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#35 initial rdock enhancements
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‎data/nudt7/ligand.mol‎

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OpenBabel06051719483D
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18 19 0 0 0 0 2 V2000
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29.0700 -43.2240 73.7660 C 0 0 0 0 0
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36.2650 -44.8070 74.9140 C 0 0 0 0 0
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37.1260 -44.6280 73.8270 C 0 0 0 0 0
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38.5050 -44.6030 73.9960 C 0 0 0 0 0
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39.0530 -44.7650 75.2580 C 0 0 0 0 0
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38.2200 -44.9420 76.3450 C 0 0 0 0 0
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36.8400 -44.9680 76.1790 C 0 0 0 0 0
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30.0630 -44.1750 73.1160 C 0 0 0 0 0
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29.4310 -45.1480 72.1250 C 0 0 0 0 0
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32.0050 -44.9160 74.3360 C 0 0 0 0 0
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32.8370 -45.6680 73.5100 C 0 0 0 0 0
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34.2080 -45.6230 73.7110 C 0 0 0 0 0
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34.7860 -44.8390 74.7200 C 0 0 0 0 0
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33.9230 -44.0930 75.5330 C 0 0 0 0 0
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32.5490 -44.1280 75.3490 C 0 0 0 0 0
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30.2050 -45.7640 71.3670 O 0 0 0 0 0
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28.1910 -45.2760 72.1490 O 0 0 0 0 0
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30.6380 -44.9430 74.1670 O 0 0 0 0 0
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M CHG 1 17 -1
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M END

‎data/nudt7/ligands.data.gz‎

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‎data/nudt7/receptor.mol2‎

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‎src/nextflow/docking/.gitignore‎

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results

‎src/nextflow/docking/rdock-filter.nsd.config‎

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// Intentionally Empty

‎src/nextflow/docking/rdock-filter.nsd.nf‎

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#!/usr/bin/env nextflow
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/* Squonk Nextflow pipline that runs Docking using rDock, filtering the poses relative to the score from docking the
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* reference ligand.
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*
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* To test this manually run something like this:
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* nextflow -c src/nextflow/nextflow-docker.config run src/nextflow/docking/rdock-filter.nsd.nf --ligands data/nudt7/ligands.data.gz --ligand data/nudt7/ligand.mol --receptor data/nudt7/receptor.mol2 --num_dockings 5 -with-docker informaticsmatters/rdkit_pipelines
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*/
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params.ligand = "$baseDir/ligand.mol"
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params.ligands = "$baseDir/ligands.data.gz"
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params.receptor = "$baseDir/receptor.mol2"
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params.chunk = 25
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params.num_dockings = 25
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params.top = 1
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params.score = null
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params.nscore = null
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params.limit = 0
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params.digits = 4
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params.threshold = 0.0
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params.field = 'SCORE.norm'
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ligand = file(params.ligand)
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ligands = file(params.ligands)
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receptor = file(params.receptor)
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process create_cavity {
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container 'informaticsmatters/rdock-mini:latest'
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beforeScript 'chmod g+w .'
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input:
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file ligand
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file receptor
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output:
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file 'receptor.prm' into prmfile
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file 'receptor.as' into asfile
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"""
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cat << EOF > receptor.prm
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RBT_PARAMETER_FILE_V1.00
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RECEPTOR_FILE $receptor
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RECEPTOR_FLEX 3.0
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SECTION MAPPER
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SITE_MAPPER RbtLigandSiteMapper
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REF_MOL $ligand
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RADIUS 3.0
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SMALL_SPHERE 1.0
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MIN_VOLUME 100
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MAX_CAVITIES 1
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VOL_INCR 0.0
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GRIDSTEP 0.5
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END_SECTION
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SECTION CAVITY
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SCORING_FUNCTION RbtCavityGridSF
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WEIGHT 1.0
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END_SECTION
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EOF
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rbcavity -was -d -r receptor.prm > rbcavity.log
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"""
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}
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/* Docks the reference ligand
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*/
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process dock_reference_ligand {
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container 'informaticsmatters/rdock-mini:latest'
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beforeScript 'chmod g+w .'
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publishDir "$baseDir/results", mode: 'copy'
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input:
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file receptor
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file 'receptor.as' from asfile
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file 'receptor.prm' from prmfile
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file ligand
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output:
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file 'best_ligand.sdf' into best_ligand
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"""
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rbdock -i ligand.mol -r receptor.prm -p dock.prm -n $params.num_dockings -o docked_ligand > docked_ligand_out.log
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sdsort -n -s -fSCORE docked_ligand.sd | sdfilter -f'\$_COUNT <= 1' > best_ligand.sdf
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"""
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}
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/* Splits the input into multiple files of ${params.chunk} records.
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*/
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process splitter {
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//beforeScript 'chmod g+w .'
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container 'informaticsmatters/rdkit_pipelines:latest'
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input:
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file ligands
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output:
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file 'ligands_part*.sdf' into ligands_parts mode flatten
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file 'ligands_part_metrics.txt' into splitter_metrics
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"""
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python -m pipelines_utils_rdkit.filter -i $ligands -c $params.chunk -l $params.limit -d $params.digits -o ligands_part -of sdf --no-gzip --meta
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"""
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}
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/* Docks each file from the ligands_parts channel sending each resulting SD file to the results channel
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*/
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process dock_ligands {
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container 'informaticsmatters/rdock-mini:latest'
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// change permissions on the work dir so that the rdock user in the container
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// can write to the directory that is owned by root
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beforeScript 'chmod g+w .'
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input:
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file part from ligands_parts
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file receptor
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file 'receptor.as' from asfile
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file 'receptor.prm' from prmfile
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output:
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file 'docked_part*.sd' into docked_parts
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"""
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rbdock -i $part -r receptor.prm -p dock.prm -n $params.num_dockings -o ${part.name.replace('ligands', 'docked')[0..-5]} > docked_out.log
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"""
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}
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/* Filter, combine and publish the results.
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* Poses are only included if they are within ${params.threshold} of the best score obtained from docking the
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* target ligand into the same receptor (output of the dock_ligand process).
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*/
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process combine_and_filter {
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container 'informaticsmatters/rdock-mini:latest'
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beforeScript 'chmod g+w .'
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input:
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file parts from docked_parts.collect()
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file best from best_ligand
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output:
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file 'rdock_results.sdf' into results
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"""
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FSCORE=\$(sdreport -nh -t${params.field} best_ligand.sdf | cut -f 2 | awk '{\$1=\$1};1')
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ASCORE=\$(awk "BEGIN {print \$FSCORE + ${params.threshold}}")
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echo "Processing $parts with normalised score filter of \$ASCORE"
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sdsort -n -s -f${params.field} docked_part*.sd | sdfilter -f"\\\$${params.field} < \$ASCORE" | sdfilter -f'\$_COUNT <= ${params.top}' > rdock_results.sdf
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"""
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}
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process results {
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beforeScript 'chmod g+w .'
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container 'informaticsmatters/rdkit_pipelines:latest'
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beforeScript 'chmod g+w .'
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publishDir "$baseDir/results", mode: 'copy'
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input:
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file 'results.sdf' from results
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file 'splitter_metrics.txt' from splitter_metrics
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output:
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file 'output.data.gz'
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file 'output.metadata'
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file 'output_metrics.txt'
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"""
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python -m pipelines_utils_rdkit.filter -i results.sdf -of json -o output --meta
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mv output_metrics.txt old_metrics.txt
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echo -n 'DockingRDock=' >> output_metrics.txt
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echo \$((`grep '__InputCount__' splitter_metrics.txt | cut -d '=' -f 2` * ${params.num_dockings})) >> output_metrics.txt
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grep '__InputCount__' splitter_metrics.txt >> output_metrics.txt
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grep '__OutputCount__' old_metrics.txt >> output_metrics.txt
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"""
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}

‎src/nextflow/nextflow-docker.config‎

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docker.enabled = true
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docker.mountFlags = 'z'
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docker.runOptions = '-u $(id -u):$(id -g)'
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process.container = 'busybox'

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