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AlignMolecules.h File Reference
`#include <RDGeneral/export.h>`
`#include <Geometry/Transform3D.h>`
`#include <Numerics/Vector.h>`
`#include <vector>`

Go to the source code of this file.

## Classes

class | RDKit::MolAlign::MolAlignException

## Namespaces

namespace | RDKit
| Std stuff.
namespace | RDKit::MolAlign
namespace | RDKit::MolAlign::details

## Functions

RDKIT_MOLALIGN_EXPORT double | RDKit::MolAlign::getAlignmentTransform (const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &trans, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=nullptr, const RDNumeric::DoubleVector *weights=nullptr, bool reflect=false, unsigned int maxIters=50)
| Alignment functions.
RDKIT_MOLALIGN_EXPORT double | RDKit::MolAlign::alignMol (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=nullptr, const RDNumeric::DoubleVector *weights=nullptr, bool reflect=false, unsigned int maxIters=50)
| Optimally (minimum RMSD) align a molecule to another molecule.

RDKIT_MOLALIGN_EXPORT double

RDKit::MolAlign::getBestAlignmentTransform (const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &bestTrans, MatchVectType &bestMatch, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, bool reflect=false, unsigned int maxIters=50, int numThreads=1)

RDKIT_MOLALIGN_EXPORT double | RDKit::MolAlign::getBestRMS (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, int numThreads=1)
RDKIT_MOLALIGN_EXPORT std::vector< double > | RDKit::MolAlign::getAllConformerBestRMS (const ROMol &mol, int numThreads=1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr)
RDKIT_MOLALIGN_EXPORT double | RDKit::MolAlign::CalcRMS (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr)
RDKIT_MOLALIGN_EXPORT double | RDKit::MolAlign::CalcRMS (ROMol &prbMol, const ROMol &refMol, int prbCid, int refCid, const std::vector< MatchVectType > &map, int maxMatches, const RDNumeric::DoubleVector *weights)
RDKIT_MOLALIGN_EXPORT void | RDKit::MolAlign::alignMolConformers (ROMol &mol, const std::vector< unsigned int > *atomIds=nullptr, const std::vector< unsigned int > *confIds=nullptr, const RDNumeric::DoubleVector *weights=nullptr, bool reflect=false, unsigned int maxIters=50, std::vector< double > *RMSlist=nullptr)
RDKIT_MOLALIGN_EXPORT void | RDKit::MolAlign::details::symmetrizeTerminalAtoms (RWMol &mol)