mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
Made changes as requested in review of PR.
Most notably, added test cases for C++ and Python which just make sure the code runs without crashing, no comparison of results with existing test files.
This commit is contained in:
DavidACosgrove
@@ -431,31 +431,8 @@ unsigned int compute2DCoordsMimicDistMat(
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//! \brief Compute 2D coordinates where a piece of the molecule is
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// constrained to have the same coordinates as a reference.
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/*!
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This function generates a depiction for a molecule where a piece of the
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molecule is constrained to have the same coordinates as a reference.
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This is useful for, for example, generating depictions of SAR data
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sets so that the cores of the molecules are all oriented the same way.
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ARGUMENTS:
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\param mol - the molecule to be aligned, this will come back
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with a single conformer.
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\param reference - a molecule with the reference atoms to align to;
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this should have a depiction.
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\param confId - (optional) the id of the reference conformation to use
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\param referencePattern - (optional) an optional molecule to be used to
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generate the atom mapping between the molecule
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and the reference.
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\param acceptFailure - (optional) if True, standard depictions will be generated
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for molecules that don't have a substructure match to the
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reference; if false, throws a DepictException.
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*/
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void generateDepictionMatching2DStructure( RDKit::ROMol &mol ,
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RDKit::ROMol &reference ,
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const RDKit::ROMol &reference ,
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int confId ,
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RDKit::ROMol *referencePattern ,
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bool acceptFailure ) {
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@@ -469,34 +446,34 @@ void generateDepictionMatching2DStructure( RDKit::ROMol &mol ,
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RDKit::MatchVectType refMatchVect;
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RDKit::SubstructMatch( reference , *referencePattern , refMatchVect );
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if( refMatchVect.empty() ) {
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throw RDDepict::DepictException( "Reference does not map to itself." );
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throw RDDepict::DepictException( "Reference pattern does not map to reference." );
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}
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refMatch.reserve( refMatchVect.size() );
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for( size_t i = 0 , is = refMatchVect.size() ; i < is ; ++i ) {
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for( size_t i = 0 ; i < refMatchVect.size() ; ++i ) {
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refMatch.push_back( refMatchVect[i].second );
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}
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RDKit::SubstructMatch( mol , *referencePattern , matchVect );
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} else {
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refMatch.reserve( reference.getNumAtoms( true ) );
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for( int i = 0 , is = reference.getNumAtoms( true ) ; i < is ; ++i ) {
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for( unsigned int i = 0 ; i < reference.getNumAtoms( true ) ; ++i ) {
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refMatch.push_back( i );
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}
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RDKit::SubstructMatch( mol , reference , matchVect );
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}
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RDGeom::INT_POINT2D_MAP coordMap;
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if( RDKit::SubstructMatch( mol , reference , matchVect ) ) {
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RDKit::Conformer &conf = reference.getConformer( confId );
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if( matchVect.empty() ) {
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if( !acceptFailure ) {
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throw RDDepict::DepictException( "Substructure match with reference not found." );
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}
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} else {
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const RDKit::Conformer &conf = reference.getConformer( confId );
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for( RDKit::MatchVectType::const_iterator mv = matchVect.begin() ;
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mv != matchVect.end() ; ++mv ) {
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RDGeom::Point3D pt3 = conf.getAtomPos( refMatch[mv->first] );
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RDGeom::Point2D pt2( pt3.x , pt3.y );
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coordMap[mv->second] = pt2;
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}
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} else {
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if( !acceptFailure ) {
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throw RDDepict::DepictException( "Substructure match with reference not found." );
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}
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}
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RDDepict::compute2DCoords( mol , &coordMap , false /* canonOrient */ ,
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true /* clearConfs */ );
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@@ -505,27 +482,8 @@ void generateDepictionMatching2DStructure( RDKit::ROMol &mol ,
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//! \brief Generate a 2D depiction for a molecule where all or part of
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// it mimics the coordinates of a 3D reference structure.
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/*!
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Generates a depiction for a molecule where a piece of the molecule
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is constrained to have coordinates similar to those of a 3D reference
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structure.
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ARGUMENTS:
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\param mol - the molecule to be aligned, this will come back
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with a single conformer containing 2D coordinates
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\param reference - a molecule with the reference atoms to align to.
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By default this should be the same as mol, but with
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3D coordinates
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\param confId - (optional) the id of the reference conformation to use
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\param refPattern - (optional) a query molecule to map a subset of
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the reference onto the mol, so that only some of the
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atoms are aligned.
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\param acceptFailure - (optional) if true, standard depictions will be generated
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for molecules that don't have a substructure match to the
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reference; if false, throws a DepictException.
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*/
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void generateDepictionMatching3DStructure( RDKit::ROMol &mol ,
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RDKit::ROMol &reference ,
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const RDKit::ROMol &reference ,
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int confId ,
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RDKit::ROMol *referencePattern ,
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bool acceptFailure ) {
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@@ -553,7 +511,7 @@ void generateDepictionMatching3DStructure( RDKit::ROMol &mol ,
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throw RDDepict::DepictException( "Reference pattern didn't match molecule or reference." );
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}
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}
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for( size_t i = 0 , is = molMatchVect.size() ; i < is ; ++i ) {
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for( size_t i = 0 ; i < molMatchVect.size() ; ++i ) {
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mol_to_ref[molMatchVect[i].second] = refMatchVect[i].second;
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}
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@@ -563,7 +521,7 @@ void generateDepictionMatching3DStructure( RDKit::ROMol &mol ,
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}
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}
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RDKit::Conformer &conf = reference.getConformer( confId );
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const RDKit::Conformer &conf = reference.getConformer( confId );
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// the distance matrix is a triangular representation
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RDDepict::DOUBLE_SMART_PTR dmat( new double[num_ats * ( num_ats - 1 ) / 2] );
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// negative distances are ignored, so initialise to -1.0 so subset by
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@@ -151,7 +151,7 @@ unsigned int compute2DCoordsMimicDistMat(
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*/
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void generateDepictionMatching2DStructure( RDKit::ROMol &mol ,
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RDKit::ROMol &reference ,
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const RDKit::ROMol &reference ,
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int confId = -1 ,
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RDKit::ROMol *referencePattern = static_cast<RDKit::ROMol *>( 0 ) ,
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bool acceptFailure = false );
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@@ -178,7 +178,7 @@ void generateDepictionMatching2DStructure( RDKit::ROMol &mol ,
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referencePattern; if false, throws a DepictException.
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*/
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void generateDepictionMatching3DStructure( RDKit::ROMol &mol ,
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RDKit::ROMol &reference ,
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const RDKit::ROMol &reference ,
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int confId = -1 ,
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RDKit::ROMol *referencePattern = 0 ,
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bool acceptFailure = false );
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@@ -107,7 +107,7 @@ unsigned int Compute2DCoordsMimicDistmat(
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bool acceptFailure ) {
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RDKit::ROMol *referencePattern = 0;
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if( refPatt ) {
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if( refPatt != python::object() ) {
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referencePattern = python::extract<RDKit::ROMol *>( refPatt );
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}
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@@ -231,7 +231,7 @@ BOOST_PYTHON_MODULE(rdDepictor) {
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RDDepict::GenerateDepictionMatching2DStructure,
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(python::arg( "mol" ) , python::arg( "reference" ) ,
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python::arg( "confId" ) = -1 ,
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python::arg( "refPatt" ) = 0 ,
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python::arg( "refPatt" ) = python::object() ,
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python::arg( "acceptFailure" ) = false ),
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docString.c_str() );
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@@ -257,7 +257,7 @@ BOOST_PYTHON_MODULE(rdDepictor) {
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RDDepict::GenerateDepictionMatching3DStructure,
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(python::arg( "mol" ) , python::arg( "reference" ) ,
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python::arg( "confId" ) = -1 ,
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python::arg( "refPatt" ) = 0 ,
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python::arg( "refPatt" ) = python::object() ,
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python::arg( "acceptFailure" ) = false ),
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docString.c_str() );
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}
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@@ -216,6 +216,24 @@ class TestCase(unittest.TestCase):
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self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.750, 3)
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self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.750, 3)
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def testConstrainedCoords(self) :
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templ = Chem.MolFromSmiles( 'c1nccc2n1ccc2' )
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rdDepictor.Compute2DCoords( templ )
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m1 = Chem.MolFromSmiles( 'c1cccc2ncn3cccc3c21' )
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rdDepictor.GenerateDepictionMatching2DStructure(m1,templ)
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m2 = Chem.MolFromSmiles( 'c1cc(Cl)cc2ncn3cccc3c21' )
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rdDepictor.Compute2DCoords(m2)
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refPatt1 = Chem.MolFromSmarts( '*1****2*1***2' )
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rdDepictor.GenerateDepictionMatching2DStructure( m2 , templ , -1 , refPatt1 )
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fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
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'1XP0_ligand.sdf')
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xp0_lig = Chem.MolFromMolFile( fileN )
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xp0_lig_2d = Chem.Mol( xp0_lig )
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rdDepictor.GenerateDepictionMatching3DStructure( xp0_lig_2d , xp0_lig )
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xp0_ref = Chem.MolFromSmarts( '[#6]1~[#7][#6]~[#6]2[#6](=[#8])[#7]~[#6](c3ccccc3)[#7][#7]12' )
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rdDepictor.GenerateDepictionMatching3DStructure( xp0_lig_2d , xp0_lig , -1 , xp0_ref )
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if __name__ == '__main__':
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unittest.main()
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@@ -823,6 +823,46 @@ void testGitHubIssue1073() {
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}
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}
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void testConstrainedCoords() {
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std::string rdbase = getenv("RDBASE");
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std::string ofile =
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rdbase + "/Code/GraphMol/Depictor/test_data/constrainedCoords.out.sdf";
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SDWriter writer(ofile);
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std::string templ_smiles= "c1nccc2n1ccc2";
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ROMol *templ = SmilesToMol( templ_smiles );
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TEST_ASSERT( templ );
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RDDepict::compute2DCoords( *templ );
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std::string smiles = "c1cccc2ncn3cccc3c21";
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ROMol *m = SmilesToMol( smiles );
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TEST_ASSERT( m );
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RDDepict::generateDepictionMatching2DStructure( *m , *templ );
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writer.write( *m );
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std::string smarts = "*1****2*1***2";
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ROMol *refPatt = SmartsToMol( smarts );
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RDDepict::generateDepictionMatching2DStructure( *m , *templ , -1 , refPatt );
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writer.write( *m );
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delete templ;
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delete m;
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delete refPatt;
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std::string xp0_file =
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rdbase + "/Code/GraphMol/Depictor/test_data/1XP0_ligand.sdf";
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RDKit::ROMol *xp0_lig = RDKit::MolFileToMol( xp0_file );
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RDKit::ROMol *xp0_lig_2d = new RDKit::ROMol( *xp0_lig );
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RDDepict::compute2DCoords( *xp0_lig_2d );
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writer.write( *xp0_lig_2d );
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RDDepict::generateDepictionMatching3DStructure( *xp0_lig_2d , *xp0_lig );
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writer.write( *xp0_lig_2d );
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delete xp0_lig;
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delete xp0_lig_2d;
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}
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int main() {
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RDLog::InitLogs();
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#if 1
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@@ -994,5 +1034,12 @@ int main() {
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BOOST_LOG(rdInfoLog)
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<< "***********************************************************\n";
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BOOST_LOG(rdInfoLog)
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<< "***********************************************************\n";
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BOOST_LOG(rdInfoLog) << " testConstrainedCoords\n";
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testConstrainedCoords();
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BOOST_LOG(rdInfoLog)
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<< "***********************************************************\n";
|
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|
||||
return (0);
|
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}
|
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|
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217
Code/GraphMol/Depictor/test_data/1XP0_ligand.sdf
Normal file
217
Code/GraphMol/Depictor/test_data/1XP0_ligand.sdf
Normal file
@@ -0,0 +1,217 @@
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1XP0_VDN_A_201
|
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RCSB PDB01141521343D
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Coordinates from PDB:1XP0:A:201 Model:1 without hydrogens
|
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34 37 0 0 0 0 999 V2000
|
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-17.3110 28.7690 59.4250 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-18.4240 27.7500 59.5520 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-19.4990 28.3170 60.2890 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-20.6790 27.6470 60.5320 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-20.8720 26.3220 60.1320 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-22.0880 25.7000 60.4070 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.1120 26.3870 61.0750 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-22.9030 27.7070 61.4740 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.7100 28.3360 61.1660 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-24.5130 25.6830 61.4210 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-25.6280 26.5010 61.0510 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-24.5590 24.4480 60.7000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.9260 24.9690 67.8530 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-24.6520 25.3890 62.9190 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.5890 24.5300 63.4650 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.7010 24.3520 64.9680 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.9540 25.6730 65.5070 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-25.3030 26.1390 65.2360 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-25.4770 26.3040 63.7200 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.3800 25.9480 66.8200 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.3890 29.7160 61.6140 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.0380 30.7260 60.6430 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-20.9950 32.0290 60.9210 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.5360 32.3970 62.2430 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.9910 31.5330 63.1240 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-22.0380 30.1810 62.8070 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-20.5730 32.8270 60.0980 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.7100 33.6360 62.8500 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-22.2670 33.3890 64.0670 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-22.4610 32.0570 64.2250 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.3840 35.0070 62.3250 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-23.0180 31.3240 65.4100 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-21.8600 30.6260 66.1240 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-22.4100 29.8920 67.3240 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0 0 0 0
|
||||
2 3 1 0 0 0 0
|
||||
3 4 1 0 0 0 0
|
||||
4 5 2 0 0 0 0
|
||||
4 9 1 0 0 0 0
|
||||
5 6 1 0 0 0 0
|
||||
6 7 2 0 0 0 0
|
||||
7 8 1 0 0 0 0
|
||||
7 10 1 0 0 0 0
|
||||
8 9 2 0 0 0 0
|
||||
9 21 1 0 0 0 0
|
||||
10 11 2 0 0 0 0
|
||||
10 12 2 0 0 0 0
|
||||
10 14 1 0 0 0 0
|
||||
13 20 1 0 0 0 0
|
||||
14 15 1 0 0 0 0
|
||||
14 19 1 0 0 0 0
|
||||
15 16 1 0 0 0 0
|
||||
16 17 1 0 0 0 0
|
||||
17 18 1 0 0 0 0
|
||||
17 20 1 0 0 0 0
|
||||
18 19 1 0 0 0 0
|
||||
21 22 2 0 0 0 0
|
||||
21 26 1 0 0 0 0
|
||||
22 23 1 0 0 0 0
|
||||
23 24 1 0 0 0 0
|
||||
23 27 2 0 0 0 0
|
||||
24 25 1 0 0 0 0
|
||||
24 28 2 0 0 0 0
|
||||
25 26 1 0 0 0 0
|
||||
25 30 1 0 0 0 0
|
||||
28 29 1 0 0 0 0
|
||||
28 31 1 0 0 0 0
|
||||
29 30 2 0 0 0 0
|
||||
30 32 1 0 0 0 0
|
||||
32 33 1 0 0 0 0
|
||||
33 34 1 0 0 0 0
|
||||
A 1
|
||||
C1
|
||||
A 2
|
||||
C2
|
||||
A 3
|
||||
O3
|
||||
A 4
|
||||
C4
|
||||
A 5
|
||||
C5
|
||||
A 6
|
||||
C6
|
||||
A 7
|
||||
C7
|
||||
A 8
|
||||
C8
|
||||
A 9
|
||||
C9
|
||||
A 10
|
||||
S10
|
||||
A 11
|
||||
O11
|
||||
A 12
|
||||
O12
|
||||
A 13
|
||||
C13
|
||||
A 14
|
||||
N14
|
||||
A 15
|
||||
C15
|
||||
A 16
|
||||
C16
|
||||
A 17
|
||||
N17
|
||||
A 18
|
||||
C18
|
||||
A 19
|
||||
C19
|
||||
A 20
|
||||
C20
|
||||
A 21
|
||||
C21
|
||||
A 22
|
||||
N22
|
||||
A 23
|
||||
C23
|
||||
A 24
|
||||
C24
|
||||
A 25
|
||||
N25
|
||||
A 26
|
||||
N26
|
||||
A 27
|
||||
O27
|
||||
A 28
|
||||
C28
|
||||
A 29
|
||||
N29
|
||||
A 30
|
||||
C30
|
||||
A 31
|
||||
C31
|
||||
A 32
|
||||
C32
|
||||
A 33
|
||||
C33
|
||||
A 34
|
||||
C34
|
||||
M END
|
||||
> <InstanceId>
|
||||
1XP0_VDN_A_201
|
||||
|
||||
> <ChemCompId>
|
||||
VDN
|
||||
|
||||
> <PdbId>
|
||||
1XP0
|
||||
|
||||
> <ChainId>
|
||||
A
|
||||
|
||||
> <ResidueNumber>
|
||||
201
|
||||
|
||||
> <InsertionCode>
|
||||
|
||||
|
||||
> <Model>
|
||||
1
|
||||
|
||||
> <AltIds>
|
||||
|
||||
|
||||
> <MissingHeavyAtoms>
|
||||
0
|
||||
|
||||
> <ObservedFormula>
|
||||
C23 N6 O4 S
|
||||
|
||||
> <Name>
|
||||
2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE
|
||||
|
||||
> <SystematicName>
|
||||
2-[2-ethoxy-5-(4-ethylpiperazin-1-yl)sulfonyl-phenyl]-5-methyl-7-propyl-1H-imidazo[5,1-f][1,2,4]triazin-4-one
|
||||
|
||||
> <Synonyms>
|
||||
VARDENAFIL, LEVITRA
|
||||
|
||||
> <Type>
|
||||
NON-POLYMER
|
||||
|
||||
> <Formula>
|
||||
C23 H32 N6 O4 S
|
||||
|
||||
> <MolecularWeight>
|
||||
488.603
|
||||
|
||||
> <ModifiedDate>
|
||||
2011-06-04
|
||||
|
||||
> <Parent>
|
||||
|
||||
|
||||
> <OneLetterCode>
|
||||
|
||||
|
||||
> <SubcomponentList>
|
||||
|
||||
|
||||
> <AmbiguousFlag>
|
||||
N
|
||||
|
||||
> <InChI>
|
||||
InChI=1S/C23H32N6O4S/c1-5-8-20-24-16(4)21-23(30)25-22(26-29(20)21)18-15-17(9-10-19(18)33-7-3)34(31,32)28-13-11-27(6-2)12-14-28/h9-10,15H,5-8,11-14H2,1-4H3,(H,25,26,30)
|
||||
|
||||
> <InChIKey>
|
||||
SECKRCOLJRRGGV-UHFFFAOYSA-N
|
||||
|
||||
> <SMILES>
|
||||
CCCc1nc(c2n1NC(=NC2=O)c3cc(ccc3OCC)S(=O)(=O)N4CCN(CC4)CC)C
|
||||
|
||||
$$$$
|
||||
Reference in New Issue
Block a user