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* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
104 lines
3.7 KiB
C++
104 lines
3.7 KiB
C++
//
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// Copyright (C) 2024 Niels Maeder 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_UFFINVERSIONS_H
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#define RD_UFFINVERSIONS_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 UFF {
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class AtomicParams;
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struct RDKIT_FORCEFIELD_EXPORT InversionContribsParams {
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unsigned int idx1{0}; //!< index of atom1 in the ForceField's positions
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unsigned int idx2{0}; //!< index of atom2 in the ForceField's positions
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unsigned int idx3{0}; //!< index of atom3 in the ForceField's positions
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unsigned int idx4{0}; //!< index of atom4 in the ForceField's positions
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int at2AtomicNum{0}; //!< atomic number for atom 2
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bool isCBoundToO{false}; //!< boolean flag; true if atom 2 is sp2 carbon
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//!< bound to sp2 oxygen
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double C0{0.0}; //!< inversion coefficient 0
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double C1{0.0}; //!< inversion coefficient 1
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double C2{0.0}; //!< inversion coefficient 2
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double forceConstant{1.0}; //!< force constant
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InversionContribsParams(unsigned int idx1, unsigned int idx2,
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unsigned int idx3, unsigned int idx4,
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int at2AtomicNum, bool isCBoundToO, double C0,
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double C1, double C2, double forceConstant = 1.0)
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: idx1(idx1),
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idx2(idx2),
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idx3(idx3),
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idx4(idx4),
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at2AtomicNum(at2AtomicNum),
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isCBoundToO(isCBoundToO),
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C0(C0),
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C1(C1),
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C2(C2),
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forceConstant(forceConstant) {};
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};
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//! A term to capture all Inversion Contributionss.
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class RDKIT_FORCEFIELD_EXPORT InversionContribs : public ForceFieldContrib {
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public:
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InversionContribs() = default;
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//! Constructor
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/*!
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\param owner pointer to the owning ForceField
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*/
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InversionContribs(ForceField *owner);
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~InversionContribs() override = default;
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//! Add contribution to this contrib.
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/*!
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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 idx4 index of atom4 in the ForceField's positions
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\param at2AtomicNum atomic number for atom 2
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\param isCBoundToO boolean flag; true if atom 2 is sp2 C bound to
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sp2 O
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\param oobForceScalingFactor scaling factor for force constant
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*/
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void addContrib(unsigned int idx1, unsigned int idx2, unsigned int idx3,
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unsigned int idx4, int at2AtomicNum, bool isCBoundToO,
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double oobForceScalingFactor = 1.0);
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//! return the contribution of this contrib to the energy of a given state
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/*!
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\param pos positions of the atoms in the current state
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*/
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double getEnergy(double *pos) const override;
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//! calculate the contribution of this contrib to the gradient at a given
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/// state
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/*!
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\param pos positions of the atoms in the current state
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\param grad gradients to be adapted
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*/
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void getGrad(double *pos, double *grad) const override;
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//! Copy constructor
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InversionContribs *copy() const override {
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return new InversionContribs(*this);
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}
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//! Return true if there are no contributions in this contrib
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bool empty() const { return d_contribs.empty(); }
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//! Get number of contributions in this contrib
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unsigned int size() const { return d_contribs.size(); }
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private:
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std::vector<InversionContribsParams> d_contribs;
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};
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} // namespace UFF
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} // namespace ForceFields
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#endif |