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266 lines
8.6 KiB
C++
266 lines
8.6 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2013 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 "AngleBend.h"
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#include "BondStretch.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 calcAngleForceConstant(double theta0,
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double bondOrder12,double bondOrder23,
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const AtomicParams *at1Params,
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const AtomicParams *at2Params,
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const AtomicParams *at3Params){
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double cosTheta0=cos(theta0);
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double r12 = calcBondRestLength(bondOrder12,at1Params,at2Params);
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double r23 = calcBondRestLength(bondOrder23,at2Params,at3Params);
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double r13 = sqrt(r12*r12 + r23*r23 - 2.*r12*r23*cosTheta0);
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double beta = 2.*Params::G/(r12*r23);
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double preFactor = beta*at1Params->Z1*at3Params->Z1 / int_pow<5>(r13);
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double rTerm = r12*r23;
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double innerBit = 3.*rTerm*(1.-cosTheta0*cosTheta0) - r13*r13*cosTheta0;
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double res=preFactor*rTerm*innerBit;
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return res;
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}
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void calcAngleBendGrad(RDGeom::Point3D *r, double *dist,
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double **g, double &dE_dTheta, double &cosTheta, double &sinTheta)
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{
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// -------
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// dTheta/dx is trickier:
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double dCos_dS[6] = {
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1.0 / dist[0] * (r[1].x - cosTheta * r[0].x),
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1.0 / dist[0] * (r[1].y - cosTheta * r[0].y),
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1.0 / dist[0] * (r[1].z - cosTheta * r[0].z),
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1.0 / dist[1] * (r[0].x - cosTheta * r[1].x),
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1.0 / dist[1] * (r[0].y - cosTheta * r[1].y),
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1.0 / dist[1] * (r[0].z - cosTheta * r[1].z)
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};
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g[0][0] += dE_dTheta * dCos_dS[0] / (-sinTheta);
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g[0][1] += dE_dTheta * dCos_dS[1] / (-sinTheta);
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g[0][2] += dE_dTheta * dCos_dS[2] / (-sinTheta);
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g[1][0] += dE_dTheta * (-dCos_dS[0] - dCos_dS[3]) / (-sinTheta);
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g[1][1] += dE_dTheta * (-dCos_dS[1] - dCos_dS[4]) / (-sinTheta);
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g[1][2] += dE_dTheta * (-dCos_dS[2] - dCos_dS[5]) / (-sinTheta);
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g[2][0] += dE_dTheta * dCos_dS[3] / (-sinTheta);
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g[2][1] += dE_dTheta * dCos_dS[4] / (-sinTheta);
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g[2][2] += dE_dTheta * dCos_dS[5] / (-sinTheta);
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>>>>>>> 5b70cdbdc12c19eee9ddb20f2a0ef60be1fb098d
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}
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} // end of namespace Utils
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AngleBendContrib::AngleBendContrib(ForceField *owner,
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unsigned int idx1,unsigned int idx2,unsigned int idx3,
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double bondOrder12,double bondOrder23,
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const AtomicParams *at1Params,
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const AtomicParams *at2Params,
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const AtomicParams *at3Params,
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unsigned int order){
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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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PRECONDITION(at3Params,"bad params pointer");
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PRECONDITION((idx1!=idx2&&idx2!=idx3&&idx1!=idx3),"degenerate points");
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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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RANGE_CHECK(0,idx3,owner->positions().size()-1);
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// the following is a hack to get decent geometries
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// with 3- and 4-membered rings incorporating sp2 atoms
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double theta0 = at2Params->theta0;
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if (order >= 30) {
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switch (order) {
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case 30:
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theta0 = 150.0 / 180.0 * M_PI;
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break;
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case 35:
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theta0 = 60.0 / 180.0 * M_PI;
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break;
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case 40:
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theta0 = 135.0 / 180.0 * M_PI;
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break;
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case 45:
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theta0 = 90.0 / 180.0 * M_PI;
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break;
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}
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order = 0;
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}
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// end of the hack
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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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d_at3Idx = idx3;
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d_order = order;
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d_forceConstant = Utils::calcAngleForceConstant
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(theta0, bondOrder12,bondOrder23,
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at1Params,at2Params,at3Params);
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if(order==0){
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double sinTheta0=sin(theta0);
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double cosTheta0=cos(theta0);
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d_C2 = 1./(4.*std::max(sinTheta0*sinTheta0,1e-8));
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d_C1 = -4.*d_C2*cosTheta0;
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d_C0 = d_C2*(2.*cosTheta0*cosTheta0 + 1.);
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}
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}
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double AngleBendContrib::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 dist1=dp_forceField->distance(d_at1Idx,d_at2Idx,pos);
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double dist2=dp_forceField->distance(d_at2Idx,d_at3Idx,pos);
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RDGeom::Point3D p1(pos[3*d_at1Idx],
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pos[3*d_at1Idx+1],
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pos[3*d_at1Idx+2]);
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RDGeom::Point3D p2(pos[3*d_at2Idx],
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pos[3*d_at2Idx+1],
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pos[3*d_at2Idx+2]);
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RDGeom::Point3D p3(pos[3*d_at3Idx],
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pos[3*d_at3Idx+1],
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pos[3*d_at3Idx+2]);
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RDGeom::Point3D p12=p1-p2;
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RDGeom::Point3D p32=p3-p2;
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double cosTheta = p12.dotProduct(p32)/(dist1*dist2);
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// we need sin^2(theta) to get cos(2*theta), so compute that:
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double sinThetaSq = 1.-cosTheta*cosTheta;
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double angleTerm = getEnergyTerm(cosTheta,sinThetaSq);
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double res = d_forceConstant*angleTerm;
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return res;
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}
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void AngleBendContrib::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[2] = {
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dp_forceField->distance(d_at1Idx, d_at2Idx, pos),
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dp_forceField->distance(d_at2Idx, d_at3Idx, pos)
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};
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RDGeom::Point3D p1(pos[3 * d_at1Idx],
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pos[3 * d_at1Idx + 1], pos[3 * d_at1Idx + 2]);
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RDGeom::Point3D p2(pos[3 * d_at2Idx],
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pos[3 * d_at2Idx + 1], pos[3 * d_at2Idx + 2]);
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RDGeom::Point3D p3(pos[3 * d_at3Idx],
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pos[3 * d_at3Idx + 1], pos[3 * d_at3Idx + 2]);
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double *g[3] = {
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&(grad[3 * d_at1Idx]),
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&(grad[3 * d_at2Idx]),
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&(grad[3 * d_at3Idx])
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};
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RDGeom::Point3D r[2] = {
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(p1 - p2) / dist[0],
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(p3 - p2) / dist[1]
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};
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double cosTheta = r[0].dotProduct(r[1]);
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double sinThetaSq = 1.0 - cosTheta * cosTheta;
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double sinTheta = std::max(((sinThetaSq > 0.0) ? sqrt(sinThetaSq) : 0.0), 1.0e-8);
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//std::cerr << "GRAD: " << cosTheta << " (" << acos(cosTheta)<< "), ";
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//std::cerr << sinTheta << " (" << asin(sinTheta)<< ")" << std::endl;
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// use the chain rule:
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// dE/dx = dE/dTheta * dTheta/dx
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// dE/dTheta is independent of cartesians:
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double dE_dTheta=getThetaDeriv(cosTheta,sinTheta);
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Utils::calcAngleBendGrad(r, dist, g, dE_dTheta, cosTheta, sinTheta);
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}
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double AngleBendContrib::getEnergyTerm(double cosTheta,double sinThetaSq) const {
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PRECONDITION(d_order==0||d_order==1||d_order==2||d_order==3||d_order==4,"bad order");
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// cos(2x) = cos^2(x) - sin^2(x);
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double cos2Theta = cosTheta*cosTheta - sinThetaSq;
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double res=0.0;
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if(d_order==0){
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res=d_C0 + d_C1*cosTheta + d_C2*cos2Theta;
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} else {
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switch(d_order){
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case 1:
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res=-cosTheta;
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break;
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case 2:
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res=cos2Theta;
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break;
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case 3:
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// cos(3x) = cos^3(x) - 3*cos(x)*sin^2(x)
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res = cosTheta*(cosTheta*cosTheta-3.*sinThetaSq);
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break;
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case 4:
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// cos(4x) = cos^4(x) - 6*cos^2(x)*sin^2(x)+sin^4(x)
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res = int_pow<4>(cosTheta) - 6.*cosTheta*cosTheta*sinThetaSq + sinThetaSq*sinThetaSq;
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break;
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}
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res = 1.-res;
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res /= (double)(d_order*d_order);
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}
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return res;
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}
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double AngleBendContrib::getThetaDeriv(double cosTheta,double sinTheta) const {
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PRECONDITION(d_order==0||d_order==1||d_order==2||d_order==3||d_order==4,"bad order");
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double dE_dTheta=0.0;
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double sin2Theta = 2.*sinTheta*cosTheta;
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if(d_order==0){
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dE_dTheta = -1.*d_forceConstant*(d_C1*sinTheta +
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2.*d_C2*sin2Theta);
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} else {
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// E = k/n^2 [1-cos(n theta)]
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// dE = - k/n^2 * d cos(n theta)
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// these all use:
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// d cos(ax) = -a sin(ax)
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switch(d_order){
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case 1:
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dE_dTheta = -sinTheta;
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break;
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case 2:
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// sin(2*x) = 2*cos(x)*sin(x)
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dE_dTheta = sin2Theta;
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break;
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case 3:
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// sin(3*x) = 3*sin(x) - 4*sin^3(x)
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dE_dTheta = sinTheta*(3.-4.*sinTheta*sinTheta);
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break;
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case 4:
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// sin(4*x) = cos(x)*(4*sin(x) - 8*sin^3(x))
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dE_dTheta = cosTheta*sinTheta*(4.-8.*sinTheta*sinTheta);
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break;
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}
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dE_dTheta *= d_forceConstant/(double)(d_order);
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}
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return dE_dTheta;
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}
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}
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}
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