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RDKit
Open-source cheminformatics and machine learning.
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Go to the source code of this file.
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::DoubleSymmMatrix * | MolTransforms::computeCovarianceMatrix (const RDKit::Conformer &conf, const RDGeom::Point3D ¢er, bool normalize=false, bool ignoreHs=true) |
Compute the covariance matrix for a conformer. More... | |
RDGeom::Transform3D * | MolTransforms::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) |