Mercurial > repos > bgruening > xchem_transfs_scoring

annotate transfs.xml @ 2:8f9269d95f91 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit 9955c29ac23ce80b2fbfd4082845a7809c8f2121"
author bgruening
date Mon, 13 Apr 2020 15:00:39 +0000
parents 189f598faea1
children
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8f9269d95f91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit 9955c29ac23ce80b2fbfd4082845a7809c8f2121"
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1 <tool id="xchem_transfs_scoring" name="XChem TransFS pose scoring" version="0.4.0">
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2 <description>using deep learning</description>
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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4 <requirements>
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5 <!--requirement type="package" version="3.0.0">openbabel</requirement-->
69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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6 <!--requirement type="package" version="3.7">python</requirement-->
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7 <!-- many other requirements are needed -->
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8f9269d95f91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit 9955c29ac23ce80b2fbfd4082845a7809c8f2121"
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8 <container type="docker">informaticsmatters/transfs:1.3</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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12 cd /train/fragalysis_test_files/ &&
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8f9269d95f91 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit 9955c29ac23ce80b2fbfd4082845a7809c8f2121"
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13 mkdir -p workdir/tfs &&
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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14 cd workdir &&
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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16 cp '$ligands' ligands.sdf &&
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17 cp '$receptor' receptor.pdb &&
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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19 cd ../ &&
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20 python transfs.py -i /train/fragalysis_test_files/workdir/ligands.sdf -r /train/fragalysis_test_files/workdir/receptor.pdb -d $distance -w workdir/tfs --model '$model' '$mock' &&
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21 ls -l &&
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22 ls -l workdir &&
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23 cp ./workdir/tfs/output.sdf '$output' &&
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24 head -n 1000 ./workdir/tfs/output.sdf &&
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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26 mkdir -p ./pdb &&
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27 cp -r ./workdir/tfs/receptor*.pdb ./pdb &&
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28 tar -cvhf archiv.tar ./pdb &&
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29 cp archiv.tar '$output_receptors' &&
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30
2
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31 cp ./workdir/tfs/predictions.txt '$predictions'
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69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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33 ]]></command>
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34
69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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35 <inputs>
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36 <param type="data" name="receptor" format="pdb" label="Receptor" help="Select a receptor (PDB format)."/>
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37 <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands (docked poses) in SDF format)"/>
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38 <param name="distance" type="float" value="0" min="0" max="5.0" label="Distance to waters"
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39 help="Remove waters closer than this distance to any ligand heavy atom (0 means skip this process)."/>
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40 <param name="model" type="select" label="Model for predictions">
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41 <option value="weights.caffemodel">No threshold (original model)</option>
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42 <option value="10nm.0_iter_50000.caffemodel">10nM threshold</option>
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43 <option value="50nm.0_iter_50000.caffemodel">50nM threshold</option>
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44 <option value="200nm.0_iter_50000.caffemodel">200nM threshold</option>
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45 </param>
0
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46 <param type="hidden" name="mock" value="" label="Mock calculations" help="Use random numbers instead of running on GPU"/>
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47 </inputs>
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48 <outputs>
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49 <data name="output" format="sdf" label="XChem pose scoring on ${on_string}"/>
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50 <data name="predictions" format="txt" label="Predictions on ${on_string}"/>
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51 <data name="output_receptors" format="tar" label="Receptors ${on_string}"/>
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52
69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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53 <!--collection name="pdb_files" type="list" label="PDB files with variable number of waters">
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54 <discover_datasets pattern="__name_and_ext__" directory="pdb" />
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55 </collection-->
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56 </outputs>
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57
69fe50d03b80 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/transfs commit d9a9e2f0e12fe9d2c37f632d99f2164df577b4af"
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58 <tests>
2
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59 <test>
0
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60 <param name="receptor" value="receptor.pdb"/>
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61 <param name="ligands" value="ligands.sdf"/>
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62 <param name="mock" value="--mock" />
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63 <param name="distance" value="4.0"/>
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64 <output name="output" ftype="sdf">
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65 <assert_contents>
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66 <has_text text="TransFSReceptor"/>
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67 <has_text text="TransFSScore"/>
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68 </assert_contents>
2
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69 </output> -->
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70 <!---output_collection name="pdb_files" type="list" count="2" /-->
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71 </test>
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72 <test>
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73 <param name="receptor" value="receptor.pdb"/>
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74 <param name="ligands" value="ligands.sdf"/>
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75 <param name="mock" value="--mock" />
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76 <param name="distance" value="0"/>
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77 <output name="output" ftype="sdf">
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78 <assert_contents>
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79 <not_has_text text="TransFSReceptor"/>
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80 <has_text text="TransFSScore"/>
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81 </assert_contents>
0
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82 </output>
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83 <!--output_collection name="pdb_files" type="list" count="1" /-->
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84 </test>
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85 </tests>
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86 <help><![CDATA[
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87
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88 .. class:: infomark
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89
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90 This tool performs scoring of docked ligand poses using deep learning.
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91 It uses the gnina and libmolgrid toolkits to perform the scoring to generate
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92 a prediction for how good the pose is.
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93
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94
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95 -----
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96
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97 .. class:: infomark
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98
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99 **Inputs**
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100
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101 1. The protein receptor to dock into as a file in PDB format. This should have the ligand removed but can
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102 retain the waters. This is specified by the 'receptor' parameter.
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103 2. A set of ligand poses to score in SDF format. This is specified by the 'ligands' parameter.
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104
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105 Other parameters:
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106
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107 'distance': Distance in Angstroms. Waters closer than this to any heavy atom in each ligand are removed.
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108 A discrete set of PDB files are created missing certain waters and the ligands corresponding to that PDB file are
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109 scored against it. If a distance of zero is specified then this process is skipped and all ligands are scored against
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110 the receptor 'as is'. The assumption is that all waters have already been removed in this case. Specifying a
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111 distance of 0 provides a significant boost in performance as the water checking step is avoided..
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112
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113 'model': A number of models are provided:
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114 - weights.caffemodel - No threshold for distinction of actives and inactives (original model)
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115 - 10nm.0_iter_50000.caffemodel: actives are molecules from DUDE that have better than 10nM activity
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116 - 50nm.0_iter_50000.caffemodel: actives are molecules from DUDE that have better than 50nM activity
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117 - 200nm.0_iter_50000.caffemodel: actives are molecules from DUDE that have better than 200nM activity
0
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118
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119 -----
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120
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121 .. class:: infomark
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122
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123 **Outputs**
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124
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125 An SDF file is produced as output. The predicted scores are contained within the SDF file
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126 as the TransFSScore property and the PDB file (with the waters that clash with the ligand removed)
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127 that was used for the scoring as the TransFSReceptor property.
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128 Values for the score range from 0 (poor binding) to 1 (good binding).
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129
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130 The raw predictions (predictions.txt) is also provided as an output.
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131
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132 A set of PDB files is also output, each one with different crystallographic waters removed. Each ligand is
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133 examined against input PDB structure and the with waters that clash (any heavy atom of the ligand closer than
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134 the 'distance' parameter being removed. The file names are encoded with the water numbers that are removed.
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135
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136 ]]></help>
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137 </tool>