adding crippen contributions to Open3DAlign

Author: tdudgeon

src/python/pipelines/rdkit/o3dAlign.dsd.json

@@ -71,6 +71,23 @@
         },
         "@class": "org.squonk.options.OptionDescriptor"
       },
+      {
+        "modes": [
+          "User"
+        ],
+        "editable": true,
+        "visible": true,
+        "description": "Use Crippen (logP) contributions",
+        "label": "Use Crippen (logP) contributions",
+        "key": "arg.crippen",
+        "minValues": 1,
+        "maxValues": 1,
+        "typeDescriptor": {
+          "type": "java.lang.Boolean",
+          "@class": "org.squonk.options.SimpleTypeDescriptor"
+        },
+        "@class": "org.squonk.options.OptionDescriptor"
+      },
       {
         "@class": "org.squonk.options.OptionDescriptor",
         "modes": [
@@ -110,5 +127,5 @@
     }
   ],
   "imageName": "informaticsmatters/rdkit_pipelines",
-  "command": "python -m pipelines.rdkit.o3dAlign queryMol.data.gz -i ${PIN}input.data.gz -o ${POUT}output -of json${binding.variables.containsKey('qmolidx') ? ' --qmolidx ' + binding.variables.get('qmolidx') : ''}${binding.variables.containsKey('num') ? ' --num ' + binding.variables.get('num') : ''}${binding.variables.containsKey('threshold') ? ' --threshold ' + binding.variables.get('threshold') : ''} --meta"
+  "command": "python -m pipelines.rdkit.o3dAlign queryMol.data.gz -i ${PIN}input.data.gz -o ${POUT}output -of json${binding.variables.containsKey('qmolidx') ? ' --qmolidx ' + binding.variables.get('qmolidx') : ''}${binding.variables.containsKey('num') ? ' --num ' + binding.variables.get('num') : ''}${binding.variables.containsKey('threshold') ? ' --threshold ' + binding.variables.get('threshold') : ''}${crippen ? ' --crippen' : ''} --meta"
 }

src/python/pipelines/rdkit/o3dAlign.py

@@ -29,8 +29,13 @@
 
 ### start function definitions #########################################
 
-def doO3Dalign(i, mol, qmol, threshold, perfect_score, writer, conformerProps=None, minEnergy=None):
-    pyO3As = rdMolAlign.GetO3AForProbeConfs(mol, qmol)
+def doO3Dalign(i, mol, qmol, use_crippen, threshold, perfect_score, writer, conformerProps=None, minEnergy=None):
+
+    if use_crippen:
+        pyO3As = rdMolAlign.GetCrippenO3AForProbeConfs(mol, qmol)
+    else:
+        pyO3As = rdMolAlign.GetO3AForProbeConfs(mol, qmol)
+
     if len(pyO3As) == 0:
         return 0
 
@@ -68,6 +73,7 @@ def main():
     parser = argparse.ArgumentParser(description='Open3DAlign with RDKit')
     parser.add_argument('query', help='query molfile')
     parser.add_argument('--qmolidx', help="Query molecule index in SD file if not the first", type=int, default=1)
+    parser.add_argument('--crippen', action='store_true', help='Use Crippen (logP) contributions')
     parser.add_argument('-t', '--threshold', type=float, help='score cuttoff relative to alignment of query to itself')
     parser.add_argument('-n', '--num', default=0, type=int, help='number of conformers to generate, if None then input structures are assumed to already be 3D')
     parser.add_argument('-a', '--attempts', default=0, type=int, help='number of attempts to generate conformers')
@@ -106,7 +112,11 @@ def main():
                                   datasetMetaProps=datasetMetaProps,
                                   fieldMetaProps=fieldMetaProps)
 
-    pyO3A = rdMolAlign.GetO3A(qmol2, qmol)
+    if args.crippen:
+        pyO3A = rdMolAlign.GetCrippenO3A(qmol2, qmol)
+    else:
+        pyO3A = rdMolAlign.GetO3A(qmol2, qmol)
+
     perfect_align = pyO3A.Align()
     perfect_score = pyO3A.Score()
     utils.log('Perfect score:', perfect_align, perfect_score, Chem.MolToSmiles(qmol, isomericSmiles=True), qmol.GetNumAtoms())
@@ -124,10 +134,10 @@ def main():
                 mol.RemoveAllConformers()
                 conformerProps, minEnergy = conformers.process_mol_conformers(mol, i, args.num, args.attempts, args.rmsd, None, None, 0)
                 mol = Chem.RemoveHs(mol)
-                count += doO3Dalign(i, mol, qmol, args.threshold, perfect_score, writer, conformerProps=conformerProps, minEnergy=minEnergy)
+                count += doO3Dalign(i, mol, qmol, args.crippen, args.threshold, perfect_score, writer, conformerProps=conformerProps, minEnergy=minEnergy)
             else:
                 mol = Chem.RemoveHs(mol)
-                count += doO3Dalign(i, mol, qmol, args.threshold, perfect_score, writer)
+                count += doO3Dalign(i, mol, qmol, args.crippen, args.threshold, perfect_score, writer)
             total += mol.GetNumConformers()
         except ValueError as e:
             errors +=1

src/python/pipelines/rdkit/o3dAlign.test

@@ -43,6 +43,21 @@
         creates: [ 'output.data.gz',
                    'output.metadata'],
 
+    ],
+
+         // Testing o3dAlign.py using crippen contributions
+         test_raw_o3dalign_sdf_to_json = [
+
+             command: '''python -m pipelines.rdkit.o3dAlign --crippen
+                      ${PIN}pyrimethamine.mol -n 2 -t 10
+                      -i ${PIN}Kinase_inhibs.sdf.gz -if sdf
+                      -o ${POUT}output -of json''',
+
+             stderr: [ 'Molecule 36 generated [1-9]\\d* conformers' ],
+
+             creates: [ 'output.data.gz',
+                        'output.metadata'],
+
     ],
 
     // Uses an invalid file - but here just to improve coverage