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* Condense MMFF electrostatics and contrib instances. Previously, a separate contrib had been added for each common term. Each of these required a separate allocation, and a separate dynamic dispatch on call. This change moves to an SOA style, making data access contiguous and drastically reducing the number of calls. * Make suggested copyright fixes and svn artifact removals
77 lines
2.9 KiB
C++
77 lines
2.9 KiB
C++
// Copyright (C) 2013-2025 Paolo Tosco and other RDKit contributors
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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_MMFFANGLEBEND_H__
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#define __RD_MMFFANGLEBEND_H__
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#include <ForceField/ForceField.h>
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#include <ForceField/Contrib.h>
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namespace ForceFields {
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namespace MMFF {
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class MMFFBond;
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class MMFFAngle;
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class MMFFProp;
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//! The angle-bend term for MMFF
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class RDKIT_FORCEFIELD_EXPORT AngleBendContrib : public ForceFieldContrib {
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public:
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AngleBendContrib() {}
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//! Constructor
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AngleBendContrib(ForceField *owner);
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/*! Adds an angle to the contrib
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The angle is between atom1 - atom2 - atom3
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\param idx1 index of atom1 in the ForceField's positions
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\param idx2 index of atom2 in the ForceField's positions
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\param idx3 index of atom3 in the ForceField's positions
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\param angleType MMFF type of the angle (as an unsigned int)
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*/
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void addTerm(unsigned int idx1, unsigned int idx2,
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unsigned int idx3, const MMFFAngle *mmffAngleParams,
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const MMFFProp *mmffPropParamsCentralAtom);
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double getEnergy(double *pos) const override;
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void getGrad(double *pos, double *grad) const override;
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AngleBendContrib *copy() const override {
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return new AngleBendContrib(*this);
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}
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private:
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std::vector<bool> d_isLinear;
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std::vector<int16_t> d_at1Idxs, d_at2Idxs, d_at3Idxs;
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std::vector<double> d_ka, d_theta0;
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};
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namespace Utils {
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//! returns the MMFF rest value for an angle
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RDKIT_FORCEFIELD_EXPORT double calcAngleRestValue(
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const MMFFAngle *mmffAngleParams);
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//! returns the MMFF force constant for an angle
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RDKIT_FORCEFIELD_EXPORT double calcAngleForceConstant(
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const MMFFAngle *mmffAngleParams);
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//! calculates and returns the cosine of the angle between points p1, p2, p3
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RDKIT_FORCEFIELD_EXPORT double calcCosTheta(RDGeom::Point3D p1,
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RDGeom::Point3D p2,
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RDGeom::Point3D p3, double dist1,
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double dist2);
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//! calculates and returns the angle bending MMFF energy
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RDKIT_FORCEFIELD_EXPORT double calcAngleBendEnergy(const double theta0,
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const double ka,
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bool isLinear,
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const double cosTheta);
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RDKIT_FORCEFIELD_EXPORT void calcAngleBendGrad(RDGeom::Point3D *r, double *dist,
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double **g, double &dE_dTheta,
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double &cosTheta,
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double &sinTheta);
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} // namespace Utils
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} // namespace MMFF
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} // namespace ForceFields
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#endif
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