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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
68 lines
2.3 KiB
C++
68 lines
2.3 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_MMFFBONDSTRETCH_H__
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#define __RD_MMFFBONDSTRETCH_H__
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#include <ForceField/Contrib.h>
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#include <vector>
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namespace ForceFields {
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namespace MMFF {
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class MMFFBond;
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class MMFFBondStretchEmpiricalRule;
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//! The bond-stretch term for MMFF
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class RDKIT_FORCEFIELD_EXPORT BondStretchContrib : public ForceFieldContrib {
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public:
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BondStretchContrib() {}
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//! Constructor
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BondStretchContrib(ForceField *owner);
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/*! Adds a bond stretch to the contrib
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\param idx1 index of end1 in the ForceField's positions
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\param idx2 index of end2 in the ForceField's positions
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\param bondType MMFF94 type of the bond (as an unsigned int)
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\param end1Params pointer to the parameters for end1
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\param end2Params pointer to the parameters for end2
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*/
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void addTerm(const unsigned int idx1,
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const unsigned int idx2,
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const MMFFBond *mmffBondParams);
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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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BondStretchContrib *copy() const override {
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return new BondStretchContrib(*this);
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}
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private:
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std::vector<int> d_at1Idxs, d_at2Idxs; //!< indices of end points
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std::vector<double> d_r0; //!< rest length of the bond
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std::vector<double> d_kb; //!< force constant of the bond
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};
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namespace Utils {
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//! returns the MMFF rest length for a bond
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RDKIT_FORCEFIELD_EXPORT double calcBondRestLength(
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const MMFFBond *mmffBondParams);
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//! returns the MMFF force constant for a bond
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RDKIT_FORCEFIELD_EXPORT double calcBondForceConstant(
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const MMFFBond *mmffBondParams);
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//! calculates and returns the bond stretching MMFF energy
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RDKIT_FORCEFIELD_EXPORT double calcBondStretchEnergy(const double r0,
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const double kb,
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const double distance);
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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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