10 #ifndef _RD_ALIGNMOLECULES_H_ 11 #define _RD_ALIGNMOLECULES_H_ 30 const char *
message()
const {
return _msg.c_str(); };
67 int refCid = -1,
const MatchVectType *atomMap = 0,
69 bool reflect =
false,
unsigned int maxIters = 50);
99 int refCid = -1,
const MatchVectType *atomMap = 0,
101 bool reflect =
false,
unsigned int maxIters = 50);
128 int probeId = -1,
int refId = -1,
129 const std::vector<MatchVectType>& map =
130 std::vector<MatchVectType>(),
131 int maxMatches = 1e6);
150 const std::vector<unsigned int> *atomIds = 0,
151 const std::vector<unsigned int> *confIds = 0,
153 bool reflect =
false,
unsigned int maxIters = 50,
154 std::vector<double> *RMSlist = 0);
const char * message() const
get the error message
double getBestRMS(ROMol &probeMol, ROMol &refMol, int probeId=-1, int refId=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6)
Returns the optimal RMS for aligning two molecules, taking.
void alignMolConformers(ROMol &mol, const std::vector< unsigned int > *atomIds=0, const std::vector< unsigned int > *confIds=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50, std::vector< double > *RMSlist=0)
Align the conformations of a molecule using a common set of atoms. If.
MolAlignException(const char *msg)
construct with an error message
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) ...
const RDGeom::POINT3D_VECT * reflect(const Conformer &conf)
MolAlignException(const std::string msg)
construct with an error message
ROMol is a molecule class that is intended to have a fixed topology.
double alignMol(ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50)
Optimally (minimum RMSD) align a molecule to another molecule.
double getAlignmentTransform(const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &trans, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50)
Alignment functions.
A class to represent vectors of numbers.