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tdudgeontdudgeon
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fixing obabel_prepare_pdb service and docker images
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‎Dockerfile-pli‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ LABEL maintainer="Tim Dudgeon<[email protected]>"
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USER root
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RUN apt-get install zlib1g-dev make gcc git -y
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RUN apt-get update -y && apt-get install zlib1g-dev make gcc git -y
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RUN mkdir -p /usr/local/
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WORKDIR /usr/local/
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RUN git clone https://bitbucket.org/AstexUK/pli.git

‎Dockerfile-smog‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,10 @@ LABEL maintainer="Tim Dudgeon<[email protected]>"
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USER root
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RUN apt-get install libopenbabel-dev g++ -y
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RUN echo 'deb http://deb.debian.org/debian experimental main' >> /etc/apt/sources.list
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RUN apt-get update -y && apt-get install -t experimental libopenbabel-dev g++ -y
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WORKDIR /usr/local
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RUN wget https://sourceforge.net/projects/opengrowth/files/SMoG2016.tar.gz/download -O smog.tar.gz &&\

‎build.gradle‎

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -84,18 +84,28 @@ task buildSmogImage(type: DockerBuildImage) {
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tag = "informaticsmatters/smog:latest"
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}
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87-
task buildSdPosterDockerImage(type: DockerBuildImage) {
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task buildSdPosterImage(type: DockerBuildImage) {
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description 'Builds the pipelines SD-poster Docker image'
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dockerFile = file('Dockerfile-sdposter')
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inputDir = file('.')
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tag = "squonk/rdkit-${pipeline}-sdposter:latest"
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}
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95+
task buildObabelImage(type: DockerBuildImage) {
96+
// TODO - remove this once the pipelines-obabel project becomes active
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description 'Builds the obabel Docker image'
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dockerFile = file('Dockerfile-obabel')
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inputDir = file('.')
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tag = "informaticsmatters/pipelines-obabel:latest"
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}
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task buildDockerImages() {
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dependsOn buildPliImage // that one depends on buildPipelinesImage
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dependsOn buildSmogImage // and so does this one
98-
dependsOn buildSdPosterDockerImage
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dependsOn buildSdPosterImage
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dependsOn buildObabelImage
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group 'Docker'
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description 'Builds all the project Docker images'

‎src/python/pipelines/docking/obabel_prepare_pdb.dsd.json‎

Lines changed: 43 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -1,50 +1,50 @@
1-
{ "@class":"org.squonk.core.DockerServiceDescriptor",
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{ "@class": "org.squonk.core.DockerServiceDescriptor",
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"serviceConfig": {
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"id": "pipelines.xchem.obabel.prepare.pdb.v1",
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"name": "OBabelPreparePDB",
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"description": "Prepare PDB file uisng Open Babel",
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"tags": [ "rdkit", "xchem", "docker", "openbabel", "obabel", "prepare", "pdb", "convert"],
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"resourceUrl": null,
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"icon": "icons/transform_molecule.png",
3+
"id": "pipelines.xchem.obabel.prepare.pdb.v1",
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"name": "OBabelPreparePDB",
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"description": "Prepare PDB file using Open Babel",
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"tags": [ "rdkit", "xchem", "docker", "openbabel", "obabel", "prepare", "pdb", "convert", "protein"],
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"resourceUrl": null,
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"icon": "icons/transform_molecule.png",
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10-
"inputDescriptors": [
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{
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"primaryType": "org.squonk.types.PDBFile",
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"mediaType": "chemical/x-pdb",
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"name": "pdb"
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}
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],
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"outputDescriptors": [
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{
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"primaryType": "org.squonk.types.Mol2File",
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"mediaType": "chemical/x-mol2",
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"name": "mol2"
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}
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],
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"inputDescriptors": [
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{
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"primaryType": "org.squonk.types.PDBFile",
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"mediaType": "chemical/x-pdb",
14+
"name": "pdb"
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}
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],
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"outputDescriptors": [
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{
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"primaryType": "org.squonk.types.Mol2File",
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"mediaType": "chemical/x-mol2",
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"name": "mol2"
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}
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],
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"optionDescriptors": [
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{
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"modes": [
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"User"
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],
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"editable": true,
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"@class": "org.squonk.options.OptionDescriptor",
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"typeDescriptor": {
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"type": "java.lang.Float",
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"@class": "org.squonk.options.SimpleTypeDescriptor"
35-
},
36-
"key": "arg.protonate",
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"label": "Protonate at pH",
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"description": "Optionally protonate side chains at this pH",
39-
"visible": true,
40-
"minValues": 0,
41-
"maxValues": 1
42-
}
43-
],
44-
"executorClassName": "org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep"
25+
"optionDescriptors": [
26+
{
27+
"modes": [
28+
"User"
29+
],
30+
"editable": true,
31+
"@class": "org.squonk.options.OptionDescriptor",
32+
"typeDescriptor": {
33+
"type": "java.lang.Float",
34+
"@class": "org.squonk.options.SimpleTypeDescriptor"
35+
},
36+
"key": "arg.protonate",
37+
"label": "Protonate at pH",
38+
"description": "Optionally protonate side chains at this pH",
39+
"visible": true,
40+
"minValues": 0,
41+
"maxValues": 1
42+
}
43+
],
44+
"executorClassName": "org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep"
4545
},
4646
"inputRoutes": [ {"route": "FILE"} ],
4747
"outputRoutes": [ {"route": "FILE"} ],
48-
"imageName": "informaticsmatters/rdkit_pipelines",
49-
"command": "python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2${protonate ? ' -prot ' + protonate : ''} --meta"
48+
"imageName": "informaticsmatters/pipelines-obabel:latest",
49+
"command": "python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2${binding.variables.containsKey('protonate') ? ' -prot ' + protonate : ''} --meta"
5050
}

‎src/python/pipelines/docking/obabel_prepare_pdb.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#!/usr/bin/env python
22

3-
# Copyright 2017 Informatics Matters Ltd.
3+
# Copyright 2018 Informatics Matters Ltd.
44
#
55
# Licensed under the Apache License, Version 2.0 (the "License");
66
# you may not use this file except in compliance with the License.
@@ -21,15 +21,19 @@
2121

2222

2323
def execute(input, output, extension, format, ph, noGzip):
24+
25+
# TODO - convert this to use the Python API rather than an external process
26+
2427
filename = output + "." + extension
2528
base_args = ["obabel", "-ipdb", input, format, "-O", filename]
2629
if ph:
2730
base_args.append("-p")
28-
base_args.append("ph")
31+
base_args.append(str(ph))
32+
utils.log("Command: " + " ".join(base_args))
2933

3034
subprocess.check_call(base_args, stdout=sys.stderr, stderr=sys.stderr)
3135

32-
# NOTE the -z argument does not seem to work correctly with obabel (truncted files generated) so we
36+
# NOTE the -z argument does not seem to work correctly with obabel (truncated files generated) so we
3337
# fall back to good old gzip to handle the compression once the uncompressed file is created
3438
if not noGzip:
3539
subprocess.check_call(['gzip', filename], stdout=sys.stderr, stderr=sys.stderr)

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