com.actelion.research.chem.forcefield.mmff.Electrostatic Maven / Gradle / Ivy
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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.chem.forcefield.mmff;
import java.util.ArrayList;
import java.util.List;
/**
* Nonbonded electrostatic energy term class. This energy term represents
* the energy from the electrostatic attraction/repulsion between any two
* atoms A1..A2 which are in a 1,X relationship (X > 3; interactions where
* X = 4 are scaled by 0.75). A cutoff (default: 100.0 angstrom) can be
* set to skip computation of electrostatic interactions between atoms
* separated by distances larger than the cutoff.
* A constant or distance-dependent dielectric model can be used (default:
* constant).
*/
public class Electrostatic implements EnergyTerm {
public final MMFFMolecule mol;
public final int a1;
public final int a2;
public final Separation.Relation rel;
public final double charge_term;
public final boolean distModel;
/**
* Construct a new electrostatic energy term.
* @param mol The molecule.
* @param a1 Index of atom 1 in mol.
* @param a2 Index of atom 2 in mol.
* @param rel The 1,X relationship between the two atoms (e.g., 1,2;
* 1,3; 1,4; 1,X).
* @param chge1 The charge of atom 1.
* @param chge2 The charge of atom 2.
* @param distModel The distance model to use, true for "distance"
* and false for "constant".
* @param dielConst The dielectric constant.
*/
public Electrostatic(MMFFMolecule mol, int a1, int a2,
Separation.Relation rel, double chge1, double chge2,
boolean distModel, double dielConst) {
this.mol = mol;
this.a1 = a1;
this.a2 = a2;
this.rel = rel;
this.distModel = distModel;
charge_term = chge1 * chge2 / dielConst;
}
/**
* Constructor with default values for distModel and dielConst.
* @param mol The molecule.
* @param a1 Index of atom 1 in mol.
* @param a2 Index of atom 2 in mol.
* @param rel The separation relation between the two atoms (how many
* degrees of separation are between them).
* @param chge1 The charge of atom 1.
* @param chge2 The charge of atom 2.
*/
public Electrostatic(MMFFMolecule mol, int a1, int a2,
Separation.Relation rel, double chge1, double chge2) {
this(mol, a1, a2, rel, chge1, chge2, false, 1.0);
}
/**
* Calculates the electrostatic energy.
* @return The energy.
*/
@Override
public double getEnergy(double[] pos) {
double dist = new Vector3(pos, a1, a2).length();
double corr_dist = dist + 0.05;
double diel = 332.0716;
if (distModel)
corr_dist *= corr_dist;
return diel * charge_term / corr_dist *
(rel == Separation.Relation.ONE_FOUR ? 0.75 : 1.0);
}
/**
* Calculates the gradient and adds it to the gradients array.
* @param pos The atoms current positions array.
* @param grad the atoms current gradients array.
*/
@Override
public void getGradient(double[] pos, double[] grad) {
double dist = new Vector3(pos, a1, a2).length();
double corr_dist = dist + 0.05;
corr_dist *= (distModel ? corr_dist * corr_dist : corr_dist);
double dE_dr = -332.0716 * (distModel ? 2.0 : 1.0)
* charge_term / corr_dist
* (rel == Separation.Relation.ONE_FOUR ? 0.75 : 1.0);
for (int i=0; i<3; i++) {
double dGrad = 0.02;
if (dist > 0.0)
dGrad = dE_dr * (pos[3*a1+i] - pos[3*a2+i]) / dist;
grad[3*a1+i] += dGrad;
grad[3*a2+i] -= dGrad;
}
}
/**
* Finds all Electrostatic energy terms in the current molecule.
* @param table The parameter tables to use.
* @param mol The molecule to search for Electrostatic forces.
* @param sep The separations table for molecule mol.
* @param nonbondedCutoff The nonbonded energy terms cutoff distance.
* Electrostatic energy terms between atoms further than this are
* not added.
* @param dielModel The dielectric model to use. True for 'distance'
* and False for 'linear'.
* @param dielConst The dielectric constant.
* @return The Electrostatic energy terms for this molecule.
*/
public static List findIn(Tables table,
MMFFMolecule mol, Separation sep, double nonbondedCutoff,
boolean dielModel, double dielConst) {
ArrayList eles = new ArrayList();
double[] charges = com.actelion.research.chem.forcefield.mmff.type.Charge.getCharges(table, mol);
for (int i=0; i 0.00001
&& Math.abs(charges[j]) > 0.00001) {
if (new Vector3(mol, i, j).length() < nonbondedCutoff) {
eles.add(new Electrostatic(mol, i, j, relation,
charges[i], charges[j], dielModel,
dielConst));
}
}
}
}
return eles;
}
/**
* Overloaded wrapper function for 'findIn' which sets default values
* for the nonbonded cutoff, dielectric model and dielectric constant.
* @param table The parameter tables to use.
* @param mol The molecule to search for Electrostatic forces.
* @param sep The separations table for molecule mol.
* @return The Electrostatic energy terms for this molecule.
*/
public static List findIn(Tables table,
MMFFMolecule mol, Separation sep) {
return findIn(table, mol, sep, 100.0, false, 1.0);
}
}