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add substructure searches of Mols using MolBundles from Python (#1603)

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This commit is contained in:
Greg Landrum
2017-10-03 23:46:44 +02:00
committed by Brian Kelley
parent 28f8421644
commit 0775cf0da5
2 changed files with 50 additions and 3 deletions
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30
Code/GraphMol/Wrap/Mol.cpp
View File

@@ -22,6 +22,7 @@
#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryOps.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/MolBundle.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <boost/python/iterator.hpp>
#include <boost/python/copy_non_const_reference.hpp>
@@ -374,8 +375,8 @@ struct mol_wrapper {
" - useQueryQueryMatches: use query-query matching logic\n\n"
" RETURNS: True or False\n")
.def("GetSubstructMatch",
(PyObject * (*)(const ROMol &m, const ROMol &query, bool, bool))
GetSubstructMatch,
(PyObject * (*)(const ROMol &m, const ROMol &query, bool,
bool))GetSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false),
@@ -398,7 +399,7 @@ struct mol_wrapper {
.def("GetSubstructMatches",
(PyObject * (*)(const ROMol &m, const ROMol &query, bool, bool,
bool, unsigned int)) GetSubstructMatches,
bool, unsigned int))GetSubstructMatches,
(python::arg("self"), python::arg("query"),
python::arg("uniquify") = true,
python::arg("useChirality") = false,
@@ -434,6 +435,29 @@ struct mol_wrapper {
" this molecule that matches the first atom in the "
"query.\n")
.def("HasSubstructMatch",
(bool (*)(const ROMol &m, const MolBundle &query, bool, bool,
bool))HasSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("recursionPossible") = true,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false))
.def("GetSubstructMatch",
(PyObject * (*)(const ROMol &m, const MolBundle &query, bool,
bool))GetSubstructMatch,
(python::arg("self"), python::arg("query"),
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false))
.def("GetSubstructMatches",
(PyObject * (*)(const ROMol &m, const MolBundle &query, bool, bool,
bool, unsigned int))GetSubstructMatches,
(python::arg("self"), python::arg("query"),
python::arg("uniquify") = true,
python::arg("useChirality") = false,
python::arg("useQueryQueryMatches") = false,
python::arg("maxMatches") = 1000))
// properties
.def("SetProp", MolSetProp<std::string>,
(python::arg("self"), python::arg("key"), python::arg("val"),

23
Code/GraphMol/Wrap/rough_test.py
View File

@@ -4397,6 +4397,29 @@ M END
self.assertEqual(len(b.GetSubstructMatches(Chem.MolFromSmiles('C[C@](Cl)(F)C[C@@H](F)(Br)'),useChirality=True)[0]),8)
self.assertEqual(len(b.GetSubstructMatches(Chem.MolFromSmiles('C[C@@](Cl)(F)C[C@@H](F)(Br)'),useChirality=False)[0]),8)
def testMolBundles2(self):
b = Chem.MolBundle()
smis = ('Fc1c(Cl)cccc1','Fc1cc(Cl)ccc1','Fc1ccc(Cl)cc1')
for smi in smis:
b.AddMol(Chem.MolFromSmiles(smi))
self.assertEqual(len(b),3)
self.assertEqual(b.Size(),3)
self.failUnless(Chem.MolFromSmiles('Fc1c(Cl)cccc1').HasSubstructMatch(b))
self.failUnless(Chem.MolFromSmiles('Fc1cc(Cl)ccc1').HasSubstructMatch(b))
self.failUnless(Chem.MolFromSmiles('Fc1c(Cl)cccc1C').HasSubstructMatch(b))
self.failUnless(Chem.MolFromSmiles('Fc1cc(Cl)ccc1C').HasSubstructMatch(b))
self.failIf(Chem.MolFromSmiles('Fc1c(Br)cccc1').HasSubstructMatch(b))
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(Cl)cccc1').GetSubstructMatch(b)),8)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(Cl)cccc1').GetSubstructMatches(b)),1)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(Cl)cccc1').GetSubstructMatches(b)[0]),8)
self.assertEqual(len(Chem.MolFromSmiles('Fc1ccc(Cl)cc1').GetSubstructMatches(b)),1)
self.assertEqual(len(Chem.MolFromSmiles('Fc1ccc(Cl)cc1').GetSubstructMatches(b,uniquify=False)),2)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(C)cccc1').GetSubstructMatch(b)),0)
self.assertEqual(len(Chem.MolFromSmiles('Fc1c(C)cccc1').GetSubstructMatches(b)),0)
if __name__ == '__main__':
if "RDTESTCASE" in os.environ:
suite = unittest.TestSuite()