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Open Source Chemistry Library
/*
* Copyright 2013-2020 Thomas Sander, openmolecules.org
*
* 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 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 HOLDER 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.
*
* @author Thomas Sander
*/
package org.openmolecules.chem.conf.so;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.conf.TorsionDB;
import com.actelion.research.chem.conf.TorsionDetail;
import com.actelion.research.chem.conf.TorsionPrediction;
import java.util.ArrayList;
public class TorsionRule extends ConformationRule {
final static double COLLIDING_ATOM_STRAIN = 0.1;
private int mSmallerSubstituentIndex;
private int[] mAtomToRotate;
private short[] mTorsion,mFrequency;
private short[][] mRange;
public TorsionRule(short[] torsion, short[] frequency, short[][] range, int[] torsionAtom, int[] atomToRotate, int smallerSubstituentIndex) {
super(torsionAtom);
mTorsion = torsion;
mFrequency = frequency;
mRange = range;
mAtomToRotate = atomToRotate;
mSmallerSubstituentIndex = smallerSubstituentIndex;
}
@Override
public int getRuleType() {
return RULE_TYPE_TORSION;
}
public static void calculateRules(ArrayList ruleList, StereoMolecule mol) {
TorsionDB.initialize(TorsionDB.MODE_ANGLES);
boolean[] isRotatableBond = new boolean[mol.getAllBonds()];
TorsionDB.findRotatableBonds(mol, true, isRotatableBond);
for (int bond=0; bond 6 && mol.getAtomPi(rearAtom) == 1)
addHeteroPiRule(mol, bondAtom, rearAtom, hCount, ruleList);
else if (mol.getAtomPi(rearAtom) != 2 && mol.getAllConnAtoms(rearAtom) > 1)
addDegree60Rule(mol, bondAtom, rearAtom, hCount, ruleList);
break;
}
}
}
}
}
private static void addHeteroPiRule(StereoMolecule mol, int bondAtom, int piAtom, int hCount, ArrayList ruleList) {
int piNeighbour = -1;
for (int j=0; j ruleList) {
int[] atomToRotate = new int[hCount];
int[] torsionAtom = new int[4];
torsionAtom[0] = mol.getConnAtom(rearAtom, (mol.getConnAtom(rearAtom, 0) == bondAtom) ? 1 : 0);
torsionAtom[1] = rearAtom;
torsionAtom[2] = bondAtom;
torsionAtom[3] = mol.getConnAtom(bondAtom, (mol.getConnAtom(bondAtom, 0) == rearAtom) ? 1 : 0);
int hIndex = 0;
for (int i = 0; i ruleList) {
for (ConformationRule rule:ruleList) {
if (rule.getRuleType() == ConformationRule.RULE_TYPE_PLANE) {
int[] planeAtom = rule.getAtomList();
for (int ta:torsionAtom) {
if (ta == -1)
return false;
boolean found = false;
for (int pa : planeAtom) {
if (ta == pa) {
found = true;
break;
}
}
if (!found)
return false;
}
return true;
}
}
return false;
}
@Override
public boolean apply(Conformer conformer, double cycleFactor) {
double currentTorsion = TorsionDB.calculateTorsionExtended(conformer, mAtom);
if (Double.isNaN(currentTorsion))
return false;
if (currentTorsion < 0.0)
currentTorsion += 2 * Math.PI;
int index = findApplicableTorsionIndex(currentTorsion);
double severity = getSeverity(currentTorsion, index);
if (severity == 0.0)
return false;
double angleCorrection = Math.PI * mTorsion[index] / 180.0 - currentTorsion;
if (Math.abs(angleCorrection) > Math.PI)
angleCorrection = (angleCorrection < 0) ? 2*Math.PI + angleCorrection : angleCorrection - 2*Math.PI;
if (Math.abs(angleCorrection) < 0.001 * Math.PI)
return false;
Coordinates unit = conformer.getCoordinates(mAtom[2]).subC(conformer.getCoordinates(mAtom[1]));
unit.unit();
angleCorrection *= cycleFactor * severity;
StereoMolecule mol = conformer.getMolecule();
if (mAtomToRotate != null) { // rotate smaller side of the molecule
double rotation = (mSmallerSubstituentIndex == 0) ? -angleCorrection : angleCorrection;
for (int a:mAtomToRotate)
rotateAtom(conformer, a, conformer.getCoordinates(mAtom[1]), unit, rotation);
}
else { // rotate first and second atom shell from bond atoms; reduce angle for second shell atoms and if one side is more rigid
int bond = mol.getBond(mAtom[1], mAtom[2]);
boolean isFiveMemberedRing = (bond != -1 && mol.getBondRingSize(bond) <= 5);
for (int i=1; i<=2; i++) {
double factor = (i==1 ? -2.0 : 2.0) * mol.getAtomRingBondCount(mAtom[i]);
for (int j=0; j Math.PI)
dif = 2*Math.PI - dif;
dif /= (10+Math.sqrt(mFrequency[i])); // normalize somewhat by frequency
if (minDif > dif) {
minDif = dif;
index = i;
}
}
return index;
}
/**
* Calculates a severity factor for the torsion depending on how
* far it is from the optimum and whether it is still in the range.
* @param angle from 0 to 2pi
* @param index of the torsion
* @return severity from 0 to 1
*/
private double getSeverity(double angle, int index) {
double range0 = mRange[index][0] * Math.PI / 180;
double range1 = mRange[index][1] * Math.PI / 180;
double torsion = mTorsion[index] * Math.PI / 180;
if (angle < torsion - Math.PI)
angle += 2 * Math.PI;
else if (angle > torsion + Math.PI)
angle -= 2 * Math.PI;
double dif = (torsion - angle) / (torsion - ((angle 180)
dif = 360 - dif;
if (dif > 60)
dif = 60;
StereoMolecule mol = conformer.getMolecule();
// Use 50% the rotation barrier of butane (6 kcal/mol), if 60 degrees off.
// The major strain contribution should come from atom repulsion strains if a torsion is not optimal.
double strain = 3.0 * severity * dif*dif/3600;
double totalStrain = 0;
for (int i=0; i maxAtomStrain)
maxAtomStrain = conformer.getAtomStrain(connAtom);
}
}
System.out.println(((maxAtomStrain < COLLIDING_ATOM_STRAIN) ? "kept:" : "disabled:")+toString());
if (maxAtomStrain < COLLIDING_ATOM_STRAIN)
return false;
mIsEnabled = false;
return true;
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder("torsion rule:");
super.addAtomList(sb);
sb.append(" torsions:");
for (int i=0; i