RDKit
Open-source cheminformatics and machine learning.
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MolTransforms.h File Reference

Go to the source code of this file.

Namespaces

namespace  RDKit
 Std stuff.
 
namespace  RDGeom
 
namespace  MolTransforms
 

Functions

RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::transformMolsAtoms (RDKit::ROMol *mol, RDGeom::Transform3D &tform)
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::transformAtom (RDKit::Atom *atom, RDGeom::Transform3D &tform)
 
RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Point3D MolTransforms::computeCentroid (const RDKit::Conformer &conf, bool ignoreHs=true, const std::vector< double > *weights=nullptr)
 Compute the centroid of a conformer.
 
RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Transform3DMolTransforms::computeCanonicalTransform (const RDKit::Conformer &conf, const RDGeom::Point3D *center=nullptr, bool normalizeCovar=false, bool ignoreHs=true)
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::transformConformer (RDKit::Conformer &conf, const RDGeom::Transform3D &trans)
 Transform the conformation using the specified transformation.
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::transformMolSubstanceGroups (RDKit::ROMol &mol, const RDGeom::Transform3D &trans)
 Transforms coordinates in a molecule's substance groups.
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::canonicalizeConformer (RDKit::Conformer &conf, const RDGeom::Point3D *center=nullptr, bool normalizeCovar=false, bool ignoreHs=true)
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::canonicalizeMol (RDKit::ROMol &mol, bool normalizeCovar=false, bool ignoreHs=true)
 Canonicalize all the conformations in a molecule.
 
RDKIT_MOLTRANSFORMS_EXPORT double MolTransforms::getBondLength (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId)
 Get the bond length between the specified atoms i, j.
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::setBondLength (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, double value)
 
RDKIT_MOLTRANSFORMS_EXPORT double MolTransforms::getAngleRad (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId)
 Get the angle in radians among the specified atoms i, j, k.
 
double MolTransforms::getAngleDeg (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId)
 Get the angle in degrees among the specified atoms i, j, k.
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::setAngleRad (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, double value)
 
void MolTransforms::setAngleDeg (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, double value)
 
RDKIT_MOLTRANSFORMS_EXPORT double MolTransforms::getDihedralRad (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId)
 Get the dihedral angle in radians among the specified atoms i, j, k, l.
 
double MolTransforms::getDihedralDeg (const RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId)
 Get the dihedral angle in degrees among the specified atoms i, j, k, l.
 
RDKIT_MOLTRANSFORMS_EXPORT void MolTransforms::setDihedralRad (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId, double value)
 
void MolTransforms::setDihedralDeg (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId, unsigned int lAtomId, double value)