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Fixes #2246 (#2248)

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* Fixes #2246

* Fixes #2247
This commit is contained in:
Greg Landrum
2019-02-04 16:32:33 +01:00
committed by Brian Kelley
parent 4d14a819e6
commit 8524652a86
5 changed files with 362 additions and 257 deletions
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33
Code/DistGeom/DistGeomUtils.cpp
View File

@@ -1,6 +1,5 @@
// $Id$
//
// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
// Copyright (C) 2004-2019 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -182,7 +181,8 @@ bool computeRandomCoords(RDGeom::PointPtrVect &positions, double boxSize,
ForceFields::ForceField *constructForceField(
const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions,
const VECT_CHIRALSET &csets, double weightChiral, double weightFourthDim,
std::map<std::pair<int, int>, double> *extraWeights, double basinSizeTol) {
std::map<std::pair<int, int>, double> *extraWeights, double basinSizeTol,
boost::dynamic_bitset<> *fixedPts) {
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
auto *field = new ForceFields::ForceField(positions[0]->dimension());
@@ -192,6 +192,9 @@ ForceFields::ForceField *constructForceField(
for (unsigned int i = 1; i < N; i++) {
for (unsigned int j = 0; j < i; j++) {
if (fixedPts != nullptr && (*fixedPts)[i] && (*fixedPts)[j]) {
continue;
}
double w = 1.0;
double l = mmat.getLowerBound(i, j);
double u = mmat.getUpperBound(i, j);
@@ -225,7 +228,7 @@ ForceFields::ForceField *constructForceField(
// finally the contribution from the fourth dimension if we need to
if ((field->dimension() == 4) && (weightFourthDim > 1.e-8)) {
for (unsigned int i = 1; i < N; i++) {
for (unsigned int i = 0; i < N; i++) {
auto *contrib = new FourthDimContrib(field, i, weightFourthDim);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
@@ -238,7 +241,9 @@ ForceFields::ForceField *construct3DForceField(
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails) {
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
CHECK_INVARIANT(etkdgDetails.expTorsionAtoms.size() == etkdgDetails.expTorsionAngles.size(), "");
CHECK_INVARIANT(etkdgDetails.expTorsionAtoms.size() ==
etkdgDetails.expTorsionAngles.size(),
"");
auto *field = new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
@@ -291,8 +296,8 @@ ForceFields::ForceField *construct3DForceField(
}
auto *contrib = new ForceFields::UFF::InversionContrib(
field, improperAtom[n[0]], improperAtom[n[1]], improperAtom[n[2]],
improperAtom[n[3]], improperAtom[4], static_cast<bool>(improperAtom[5]),
oobForceScalingFactor);
improperAtom[n[3]], improperAtom[4],
static_cast<bool>(improperAtom[5]), oobForceScalingFactor);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
@@ -360,7 +365,9 @@ ForceFields::ForceField *constructPlain3DForceField(
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails) {
unsigned int N = mmat.numRows();
CHECK_INVARIANT(N == positions.size(), "");
CHECK_INVARIANT(etkdgDetails.expTorsionAtoms.size() == etkdgDetails.expTorsionAngles.size(), "");
CHECK_INVARIANT(etkdgDetails.expTorsionAtoms.size() ==
etkdgDetails.expTorsionAngles.size(),
"");
auto *field = new ForceFields::ForceField(positions[0]->dimension());
for (unsigned int i = 0; i < N; ++i) {
field->positions().push_back(positions[i]);
@@ -438,7 +445,7 @@ ForceFields::ForceField *constructPlain3DForceField(
ForceFields::ForceField *construct3DImproperForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const std::vector<std::vector<int> > &improperAtoms,
const std::vector<std::vector<int>> &improperAtoms,
const std::vector<int> &atomNums) {
(void)atomNums;
unsigned int N = mmat.numRows();
@@ -475,13 +482,13 @@ ForceFields::ForceField *construct3DImproperForceField(
}
auto *contrib = new ForceFields::UFF::InversionContrib(
field, improperAtom[n[0]], improperAtom[n[1]], improperAtom[n[2]],
improperAtom[n[3]], improperAtom[4], static_cast<bool>(improperAtom[5]),
oobForceScalingFactor);
improperAtom[n[3]], improperAtom[4],
static_cast<bool>(improperAtom[5]), oobForceScalingFactor);
field->contribs().push_back(ForceFields::ContribPtr(contrib));
}
}
return field;
} // construct3DImproperForceField
}
} // construct3DImproperForceField
} // namespace DistGeom

64
Code/DistGeom/DistGeomUtils.h
View File

@@ -1,5 +1,5 @@
//
// Copyright (C) 2004-2007 Greg Landrum and Rational Discovery LLC
// Copyright (C) 2004-2019 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -17,13 +17,14 @@
#include <Geometry/point.h>
#include "ChiralSet.h"
#include <RDGeneral/utils.h>
#include <boost/dynamic_bitset.hpp>
namespace ForceFields {
class ForceField;
namespace CrystalFF {
struct CrystalFFDetails;
}
struct CrystalFFDetails;
}
} // namespace ForceFields
namespace DistGeom {
@@ -36,12 +37,13 @@ namespace DistGeom {
\return the largest element of the distance matrix
*/
RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(const BoundsMatrix &mmat,
RDNumeric::SymmMatrix<double> &distmat, int seed = -1);
RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(
const BoundsMatrix &mmat, RDNumeric::SymmMatrix<double> &distmat,
int seed = -1);
//! \overload
RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(const BoundsMatrix &mmat,
RDNumeric::SymmMatrix<double> &distmat,
RDKit::double_source_type &rng);
RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(
const BoundsMatrix &mmat, RDNumeric::SymmMatrix<double> &distmat,
RDKit::double_source_type &rng);
//! Compute an initial embedded in 3D based on a distance matrix
/*!
@@ -62,16 +64,15 @@ RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(const BoundsMatrix &mmat,
\return true if the embedding was successful
*/
RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(const RDNumeric::SymmMatrix<double> &distmat,
RDGeom::PointPtrVect &positions,
bool randNegEig = false, unsigned int numZeroFail = 2,
int seed = -1);
RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(
const RDNumeric::SymmMatrix<double> &distmat,
RDGeom::PointPtrVect &positions, bool randNegEig = false,
unsigned int numZeroFail = 2, int seed = -1);
//! \overload
RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(const RDNumeric::SymmMatrix<double> &distmat,
RDGeom::PointPtrVect &positions,
RDKit::double_source_type &rng,
bool randNegEig = false,
unsigned int numZeroFail = 2);
RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(
const RDNumeric::SymmMatrix<double> &distmat,
RDGeom::PointPtrVect &positions, RDKit::double_source_type &rng,
bool randNegEig = false, unsigned int numZeroFail = 2);
//! places atoms randomly in a box
/*!
@@ -82,11 +83,12 @@ RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(const RDNumeric::SymmMatrix<
\return true if the coordinate generation was successful
*/
RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(RDGeom::PointPtrVect &positions, double boxSize,
int seed = -1);
RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(
RDGeom::PointPtrVect &positions, double boxSize, int seed = -1);
//! \overload
RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(RDGeom::PointPtrVect &positions, double boxSize,
RDKit::double_source_type &rng);
RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(
RDGeom::PointPtrVect &positions, double boxSize,
RDKit::double_source_type &rng);
//! Setup the error function for violation of distance bounds as a forcefield
/*!
@@ -118,10 +120,10 @@ RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *constructForceField(
const VECT_CHIRALSET &csets, double weightChiral = 1.0,
double weightFourthDim = 0.1,
std::map<std::pair<int, int>, double> *extraWeights = 0,
double basinSizeTol = 5.0);
double basinSizeTol = 5.0, boost::dynamic_bitset<> *fixedPts = nullptr);
//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
//constraints
// constraints
/*!
\param mmat Distance bounds matrix
@@ -136,7 +138,7 @@ RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *construct3DForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails);
//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
//constraints
// constraints
/*!
\param mmat Distance bounds matrix
@@ -155,19 +157,21 @@ RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *constructPlain3DForceField(
/*!
\param mmat Distance bounds matrix
\param positions A vector of pointers to 3D Points to write out the resulting coordinates
\param improperAtoms A list of groups of 4 atom indices for inversion terms
\param atomNums A list of atomic numbers for all atoms in the molecule
\param positions A vector of pointers to 3D Points to write out the
resulting coordinates \param improperAtoms A list of groups of 4 atom
indices for inversion terms \param atomNums A list of atomic numbers
for all atoms in the molecule
\return a pointer to a ForceField with improper terms
<b>NOTE:</b> the caller is responsible for deleting this force field.
*/
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *construct3DImproperForceField(
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *
construct3DImproperForceField(
const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
const std::vector<std::vector<int> > &improperAtoms,
const std::vector<std::vector<int>> &improperAtoms,
const std::vector<int> &atomNums);
}
} // namespace DistGeom
#endif