RDKit: MolTransforms.h File Reference

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MolTransforms.h File Reference
`#include <Geometry/point.h>`
`#include <Numerics/SymmMatrix.h>`

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 &center, 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)
| origin, the largest princiapl axis with the x-axis, the next largest with More...
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 (const 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 (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. More...
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. 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 (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. More...
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. 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)