Mercurial > repos > bgruening > openbabel_remove_protonation_state

annotate cheminfolib.py @ 14:e376ba0fcde0 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:34:01 +0000
parents b578d0c101cd
children 22a866858b81
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0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 Small library with cheminformatic functions based on openbabel and pgchem.
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 Copyright 2012, Bjoern Gruening and Xavier Lucas
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5 """
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6
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7 import glob
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8 import re
b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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9 import subprocess
b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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10 import sys
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11 import tempfile
b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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12 from multiprocessing import Pool
b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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13
0
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14
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15 try:
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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16 from galaxy import eggs
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17 eggs.require('psycopg2')
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18 except ImportError:
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19 psycopg2 = None
0
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20 print('psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB')
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22 try:
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23 from openbabel import openbabel, pybel
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24 openbabel.obErrorLog.StopLogging()
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25 except ImportError:
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26 openbabel, pybel = None, None
0
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27 print('OpenBabel could not be found. A few functions are not available without OpenBabel.')
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28
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30 def CountLines(path):
0
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31 out = subprocess.Popen(['wc', '-l', path],
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32 stdout=subprocess.PIPE,
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33 stderr=subprocess.STDOUT
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34 ).communicate()[0]
0
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35 return int(out.partition(b' ')[0])
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37
0
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38 def grep(pattern, file_obj):
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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39 grepper = re.compile(pattern)
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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40 for line in file_obj:
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41 if grepper.search(line):
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42 return True
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43 return False
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44
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45
0
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46 def check_filetype(filepath):
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47 mol = False
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48 possible_inchi = True
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49 for line_counter, line in enumerate(open(filepath)):
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50 if line_counter > 10000:
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51 break
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52 if line.find('$$$$') != -1:
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53 return 'sdf'
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54 elif line.find('@<TRIPOS>MOLECULE') != -1:
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55 return 'mol2'
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56 elif line.find('ligand id') != -1:
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57 return 'drf'
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58 elif possible_inchi and re.findall('^InChI=', line):
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59 return 'inchi'
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60 elif re.findall(r'^M\s+END', line):
0
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61 mol = True
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62 # first line is not an InChI, so it can't be an InChI file
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63 possible_inchi = False
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64
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65 if mol:
13
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66 # END can occures before $$$$, so and SDF file will
0
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67 # be recognised as mol, if you not using this hack'
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68 return 'mol'
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69 return 'smi'
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70
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71
0
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72 def db_connect(args):
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73 try:
13
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74 db_conn = psycopg2.connect("dbname=%s user=%s host=%s password=%s" % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd))
0
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75 return db_conn
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76 except psycopg2.Error:
0
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77 sys.exit('Unable to connect to the db')
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78
13
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79
0
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80 ColumnNames = {
13
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81 'can_smiles': 'Canonical SMILES',
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82 'can': 'Canonical SMILES',
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83 'inchi': 'InChI',
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84 'inchi_key': 'InChI key',
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85 'inchi_key_first': 'InChI key first',
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86 'inchi_key_last': 'InChI key last',
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87 'molwt': 'Molecular weight',
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88 'hbd': 'Hydrogen-bond donors',
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89 'donors': 'Hydrogen-bond donors',
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90 'hba': 'Hydrogen-bond acceptors',
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91 'acceptors': 'Hydrogen-bond acceptors',
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92 'rotbonds': 'Rotatable bonds',
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93 'logp': 'logP',
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94 'psa': 'Polar surface area',
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95 'mr': 'Molecular refractivity',
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96 'atoms': 'Number of heavy atoms',
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97 'rings': 'Number of rings',
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98 'set_bits': 'FP2 bits',
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99 'id': 'Internal identifier',
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100 'tani': 'Tanimoto coefficient',
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101 'spectrophore': 'Spectrophores(TM)',
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102 'dist_spectrophore': 'Spectrophores(TM) distance to target',
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103 'synonym': 'Entry id',
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104 }
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105
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106 OBDescriptor = {
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107 'atoms': ["atoms", "Number of atoms"],
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108 'hatoms': ["hatoms", "Number of heavy atoms"], # self defined tag hatoms in plugindefines.txt
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109 'can_smiles': ["cansmi", "Canonical SMILES"],
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110 'can_smilesNS': ["cansmiNS", "Canonical SMILES without isotopes or stereo"],
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111 # ["abonds", "Number of aromatic bonds"],
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112 # ["bonds", "Number of bonds"],
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113 # ["dbonds", "Number of double bonds"],
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114 # ["formula", "Chemical formula"],
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115 'hba': ["HBA1", "Number of Hydrogen Bond Acceptors 1 (JoelLib)"],
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116 'hba2': ["HBA2", "Number of Hydrogen Bond Acceptors 2 (JoelLib)"],
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117 'hbd': ["HBD", "Number of Hydrogen Bond Donors (JoelLib)"],
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118 'inchi': ["InChI", "IUPAC InChI identifier"],
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119 'inchi_key': ["InChIKey", "InChIKey"],
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120 # ["L5", "Lipinski Rule of Five"],
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121 'logp': ["logP", "octanol/water partition coefficient"],
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122 'mr': ["MR", "molar refractivity"],
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123 'molwt': ["MW", "Molecular Weight filter"],
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124 # ["nF", "Number of Fluorine Atoms"],
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125 # ["s", "SMARTS filter"],
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126 # ["sbonds", "Number of single bonds"],
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127 # ["smarts", "SMARTS filter"],
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128 # ["tbonds", "Number of triple bonds"],
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129 # ["title", "For comparing a molecule's title"],
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130 'psa': ["TPSA", "topological polar surface area"],
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131 'rotbonds': ['ROTATABLE_BOND', 'rotatable bonds'],
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132 }
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133
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134
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135 def print_output(args, rows):
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136 if args.oformat == 'table':
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137 outfile = open(args.output, 'w')
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138 requested_fields = (filter(lambda x: x not in ["[", "]", "'"], args.fetch)).split(', ')
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139 if args.header:
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140 outfile.write('Identifier\t' + '\t'.join([ColumnNames[key] for key in requested_fields]) + '\n')
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141 for row in rows:
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142 outfile.write(row['synonym'] + '\t' + '\t'.join([str(row[key]) for key in requested_fields]) + '\n')
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143
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144 elif args.oformat in ['sdf', 'mol2']:
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145 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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146 for row in rows:
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147 try:
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148 mol = pybel.readstring('sdf', row['mol'])
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149 if args.oformat == 'sdf':
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150 keys = filter(lambda x: x not in ["[", "]", "'"], args.fetch).split(', ')
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151 mol.data.update({ColumnNames['synonym']: row['synonym']})
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152 if 'inchi_key' in keys:
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153 keys = (', '.join(keys).replace("inchi_key", "inchi_key_first, inchi_key_last")).split(', ')
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154 [mol.data.update({ColumnNames[key]: row[key]}) for key in keys if key]
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155 outfile.write(mol)
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156 except OSError:
0
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157 pass
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158 else:
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159 outfile = open(args.output, 'w')
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160 outfile.write('\n'.join(['%s\t%s' % (row[args.oformat], row['synonym']) for row in rows]))
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161 outfile.close()
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162
13
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163
0
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164 def pybel_stop_logging():
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165 openbabel.obErrorLog.StopLogging()
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166
13
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167
0
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168 def get_properties_ext(mol):
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169 HBD = pybel.Smarts("[!#6;!H0]")
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170 HBA = pybel.Smarts(("[$([$([#8,#16]);!$(*=N~O);"
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171 "!$(*~N=O);X1,X2]),$([#7;v3;"
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172 "!$([nH]);!$(*(-a)-a)])]"
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173 ))
0
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174 calc_desc_dict = mol.calcdesc()
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175
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176 try:
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177 logp = calc_desc_dict['logP']
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178 except KeyError:
0
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179 logp = calc_desc_dict['LogP']
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180
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181 return {"molwt": mol.molwt,
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182 "logp": logp,
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183 "donors": len(HBD.findall(mol)),
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184 "acceptors": len(HBA.findall(mol)),
0
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185 "psa": calc_desc_dict['TPSA'],
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186 "mr": calc_desc_dict['MR'],
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187 "rotbonds": mol.OBMol.NumRotors(),
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188 "can": mol.write("can").split()[0].strip(), # tthis one works fine for both zinc and chembl (no ZINC code added after can descriptor string)
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189 "inchi": mol.write("inchi").strip(),
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190 "inchi_key": get_inchikey(mol).strip(),
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191 "rings": len(mol.sssr),
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192 "atoms": mol.OBMol.NumHvyAtoms(),
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193 "spectrophore": OBspectrophore(mol),
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194 }
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195
0
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196
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197 def get_inchikey(mol):
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198 conv = openbabel.OBConversion()
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199 conv.SetInAndOutFormats("mol", "inchi")
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200 conv.SetOptions("K", conv.OUTOPTIONS)
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201 inchikey = conv.WriteString(mol.OBMol)
0
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202 return inchikey
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203
13
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204
0
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205 def OBspectrophore(mol):
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206 spectrophore = pybel.ob.OBSpectrophore()
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207 # Parameters: rotation angle = 20, normalization for mean and sd, accuracy = 3.0 A and non-stereospecific cages.
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208 spectrophore.SetNormalization(spectrophore.NormalizationTowardsZeroMeanAndUnitStd)
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209 return ', '.join(["%.3f" % value for value in spectrophore.GetSpectrophore(mol.OBMol)])
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210
0
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211
13
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212 def split_library(lib_path, lib_format='sdf', package_size=None):
0
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213 """
13
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214 Split a library of compounds. Usage: split_library(lib_path, lib_format, package_size)
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215 IT currently ONLY WORKS FOR SD-Files
0
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216 """
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217 pack = 1
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218 mol_counter = 0
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219
13
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220 outfile = open('/%s/%s_pack_%i.%s' % ('/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w')
0
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221
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222 for line in open(lib_path, 'r'):
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223 outfile.write(line)
0
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224 if line.strip() == '$$$$':
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225 mol_counter += 1
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226 if mol_counter % package_size == 0:
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227 outfile.close()
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228 pack += 1
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229 outfile = open('/%s/%s_pack_%i.%s' % ('/'.join(lib_path.split('/')[:-1]), lib_path.split('/')[-1].split('.')[0], pack, 'sdf'), 'w')
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230 if mol_counter * 10 % package_size == 0:
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231 print('%i molecules parsed, starting pack nr. %i' % (mol_counter, pack - 1))
0
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232 outfile.close()
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233
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234 return True
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235
13
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236
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237 def split_smi_library(smiles_file, structures_in_one_file):
0
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238 """
13
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239 Split a file with SMILES to several files for multiprocessing usage.
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240 Usage: split_smi_library(smiles_file, 10)
0
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241 """
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242 output_files = []
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243 tfile = tempfile.NamedTemporaryFile(delete=False)
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244
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245 smiles_handle = open(smiles_file, 'r')
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246 for count, line in enumerate(smiles_handle):
0
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247 if count % structures_in_one_file == 0 and count != 0:
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248 tfile.close()
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249 output_files.append(tfile.name)
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250 tfile = tempfile.NamedTemporaryFile(delete=False)
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251 tfile.write(line)
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252 tfile.close()
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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253 output_files.append(tfile.name)
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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254 smiles_handle.close()
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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255 return output_files
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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256
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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257
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b578d0c101cd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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258 def mp_run(input_path, regex, PROCESSES, function_to_call):
0
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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259 paths = []
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260 [paths.append(compound_file) for compound_file in glob.glob(str(input_path) + str(regex))]
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0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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261 paths.sort()
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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262
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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263 pool = Pool(processes=PROCESSES)
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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264 print('Process initialized with', PROCESSES, 'processors')
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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265 result = pool.map_async(function_to_call, paths)
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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266 result.get()
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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267
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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268 return paths
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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269
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270
0
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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271 if __name__ == '__main__':
0eabdfaef1d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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272 print(check_filetype(sys.argv[1]))