mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
4f2ec84e7b
* update .gitignore * foundation for 3D descriptors move PBF into core * cleanup work * a bit more cleanup * move the principal moments calc to MolTransforms * cleanup * cleanups * add caching of the principal moments and values * do not include the 3D descriptors in MolDescriptors.h * the properties are computed * add PMI descriptors and tests * add tests for NPR descriptors * return 0 when the largest PMI is zero * PMI edge case tests * NPR edge case tests * PBF edge case tests * PBF edge case tests * more edge cases * add a few more 3d descriptors * add defns to docs * tests for the new descriptors * add versions to new descriptors * add 3d descriptors to python wrapper * add eigen support to the travis build * try to get non-windows builds working * remove computeCovarianceMatrix() from java wrapper * make pmi property names "private"
179 lines
6.7 KiB
C++
179 lines
6.7 KiB
C++
//
|
|
// Copyright (C) 2003-2006 Rational Discovery LLC
|
|
//
|
|
// @@ All Rights Reserved @@
|
|
// This file is part of the RDKit.
|
|
// The contents are covered by the terms of the BSD license
|
|
// which is included in the file license.txt, found at the root
|
|
// of the RDKit source tree.
|
|
//
|
|
#ifndef _RD_MOLTRANSFORMS_H_
|
|
#define _RD_MOLTRANSFORMS_H_
|
|
|
|
#include <Geometry/point.h>
|
|
#include <Numerics/SymmMatrix.h>
|
|
|
|
#ifdef RDK_HAS_EIGEN3
|
|
#include <Eigen/Dense>
|
|
#endif
|
|
|
|
namespace RDKit {
|
|
class ROMol;
|
|
class Atom;
|
|
class Conformer;
|
|
}
|
|
|
|
namespace RDGeom {
|
|
class Transform3D;
|
|
}
|
|
|
|
namespace MolTransforms {
|
|
void transformMolsAtoms(RDKit::ROMol *mol, RDGeom::Transform3D &tform);
|
|
void transformAtom(RDKit::Atom *atom, RDGeom::Transform3D &tform);
|
|
|
|
//! Compute the centroid of a conformer
|
|
/*!
|
|
This is simple the average of the heavy atom locations in the conformer,
|
|
not attention is paid to hydrogens or the differences in atomic radii
|
|
|
|
\param conf Conformer of interest
|
|
\param ignoreHs If true, ignore hydrogen atoms
|
|
*/
|
|
RDGeom::Point3D computeCentroid(const RDKit::Conformer &conf,
|
|
bool ignoreHs = true);
|
|
|
|
#ifdef RDK_HAS_EIGEN3
|
|
//! Compute principal axes and moments for a conformer
|
|
/*!
|
|
\param conf Conformer of interest
|
|
\param axes used to return the principal axes
|
|
\param moments used to return the principal moments
|
|
\param ignoreHs If true, ignore hydrogen atoms
|
|
\param force If true, the calculation will be carried out even if a cached value is present
|
|
\param weights If present used to weight the atomic coordinates
|
|
|
|
\returns whether or not the calculation was successful
|
|
*/
|
|
bool computePrincipalAxesAndMoments(
|
|
const RDKit::Conformer &conf,
|
|
Eigen::Matrix3d &axes,
|
|
Eigen::Vector3d &moments,
|
|
bool ignoreHs = true,
|
|
bool force = false,
|
|
const std::vector<double> *weights = NULL);
|
|
#endif
|
|
|
|
|
|
|
|
//! Compute the transformation require to orient the conformation
|
|
//! along the principal axes about the center; i.e. center is made to coincide
|
|
// with the
|
|
//! origin, the largest princiapl axis with the x-axis, the next largest with
|
|
// the y-axis
|
|
//! and the smallest with the z-axis
|
|
/*!
|
|
If center is not specified the the centroid of the conformer will be used
|
|
\param conf Conformer of interest
|
|
\param center Center to be used for canonicalization, defaults to
|
|
the centroid of the
|
|
conformation
|
|
\param normalizeCovar Normalize the covariance matrix with the number of
|
|
atoms
|
|
\param ignoreHs Optinally ignore hydrogens
|
|
*/
|
|
RDGeom::Transform3D *computeCanonicalTransform(
|
|
const RDKit::Conformer &conf, const RDGeom::Point3D *center = 0,
|
|
bool normalizeCovar = false, bool ignoreHs = true);
|
|
|
|
//! Transform the conformation using the specified transformation
|
|
void transformConformer(RDKit::Conformer &conf,
|
|
const RDGeom::Transform3D &trans);
|
|
|
|
//! Canonicalize the orientation of a conformer so that its principal axes
|
|
//! around the specified center point coincide with the x, y, z axes
|
|
/*!
|
|
\param conf The conformer of interest
|
|
\param center Optional center point about which the principal axes are
|
|
computed
|
|
if not specified the centroid of the conformer will be
|
|
used
|
|
\param normalizeCovar Optionally normalize the covariance matrix by the number
|
|
of atoms
|
|
\param ignoreHs If true, ignore hydrogen atoms
|
|
|
|
*/
|
|
void canonicalizeConformer(RDKit::Conformer &conf,
|
|
const RDGeom::Point3D *center = 0,
|
|
bool normalizeCovar = false, bool ignoreHs = true);
|
|
|
|
//! Canonicalize all the conformations in a molecule
|
|
/*!
|
|
\param mol the molecule of interest
|
|
\param normalizeCovar Optionally normalize the covariance matrix by the number
|
|
of atoms
|
|
\param ignoreHs If true, ignore hydrogens
|
|
*/
|
|
void canonicalizeMol(RDKit::ROMol &mol, bool normalizeCovar = false,
|
|
bool ignoreHs = true);
|
|
|
|
//! Get the bond length between the specified atoms i, j
|
|
double getBondLength(const RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId);
|
|
|
|
//! Set the bond length between the specified atoms i, j
|
|
//! (all atoms bonded to atom j are moved)
|
|
void setBondLength(RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, double value);
|
|
|
|
//! Get the angle in radians among the specified atoms i, j, k
|
|
double getAngleRad(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
|
|
inline double getAngleDeg(const RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, unsigned int kAtomId) {
|
|
return (180. / M_PI * getAngleRad(conf, iAtomId, jAtomId, kAtomId));
|
|
}
|
|
|
|
//! Set the angle in radians among the specified atoms i, j, k
|
|
//! (all atoms bonded to atom k are moved)
|
|
void setAngleRad(RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, unsigned int kAtomId, double value);
|
|
|
|
//! Set the angle in degrees among the specified atoms i, j, k
|
|
//! (all atoms bonded to atom k are moved)
|
|
inline void setAngleDeg(RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, unsigned int kAtomId,
|
|
double value) {
|
|
setAngleRad(conf, iAtomId, jAtomId, kAtomId, value / 180. * M_PI);
|
|
}
|
|
|
|
//! Get the dihedral angle in radians among the specified atoms i, j, k, l
|
|
double getDihedralRad(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
|
|
inline double getDihedralDeg(const RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, unsigned int kAtomId,
|
|
unsigned int lAtomId) {
|
|
return (180. / M_PI *
|
|
getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId));
|
|
}
|
|
|
|
//! Set the dihedral angle in radians among the specified atoms i, j, k, l
|
|
//! (all atoms bonded to atom l are moved)
|
|
void setDihedralRad(RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, unsigned int kAtomId,
|
|
unsigned int lAtomId, double value);
|
|
|
|
//! Set the dihedral angle in degrees among the specified atoms i, j, k, l
|
|
//! (all atoms bonded to atom l are moved)
|
|
inline void setDihedralDeg(RDKit::Conformer &conf, unsigned int iAtomId,
|
|
unsigned int jAtomId, unsigned int kAtomId,
|
|
unsigned int lAtomId, double value) {
|
|
setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value / 180. * M_PI);
|
|
}
|
|
}
|
|
#endif
|