Mercurial > repos > bgruening > enumerate_charges

annotate dimorphite_dl.py @ 5:67ee76f0e497 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
author bgruening
date Sat, 04 Dec 2021 16:40:23 +0000
parents bbbf5fb356dd
children
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bbbf5fb356dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
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1 # flake8: noqa
0
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2 # Copyright 2018 Jacob D. Durrant
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3 #
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4 # Licensed under the Apache License, Version 2.0 (the "License");
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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5 # you may not use this file except in compliance with the License.
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6 # You may obtain a copy of the License at
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7 #
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8 # http://www.apache.org/licenses/LICENSE-2.0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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9 #
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10 # Unless required by applicable law or agreed to in writing, software
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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11 # distributed under the License is distributed on an "AS IS" BASIS,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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12 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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13 # See the License for the specific language governing permissions and
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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14 # limitations under the License.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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15
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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16 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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17 This script identifies and enumerates the possible protonation sites of SMILES
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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18 strings.
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19 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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20
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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21 from __future__ import print_function
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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22
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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23 import argparse
0
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24 import os
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25 import sys
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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26
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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27 try:
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28 # Python2
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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29 from StringIO import StringIO
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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30 except ImportError:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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31 # Python3
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32 from io import StringIO
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33
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34 # Always let the user know a help file is available.
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35 print("\nFor help, use: python dimorphite_dl.py --help")
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36
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37 # And always report citation information.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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38 print("\nIf you use Dimorphite-DL in your research, please cite:")
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39 print("Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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40 print("open-source program for enumerating the ionization states of drug-like small")
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41 print("molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.\n")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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42
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43 try:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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44 import rdkit
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45 from rdkit import Chem
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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46 from rdkit.Chem import AllChem
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47 except Exception:
0
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48 msg = "Dimorphite-DL requires RDKit. See https://www.rdkit.org/"
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49 print(msg)
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50 raise Exception(msg)
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51
5
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52
0
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53 def main(params=None):
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54 """The main definition run when you call the script from the commandline.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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55
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56 :param params: The parameters to use. Entirely optional. If absent,
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57 defaults to None, in which case argments will be taken from
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58 those given at the command line.
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59 :param params: dict, optional
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60 :return: Returns a list of the SMILES strings return_as_list parameter is
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61 True. Otherwise, returns None.
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62 """
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63
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64 parser = ArgParseFuncs.get_args()
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65 args = vars(parser.parse_args())
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66
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67 # Add in any parameters in params.
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68 if params is not None:
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69 for k, v in params.items():
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70 args[k] = v
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71
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72 # If being run from the command line, print out all parameters.
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73 if __name__ == "__main__":
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74 print("\nPARAMETERS:\n")
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75 for k in sorted(args.keys()):
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76 print(k.rjust(13) + ": " + str(args[k]))
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77 print("")
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78
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79 if args["test"]:
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80 # Run tests.
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81 TestFuncs.test()
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82 else:
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83 # Run protonation
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84 if "output_file" in args and args["output_file"] is not None:
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85 # An output file was specified, so write to that.
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86 with open(args["output_file"], "w") as file:
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87 for protonated_smi in Protonate(args):
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88 file.write(protonated_smi + "\n")
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89 elif "return_as_list" in args and args["return_as_list"]:
0
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90 return list(Protonate(args))
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91 else:
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92 # No output file specified. Just print it to the screen.
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93 for protonated_smi in Protonate(args):
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94 print(protonated_smi)
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95
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96
0
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97 class MyParser(argparse.ArgumentParser):
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98 """Overwrite default parse so it displays help file on error. See
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99 https://stackoverflow.com/questions/4042452/display-help-message-with-python-argparse-when-script-is-called-without-any-argu"""
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100
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101 def error(self, message):
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102 """Overwrites the default error message.
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103
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104 :param message: The default error message.
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105 """
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106
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107 self.print_help()
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108 msg = "ERROR: %s\n\n" % message
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109 print(msg)
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110 raise Exception(msg)
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111
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112 def print_help(self, file=None):
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113 """Overwrite the default print_help function
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114
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115 :param file: Output file, defaults to None
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116 """
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117
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118 print("")
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119
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120 if file is None:
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121 file = sys.stdout
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122 self._print_message(self.format_help(), file)
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123 print(
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124 """
0
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125 examples:
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126 python dimorphite_dl.py --smiles_file sample_molecules.smi
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127 python dimorphite_dl.py --smiles "CCC(=O)O" --min_ph -3.0 --max_ph -2.0
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128 python dimorphite_dl.py --smiles "CCCN" --min_ph -3.0 --max_ph -2.0 --output_file output.smi
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129 python dimorphite_dl.py --smiles_file sample_molecules.smi --pka_precision 2.0 --label_states
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130 python dimorphite_dl.py --test"""
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131 )
0
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132 print("")
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133
5
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134
0
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135 class ArgParseFuncs:
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136 """A namespace for storing functions that are useful for processing
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137 command-line arguments. To keep things organized."""
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138
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139 @staticmethod
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140 def get_args():
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141 """Gets the arguments from the command line.
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142
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143 :return: A parser object.
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144 """
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145
5
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146 parser = MyParser(
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147 description="Dimorphite 1.2: Creates models of "
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148 + "appropriately protonated small moleucles. "
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149 + "Apache 2.0 License. Copyright 2018 Jacob D. "
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150 + "Durrant."
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151 )
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152 parser.add_argument(
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153 "--min_ph",
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154 metavar="MIN",
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155 type=float,
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156 default=6.4,
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157 help="minimum pH to consider (default: 6.4)",
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158 )
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159 parser.add_argument(
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160 "--max_ph",
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161 metavar="MAX",
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162 type=float,
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163 default=8.4,
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164 help="maximum pH to consider (default: 8.4)",
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165 )
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166 parser.add_argument(
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167 "--pka_precision",
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168 metavar="PRE",
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169 type=float,
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170 default=1.0,
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171 help="pKa precision factor (number of standard devations, default: 1.0)",
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172 )
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173 parser.add_argument(
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174 "--smiles", metavar="SMI", type=str, help="SMILES string to protonate"
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175 )
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176 parser.add_argument(
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177 "--smiles_file",
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178 metavar="FILE",
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179 type=str,
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180 help="file that contains SMILES strings to protonate",
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181 )
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182 parser.add_argument(
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183 "--output_file",
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184 metavar="FILE",
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185 type=str,
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186 help="output file to write protonated SMILES (optional)",
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187 )
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188 parser.add_argument(
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189 "--label_states",
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190 action="store_true",
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191 help="label protonated SMILES with target state "
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192 + '(i.e., "DEPROTONATED", "PROTONATED", or "BOTH").',
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193 )
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194 parser.add_argument(
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195 "--test", action="store_true", help="run unit tests (for debugging)"
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196 )
0
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197
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198 return parser
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199
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200 @staticmethod
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201 def clean_args(args):
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202 """Cleans and normalizes input parameters
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203
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204 :param args: A dictionary containing the arguments.
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205 :type args: dict
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206 :raises Exception: No SMILES in params.
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207 """
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208
5
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209 defaults = {
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210 "min_ph": 6.4,
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211 "max_ph": 8.4,
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212 "pka_precision": 1.0,
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213 "label_states": False,
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214 "test": False,
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215 }
0
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216
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217 for key in defaults:
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218 if key not in args:
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219 args[key] = defaults[key]
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220
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221 keys = list(args.keys())
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222 for key in keys:
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223 if args[key] is None:
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224 del args[key]
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225
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226 if not "smiles" in args and not "smiles_file" in args:
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227 msg = "Error: No SMILES in params. Use the -h parameter for help."
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228 print(msg)
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229 raise Exception(msg)
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230
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231 # If the user provides a smiles string, turn it into a file-like StringIO
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232 # object.
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233 if "smiles" in args:
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234 if isinstance(args["smiles"], str):
5
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235 args["smiles_file"] = StringIO(args["smiles"])
0
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236
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237 args["smiles_and_data"] = LoadSMIFile(args["smiles_file"])
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238
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239 return args
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240
5
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241
0
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242 class UtilFuncs:
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243 """A namespace to store functions for manipulating mol objects. To keep
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244 things organized."""
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245
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246 @staticmethod
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247 def neutralize_mol(mol):
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248 """All molecules should be neuralized to the extent possible. The user
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249 should not be allowed to specify the valence of the atoms in most cases.
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250
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251 :param rdkit.Chem.rdchem.Mol mol: The rdkit Mol objet to be neutralized.
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252 :return: The neutralized Mol object.
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253 """
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254
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255 # Get the reaction data
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256 rxn_data = [
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257 [
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258 "[Ov1-1:1]",
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259 "[Ov2+0:1]-[H]",
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260 ], # To handle O- bonded to only one atom (add hydrogen).
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261 [
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262 "[#7v4+1:1]-[H]",
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263 "[#7v3+0:1]",
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264 ], # To handle N+ bonded to a hydrogen (remove hydrogen).
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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265 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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266 "[Ov2-:1]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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267 "[Ov2+0:1]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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268 ], # To handle O- bonded to two atoms. Should not be Negative.
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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269 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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270 "[#7v3+1:1]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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271 "[#7v3+0:1]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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272 ], # To handle N+ bonded to three atoms. Should not be positive.
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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273 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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274 "[#7v2-1:1]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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275 "[#7+0:1]-[H]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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276 ], # To handle N- Bonded to two atoms. Add hydrogen.
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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277 # ['[N:1]=[N+0:2]=[N:3]-[H]', '[N:1]=[N+1:2]=[N+0:3]-[H]'], # To
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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278 # handle bad azide. Must be protonated. (Now handled elsewhere, before
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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279 # SMILES converted to Mol object.)
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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280 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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281 "[H]-[N:1]-[N:2]#[N:3]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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282 "[N:1]=[N+1:2]=[N:3]-[H]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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283 ], # To handle bad azide. R-N-N#N should be R-N=[N+]=N
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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284 ]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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285
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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286 # Add substructures and reactions (initially none)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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287 for i, rxn_datum in enumerate(rxn_data):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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288 rxn_data[i].append(Chem.MolFromSmarts(rxn_datum[0]))
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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289 rxn_data[i].append(None)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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290
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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291 # Add hydrogens (respects valence, so incomplete).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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292 # Chem.calcImplicitValence(mol)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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293 mol.UpdatePropertyCache(strict=False)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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294 mol = Chem.AddHs(mol)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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295
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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296 while True: # Keep going until all these issues have been resolved.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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297 current_rxn = None # The reaction to perform.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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298 current_rxn_str = None
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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299
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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300 for i, rxn_datum in enumerate(rxn_data):
5
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bgruening
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301 (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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302 reactant_smarts,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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303 product_smarts,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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304 substruct_match_mol,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
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305 rxn_placeholder,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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306 ) = rxn_datum
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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307 if mol.HasSubstructMatch(substruct_match_mol):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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308 if rxn_placeholder is None:
5
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309 current_rxn_str = reactant_smarts + ">>" + product_smarts
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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310 current_rxn = AllChem.ReactionFromSmarts(current_rxn_str)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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311 rxn_data[i][3] = current_rxn # Update the placeholder.
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312 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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313 current_rxn = rxn_data[i][3]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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314 break
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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315
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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316 # Perform the reaction if necessary
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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317 if current_rxn is None: # No reaction left, so break out of while loop.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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318 break
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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319 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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320 mol = current_rxn.RunReactants((mol,))[0][0]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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321 mol.UpdatePropertyCache(strict=False) # Update valences
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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322
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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323 # The mols have been altered from the reactions described above, we need
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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324 # to resanitize them. Make sure aromatic rings are shown as such This
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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325 # catches all RDKit Errors. without the catchError and sanitizeOps the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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326 # Chem.SanitizeMol can crash the program.
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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327 sanitize_string = Chem.SanitizeMol(
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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328 mol,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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329 sanitizeOps=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL,
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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330 catchErrors=True,
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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331 )
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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332
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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333 return mol if sanitize_string.name == "SANITIZE_NONE" else None
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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334
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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335 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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336 def convert_smiles_str_to_mol(smiles_str):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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337 """Given a SMILES string, check that it is actually a string and not a
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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338 None. Then try to convert it to an RDKit Mol Object.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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339
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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340 :param string smiles_str: The SMILES string.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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341 :return: A rdkit.Chem.rdchem.Mol object, or None if it is the wrong type or
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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342 if it fails to convert to a Mol Obj
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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343 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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344
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
345 # Check that there are no type errors, ie Nones or non-string
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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346 # A non-string type will cause RDKit to hard crash
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
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347 if smiles_str is None or type(smiles_str) is not str:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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348 return None
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
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349
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
350 # Try to fix azides here. They are just tricky to deal with.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
351 smiles_str = smiles_str.replace("N=N=N", "N=[N+]=N")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
352 smiles_str = smiles_str.replace("NN#N", "N=[N+]=N")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
353
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
354 # Now convert to a mol object. Note the trick that is necessary to
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
355 # capture RDKit error/warning messages. See
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
356 # https://stackoverflow.com/questions/24277488/in-python-how-to-capture-the-stdout-from-a-c-shared-library-to-a-variable
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
357 stderr_fileno = sys.stderr.fileno()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
358 stderr_save = os.dup(stderr_fileno)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
359 stderr_pipe = os.pipe()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
360 os.dup2(stderr_pipe[1], stderr_fileno)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
361 os.close(stderr_pipe[1])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
362
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
363 mol = Chem.MolFromSmiles(smiles_str)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
364
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
365 os.close(stderr_fileno)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
366 os.close(stderr_pipe[0])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
367 os.dup2(stderr_save, stderr_fileno)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
368 os.close(stderr_save)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
369
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
370 # Check that there are None type errors Chem.MolFromSmiles has sanitize on
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
371 # which means if there is even a small error in the SMILES (kekulize,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
372 # nitrogen charge...) then mol=None. ie.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
373 # Chem.MolFromSmiles("C[N]=[N]=[N]") = None this is an example of an
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
374 # nitrogen charge error. It is cased in a try statement to be overly
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
375 # cautious.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
376
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
377 return None if mol is None else mol
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
378
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
379 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
380 def eprint(*args, **kwargs):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
381 """Error messages should be printed to STDERR. See
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
382 https://stackoverflow.com/questions/5574702/how-to-print-to-stderr-in-python"""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
383
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
384 print(*args, file=sys.stderr, **kwargs)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
385
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
386
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
387 class LoadSMIFile(object):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
388 """A generator class for loading in the SMILES strings from a file, one at
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
389 a time."""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
390
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
391 def __init__(self, filename):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
392 """Initializes this class.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
393
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
394 :param filename: The filename or file object (i.e., StringIO).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
395 :type filename: str or StringIO
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
396 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
397
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
398 if type(filename) is str:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
399 # It's a filename
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
400 self.f = open(filename, "r")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
401 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
402 # It's a file object (i.e., StringIO)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
403 self.f = filename
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
404
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
405 def __iter__(self):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
406 """Returns this generator object.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
407
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
408 :return: This generator object.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
409 :rtype: LoadSMIFile
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
410 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
411
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
412 return self
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
413
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
414 def __next__(self):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
415 """Ensure Python3 compatibility.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
416
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
417 :return: A dict, where the "smiles" key contains the canonical SMILES
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
418 string and the "data" key contains the remaining information
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
419 (e.g., the molecule name).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
420 :rtype: dict
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
421 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
422
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
423 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
424
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
425 def next(self):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
426 """Get the data associated with the next line.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
427
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
428 :raises StopIteration: If there are no more lines left iin the file.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
429 :return: A dict, where the "smiles" key contains the canonical SMILES
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
430 string and the "data" key contains the remaining information
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
431 (e.g., the molecule name).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
432 :rtype: dict
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
433 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
434
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
435 line = self.f.readline()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
436
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
437 if line == "":
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
438 # EOF
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
439 self.f.close()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
440 raise StopIteration()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
441 return
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
442
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
443 # Divide line into smi and data
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
444 splits = line.split()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
445 if len(splits) != 0:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
446 # Generate mol object
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
447 smiles_str = splits[0]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
448
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
449 # Convert from SMILES string to RDKIT Mol. This series of tests is
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
450 # to make sure the SMILES string is properly formed and to get it
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
451 # into a canonical form. Filter if failed.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
452 mol = UtilFuncs.convert_smiles_str_to_mol(smiles_str)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
453 if mol is None:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
454 UtilFuncs.eprint(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
455 "WARNING: Skipping poorly formed SMILES string: " + line
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
456 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
457 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
458
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
459 # Handle nuetralizing the molecules. Filter if failed.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
460 mol = UtilFuncs.neutralize_mol(mol)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
461 if mol is None:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
462 UtilFuncs.eprint(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
463 "WARNING: Skipping poorly formed SMILES string: " + line
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
464 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
465 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
466
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
467 # Remove the hydrogens.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
468 try:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
469 mol = Chem.RemoveHs(mol)
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
470 except Exception:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
471 UtilFuncs.eprint(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
472 "WARNING: Skipping poorly formed SMILES string: " + line
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
473 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
474 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
475
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
476 if mol is None:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
477 UtilFuncs.eprint(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
478 "WARNING: Skipping poorly formed SMILES string: " + line
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
479 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
480 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
481
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
482 # Regenerate the smiles string (to standardize).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
483 new_mol_string = Chem.MolToSmiles(mol, isomericSmiles=True)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
484
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
485 return {"smiles": new_mol_string, "data": splits[1:]}
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
486 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
487 # Blank line? Go to next one.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
488 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
489
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
490
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
491 class Protonate(object):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
492 """A generator class for protonating SMILES strings, one at a time."""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
493
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
494 def __init__(self, args):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
495 """Initialize the generator.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
496
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
497 :param args: A dictionary containing the arguments.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
498 :type args: dict
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
499 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
500
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
501 # Make the args an object variable variable.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
502 self.args = args
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
503
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
504 # A list to store the protonated SMILES strings associated with a
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
505 # single input model.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
506 self.cur_prot_SMI = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
507
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
508 # Clean and normalize the args
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
509 self.args = ArgParseFuncs.clean_args(args)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
510
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
511 # Load the substructures that can be protonated.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
512 self.subs = ProtSubstructFuncs.load_protonation_substructs_calc_state_for_ph(
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
513 self.args["min_ph"], self.args["max_ph"], self.args["pka_precision"]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
514 )
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
515
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
516 def __iter__(self):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
517 """Returns this generator object.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
518
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
519 :return: This generator object.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
520 :rtype: Protonate
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
521 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
522
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
523 return self
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
524
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
525 def __next__(self):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
526 """Ensure Python3 compatibility.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
527
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
528 :return: A dict, where the "smiles" key contains the canonical SMILES
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
529 string and the "data" key contains the remaining information
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
530 (e.g., the molecule name).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
531 :rtype: dict
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
532 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
533
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
534 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
535
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
536 def next(self):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
537 """Get the next protonated SMILES string.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
538
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
539 :raises StopIteration: If there are no more lines left iin the file.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
540 :return: TODO A dict, where the "smiles" key contains the canonical SMILES
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
541 string and the "data" key contains the remaining information
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
542 (e.g., the molecule name).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
543 :rtype: dict
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
544 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
545
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
546 # If there are any SMILES strings in self.cur_prot_SMI, just return
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
547 # the first one and update the list to include only the remaining.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
548 if len(self.cur_prot_SMI) > 0:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
549 first, self.cur_prot_SMI = self.cur_prot_SMI[0], self.cur_prot_SMI[1:]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
550 return first
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
551
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
552 # self.cur_prot_SMI is empty, so try to add more to it.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
553
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
554 # Get the next SMILES string from the input file.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
555 try:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
556 smile_and_datum = self.args["smiles_and_data"].next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
557 except StopIteration:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
558 # There are no more input smiles strings...
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
559 raise StopIteration()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
560
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
561 smi = smile_and_datum["smiles"]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
562 data = smile_and_datum["data"] # Everything on SMILES line but the
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
563 # SMILES string itself (e.g., the
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
564 # molecule name).
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
565
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
566 # Collect the data associated with this smiles (e.g., the molecule
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
567 # name).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
568 tag = " ".join(data)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
569
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
570 # sites is a list of (atom index, "PROTONATED|DEPROTONATED|BOTH").
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
571 # Note that the second entry indicates what state the site SHOULD be
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
572 # in (not the one it IS in per the SMILES string). It's calculated
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
573 # based on the probablistic distributions obtained during training.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
574 sites = ProtSubstructFuncs.get_prot_sites_and_target_states(smi, self.subs)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
575
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
576 new_smis = [smi]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
577 for site in sites:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
578 # Make a new smiles with the correct protonation state. Note that
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
579 # new_smis is a growing list. This is how multiple protonation
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
580 # sites are handled.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
581
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
582 # new_smis_to_perhaps_add = ProtSubstructFuncs.protonate_site(new_smis, site)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
583 new_smis = ProtSubstructFuncs.protonate_site(new_smis, site)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
584 # print(site, new_smis) # Good for debugging.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
585
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
586 # Only add new smiles if not already in the list.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
587 # for s in new_smis_to_perhaps_add:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
588 # if not s in new_smis:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
589 # new_smis.append(s)
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
590
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
591 # In some cases, the script might generate redundant molecules.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
592 # Phosphonates, when the pH is between the two pKa values and the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
593 # stdev value is big enough, for example, will generate two identical
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
594 # BOTH states. Let's remove this redundancy.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
595 new_smis = list(set(new_smis))
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
596
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
597 # Deprotonating protonated aromatic nitrogen gives [nH-]. Change this
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
598 # to [n-]. This is a hack.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
599 new_smis = [s.replace("[nH-]", "[n-]") for s in new_smis]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
600
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
601 # Sometimes Dimorphite-DL generates molecules that aren't actually
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
602 # possible. Simply convert these to mol objects to eliminate the bad
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
603 # ones (that are None).
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
604 new_smis = [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
605 s for s in new_smis if UtilFuncs.convert_smiles_str_to_mol(s) is not None
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
606 ]
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
607
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
608 # If there are no smi left, return the input one at the very least.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
609 # All generated forms have apparently been judged
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
610 # inappropriate/mal-formed.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
611 if len(new_smis) == 0:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
612 new_smis = [smi]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
613
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
614 # If the user wants to see the target states, add those
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
615 # to the ends of each line.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
616 if self.args["label_states"]:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
617 states = "\t".join([x[1] for x in sites])
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
618 new_lines = [x + "\t" + tag + "\t" + states for x in new_smis]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
619 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
620 new_lines = [x + "\t" + tag for x in new_smis]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
621
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
622 self.cur_prot_SMI = new_lines
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
623
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
624 return self.next()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
625
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
626
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
627 class ProtSubstructFuncs:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
628 """A namespace to store functions for loading the substructures that can
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
629 be protonated. To keep things organized."""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
630
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
631 @staticmethod
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
632 def load_protonation_substructs_calc_state_for_ph(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
633 min_ph=6.4, max_ph=8.4, pka_std_range=1
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
634 ):
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
635 """A pre-calculated list of R-groups with protonation sites, with their
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
636 likely pKa bins.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
637
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
638 :param float min_ph: The lower bound on the pH range, defaults to 6.4.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
639 :param float max_ph: The upper bound on the pH range, defaults to 8.4.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
640 :param pka_std_range: Basically the precision (stdev from predicted pKa to
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
641 consider), defaults to 1.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
642 :return: A dict of the protonation substructions for the specified pH
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
643 range.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
644 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
645
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
646 subs = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
647 pwd = os.path.dirname(os.path.realpath(__file__))
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
648
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
649 site_structures_file = "{}/{}".format(pwd, "site_substructures.smarts")
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
650 with open(site_structures_file, "r") as substruct:
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
651 for line in substruct:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
652 line = line.strip()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
653 sub = {}
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
654 if line is not "":
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
655 splits = line.split()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
656 sub["name"] = splits[0]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
657 sub["smart"] = splits[1]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
658 sub["mol"] = Chem.MolFromSmarts(sub["smart"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
659
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
660 # NEED TO DIVIDE THIS BY 3s
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
661 pka_ranges = [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
662 splits[i : i + 3] for i in range(2, len(splits) - 1, 3)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
663 ]
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
664
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
665 prot = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
666 for pka_range in pka_ranges:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
667 site = pka_range[0]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
668 std = float(pka_range[2]) * pka_std_range
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
669 mean = float(pka_range[1])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
670 protonation_state = ProtSubstructFuncs.define_protonation_state(
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
671 mean, std, min_ph, max_ph
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
672 )
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
673
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
674 prot.append([site, protonation_state])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
675
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
676 sub["prot_states_for_pH"] = prot
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
677 subs.append(sub)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
678 return subs
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
679
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
680 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
681 def define_protonation_state(mean, std, min_ph, max_ph):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
682 """Updates the substructure definitions to include the protonation state
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
683 based on the user-given pH range. The size of the pKa range is also based
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
684 on the number of standard deviations to be considered by the user param.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
685
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
686 :param float mean: The mean pKa.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
687 :param float std: The precision (stdev).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
688 :param float min_ph: The min pH of the range.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
689 :param float max_ph: The max pH of the range.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
690 :return: A string describing the protonation state.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
691 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
692
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
693 min_pka = mean - std
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
694 max_pka = mean + std
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
695
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
696 # This needs to be reassigned, and 'ERROR' should never make it past the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
697 # next set of checks.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
698 if min_pka <= max_ph and min_ph <= max_pka:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
699 protonation_state = "BOTH"
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
700 elif mean > max_ph:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
701 protonation_state = "PROTONATED"
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
702 else:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
703 protonation_state = "DEPROTONATED"
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
704
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
705 return protonation_state
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
706
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
707 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
708 def get_prot_sites_and_target_states(smi, subs):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
709 """For a single molecule, find all possible matches in the protonation
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
710 R-group list, subs. Items that are higher on the list will be matched
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
711 first, to the exclusion of later items.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
712
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
713 :param string smi: A SMILES string.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
714 :param list subs: Substructure information.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
715 :return: A list of protonation sites and their pKa bin. ('PROTONATED',
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
716 'BOTH', or 'DEPROTONATED')
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
717 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
718
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
719 # Convert the Smiles string (smi) to an RDKit Mol Obj
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
720 mol = UtilFuncs.convert_smiles_str_to_mol(smi)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
721
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
722 # Check Conversion worked
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
723 if mol is None:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
724 UtilFuncs.eprint("ERROR: ", smi)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
725 return []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
726
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
727 # Try to Add hydrogens. if failed return []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
728 try:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
729 mol = Chem.AddHs(mol)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
730 except Exception:
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
731 UtilFuncs.eprint("ERROR: ", smi)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
732 return []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
733
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
734 # Check adding Hs worked
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
735 if mol is None:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
736 UtilFuncs.eprint("ERROR: ", smi)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
737 return []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
738
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
739 ProtectUnprotectFuncs.unprotect_molecule(mol)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
740 protonation_sites = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
741
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
742 for item in subs:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
743 smart = item["mol"]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
744 if mol.HasSubstructMatch(smart):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
745 matches = ProtectUnprotectFuncs.get_unprotected_matches(mol, smart)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
746 prot = item["prot_states_for_pH"]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
747 for match in matches:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
748 # We want to move the site from being relative to the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
749 # substructure, to the index on the main molecule.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
750 for site in prot:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
751 proton = int(site[0])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
752 category = site[1]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
753 new_site = (match[proton], category, item["name"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
754
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
755 if not new_site in protonation_sites:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
756 # Because sites must be unique.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
757 protonation_sites.append(new_site)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
758
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
759 ProtectUnprotectFuncs.protect_molecule(mol, match)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
760
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
761 return protonation_sites
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
762
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
763 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
764 def protonate_site(smis, site):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
765 """Given a list of SMILES strings, we protonate the site.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
766
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
767 :param list smis: The list of SMILES strings.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
768 :param tuple site: Information about the protonation site.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
769 (idx, target_prot_state, prot_site_name)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
770 :return: A list of the appropriately protonated SMILES.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
771 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
772
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
773 # Decouple the atom index and its target protonation state from the site
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
774 # tuple
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
775 idx, target_prot_state, prot_site_name = site
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
776
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
777 # Initialize the output list
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
778 output_smis = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
779
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
780 state_to_charge = {"DEPROTONATED": [-1], "PROTONATED": [0], "BOTH": [-1, 0]}
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
781
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
782 charges = state_to_charge[target_prot_state]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
783
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
784 # Now make the actual smiles match the target protonation state.
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
785 output_smis = ProtSubstructFuncs.set_protonation_charge(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
786 smis, idx, charges, prot_site_name
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
787 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
788
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
789 return output_smis
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
790
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
791 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
792 def set_protonation_charge(smis, idx, charges, prot_site_name):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
793 """Sets the atomic charge on a particular site for a set of SMILES.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
794
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
795 :param list smis: A list of the SMILES strings.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
796 :param int idx: The index of the atom to consider.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
797 :param list charges: A list of the charges (ints) to assign at
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
798 this site.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
799 :param string prot_site_name: The name of the protonation site.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
800 :return: A list of the processed SMILES strings.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
801 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
802
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
803 # Sets up the output list and the Nitrogen charge
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
804 output = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
805
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
806 for charge in charges:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
807 # The charge for Nitrogens is 1 higher than others (i.e., protonated
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
808 # state is positively charged).
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
809 nitro_charge = charge + 1
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
810
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
811 # But there are a few nitrogen moieties where the acidic group is the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
812 # neutral one. Amides are a good example. I gave some thought re. how
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
813 # to best flag these. I decided that those nitrogen-containing
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
814 # moieties where the acidic group is neutral (rather than positively
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
815 # charged) will have "*" in the name.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
816 if "*" in prot_site_name:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
817 nitro_charge = nitro_charge - 1 # Undo what was done previously.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
818
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
819 for smi in smis:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
820
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
821 # Convert smilesstring (smi) into a RDKit Mol
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
822 mol = UtilFuncs.convert_smiles_str_to_mol(smi)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
823
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
824 # Check that the conversion worked, skip if it fails
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
825 if mol is None:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
826 continue
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
827
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
828 atom = mol.GetAtomWithIdx(idx)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
829
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
830 # Assign the protonation charge, with special care for Nitrogens
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
831 element = atom.GetAtomicNum()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
832 if element == 7:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
833 atom.SetFormalCharge(nitro_charge)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
834 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
835 atom.SetFormalCharge(charge)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
836
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
837 # Convert back to SMILE and add to output
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
838 out_smile = Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
839 output.append(out_smile)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
840
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
841 return output
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
842
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
843
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
844 class ProtectUnprotectFuncs:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
845 """A namespace for storing functions that are useful for protecting and
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
846 unprotecting molecules. To keep things organized. We need to identify and
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
847 mark groups that have been matched with a substructure."""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
848
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
849 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
850 def unprotect_molecule(mol):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
851 """Sets the protected property on all atoms to 0. This also creates the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
852 property for new molecules.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
853
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
854 :param rdkit.Chem.rdchem.Mol mol: The rdkit Mol object.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
855 :type mol: The rdkit Mol object with atoms unprotected.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
856 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
857
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
858 for atom in mol.GetAtoms():
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
859 atom.SetProp("_protected", "0")
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
860
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
861 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
862 def protect_molecule(mol, match):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
863 """Given a 'match', a list of molecules idx's, we set the protected status
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
864 of each atom to 1. This will prevent any matches using that atom in the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
865 future.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
866
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
867 :param rdkit.Chem.rdchem.Mol mol: The rdkit Mol object to protect.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
868 :param list match: A list of molecule idx's.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
869 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
870
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
871 for idx in match:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
872 atom = mol.GetAtomWithIdx(idx)
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
873 atom.SetProp("_protected", "1")
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
874
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
875 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
876 def get_unprotected_matches(mol, substruct):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
877 """Finds substructure matches with atoms that have not been protected.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
878 Returns list of matches, each match a list of atom idxs.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
879
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
880 :param rdkit.Chem.rdchem.Mol mol: The Mol object to consider.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
881 :param string substruct: The SMARTS string of the substructure ot match.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
882 :return: A list of the matches. Each match is itself a list of atom idxs.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
883 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
884
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
885 matches = mol.GetSubstructMatches(substruct)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
886 unprotected_matches = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
887 for match in matches:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
888 if ProtectUnprotectFuncs.is_match_unprotected(mol, match):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
889 unprotected_matches.append(match)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
890 return unprotected_matches
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
891
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
892 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
893 def is_match_unprotected(mol, match):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
894 """Checks a molecule to see if the substructure match contains any
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
895 protected atoms.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
896
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
897 :param rdkit.Chem.rdchem.Mol mol: The Mol object to check.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
898 :param list match: The match to check.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
899 :return: A boolean, whether the match is present or not.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
900 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
901
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
902 for idx in match:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
903 atom = mol.GetAtomWithIdx(idx)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
904 protected = atom.GetProp("_protected")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
905 if protected == "1":
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
906 return False
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
907 return True
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
908
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
909
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
910 class TestFuncs:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
911 """A namespace for storing functions that perform tests on the code. To
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
912 keep things organized."""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
913
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
914 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
915 def test():
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
916 """Tests all the 38 groups."""
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
917
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
918 smis = [
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
919 # [input smiles, pka, protonated, deprotonated, category]
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
920 ["C#CCO", "C#CCO", "C#CC[O-]", "Alcohol"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
921 ["C(=O)N", "NC=O", "[NH-]C=O", "Amide"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
922 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
923 "CC(=O)NOC(C)=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
924 "CC(=O)NOC(C)=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
925 "CC(=O)[N-]OC(C)=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
926 "Amide_electronegative",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
927 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
928 ["COC(=N)N", "COC(N)=[NH2+]", "COC(=N)N", "AmidineGuanidine2"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
929 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
930 "Brc1ccc(C2NCCS2)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
931 "Brc1ccc(C2[NH2+]CCS2)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
932 "Brc1ccc(C2NCCS2)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
933 "Amines_primary_secondary_tertiary",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
934 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
935 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
936 "CC(=O)[n+]1ccc(N)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
937 "CC(=O)[n+]1ccc([NH3+])cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
938 "CC(=O)[n+]1ccc(N)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
939 "Anilines_primary",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
940 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
941 ["CCNc1ccccc1", "CC[NH2+]c1ccccc1", "CCNc1ccccc1", "Anilines_secondary"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
942 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
943 "Cc1ccccc1N(C)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
944 "Cc1ccccc1[NH+](C)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
945 "Cc1ccccc1N(C)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
946 "Anilines_tertiary",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
947 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
948 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
949 "BrC1=CC2=C(C=C1)NC=C2",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
950 "Brc1ccc2[nH]ccc2c1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
951 "Brc1ccc2[n-]ccc2c1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
952 "Indole_pyrrole",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
953 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
954 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
955 "O=c1cc[nH]cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
956 "O=c1cc[nH]cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
957 "O=c1cc[n-]cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
958 "Aromatic_nitrogen_protonated",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
959 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
960 ["C-N=[N+]=[N@H]", "CN=[N+]=N", "CN=[N+]=[N-]", "Azide"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
961 ["BrC(C(O)=O)CBr", "O=C(O)C(Br)CBr", "O=C([O-])C(Br)CBr", "Carboxyl"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
962 ["NC(NN=O)=N", "NC(=[NH2+])NN=O", "N=C(N)NN=O", "AmidineGuanidine1"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
963 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
964 "C(F)(F)(F)C(=O)NC(=O)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
965 "CC(=O)NC(=O)C(F)(F)F",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
966 "CC(=O)[N-]C(=O)C(F)(F)F",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
967 "Imide",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
968 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
969 ["O=C(C)NC(C)=O", "CC(=O)NC(C)=O", "CC(=O)[N-]C(C)=O", "Imide2"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
970 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
971 "CC(C)(C)C(N(C)O)=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
972 "CN(O)C(=O)C(C)(C)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
973 "CN([O-])C(=O)C(C)(C)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
974 "N-hydroxyamide",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
975 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
976 ["C[N+](O)=O", "C[N+](=O)O", "C[N+](=O)[O-]", "Nitro"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
977 ["O=C1C=C(O)CC1", "O=C1C=C(O)CC1", "O=C1C=C([O-])CC1", "O=C-C=C-OH"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
978 ["C1CC1OO", "OOC1CC1", "[O-]OC1CC1", "Peroxide2"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
979 ["C(=O)OO", "O=COO", "O=CO[O-]", "Peroxide1"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
980 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
981 "Brc1cc(O)cc(Br)c1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
982 "Oc1cc(Br)cc(Br)c1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
983 "[O-]c1cc(Br)cc(Br)c1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
984 "Phenol",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
985 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
986 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
987 "CC(=O)c1ccc(S)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
988 "CC(=O)c1ccc(S)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
989 "CC(=O)c1ccc([S-])cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
990 "Phenyl_Thiol",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
991 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
992 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
993 "C=CCOc1ccc(C(=O)O)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
994 "C=CCOc1ccc(C(=O)O)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
995 "C=CCOc1ccc(C(=O)[O-])cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
996 "Phenyl_carboxyl",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
997 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
998 ["COP(=O)(O)OC", "COP(=O)(O)OC", "COP(=O)([O-])OC", "Phosphate_diester"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
999 ["CP(C)(=O)O", "CP(C)(=O)O", "CP(C)(=O)[O-]", "Phosphinic_acid"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1000 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1001 "CC(C)OP(C)(=O)O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1002 "CC(C)OP(C)(=O)O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1003 "CC(C)OP(C)(=O)[O-]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1004 "Phosphonate_ester",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1005 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1006 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1007 "CC1(C)OC(=O)NC1=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1008 "CC1(C)OC(=O)NC1=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1009 "CC1(C)OC(=O)[N-]C1=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1010 "Ringed_imide1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1011 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1012 ["O=C(N1)C=CC1=O", "O=C1C=CC(=O)N1", "O=C1C=CC(=O)[N-]1", "Ringed_imide2"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1013 ["O=S(OC)(O)=O", "COS(=O)(=O)O", "COS(=O)(=O)[O-]", "Sulfate"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1014 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1015 "COc1ccc(S(=O)O)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1016 "COc1ccc(S(=O)O)cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1017 "COc1ccc(S(=O)[O-])cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1018 "Sulfinic_acid",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1019 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1020 ["CS(N)(=O)=O", "CS(N)(=O)=O", "CS([NH-])(=O)=O", "Sulfonamide"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1021 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1022 "CC(=O)CSCCS(O)(=O)=O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1023 "CC(=O)CSCCS(=O)(=O)O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1024 "CC(=O)CSCCS(=O)(=O)[O-]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1025 "Sulfonate",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1026 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1027 ["CC(=O)S", "CC(=O)S", "CC(=O)[S-]", "Thioic_acid"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1028 ["C(C)(C)(C)(S)", "CC(C)(C)S", "CC(C)(C)[S-]", "Thiol"],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1029 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1030 "Brc1cc[nH+]cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1031 "Brc1cc[nH+]cc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1032 "Brc1ccncc1",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1033 "Aromatic_nitrogen_unprotonated",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1034 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1035 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1036 "C=C(O)c1c(C)cc(C)cc1C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1037 "C=C(O)c1c(C)cc(C)cc1C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1038 "C=C([O-])c1c(C)cc(C)cc1C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1039 "Vinyl_alcohol",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1040 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1041 ["CC(=O)ON", "CC(=O)O[NH3+]", "CC(=O)ON", "Primary_hydroxyl_amine"],
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1042 ]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1043
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1044 smis_phos = [
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1045 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1046 "O=P(O)(O)OCCCC",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1047 "CCCCOP(=O)(O)O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1048 "CCCCOP(=O)([O-])O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1049 "CCCCOP(=O)([O-])[O-]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1050 "Phosphate",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1051 ],
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1052 [
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1053 "CC(P(O)(O)=O)C",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1054 "CC(C)P(=O)(O)O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1055 "CC(C)P(=O)([O-])O",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1056 "CC(C)P(=O)([O-])[O-]",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1057 "Phosphonate",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1058 ],
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1059 ]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1060
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1061 # Load the average pKa values.
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1062 average_pkas = {
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1063 l.split()[0].replace("*", ""): float(l.split()[3])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1064 for l in open("site_substructures.smarts")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1065 if l.split()[0] not in ["Phosphate", "Phosphonate"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1066 }
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1067 average_pkas_phos = {
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1068 l.split()[0].replace("*", ""): [float(l.split()[3]), float(l.split()[6])]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1069 for l in open("site_substructures.smarts")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1070 if l.split()[0] in ["Phosphate", "Phosphonate"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1071 }
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1072
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1073 print("Running Tests")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1074 print("=============")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1075 print("")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1076
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1077 print("Very Acidic (pH -10000000)")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1078 print("--------------------------")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1079 print("")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1080
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1081 args = {
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1082 "min_ph": -10000000,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1083 "max_ph": -10000000,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1084 "pka_precision": 0.5,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1085 "smiles": "",
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1086 "label_states": True,
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1087 }
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1088
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1089 for smi, protonated, deprotonated, category in smis:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1090 args["smiles"] = smi
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1091 TestFuncs.test_check(args, [protonated], ["PROTONATED"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1092
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1093 for smi, protonated, mix, deprotonated, category in smis_phos:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1094 args["smiles"] = smi
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1095 TestFuncs.test_check(args, [protonated], ["PROTONATED"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1096
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1097 args["min_ph"] = 10000000
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1098 args["max_ph"] = 10000000
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1099
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1100 print("")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1101 print("Very Basic (pH 10000000)")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1102 print("------------------------")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1103 print("")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1104
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1105 for smi, protonated, deprotonated, category in smis:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1106 args["smiles"] = smi
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1107 TestFuncs.test_check(args, [deprotonated], ["DEPROTONATED"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1108
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1109 for smi, protonated, mix, deprotonated, category in smis_phos:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1110 args["smiles"] = smi
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1111 TestFuncs.test_check(args, [deprotonated], ["DEPROTONATED"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1112
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1113 print("")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1114 print("pH is Category pKa")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1115 print("------------------")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1116 print("")
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1117
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1118 for smi, protonated, deprotonated, category in smis:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1119 avg_pka = average_pkas[category]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1120
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1121 args["smiles"] = smi
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1122 args["min_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1123 args["max_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1124
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1125 TestFuncs.test_check(args, [protonated, deprotonated], ["BOTH"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1126
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1127 for smi, protonated, mix, deprotonated, category in smis_phos:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1128 args["smiles"] = smi
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1129
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1130 avg_pka = average_pkas_phos[category][0]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1131 args["min_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1132 args["max_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1133
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1134 TestFuncs.test_check(args, [mix, protonated], ["BOTH"])
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1135
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1136 avg_pka = average_pkas_phos[category][1]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1137 args["min_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1138 args["max_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1139
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1140 TestFuncs.test_check(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1141 args, [mix, deprotonated], ["DEPROTONATED", "DEPROTONATED"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1142 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1143
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1144 avg_pka = 0.5 * (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1145 average_pkas_phos[category][0] + average_pkas_phos[category][1]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1146 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1147 args["min_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1148 args["max_ph"] = avg_pka
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1149 args["pka_precision"] = 5 # Should give all three
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1150
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1151 TestFuncs.test_check(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1152 args, [mix, deprotonated, protonated], ["BOTH", "BOTH"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1153 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1154
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1155 @staticmethod
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1156 def test_check(args, expected_output, labels):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1157 """Tests most ionizable groups. The ones that can only loose or gain a single proton.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1158
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1159 :param args: The arguments to pass to protonate()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1160 :param expected_output: A list of the expected SMILES-strings output.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1161 :param labels: The labels. A list containing combo of BOTH, PROTONATED,
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1162 DEPROTONATED.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1163 :raises Exception: Wrong number of states produced.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1164 :raises Exception: Unexpected output SMILES.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1165 :raises Exception: Wrong labels.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1166 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1167
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1168 output = list(Protonate(args))
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1169 output = [o.split() for o in output]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1170
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1171 num_states = len(expected_output)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1172
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1173 if len(output) != num_states:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1174 msg = (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1175 args["smiles"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1176 + " should have "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1177 + str(num_states)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1178 + " states at at pH "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1179 + str(args["min_ph"])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1180 + ": "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1181 + str(output)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1182 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1183 print(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1184 raise Exception(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1185
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1186 if len(set([l[0] for l in output]) - set(expected_output)) != 0:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1187 msg = (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1188 args["smiles"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1189 + " is not "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1190 + " AND ".join(expected_output)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1191 + " at pH "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1192 + str(args["min_ph"])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1193 + " - "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1194 + str(args["max_ph"])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1195 + "; it is "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1196 + " AND ".join([l[0] for l in output])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1197 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1198 print(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1199 raise Exception(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1200
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1201 if len(set([l[1] for l in output]) - set(labels)) != 0:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1202 msg = (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1203 args["smiles"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1204 + " not labeled as "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1205 + " AND ".join(labels)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1206 + "; it is "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1207 + " AND ".join([l[1] for l in output])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1208 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1209 print(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1210 raise Exception(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1211
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1212 ph_range = sorted(list(set([args["min_ph"], args["max_ph"]])))
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1213 ph_range_str = "(" + " - ".join("{0:.2f}".format(n) for n in ph_range) + ")"
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1214 print(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1215 "(CORRECT) "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1216 + ph_range_str.ljust(10)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1217 + " "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1218 + args["smiles"]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1219 + " => "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1220 + " AND ".join([l[0] for l in output])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1221 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1222
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1223
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1224 def run(**kwargs):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1225 """A helpful, importable function for those who want to call Dimorphite-DL
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1226 from another Python script rather than the command line. Note that this
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1227 function accepts keyword arguments that match the command-line parameters
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1228 exactly. If you want to pass and return a list of RDKit Mol objects, import
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1229 run_with_mol_list() instead.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1230
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1231 :param **kwargs: For a complete description, run dimorphite_dl.py from the
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1232 command line with the -h option.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1233 :type kwargs: dict
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1234 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1235
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1236 # Run the main function with the specified arguments.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1237 main(kwargs)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1238
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1239
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1240 def run_with_mol_list(mol_lst, **kwargs):
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1241 """A helpful, importable function for those who want to call Dimorphite-DL
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1242 from another Python script rather than the command line. Note that this
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1243 function is for passing Dimorphite-DL a list of RDKit Mol objects, together
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1244 with command-line parameters. If you want to use only the same parameters
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1245 that you would use from the command line, import run() instead.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1246
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1247 :param mol_lst: A list of rdkit.Chem.rdchem.Mol objects.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1248 :type mol_lst: list
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1249 :raises Exception: If the **kwargs includes "smiles", "smiles_file",
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1250 "output_file", or "test" parameters.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1251 :return: A list of properly protonated rdkit.Chem.rdchem.Mol objects.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1252 :rtype: list
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1253 """
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1254
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1255 # Do a quick check to make sure the user input makes sense.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1256 for bad_arg in ["smiles", "smiles_file", "output_file", "test"]:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1257 if bad_arg in kwargs:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1258 msg = (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1259 "You're using Dimorphite-DL's run_with_mol_list(mol_lst, "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1260 + '**kwargs) function, but you also passed the "'
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1261 + bad_arg
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1262 + '" argument. Did you mean to use the '
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1263 + "run(**kwargs) function instead?"
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1264 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1265 print(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1266 raise Exception(msg)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1267
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1268 # Set the return_as_list flag so main() will return the protonated smiles
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1269 # as a list.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1270 kwargs["return_as_list"] = True
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1271
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1272 # Having reviewed the code, it will be very difficult to rewrite it so
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1273 # that a list of Mol objects can be used directly. Intead, convert this
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1274 # list of mols to smiles and pass that. Not efficient, but it will work.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1275 protonated_smiles_and_props = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1276 for m in mol_lst:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1277 props = m.GetPropsAsDict()
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1278 kwargs["smiles"] = Chem.MolToSmiles(m, isomericSmiles=True)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1279 protonated_smiles_and_props.extend(
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1280 [(s.split("\t")[0], props) for s in main(kwargs)]
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1281 )
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1282
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1283 # Now convert the list of protonated smiles strings back to RDKit Mol
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1284 # objects. Also, add back in the properties from the original mol objects.
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1285 mols = []
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1286 for s, props in protonated_smiles_and_props:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1287 m = Chem.MolFromSmiles(s)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1288 if m:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1289 for prop, val in props.items():
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1290 if type(val) is int:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1291 m.SetIntProp(prop, val)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1292 elif type(val) is float:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1293 m.SetDoubleProp(prop, val)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1294 elif type(val) is bool:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1295 m.SetBoolProp(prop, val)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1296 else:
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1297 m.SetProp(prop, str(val))
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1298 mols.append(m)
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1299 else:
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1300 UtilFuncs.eprint(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1301 "WARNING: Could not process molecule with SMILES string "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1302 + s
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1303 + " and properties "
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1304 + str(props)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1305 )
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1306
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1307 return mols
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1308
5
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents: 4
diff changeset
1309
0
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1310 if __name__ == "__main__":
0f3e5c69251e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
bgruening
parents:
diff changeset
1311 main()