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Alan Christie
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Merge remote-tracking branch 'origin/master'
2 parents 393e998 + c1005f4 commit f6e10b0

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‎data/sucos/4e3g_lig.sdf‎ renamed to ‎data/sucos/4e3g_lig.mol‎

File renamed without changes.

‎data/sucos/mols.sdf‎

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RDKit 3D
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M END
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$$$$
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OpenBabel11011818103D
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16 16 0 0 0 0 0 0 0 0999 V2000
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16.4400 2.1870 15.2350 C 0 0 0 0 0 0 0 0 0 0 0 0
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M END
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$$$$
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obj02
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PyMOL2.1 3D 0
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10 10 0 0 0 0 0 0 0 0999 V2000
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16.4400 2.1870 15.2350 C 0 0 0 0 0 0 0 0 0 0 0 0
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15.2530 1.8470 15.5410 O 0 0 0 0 0 0 0 0 0 0 0 0
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M END
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$$$$
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RDKit 3D
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10 10 0 0 0 0 0 0 0 0999 V2000
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M END
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$$$$
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4e3g_lig
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M END
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$$$$
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4e3g_lig
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5 6 2 0 0 0 0
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M END
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$$$$

‎src/python/pipelines/rdkit/sucos.dsd.json‎

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"visible": true,
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"description": "Target molecule index (default is the first)",
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"label": "Target mol index",
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"key": "arg.target",
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"key": "arg.targetidx",
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"minValues": 0,
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"maxValues": 1,
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"typeDescriptor": {
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}
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],
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"imageName": "informaticsmatters/rdkit_pipelines",
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"command": "python -m pipelines.rdkit.sucos --target target.data.gz -i ${PIN}input.data.gz -o ${POUT}output -of json${binding.variables.containsKey('target') ? ' --targetidx ' + binding.variables.get('targetidx') : ''} --meta"
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"command": "python -m pipelines.rdkit.sucos --target ${PIN}target.data.gz -i ${PIN}input.data.gz -o ${POUT}output -of json${binding.variables.containsKey('targetidx') ? ' --targetidx ' + binding.variables.get('targetidx') : ''} --meta"
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}

‎src/python/pipelines/rdkit/sucos.test‎

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version = 1,
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// Testing sucos.py reading from file and writing to file
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test_raw_sucos_sdf_to_sdf = [
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test_raw_sucos_sdf_to_mol = [
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command: '''python -m pipelines.rdkit.sucos
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--target ${PIN}/sucos/4e3g_lig.sdf
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--target ${PIN}/sucos/4e3g_lig.mol
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-i ${PIN}/sucos/benzene.sdf -if sdf
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-o ${POUT}output -of sdf''',
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stderr: [ 'Score: 0.843' ],
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creates: [ 'output.sdf.gz' ],
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],
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test_raw_sucos_sdf_pick_target_1 = [
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command: '''python -m pipelines.rdkit.sucos
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--target ${PIN}/sucos/mols.sdf
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--targetidx 1
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-i ${PIN}/sucos/mols.sdf -if sdf
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-o ${POUT}output -of sdf''',
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stderr: [ 'Score: 0.843' ],
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creates: [ 'output.sdf.gz' ],
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],
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test_raw_sucos_sdf_pick_target_6 = [
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command: '''python -m pipelines.rdkit.sucos
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--target ${PIN}/sucos/mols.sdf
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--targetidx 6
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-i ${PIN}/sucos/mols.sdf -if sdf
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-o ${POUT}output -of sdf''',
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stderr: [ 'Score: 1.0' ],
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creates: [ 'output.sdf.gz' ],
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]
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