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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;
private Coordinates mAxisOfRotation;
public TetrahedralStereoRule(StereoMolecule mol, int[] atom) {
super(atom);
mRotatableAtom = getRotatableAtoms(mol, atom[4]);
}
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];
for (int i=0; i atomList[index])
index++;
for (int j=i-1; j>=index; j--)
atomList[j+1] = atomList[j];
atomList[index] = connAtom;
}
if (mol.getAllConnAtoms(atom) == 3)
atomList[3] = -1;
atomList[4] = atom;
if (parity == Molecule.cAtomParity1) {
int temp = atomList[2];
atomList[2] = atomList[1];
atomList[1] = temp;
}
ruleList.add(new TetrahedralStereoRule(mol, atomList));
}
}
}
}
@Override
public boolean apply(Conformer conformer, double cycleFactor) {
double[] n = getPlaneVector(conformer);
boolean invert = (mAtom[3] == -1 && isOnSameSide(conformer, n, mAtom[0], mAtom[4]))
|| (mAtom[3] != -1 && isOnSameSide(conformer, n, mAtom[0], mAtom[3]));
if (!invert)
return false;
for (int atom:mRotatableAtom)
rotateAtom(conformer, atom, mAtom[1], mAxisOfRotation, Math.PI);
return true;
/* invert stereocenter by moving atom[3] and/or atom[4] through plane of other atoms
double d = n[0]*conformer.getX(mAtom[0])
+ n[1]*conformer.getY(mAtom[0])
+ n[2]*conformer.getZ(mAtom[0]); // distance of Hesse equation of plane
double distance3 = (mAtom[3] == -1) ? 0.0
: n[0]*conformer.getX(mAtom[3])
+ n[1]*conformer.getY(mAtom[3])
+ n[2]*conformer.getZ(mAtom[3]) - d;
double distance4 = n[0]*conformer.getX(mAtom[4])
+ n[1]*conformer.getY(mAtom[4])
+ n[2]*conformer.getZ(mAtom[4]) - d;
if (mAtom[3] == -1 || conformer.getMolecule().getConnAtoms(mAtom[3]) == 1 || !invertAtom4) {
// keep atoms 0,1,2 in plane and move atom3 and/or atom4 through plane
if (invertAtom3)
conformer.getCoordinates(mAtom[3]).add(-2.0*distance3*n[0],
-2.0*distance3*n[1],
-2.0*distance3*n[2]);
if (invertAtom4)
conformer.getCoordinates(mAtom[4]).add(-2.0*distance4*n[0],
-2.0*distance4*n[1],
-2.0*distance4*n[2]);
}
else { // for neighbors and central atom needs to be inverted: keep center of gravity
for (int i=0; i<3; i++)
conformer.getCoordinates(mAtom[i]).add(0.5*distance4*n[0],
0.5*distance4*n[1],
0.5*distance4*n[2]);
if (invertAtom3)
conformer.getCoordinates(mAtom[3]).add(0.5*distance4*n[0] - 2.0*distance3*n[0],
0.5*distance4*n[1] - 2.0*distance3*n[1],
0.5*distance4*n[2] - 2.0*distance3*n[2]);
conformer.getCoordinates(mAtom[4]).add(-1.5*distance4*n[0],
-1.5*distance4*n[1],
-1.5*distance4*n[2]);
}
return true;*/
}
@Override
public double addStrain(Conformer conformer, double[] atomStrain) {
double totalStrain = 0;
double[] n = getPlaneVector(conformer);
if ((mAtom[3] == -1 && isOnSameSide(conformer, n, mAtom[0], mAtom[4]))
|| (mAtom[3] != -1 && isOnSameSide(conformer, n, mAtom[0], mAtom[3]))) {
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 (a0->a1, a0->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+1]) - conformer.getX(mAtom[0]);
coords[i][1] = conformer.getY(mAtom[i+1]) - conformer.getY(mAtom[0]);
coords[i][2] = conformer.getZ(mAtom[i+1]) - conformer.getZ(mAtom[0]);
}
// 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 int[] getRotatableAtoms(StereoMolecule mol, int atom) {
int neighbours = mol.getAllConnAtoms(atom);
boolean[][] isMemberAtom = new boolean[neighbours][mol.getAllAtoms()];
int[] substituentSize = new int[neighbours];
// find sizes of the 3 or 4 substituents (if not in a ring)
for (int i=0; i substituentSize[i] && substituentSize[i] != 0) {
smallestSize = substituentSize[i];
smallestIndex = i;
}
}
if (smallestIndex != -1) {
rotatableAtomCount += substituentSize[smallestIndex];
substituentSize[smallestIndex] = 0; // mark to not find it again
if (isRotatableAtom == null)
isRotatableAtom = isMemberAtom[smallestIndex];
else
for (int a=0; a=0; i--) {
int connAtom = mol.getConnAtom(atom, i);
if (!isRotatableAtom[connAtom]) {
isRotatableAtom[connAtom] = true;
rotatableAtomCount++;
break;
}
}
}
}
int index = 0;
int[] rotatableAtom = new int[rotatableAtomCount];
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy