mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
5b70cdbdc1
to the current value) (C++/Python) - added absolute/relative AngleConstraints (C++/Python) - added absolute/relative TorsionConstraints (C++/Python) - added PositionConstraints (C++/Python) - exposed fixedPoints from Python - added relevant C++/Python tests - removed a number of redundant "this->" in member functions - moved some getGrad() code into Utils::calcAngleBendGrad and Utils::calcTorsionGrad to avoid repeating the same code for constraints
103 lines
3.4 KiB
C++
103 lines
3.4 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
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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 "Nonbonded.h"
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#include "Params.h"
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#include <math.h>
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#include <ForceField/ForceField.h>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/utils.h>
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namespace ForceFields {
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namespace UFF {
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namespace Utils {
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double calcNonbondedMinimum(const AtomicParams *at1Params,
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const AtomicParams *at2Params){
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return sqrt(at1Params->x1*at2Params->x1);
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}
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double calcNonbondedDepth(const AtomicParams *at1Params,
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const AtomicParams *at2Params){
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return sqrt(at1Params->D1*at2Params->D1);
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}
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} // end of namespace utils
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vdWContrib::vdWContrib(ForceField *owner,
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unsigned int idx1,unsigned int idx2,
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const AtomicParams *at1Params,
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const AtomicParams *at2Params,
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double threshMultiplier){
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PRECONDITION(owner,"bad owner");
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PRECONDITION(at1Params,"bad params pointer");
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PRECONDITION(at2Params,"bad params pointer");
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RANGE_CHECK(0,idx1,owner->positions().size()-1);
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RANGE_CHECK(0,idx2,owner->positions().size()-1);
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dp_forceField = owner;
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d_at1Idx = idx1;
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d_at2Idx = idx2;
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// UFF uses the geometric mean of the vdW parameters:
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d_xij = Utils::calcNonbondedMinimum(at1Params,at2Params);
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d_wellDepth = Utils::calcNonbondedDepth(at1Params,at2Params);
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d_thresh = threshMultiplier*d_xij;
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//std::cerr << " non-bonded: " << idx1 << "-" << idx2 << " " << d_xij << " " << d_wellDepth << " " << d_thresh << std::endl;
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}
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double vdWContrib::getEnergy(double *pos) const {
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PRECONDITION(dp_forceField,"no owner");
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PRECONDITION(pos,"bad vector");
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double dist=dp_forceField->distance(d_at1Idx,d_at2Idx,pos);
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if(dist>d_thresh || dist<=0.0) return 0.0;
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double r=d_xij/dist;
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double r6=int_pow<6>(r);
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double r12=r6*r6;
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double res = d_wellDepth*(r12 - 2.0*r6);
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//if(d_at1Idx==12 && d_at2Idx==21 ) std::cerr << " >: " << d_at1Idx << "-" << d_at2Idx << " " << r << " = " << res << std::endl;
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return res;
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}
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void vdWContrib::getGrad(double *pos,double *grad) const {
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PRECONDITION(dp_forceField,"no owner");
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PRECONDITION(pos,"bad vector");
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PRECONDITION(grad,"bad vector");
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double dist=dp_forceField->distance(d_at1Idx,d_at2Idx,pos);
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if(dist>d_thresh) return;
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if(dist<=0){
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for(int i=0;i<3;i++){
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// move in an arbitrary direction
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double dGrad=100.0;
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grad[3*d_at1Idx+i] += dGrad;
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grad[3*d_at2Idx+i] -= dGrad;
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}
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return;
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}
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double r = d_xij/dist;
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double r7 = int_pow<7>(r);
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double r13= int_pow<13>(r);
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double preFactor = 12.*d_wellDepth/d_xij * (r7-r13);
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double *at1Coords = &(pos[3*d_at1Idx]);
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double *at2Coords = &(pos[3*d_at2Idx]);
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for(int i=0;i<3;i++){
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double dGrad=preFactor * (at1Coords[i]-at2Coords[i])/dist;
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grad[3*d_at1Idx+i] += dGrad;
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grad[3*d_at2Idx+i] -= dGrad;
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}
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}
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}
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}
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