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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 java.util.ArrayList;
public class TetrahedralStereoRule extends ConformationRule {
private int[] mRotatableAtom,mStaticNeighbour,mRotatableNeighbour;
/**
* Expects neighbourAtom[5] as list of 3 or 4 neighbour atoms of the stereo center.
* The list must be sorted by atom index. In case of 3 neighbours neighbourAtom[3] is -1.
* neighbourAtom[4] contains the stereo center. If desired parity==cAtomParity1, then
* neighbourAtom[0] && neighbourAtom[1] have swapped positions.
* @param mol
* @param neighbourAtom
* @param neighbourBond
*/
public TetrahedralStereoRule(StereoMolecule mol, int[] neighbourAtom, int[] neighbourBond) {
super(neighbourAtom);
calculateRotatableAtoms(mol, neighbourAtom, neighbourBond);
}
public static void calculateRules(ArrayList ruleList, StereoMolecule mol) {
for (int atom=0; atom= 3) {
int parity = mol.getAtomParity(atom);
if ((parity == Molecule.cAtomParity1 || parity == Molecule.cAtomParity2)
&& !mol.isCentralAlleneAtom(atom)) {
int[] atomList = new int[5];
int[] bondList = new int[4];
for (int i=0; i atomList[index])
index++;
for (int j=i-1; j>=index; j--) {
atomList[j + 1] = atomList[j];
bondList[j + 1] = bondList[j];
}
atomList[index] = connAtom;
bondList[index] = connBond;
}
if (mol.getAllConnAtoms(atom) == 3) {
atomList[3] = -1;
bondList[3] = -1;
}
atomList[4] = atom;
if (parity == Molecule.cAtomParity1) {
int temp = atomList[1];
atomList[1] = atomList[0];
atomList[0] = temp;
temp = bondList[1];
bondList[1] = bondList[0];
bondList[0] = temp;
}
ruleList.add(new TetrahedralStereoRule(mol, atomList, bondList));
}
}
}
}
@Override
public boolean apply(Conformer conformer, double cycleFactor) {
double[] n = getPlaneVector(conformer);
// We invert if 3rd substituent is on wrong side (3 substituents)
// or if 3rd and 4th substituent are on wrong side (4 substituents)
boolean invert = (mAtom[3] == -1 && !isOnSameSide(conformer, n, mAtom[4], mAtom[2]))
|| (mAtom[3] != -1 && !isOnSameSide(conformer, n, mAtom[4], mAtom[2])
&& isOnSameSide(conformer, n, mAtom[4], mAtom[3]));
if (!invert)
return false;
Coordinates rotationAxis = calculateRotationAxis(conformer);
for (int atom:mRotatableAtom)
rotateAtom(conformer, atom, conformer.getCoordinates(mAtom[4]), rotationAxis, Math.PI);
return true;
}
@Override
public double addStrain(Conformer conformer, double[] atomStrain) {
double totalStrain = 0;
double[] n = getPlaneVector(conformer);
// We add a penalty for 3rd and 4th (if existing) substituent that is on the wrong side
int wrongCount = 0;
if (mAtom[3] == -1) {
if (!isOnSameSide(conformer, n, mAtom[4], mAtom[2]))
wrongCount++;
}
else {
if (!isOnSameSide(conformer, n, mAtom[4], mAtom[2]))
wrongCount++;
if (isOnSameSide(conformer, n, mAtom[4], mAtom[3]))
wrongCount++;
}
if (wrongCount != 0) {
for (int i=0; ia1 to normal vector
return v[0]*n[0]+v[1]*n[1]+v[2]*n[2] > 0;
}
/**
* Calculates the vector of plane (a4->a1, a4->a2)
* @param conformer
* @return
*/
private double[] getPlaneVector(Conformer conformer) {
double[][] coords = new double[2][3];
for (int i=0; i<2; i++) {
coords[i][0] = conformer.getX(mAtom[i]) - conformer.getX(mAtom[4]);
coords[i][1] = conformer.getY(mAtom[i]) - conformer.getY(mAtom[4]);
coords[i][2] = conformer.getZ(mAtom[i]) - conformer.getZ(mAtom[4]);
}
// calculate the vector of the plane (vector product of coords[0] and coords[1])
double[] v = new double[3];
v[0] = coords[0][1]*coords[1][2]-coords[0][2]*coords[1][1];
v[1] = coords[0][2]*coords[1][0]-coords[0][0]*coords[1][2];
v[2] = coords[0][0]*coords[1][1]-coords[0][1]*coords[1][0];
return v;
}
private void calculateRotatableAtoms(StereoMolecule mol, int[] neighbourAtom, int[] neighbourBond) {
int stereoCenter = neighbourAtom[4];
int neighbours = (neighbourAtom[3] == -1) ? 3 : 4;
int[] fragmentNo = new int[mol.getAllAtoms()];
boolean[] neglectBond = new boolean[mol.getAllBonds()];
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy