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annotate parmconv.xml @ 7:5a97cb53a456 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 27e76b3f6ed12955fd60609aad4043bc9c60cba2"
author chemteam
date Thu, 07 Oct 2021 09:52:50 +0000
parents 267a70416daf
children
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da2252f1ccab "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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1 <tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>to AMBER prmtop in preparation for MMGBSA/MMPBSA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements">
7
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8 <requirement type="package" version="3.4.3">parmed</requirement>
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9 <requirement type="package" version="2021.3">gromacs</requirement>
4
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10 <requirement type="package" version="3.0.1">jinja2</requirement>
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11 </expand>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
3
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14 #if $param_inputs.fmt == "GROMACS":
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15 python '$__tool_directory__/parmconv.py'
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16 --istr '$param_inputs.str_in'
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17 --itop '$param_inputs.top_in'
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18 $param_inputs.modbehaviour.removedihe
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19 $param_inputs.modbehaviour.removebox
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20 --iradii '$param_inputs.modbehaviour.radii'
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21 --istripmask '$stripmask_ligand'
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22 --o_prmtop '$prmtop_ligand'
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23 2>&1 &&
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24 python '$__tool_directory__/parmconv.py'
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25 --istr '$param_inputs.str_in'
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26 --itop '$param_inputs.top_in'
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27 $param_inputs.modbehaviour.removedihe
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28 $param_inputs.modbehaviour.removebox
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29 --iradii '$param_inputs.modbehaviour.radii'
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30 --istripmask '$stripmask_receptor'
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31 --o_prmtop '$prmtop_receptor'
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32 2>&1 &&
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33 python '$__tool_directory__/parmconv.py'
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34 --istr '$param_inputs.str_in'
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35 --itop '$param_inputs.top_in'
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36 $param_inputs.modbehaviour.removedihe
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37 $param_inputs.modbehaviour.removebox
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38 --iradii '$param_inputs.modbehaviour.radii'
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39 --istripmask '$stripmask_complex'
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40 --o_prmtop '$prmtop_complex'
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41 2>&1 &&
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42 python '$__tool_directory__/parmconv.py'
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43 --istr '$param_inputs.str_in'
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44 --itop '$param_inputs.top_in'
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45 $param_inputs.modbehaviour.removedihe
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46 $param_inputs.modbehaviour.removebox
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47 --iradii '$param_inputs.modbehaviour.radii'
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48 --istripmask '$stripmask_solvatedcomplex'
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49 --o_prmtop '$prmtop_solvatedcomplex'
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50 2>&1
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51 #else
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52 python '$templating_script' '$inputs' &&
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53 PATH_TO_PARMED=\$(dirname `which parmed`) &&
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54 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
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55 export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
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56 parmed -i ligand.script -O &&
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57 parmed -i receptor.script -O &&
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58 parmed -i complex.script -O &&
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59 parmed -i solvatedcomplex.script -O
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60 #end if
0
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61 ]]>
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62 </command>
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63 <configfiles>
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64 <inputs name="inputs"/>
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65 <configfile name="templating_script">
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66 <![CDATA[
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67
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68 import os
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69 import sys
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70 import json
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71
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72 from jinja2 import Environment, FileSystemLoader
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73 input_json_path = sys.argv[1]
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74 params = json.load(open(input_json_path, "r"))
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75 currentpath = "$__tool_directory__" # should work generally
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76 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
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77 template = template_environment.get_template('template_parmconv.j2')
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78 params['fmt'] = '$param_inputs.fmt'
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79 #if str($param_inputs.fmt) == 'AMBER':
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80 params["top_in"] = '$param_inputs.top_in'
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81 #else:
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82 params["top_in"] = '$param_inputs.top_in'
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83 params["str_in"] = '$param_inputs.str_in'
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84 #end if
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85 params['prmtop_ligand'] = '$prmtop_ligand'
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86 params['prmtop_receptor'] = '$prmtop_receptor'
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87 params['prmtop_complex'] = '$prmtop_complex'
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88 params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex'
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89 print(params)
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90
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91
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92 def unescape(cond_text):
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93 """
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94 # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py
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95 """
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96 mapped_chars = { '>' :'__gt__',
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97 '<' :'__lt__',
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98 "'" :'__sq__',
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99 '"' :'__dq__',
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100 '[' :'__ob__',
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101 ']' :'__cb__',
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102 '{' :'__oc__',
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103 '}' :'__cc__',
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104 '@' : '__at__',
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105 '\n' : '__cn__',
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106 '\r' : '__cr__',
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107 '\t' : '__tc__',
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108 '&' : '__and__'
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109 }
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110 for key, value in mapped_chars.items():
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111 cond_text = cond_text.replace( value, key )
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112 return cond_text
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113
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114 def run_template(params=params, system="ligand"):
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115 """
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116 # Render template on a selected system using a local parameter copy
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117 """
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118 localparams=params.copy() # shallow copy ok for simple variables
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119 localparams['stripmask']=unescape(localparams['stripmask_'+system])
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120 localparams['prmtop_out']=localparams['prmtop_'+system]
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121 print(localparams)
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122 with open(system+'.script','w+') as f:
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123 f.write(template.render(localparams))
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124
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125 systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex']
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126 for system in systems:
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127 run_template(system=system)
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128
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129 ]]>
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130 </configfile>
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131 </configfiles>
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132 <inputs>
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133 <conditional name="param_inputs">
3
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134 <param name="fmt" type="select" label="Input format">
0
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135 <option selected="True" value="AMBER">AMBER</option>
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136 <option value="GROMACS">GROMACS</option>
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137 </param>
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138 <when value="AMBER">
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139 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>
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140 </when>
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141 <when value="GROMACS">
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142 <param name="top_in" type="data" label="Input topology (top) file" format="top"/>
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143 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>
3
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144 <section name="modbehaviour" title="Modify behaviour" expanded="false">
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145 <param name="removedihe" type="boolean" truevalue="--removedihe" falsevalue="" checked="false" label="Remove all zero period dihedrals" help="This will remove zero period dihedrals from the generated topology"/>
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146 <param name="removebox" type="boolean" truevalue="--removebox" falsevalue="" checked="false" label="Remove periodic box information" help="This will remove periodic information from the generated topology"/>
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147 <param name="radii" type="select" label="Radii to use" help="Select the radii to use. Default is mbondi.">
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148 <option selected="True" value="mbondi">mbondi</option>
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149 <option value="mbondi2">mbondi2</option>
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150 <option value="mbondi3">mbondi3</option>
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151 <option value="bondi">bondi</option>
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152 <option value="amber6">amber6</option>
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153 </param>
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154 </section>
0
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155 </when>
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156 </conditional>
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157 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand">
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158 <sanitizer>
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159 <valid initial="string.printable">
3
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160 <add value="&amp;"/>
0
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161 </valid>
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162 </sanitizer>
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163 </param>
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164 <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor">
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165 <sanitizer>
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166 <valid initial="string.printable">
3
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167 <add value="&amp;"/>
0
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168 </valid>
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169 </sanitizer>
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170 </param>
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171 <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)">
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172 <sanitizer>
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173 <valid initial="string.printable">
3
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174 <add value="&amp;"/>
0
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175 </valid>
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176 </sanitizer>
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177 </param>
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178 <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)">
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179 <sanitizer>
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180 <valid initial="string.printable">
3
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181 <add value="&amp;"/>
0
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182 </valid>
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183 </sanitizer>
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184 </param>
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185 </inputs>
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186 <outputs>
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187 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/>
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188 <data format="txt" name="prmtop_receptor" label="receptor prmtop"/>
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189 <data format="txt" name="prmtop_complex" label="complex prmtop"/>
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190 <data format="txt" name="prmtop_solvatedcomplex" label="solvated complex prmtop"/>
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191 </outputs>
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192 <tests>
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193 <test>
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194 <!--example in this test is not solvated but sufficient -->
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195 <param name="fmt" value="AMBER"/>
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196 <conditional name="param_inputs">
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197 <param name="top_in" value="complex.prmtop"/>
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198 </conditional>
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199 <param name="stripmask_ligand" value="!:RAL"/>
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200 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/>
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201 <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/>
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202 <output name="prmtop_ligand">
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203 <assert_contents>
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204 <has_text text=" 61 15"/>
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205 <has_text text="%FLAG MASS"/>
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206 <has_text text="RAL"/>
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207 </assert_contents>
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208 </output>
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209 <output name="prmtop_receptor">
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210 <assert_contents>
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211 <has_text text=" 3880 15"/>
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212 <has_text text="%FLAG MASS"/>
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213 <has_text text="ALA LEU"/>
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214 <not_has_text text="RAL "/>
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215 </assert_contents>
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216 </output>
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217 <output name="prmtop_complex">
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218 <assert_contents>
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219 <has_text text=" 3941 15"/>
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220 <has_text text="%FLAG MASS"/>
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221 <has_text text="ALA LEU"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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222 <has_text text="RAL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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223 </assert_contents>
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224 </output>
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225 </test>
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226 <test>
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227 <!--example in this test is from @sbrays' gromacs tests. It has no ligand but is sufficient and will not take extra space in the repo! -->
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228 <param name="fmt" value="GROMACS"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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229 <conditional name="param_inputs">
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230 <param name="top_in" value="topol_solv.top"/>
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231 <param name="str_in" value="solv_ions.gro"/>
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232 </conditional>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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233 <!-- pretending CL is a ligand -->
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234 <param name="stripmask_ligand" value="!:CL"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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235 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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236 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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237 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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238 <output name="prmtop_ligand">
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239 <assert_contents>
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240 <has_text text="%FLAG MASS"/>
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241 <has_text text="CL"/>
3
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242 <has_text text="SOLVENT_POINTERS"/>
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243 <has_text text="BOX_DIMENSIONS"/>
0
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244 </assert_contents>
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245 </output>
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246 <output name="prmtop_receptor">
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247 <assert_contents>
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248 <has_text text="%FLAG MASS"/>
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249 <has_text text="LYS VAL PHE "/>
3
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250 <has_text text="SOLVENT_POINTERS"/>
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251 <has_text text="BOX_DIMENSIONS"/>
0
6c6cecf51bd0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
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252 <not_has_text text="CL "/>
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253 </assert_contents>
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254 </output>
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255 <output name="prmtop_solvatedcomplex">
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256 <assert_contents>
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257 <has_text text="%FLAG MASS"/>
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258 <has_text text="LYS VAL PHE"/>
3
2b82fc7bec67 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
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259 <has_text text="SOLVENT_POINTERS"/>
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260 <has_text text="BOX_DIMENSIONS"/>
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261 </assert_contents>
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262 </output>
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263 </test>
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264 <test>
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265 <!-- test with removing dihedrals and periodicity -->
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266 <param name="fmt" value="GROMACS"/>
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diff changeset
267 <conditional name="param_inputs">
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268 <param name="top_in" value="topol_solv.top"/>
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269 <param name="str_in" value="solv_ions.gro"/>
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270 </conditional>
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271 <!-- dihedrals and periodicity -->
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272 <param name="removedihe" value="--removedihe"/>
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273 <param name="removebox" value="--removebox"/>
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274 <!-- pretending CL is a ligand -->
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275 <param name="stripmask_ligand" value="!:CL"/>
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276 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
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277 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
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278 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
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279 <output name="prmtop_ligand">
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280 <assert_contents>
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281 <has_text text="%FLAG MASS"/>
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282 <has_text text="CL"/>
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283 <not_has_text text="SOLVENT_POINTERS"/>
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284 <not_has_text text="BOX_DIMENSIONS"/>
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285 </assert_contents>
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286 </output>
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287 <output name="prmtop_receptor">
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288 <assert_contents>
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289 <has_text text="%FLAG MASS"/>
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290 <has_text text="LYS VAL PHE "/>
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291 <not_has_text text="CL "/>
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292 <not_has_text text="SOLVENT_POINTERS"/>
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293 <not_has_text text="BOX_DIMENSIONS"/>
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294 </assert_contents>
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295 </output>
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296 <output name="prmtop_solvatedcomplex">
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297 <assert_contents>
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298 <has_text text="%FLAG MASS"/>
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299 <has_text text="LYS VAL PHE"/>
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300 <not_has_text text="SOLVENT_POINTERS"/>
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301 <not_has_text text="BOX_DIMENSIONS"/>
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302 </assert_contents>
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303 </output>
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304 </test>
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305 </tests>
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306 <help>
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307 <![CDATA[
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308 .. class:: infomark
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309
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310 **What it does**
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311
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312 This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMGBSA/MMPBSA calculations.
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313
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314 .. class:: infomark
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315
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316 **How it works**
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317
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318 AmberTools' ParmEd is used to strip unneeded atoms and save the parameter files. The stripmasks are defined by the user.
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319
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320 .. class:: infomark
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321
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322 **Outputs created**
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323
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324 prmtop files for the ligand, receptor, complex and solvated complex.
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325
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326 .. class:: infomark
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327
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328 **User guide and documentation**
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329
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330 - The `AmberTools Manual`_
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331 - The `Parmed Documentation`_
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332
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333
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334 .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf
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335 .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html
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336
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337
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338 ]]>
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339 </help>
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340 <expand macro="citations">
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341 <citation type="bibtex">@misc{parmed_2020, author = {ParmEd}, title = {ParmEd/ParmEd}, url={https://github.com/ParmEd/ParmEd}, abstract = {Parameter/topology editor and molecular simulator. Contribute to ParmEd/ParmEd development by creating an
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342 account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>
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343 </expand>
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344 </tool>