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Merge branch 'master' of github.com:dannyspadaro/galaxytools into alevin-fry
2 parents 1ab4818 + c658843 commit 08ce36e

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‎chemicaltoolbox/lirasearch/.shed.yml‎

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categories:
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- Computational chemistry
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description: Generate 3D descriptors for a ligand conformer
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long_description: |
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Generate 3D descriptors for a ligand conformer, based on predicting
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the electrostatic potential (ESP) using a deep neural network, and
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computing spherical harmonic coefficients.
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homepage_url: https://github.com/rwmontalvao/SHCoeffsDev
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name: lirasearch
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owner: bgruening
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/lirasearch/
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type: unrestricted
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maintainers:
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- simonbray

‎chemicaltoolbox/lirasearch/lirasearch.xml‎

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<tool id="lirasearch" name="Identify similar conformers" version="@TOOL_VERSION@" profile="20.01">
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<description>using LiraSearch spherical harmonic descriptors</description>
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<macros>
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<token name="@TOOL_VERSION@">0.1.0</token>
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</macros>
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<requirements>
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<container type="docker">sb17/lirasearch:@TOOL_VERSION@</container>
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</requirements>
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<command detect_errors="exit_code">
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<![CDATA[
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export HOME=`pwd` &&
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#if $ligand.ext == 'pdb':
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ln -s $ligand ligand.pdb &&
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#else
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python /opt/scripts/convert_sdf_to_pdb.py $ligand ligand.pdb &&
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#end if
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python -m esp_dnn.predict -m ligand -i . -o . &&
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esp-surface-generator ligand.pdb.pqr ligand.pdb.tmesh &&
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sh-coeff-calculator . &&
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micromamba run -n lirasearch python /opt/scripts/lira_search_sdf.py --in_file rid_coeffs.csv --out_file output --out_keys keys.txt --database ${database_select.fields.path}/rid_coeffs.csv --num_results $num_results &&
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mkdir search_results && rocksdb_to_sdf ${database_select.fields.path} keys.txt search_results &&
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micromamba run -n lirasearch python /opt/scripts/lira_super.py --target ligand.pdb --folder search_results &&
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cat search_results/*rotated.sdf >> '$output_sdf'
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]]>
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</command>
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<inputs>
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<param name="ligand" type="data" format="pdb,sdf" label="Ligand file" help="Query for searching database" />
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<param name="database_select" type="select" label="Select database to search">
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<options from_data_table="lirasearch">
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<filter type="sort_by" column="2" />
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<validator type="no_options" message="No databases are available!" />
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</options>
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</param>
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<param name="num_results" type="integer" value="50" label="Number of results to return" />
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</inputs>
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<outputs>
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<data name="output_sdf" format="sdf" label="SDF with LiraSearch query results" />
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</outputs>
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<tests>
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<test>
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<param name="ligand" value="ligand.pdb" ftype="pdb" />
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<param name="database_select" value="test"/>
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<param name="num_results" value="2" />
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<output name="output_sdf" value="lirasearch_output.sdf"/>
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</test>
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<test>
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<param name="ligand" value="ligand.sdf"/>
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<param name="database_select" value="test"/>
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<param name="num_results" value="2" />
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<output name="output_sdf" value="lirasearch_output.sdf"/>
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</test>
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</tests>
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<help>
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<![CDATA[
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.. class:: infomark
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**What this tool does**
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Identify similar conformers to an input ligand, based on predicting the electrostatic potential (ESP) using a deep neural network and computing spherical harmonic coefficients.
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]]>
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</help>
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<citations>
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<citation type="doi">10.1101/2022.01.19.476747</citation>
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<citation type="doi">10.1021/acs.jmedchem.9b01129</citation>
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</citations>
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</tool>
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‎chemicaltoolbox/lirasearch/test-data/ligand.pdb‎

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ATOM 1 C1 MOL 1 -15.571 -21.538 0.079 0.00 0.00 C
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ATOM 2 C2 MOL 1 -15.927 -20.222 -0.610 0.00 0.00 C
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ATOM 3 C3 MOL 1 -15.772 -20.326 -2.133 0.00 0.00 C
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ATOM 4 N4 MOL 1 -16.073 -19.033 -2.753 0.00 0.00 N
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ATOM 5 C5 MOL 1 -16.274 -19.054 -4.180 0.00 0.00 C
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ATOM 6 C6 MOL 1 -15.033 -19.345 -5.053 0.00 0.00 C
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ATOM 7 O7 MOL 1 -13.944 -19.630 -4.569 0.00 0.00 O
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ATOM 8 N8 MOL 1 -15.234 -19.261 -6.418 0.00 0.00 N
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ATOM 9 C9 MOL 1 -16.512 -18.864 -7.057 0.00 0.00 C
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ATOM 10 C10 MOL 1 -16.309 -19.152 -8.563 0.00 0.00 C
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ATOM 11 C11 MOL 1 -14.812 -19.311 -8.685 0.00 0.00 C
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ATOM 12 C12 MOL 1 -14.016 -19.403 -9.818 0.00 0.00 C
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ATOM 13 C13 MOL 1 -12.638 -19.599 -9.683 0.00 0.00 C
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ATOM 14 C14 MOL 1 -12.095 -19.706 -8.403 0.00 0.00 C
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ATOM 15 C15 MOL 1 -12.865 -19.618 -7.241 0.00 0.00 C
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ATOM 16 C16 MOL 1 -14.236 -19.411 -7.410 0.00 0.00 C
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ATOM 17 C17 MOL 1 -15.209 -17.961 -2.252 0.00 0.00 C
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ATOM 18 C18 MOL 1 -15.366 -17.863 -0.735 0.00 0.00 C
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ATOM 19 N19 MOL 1 -15.037 -19.157 -0.136 0.00 0.00 N
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ATOM 20 CL20 MOL 1 -10.358 -19.959 -8.240 0.00 0.00 CL
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ATOM 21 Hh MOL 1 -16.224 -22.349 -0.263 0.00 0.00 H
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ATOM 22 Hh MOL 1 -15.686 -21.455 1.167 0.00 0.00 H
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ATOM 23 Hh MOL 1 -14.531 -21.813 -0.131 0.00 0.00 H
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ATOM 24 Hh MOL 1 -16.989 -19.981 -0.406 0.00 0.00 H
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ATOM 25 Hh MOL 1 -16.488 -21.065 -2.518 0.00 0.00 H
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ATOM 26 Hh MOL 1 -14.757 -20.677 -2.369 0.00 0.00 H
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ATOM 27 Hh MOL 1 -16.696 -18.086 -4.489 0.00 0.00 H
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ATOM 28 Hh MOL 1 -17.043 -19.807 -4.412 0.00 0.00 H
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ATOM 29 Hh MOL 1 -16.698 -17.796 -6.882 0.00 0.00 H
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ATOM 30 Hh MOL 1 -17.348 -19.425 -6.634 0.00 0.00 H
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ATOM 31 Hh MOL 1 -16.711 -18.345 -9.184 0.00 0.00 H
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ATOM 32 Hh MOL 1 -16.825 -20.075 -8.859 0.00 0.00 H
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ATOM 33 Hh MOL 1 -14.456 -19.325 -10.809 0.00 0.00 H
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ATOM 34 Hh MOL 1 -11.997 -19.670 -10.554 0.00 0.00 H
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ATOM 35 Hh MOL 1 -12.428 -19.703 -6.258 0.00 0.00 H
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ATOM 36 Hh MOL 1 -15.526 -17.017 -2.714 0.00 0.00 H
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ATOM 37 Hh MOL 1 -14.151 -18.128 -2.502 0.00 0.00 H
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ATOM 38 Hh MOL 1 -16.399 -17.535 -0.509 0.00 0.00 H
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ATOM 39 Hh MOL 1 -14.676 -17.106 -0.344 0.00 0.00 H
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ATOM 40 Hh MOL 1 -15.096 -19.092 0.879 0.00 0.00 H
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CONECT 1 2
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CONECT 2 1 3 19
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CONECT 3 2 4
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CONECT 4 3 5 17
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CONECT 5 4 6
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CONECT 6 5 7 7 8
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CONECT 7 6 6
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CONECT 8 6 9 16
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CONECT 9 8 10
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CONECT 10 9 11
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CONECT 11 10 12 12 16
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CONECT 12 11 11 13
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CONECT 13 12 14 14
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CONECT 14 13 13 15 20
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CONECT 15 14 16 16
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CONECT 16 8 11 15 15
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CONECT 17 4 18
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CONECT 18 17 19
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CONECT 19 2 18
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CONECT 20 14
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CONECT 1 21
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CONECT 21 1
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CONECT 1 22
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CONECT 22 1
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CONECT 1 23
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CONECT 23 1
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CONECT 2 24
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CONECT 24 2
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CONECT 3 25
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CONECT 25 3
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CONECT 3 26
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CONECT 26 3
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CONECT 5 27
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CONECT 27 5
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CONECT 5 28
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CONECT 28 5
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CONECT 9 29
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CONECT 29 9
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CONECT 9 30
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CONECT 30 9
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CONECT 10 31
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CONECT 31 10
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CONECT 10 32
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CONECT 32 10
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CONECT 12 33
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CONECT 33 12
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CONECT 13 34
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CONECT 34 13
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CONECT 15 35
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CONECT 35 15
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CONECT 17 36
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CONECT 36 17
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CONECT 17 37
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CONECT 37 17
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CONECT 18 38
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CONECT 38 18
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CONECT 18 39
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CONECT 39 18
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CONECT 19 40
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CONECT 40 19

‎chemicaltoolbox/lirasearch/test-data/ligand.sdf‎

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ligand.pdb
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OpenBabel06132509543D
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40 42 0 0 1 0 0 0 0 0999 V2000
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-15.5710 -21.5380 0.0790 C 0 0 0 0 0 0 0 0 0 0 0 0
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M END
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$$$$

‎chemicaltoolbox/lirasearch/test-data/lirasearch.loc‎

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# This file lists databases that can be searched with LiraSearch.
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# The file has the format (white space characters are
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# TAB characters):
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#
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# <unique_id> <name> <version> <path>
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#
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# So, lirasearch.loc could look something like this:
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#value name version path
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#zinc20 ZINC20 1 /home/galaxy/zinc20
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#zinc22 ZINC22 1 /home/galaxy/zinc22
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#dude DUD-E 1 /home/galaxy/dude
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test test 1 ${__HERE__}/storage

‎chemicaltoolbox/lirasearch/test-data/lirasearch_output.sdf‎

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ZINCae0000002oHX.0
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RDKit 3D
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3 4 1 6
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3 5 1 0
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5 20 1 0
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6 7 1 6
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M END
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$$$$
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ZINCae0000002oRr.0
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RDKit 3D
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2 3 1 0
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3 4 1 0
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7 8 2 0
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7 17 1 0
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M END
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$$$$

‎chemicaltoolbox/lirasearch/test-data/storage/000004.log‎

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‎chemicaltoolbox/lirasearch/test-data/storage/CURRENT‎

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MANIFEST-000005

‎chemicaltoolbox/lirasearch/test-data/storage/IDENTITY‎

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