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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
67 lines
2.0 KiB
C++
67 lines
2.0 KiB
C++
//
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// Created by Santosh Putta, Nov 2006
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//
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#include <RDGeneral/export.h>
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#ifndef __RD_FOURTHDIMCONTRIB_H__
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#define __RD_FOURTHDIMCONTRIB_H__
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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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//! DEPRECATED: use FourthDimContribs instead
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//! A term used in penalizing chirality violations
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//!
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class RDKIT_DISTGEOMETRY_EXPORT FourthDimContrib
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: public ForceFields::ForceFieldContrib {
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public:
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FourthDimContrib() {}
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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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FourthDimContrib(ForceFields::ForceField *owner, unsigned int idx,
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double weight)
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: d_idx(idx), d_weight(weight) {
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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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//! 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(dp_forceField, "no owner");
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PRECONDITION(dp_forceField->dimension() == 4,
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"force field has wrong dimension");
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PRECONDITION(pos, "bad vector");
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unsigned int pid = d_idx * dp_forceField->dimension() + 3;
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return d_weight * pos[pid] * pos[pid];
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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(dp_forceField, "no owner");
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PRECONDITION(dp_forceField->dimension() == 4,
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"force field has wrong dimension");
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PRECONDITION(pos, "bad vector");
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unsigned int pid = d_idx * dp_forceField->dimension() + 3;
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grad[pid] += d_weight * pos[pid];
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}
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FourthDimContrib *copy() const override {
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return new FourthDimContrib(*this);
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}
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private:
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unsigned int d_idx{0};
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double d_weight{0.0};
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};
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} // namespace DistGeom
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#endif
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