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2c5ae534f2
* First try at using DistViolationContribs only the most basic of testing has been done also add ForceField::distance2 to allow some optimizations * allow testing using old approach * optimization At this point testUFFForceFieldHelpers fails since the check for std::max_element in the e_contribs vector at Embedder.cpp:513 is now doing something totally different (instead of a bunch of small distance violation contribs, we have one big one). We'll need to come up with something for this. With the benchmarking set that I'm using - 500 DG conformers for ~465 COD molecules using 10 threads - this runs in almost 10% less time than master. * backup; builds, tests do not pass * all tests pass except the old failure * more constification * backup/debugging * add fourthdim contribs the same way * tests now pass * deprecations * remove unused vars and code * changes in response to review
85 lines
2.4 KiB
C++
85 lines
2.4 KiB
C++
//
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// Copyright (C) 2024 Greg Landrum 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_FOURTHDIMCONTRIBS_H
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#define RD_FOURTHDIMCONTRIBS_H
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#include <vector>
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#include <RDGeneral/Invariant.h>
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#include <ForceField/Contrib.h>
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#include <ForceField/ForceField.h>
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namespace DistGeom {
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struct FourthDimContribsParams {
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unsigned int idx{0};
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double weight{0.0};
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FourthDimContribsParams(unsigned int idx, double w) : idx(idx), weight(w) {};
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};
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//! A term used in penalizing the 4th dimension in order to move from 4D->3D
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//!
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class RDKIT_DISTGEOMETRY_EXPORT FourthDimContribs
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: public ForceFields::ForceFieldContrib {
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public:
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FourthDimContribs() = 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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\param idx the index of the atom to be considered
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\param weight (optional) the weight to be used for this contrib
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*/
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FourthDimContribs(ForceFields::ForceField *owner) {
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PRECONDITION(owner, "bad force field");
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PRECONDITION(owner->dimension() == 4, "force field has wrong dimension");
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dp_forceField = owner;
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}
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void addContrib(unsigned int idx, double weight) {
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d_contribs.emplace_back(idx, weight);
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}
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//! return the contribution of this contrib to the energy of a given state
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double getEnergy(double *pos) const override {
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PRECONDITION(pos, "bad vector");
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constexpr unsigned int ffdim = 4;
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double res = 0.0;
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for (const auto &contrib : d_contribs) {
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unsigned int pid = contrib.idx * ffdim + 3;
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res += contrib.weight * pos[pid] * pos[pid];
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}
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return res;
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}
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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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void getGrad(double *pos, double *grad) const override {
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PRECONDITION(pos, "bad vector");
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constexpr unsigned int ffdim = 4;
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for (const auto &contrib : d_contribs) {
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unsigned int pid = contrib.idx * ffdim + 3;
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grad[pid] += contrib.weight * pos[pid];
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}
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}
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FourthDimContribs *copy() const override {
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return new FourthDimContribs(*this);
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}
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bool empty() const { return d_contribs.empty(); }
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unsigned int size() const { return d_contribs.size(); }
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private:
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std::vector<FourthDimContribsParams> d_contribs;
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};
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} // namespace DistGeom
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#endif
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