#35 initial rdock enhancements

data/nudt7/ligand.mol

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+
+ OpenBabel06051719483D
+
+ 18 19  0  0  0  0              2 V2000
+   29.0700  -43.2240   73.7660 C   0  0  0  0  0
+   36.2650  -44.8070   74.9140 C   0  0  0  0  0
+   37.1260  -44.6280   73.8270 C   0  0  0  0  0
+   38.5050  -44.6030   73.9960 C   0  0  0  0  0
+   39.0530  -44.7650   75.2580 C   0  0  0  0  0
+   38.2200  -44.9420   76.3450 C   0  0  0  0  0
+   36.8400  -44.9680   76.1790 C   0  0  0  0  0
+   30.0630  -44.1750   73.1160 C   0  0  0  0  0
+   29.4310  -45.1480   72.1250 C   0  0  0  0  0
+   32.0050  -44.9160   74.3360 C   0  0  0  0  0
+   32.8370  -45.6680   73.5100 C   0  0  0  0  0
+   34.2080  -45.6230   73.7110 C   0  0  0  0  0
+   34.7860  -44.8390   74.7200 C   0  0  0  0  0
+   33.9230  -44.0930   75.5330 C   0  0  0  0  0
+   32.5490  -44.1280   75.3490 C   0  0  0  0  0
+   30.2050  -45.7640   71.3670 O   0  0  0  0  0
+   28.1910  -45.2760   72.1490 O   0  0  0  0  0
+   30.6380  -44.9430   74.1670 O   0  0  0  0  0
+  1  8  1  0  0  0
+  2  3  2  0  0  0
+  2  7  1  0  0  0
+  2 13  1  0  0  0
+  3  4  1  0  0  0
+  4  5  2  0  0  0
+  5  6  1  0  0  0
+  6  7  2  0  0  0
+  8  9  1  0  0  0
+  8 18  1  0  0  0
+  9 16  2  0  0  0
+  9 17  1  0  0  0
+ 10 11  2  0  0  0
+ 10 15  1  0  0  0
+ 10 18  1  0  0  0
+ 11 12  1  0  0  0
+ 12 13  2  0  0  0
+ 13 14  1  0  0  0
+ 14 15  2  0  0  0
+M  CHG  1  17  -1
+M  END

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
+
+/* Squonk Nextflow pipline that runs Docking using rDock, filtering the poses relative to the score from docking the
+* reference ligand.
+*
+* To test this manually run something like this:
+* 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
+*/
+
+params.ligand = "$baseDir/ligand.mol"
+params.ligands = "$baseDir/ligands.data.gz"
+params.receptor = "$baseDir/receptor.mol2"
+params.chunk = 25
+params.num_dockings = 25
+params.top = 1
+params.score = null
+params.nscore = null
+params.limit = 0
+params.digits = 4
+params.threshold = 0.0
+params.field = 'SCORE.norm'
+
+ligand = file(params.ligand)
+ligands = file(params.ligands)
+receptor = file(params.receptor)
+
+process create_cavity {
+
+    container 'informaticsmatters/rdock-mini:latest'
+    beforeScript 'chmod g+w .'
+
+    input:
+    file ligand
+    file receptor
+
+    output:
+    file 'receptor.prm' into prmfile
+    file 'receptor.as' into asfile
+
+    """
+    cat << EOF > receptor.prm
+RBT_PARAMETER_FILE_V1.00
+RECEPTOR_FILE $receptor
+RECEPTOR_FLEX 3.0
+SECTION MAPPER
+    SITE_MAPPER RbtLigandSiteMapper
+    REF_MOL $ligand
+    RADIUS 3.0
+    SMALL_SPHERE 1.0
+    MIN_VOLUME 100
+    MAX_CAVITIES 1
+    VOL_INCR 0.0
+    GRIDSTEP 0.5
+END_SECTION
+SECTION CAVITY
+    SCORING_FUNCTION RbtCavityGridSF
+    WEIGHT 1.0
+END_SECTION
+EOF
+
+rbcavity -was -d -r receptor.prm > rbcavity.log
+    """
+}
+
+/* Docks the reference ligand
+*/
+process dock_reference_ligand {
+
+    container 'informaticsmatters/rdock-mini:latest'
+    beforeScript 'chmod g+w .'
+
+    publishDir "$baseDir/results", mode: 'copy'
+
+    input:
+    file receptor
+    file 'receptor.as' from asfile
+    file 'receptor.prm' from prmfile
+    file ligand
+
+    output:
+    file 'best_ligand.sdf' into best_ligand
+
+    """
+    rbdock -i ligand.mol -r receptor.prm -p dock.prm -n $params.num_dockings -o docked_ligand > docked_ligand_out.log
+    sdsort -n -s -fSCORE docked_ligand.sd | sdfilter -f'\$_COUNT <= 1' > best_ligand.sdf
+    """
+}
+
+/* Splits the input into multiple files of ${params.chunk} records.
+*/
+process splitter {
+
+    //beforeScript 'chmod g+w .'
+    container 'informaticsmatters/rdkit_pipelines:latest'
+
+    input:
+    file ligands
+
+    output:
+    file 'ligands_part*.sdf' into ligands_parts mode flatten
+    file 'ligands_part_metrics.txt' into splitter_metrics
+
+    """
+    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
+    """
+}
+
+/* Docks each file from the ligands_parts channel sending each resulting SD file to the results channel
+*/
+process dock_ligands {
+
+    container 'informaticsmatters/rdock-mini:latest'
+    // change permissions on the work dir so that the rdock user in the container
+    // can write to the directory that is owned by root
+    beforeScript 'chmod g+w .'
+
+    input:
+    file part from ligands_parts
+    file receptor
+    file 'receptor.as' from asfile
+    file 'receptor.prm' from prmfile
+
+    output:
+    file 'docked_part*.sd' into docked_parts
+
+    """
+    rbdock -i $part -r receptor.prm -p dock.prm -n $params.num_dockings -o ${part.name.replace('ligands', 'docked')[0..-5]} > docked_out.log
+    """
+}
+
+/* Filter, combine and publish the results.
+* Poses are only included if they are within ${params.threshold} of the best score obtained from docking the
+* target ligand into the same receptor (output of the dock_ligand process).
+*/
+process combine_and_filter {
+
+	container 'informaticsmatters/rdock-mini:latest'
+	beforeScript 'chmod g+w .'
+
+	input:
+	file parts from docked_parts.collect()
+	file best from best_ligand
+
+	output:
+	file 'rdock_results.sdf' into results
+
+	"""
+	FSCORE=\$(sdreport -nh -t${params.field} best_ligand.sdf | cut -f 2 | awk '{\$1=\$1};1')
+	ASCORE=\$(awk "BEGIN {print \$FSCORE + ${params.threshold}}")
+	echo "Processing $parts with normalised score filter of \$ASCORE"
+	sdsort -n -s -f${params.field} docked_part*.sd | sdfilter -f"\\\$${params.field} < \$ASCORE" | sdfilter -f'\$_COUNT <= ${params.top}' > rdock_results.sdf
+	"""
+}
+
+process results {
+
+    beforeScript 'chmod g+w .'
+    container 'informaticsmatters/rdkit_pipelines:latest'
+    beforeScript 'chmod g+w .'
+
+    publishDir "$baseDir/results", mode: 'copy'
+
+    input:
+    file 'results.sdf' from results
+    file 'splitter_metrics.txt' from splitter_metrics
+
+    output:
+    file 'output.data.gz'
+    file 'output.metadata'
+    file 'output_metrics.txt'
+
+    """
+    python -m pipelines_utils_rdkit.filter -i results.sdf -of json -o output --meta
+    mv output_metrics.txt old_metrics.txt
+    echo -n 'DockingRDock=' >> output_metrics.txt
+    echo \$((`grep '__InputCount__' splitter_metrics.txt | cut -d '=' -f 2` * ${params.num_dockings})) >> output_metrics.txt
+    grep '__InputCount__' splitter_metrics.txt >> output_metrics.txt
+    grep '__OutputCount__' old_metrics.txt >> output_metrics.txt
+    """
+}

src/nextflow/nextflow-docker.config

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