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MolTransforms.h File Reference

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Namespaces

 RDKit
 Includes a bunch of functionality for handling Atom and Bond queries.
 
 RDGeom
 
 MolTransforms
 

Functions

void MolTransforms::transformMolsAtoms (RDKit::ROMol *mol, RDGeom::Transform3D &tform)
 
void MolTransforms::transformAtom (RDKit::Atom *atom, RDGeom::Transform3D &tform)
 
RDGeom::Point3D MolTransforms::computeCentroid (const RDKit::Conformer &conf, bool ignoreHs=true)
 Compute the centroid of a conformer. More...
 
RDNumeric::DoubleSymmMatrixMolTransforms::computeCovarianceMatrix (const RDKit::Conformer &conf, const RDGeom::Point3D &center, bool normalize=false, bool ignoreHs=true)
 Compute the covariance matrix for a conformer. More...
 
RDGeom::Transform3DMolTransforms::computeCanonicalTransform (const RDKit::Conformer &conf, const RDGeom::Point3D *center=0, bool normalizeCovar=false, bool ignoreHs=true)
 
void MolTransforms::transformConformer (RDKit::Conformer &conf, const RDGeom::Transform3D &trans)
 Transform the conformation using the specified transformation. More...
 
void MolTransforms::canonicalizeConformer (RDKit::Conformer &conf, const RDGeom::Point3D *center=0, bool normalizeCovar=false, bool ignoreHs=true)
 
void MolTransforms::canonicalizeMol (RDKit::ROMol &mol, bool normalizeCovar=false, bool ignoreHs=true)
 Canonicalize all the conformations in a molecule. More...
 
double MolTransforms::getBondLength (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId)
 Get the bond length between the specified atoms i, j. More...
 
void MolTransforms::setBondLength (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, double value)
 
double MolTransforms::getAngleRad (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId)
 Get the angle in radians among the specified atoms i, j, k. More...
 
double MolTransforms::getAngleDeg (RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId, unsigned int kAtomId)
 Get the angle in degrees among the specified atoms i, j, k. More...
 
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)
 
double MolTransforms::getDihedralRad (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. More...
 
double MolTransforms::getDihedralDeg (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. More...
 
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)