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3f3ff3858a
* refactor skeleton * fix contribs * adapt documentation * clarify function names * make variable names more readable and update documentation * switch boost dynamic bitset with std::vector<bool> * clearer const name * fix typo and go back to dynamic bitset * go back to old function signature * add inline overload with fewer arguments * remove unecessary doc lines and add tol to distance directly in function call * use constexpr for known distance force constant * update documentation * enhance documentation * english Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * make changes requested by @greglandrum * make all constexprs --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
218 lines
8.2 KiB
C++
218 lines
8.2 KiB
C++
//
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// Copyright (C) 2004-2019 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef _RD_DISTGEOMUTILS_H_
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#define _RD_DISTGEOMUTILS_H_
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#include "BoundsMatrix.h"
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#include <Numerics/SymmMatrix.h>
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#include <map>
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#include <Geometry/point.h>
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#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
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#include "ChiralSet.h"
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#include <RDGeneral/utils.h>
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#include <boost/dynamic_bitset.hpp>
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namespace ForceFields {
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class ForceField;
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} // namespace ForceFields
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namespace DistGeom {
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//! Pick a distance matrix at random such that the
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//! distance satisfy the bounds in the BoundsMatrix
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/*!
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\param mmat Bounds matrix
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\param distmat Storage for randomly chosen distances
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\param seed the random number seed to use
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\return the largest element of the distance matrix
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*/
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RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(
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const BoundsMatrix &mmat, RDNumeric::SymmMatrix<double> &distmat,
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int seed = -1);
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//! \overload
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RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(
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const BoundsMatrix &mmat, RDNumeric::SymmMatrix<double> &distmat,
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RDKit::double_source_type &rng);
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//! Compute an initial embedded in 3D based on a distance matrix
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/*!
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This function follows the embed algorithm mentioned in
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"Distance Geometry and Molecular Conformation" by G.M.Crippen and T.F.Havel
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(pages 312-313)
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\param distmat Distance matrix
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\param positions A vector of pointers to Points to write out the resulting
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coordinates
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\param randNegEig If set to true and if any of the eigen values are negative,
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we will
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pick the corresponding components of the coordinates at
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random
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\param numZeroFail Fail embedding is more this many (or more) eigen values are
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zero
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\param seed the random number seed to use
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\return true if the embedding was successful
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*/
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RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(
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const RDNumeric::SymmMatrix<double> &distmat,
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RDGeom::PointPtrVect &positions, bool randNegEig = false,
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unsigned int numZeroFail = 2, int seed = -1);
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//! \overload
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RDKIT_DISTGEOMETRY_EXPORT bool computeInitialCoords(
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const RDNumeric::SymmMatrix<double> &distmat,
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RDGeom::PointPtrVect &positions, RDKit::double_source_type &rng,
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bool randNegEig = false, unsigned int numZeroFail = 2);
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//! places atoms randomly in a box
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/*!
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\param positions A vector of pointers to Points to write out the resulting
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coordinates
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\param boxSize the side-length of the cubic box
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\param seed the random number seed to use
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\return true if the coordinate generation was successful
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*/
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RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(
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RDGeom::PointPtrVect &positions, double boxSize, int seed = -1);
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//! \overload
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RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(
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RDGeom::PointPtrVect &positions, double boxSize,
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RDKit::double_source_type &rng);
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//! Setup the error function for violation of distance bounds as a forcefield
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/*!
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This is based on function E3 on page 311 of "Distance Geometry in Molecular
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Modeling" Jeffrey M.Blaney and J.Scott Dixon, Review in Computational
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Chemistry,
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Volume V
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\param mmat Distance bounds matrix
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\param positions A vector of pointers to Points to write out the
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resulting coordinates
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\param csets The vector of chiral points (type: ChiralSet)
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\param weightChiral weight to be used to enforce chirality
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\param weightFourthDim another chiral weight
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\param extraWeights an optional set of weights for distance bounds
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violations
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\param basinSizeTol Optional: any distance bound with a basin (distance
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between max and
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min bounds) larger than this value will not be included
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in the force
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field used to cleanup the structure.
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\return a pointer to a ForceField suitable for cleaning up the violations.
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<b>NOTE:</b> the caller is responsible for deleting this force field.
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*/
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RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *constructForceField(
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const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions,
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const VECT_CHIRALSET &csets, double weightChiral = 1.0,
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double weightFourthDim = 0.1,
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std::map<std::pair<int, int>, double> *extraWeights = nullptr,
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double basinSizeTol = 5.0, boost::dynamic_bitset<> *fixedPts = nullptr);
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//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
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/// constraints
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/*!
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\param mmat Distance bounds matrix
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\param positions A vector of pointers to 3D Points to write out the
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resulting coordinates
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\param etkdgDetails Contains information about the ETKDG force field
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<b>NOTE:</b> the caller is responsible for deleting this force field.
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*/
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RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *construct3DForceField(
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const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
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const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails);
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//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
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/// constraints, as well as atom pairwise Columbic interactions
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/*!
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\param mmat Distance bounds matrix
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\param positions A vector of pointers to 3D Points to write out the
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resulting coordinates
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\param etkdgDetails Contains information about the ETKDG force field
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\param CPCI Contains which atom pair(s) have what strength of
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attractive/repulsive electrostatic interaction(s)
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<b>NOTE:</b> the caller is responsible for deleting this force field.
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*/
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RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *construct3DForceField(
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const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
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const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails,
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const std::map<std::pair<unsigned int, unsigned int>, double> &CPCI);
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//! Force field with experimental torsion angle preferences and 1-2/1-3 distance
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/// constraints
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/*!
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\param mmat Distance bounds matrix
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\param positions A vector of pointers to 3D Points to write out the
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resulting coordinates
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\param etkdgDetails Contains information about the ETKDG force field
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<b>NOTE:</b> the caller is responsible for deleting this force field.
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*/
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RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *constructPlain3DForceField(
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const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
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const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails);
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//! Force field with improper terms and SP linearity contributions
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/*!
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\param mmat Distance bounds matrix
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\param positions A vector of pointers to 3D Points to write out the
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resulting coordinates
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\param improperAtoms A list of groups of 4 atom indices for inversion terms
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\param angles List of lists with the three angle indices and whether
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the center atom in the angle is SP hybridized for every angle in the molecule.
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\param atomNums A list of atomic numbers for all atoms in the molecule,
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no longer used.
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\return a pointer to a ForceField with improper terms
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<b>NOTE:</b> the caller is responsible for deleting this force field.
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*/
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RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *
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construct3DImproperForceField(
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const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
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const std::vector<std::vector<int>> &improperAtoms,
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const std::vector<std::vector<int>> &angles,
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const std::vector<int> &atomNums);
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//! Force field with improper terms and SP linearity contributions
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/*!
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\param mmat Distance bounds matrix
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\param positions A vector of pointers to 3D Points to write out the
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resulting coordinates
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\param etkdgDetails Contains information about the ETKDG force field
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\return a pointer to a ForceField with improper terms
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<b>NOTE:</b> the caller is responsible for deleting this force field.
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*/
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//! \overload
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inline ForceFields::ForceField *construct3DImproperForceField(
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const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions,
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const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails) {
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return construct3DImproperForceField(
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mmat, positions, etkdgDetails.improperAtoms, etkdgDetails.angles,
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etkdgDetails.atomNums);
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}
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} // namespace DistGeom
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#endif
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