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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
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* @author Thomas Sander
*/
package com.actelion.research.chem.conf;
import com.actelion.research.chem.StereoMolecule;
public class TorsionPrediction {
private short[] mTorsion,mFrequency;
private short[][] mTorsionRange;
public TorsionPrediction(StereoMolecule mol, int[] torsionAtom) {
int atom1 = torsionAtom[1];
int atom2 = torsionAtom[2];
int conns1 = mol.getConnAtoms(atom1) - 1;
int conns2 = mol.getConnAtoms(atom2) - 1;
if (conns1 > 3 || conns2 > 3) { // assume octahedral neighbors
mTorsion = new short[4];
mTorsion[0] = 45;
mTorsion[1] = 135;
mTorsion[2] = 225;
mTorsion[2] = 315;
mTorsionRange = new short[4][2];
mTorsionRange[0][0] = 30;
mTorsionRange[0][1] = 60;
mTorsionRange[1][0] = 120;
mTorsionRange[1][1] = 150;
mTorsionRange[2][0] = 210;
mTorsionRange[2][1] = 240;
mTorsionRange[2][0] = 300;
mTorsionRange[2][1] = 330;
mFrequency = new short[4];
mFrequency[0] = 25;
mFrequency[1] = 25;
mFrequency[2] = 25;
mFrequency[3] = 25;
}
// sp3 - sp3
else if ((mol.getAtomPi(atom1) == 0 || mol.getAtomicNo(atom1) > 9)
&& (mol.getAtomPi(atom2) == 0 || mol.getAtomicNo(atom2) > 9)) {
if ((conns1 == 3 && conns2 == 3)
|| (conns1 == 3 && conns2 == 2)
|| (conns1 == 3 && conns2 == 1)
|| (conns1 == 2 && conns2 == 3)
|| (conns1 == 1 && conns2 == 3)
|| (conns1 == 2 && conns2 == 2 && (torsionAtom[0] != -1 || torsionAtom[3] != -1))) {
mTorsion = new short[3];
mTorsion[0] = 60;
mTorsion[1] = 180;
mTorsion[2] = 300;
mTorsionRange = new short[3][2];
mTorsionRange[0][0] = 45;
mTorsionRange[0][1] = 75;
mTorsionRange[1][0] = 165;
mTorsionRange[1][1] = 195;
mTorsionRange[2][0] = 285;
mTorsionRange[2][1] = 315;
mFrequency = new short[3];
mFrequency[0] = 33;
mFrequency[1] = 33;
mFrequency[2] = 33;
}
else if ((conns1 == 1 && conns2 == 2 && torsionAtom[3] == -1)
|| (conns1 == 2 && conns2 == 1 && torsionAtom[0] == -1)) {
mTorsion = new short[3];
mTorsion[0] = 60;
mTorsion[1] = 180;
mTorsion[2] = 300;
mTorsionRange = new short[3][2];
mTorsionRange[0][0] = 45;
mTorsionRange[0][1] = 75;
mTorsionRange[1][0] = 165;
mTorsionRange[1][1] = 195;
mTorsionRange[2][0] = 285;
mTorsionRange[2][1] = 315;
mFrequency = new short[3];
mFrequency[0] = 40;
mFrequency[1] = 20;
mFrequency[2] = 40;
}
else if ((conns1 == 1 && conns2 == 1)
|| (conns1 == 1 && conns2 == 2 && torsionAtom[3] != -1)
|| (conns1 == 2 && conns2 == 1 && torsionAtom[0] != -1)
|| (conns1 == 2 && conns2 == 2 && torsionAtom[0] == -1 && torsionAtom[3] == -1)) {
mTorsion = new short[3];
mTorsion[0] = 60;
mTorsion[1] = 180;
mTorsion[2] = 300;
mTorsionRange = new short[3][2];
mTorsionRange[0][0] = 45;
mTorsionRange[0][1] = 75;
mTorsionRange[1][0] = 165;
mTorsionRange[1][1] = 195;
mTorsionRange[2][0] = 285;
mTorsionRange[2][1] = 315;
mFrequency = new short[3];
mFrequency[0] = 25;
mFrequency[1] = 50;
mFrequency[2] = 25;
}
}
else if (((mol.getAtomPi(atom1) == 0 || mol.getAtomicNo(atom1) > 9) && mol.getAtomPi(atom2) == 1)
|| ((mol.getAtomPi(atom2) == 0 || mol.getAtomicNo(atom2) > 9) && mol.getAtomPi(atom1) == 1)) {
if (conns1 == 3 || conns2 == 3) {
mTorsion = new short[6];
mTorsion[0] = 0;
mTorsion[1] = 60;
mTorsion[2] = 120;
mTorsion[3] = 180;
mTorsion[4] = 240;
mTorsion[5] = 300;
mTorsionRange = new short[6][2];
mTorsionRange[0][0] = -15;
mTorsionRange[0][1] = 15;
mTorsionRange[1][0] = 45;
mTorsionRange[1][1] = 75;
mTorsionRange[2][0] = 105;
mTorsionRange[2][1] = 135;
mTorsionRange[3][0] = 165;
mTorsionRange[3][1] = 195;
mTorsionRange[4][0] = 225;
mTorsionRange[4][1] = 255;
mTorsionRange[5][0] = 285;
mTorsionRange[5][1] = 315;
mFrequency = new short[6];
mFrequency[0] = 16;
mFrequency[1] = 16;
mFrequency[2] = 16;
mFrequency[3] = 16;
mFrequency[4] = 16;
mFrequency[5] = 16;
}
else if (conns1 == 1 && conns2 == 1) {
mTorsion = new short[2];
mTorsion[0] = 120;
mTorsion[1] = 240;
mTorsionRange = new short[2][2];
mTorsionRange[0][0] = 105;
mTorsionRange[0][1] = 135;
mTorsionRange[1][0] = 225;
mTorsionRange[1][1] = 255;
mFrequency = new short[2];
mFrequency[0] = 50;
mFrequency[1] = 50;
}
else if ((mol.getAtomPi(atom1) == 1 && conns1 == 2 && conns2 == 1)
|| (mol.getAtomPi(atom2) == 1 && conns2 == 2 && conns1 == 1)) {
mTorsion = new short[2];
mTorsion[0] = 90;
mTorsion[1] = 270;
mTorsionRange = new short[2][2];
mTorsionRange[0][0] = 75;
mTorsionRange[0][1] = 105;
mTorsionRange[1][0] = 255;
mTorsionRange[1][1] = 285;
mFrequency = new short[2];
mFrequency[0] = 50;
mFrequency[1] = 50;
}
else if ((mol.getAtomPi(atom1) == 1 && conns1 == 1 && conns2 == 2 && torsionAtom[3] == -1)
|| (mol.getAtomPi(atom2) == 1 && conns2 == 1 && conns1 == 2 && torsionAtom[0] == -1)) {
mTorsion = new short[3];
mTorsion[0] = 0;
mTorsion[1] = 120;
mTorsion[2] = 240;
mTorsionRange = new short[3][2];
mTorsionRange[0][0] = -15;
mTorsionRange[0][1] = 15;
mTorsionRange[1][0] = 105;
mTorsionRange[1][1] = 135;
mTorsionRange[2][0] = 225;
mTorsionRange[2][1] = 255;
mFrequency = new short[3];
mFrequency[0] = 60;
mFrequency[1] = 20;
mFrequency[2] = 20;
}
else if ((mol.getAtomPi(atom1) == 1 && conns1 == 1 && conns2 == 2 && torsionAtom[3] != -1)
|| (mol.getAtomPi(atom2) == 1 && conns2 == 1 && conns1 == 2 && torsionAtom[0] != -1)) {
mTorsion = new short[3];
mTorsion[0] = 0;
mTorsion[1] = 120;
mTorsion[2] = 240;
mTorsionRange = new short[3][2];
mTorsionRange[0][0] = -15;
mTorsionRange[0][1] = 15;
mTorsionRange[1][0] = 105;
mTorsionRange[1][1] = 135;
mTorsionRange[2][0] = 225;
mTorsionRange[2][1] = 255;
mFrequency = new short[3];
mFrequency[0] = 20;
mFrequency[1] = 40; // in reality the double bond is syn to the hydrogen or a hetero atom
mFrequency[2] = 40;
}
else if (conns1 == 2 && conns2 == 2) {
if (torsionAtom[0] == -1 || torsionAtom[3] == -1) {
mTorsion = new short[2];
mTorsion[0] = 0;
mTorsion[1] = 180;
mTorsionRange = new short[2][2];
mTorsionRange[0][0] = -15;
mTorsionRange[0][1] = 15;
mTorsionRange[1][0] = 165;
mTorsionRange[1][1] = 195;
mFrequency = new short[2];
mFrequency[0] = 50;
mFrequency[1] = 50;
}
else {
mTorsion = new short[2];
mTorsion[0] = 90; // this should be 60 or 120 depending on sp3 reference neighbor
mTorsion[1] = 270; // this should be 240 or 300 depending on sp3 reference neighbor
mTorsionRange = new short[2][2];
mTorsionRange[0][0] = 75;
mTorsionRange[0][1] = 105;
mTorsionRange[1][0] = 255;
mTorsionRange[1][1] = 285;
mFrequency = new short[2];
mFrequency[0] = 50;
mFrequency[1] = 50;
}
}
}
else if (mol.getAtomPi(atom1) == 1 && mol.getAtomPi(atom2) == 1) {
if (conns1 == 1 && conns2 == 1) {
mTorsion = new short[2];
mTorsion[0] = 0;
mTorsion[1] = 180;
mTorsionRange = new short[2][2];
mTorsionRange[0][0] = -15;
mTorsionRange[0][1] = 15;
mTorsionRange[1][0] = 165;
mTorsionRange[1][1] = 195;
mFrequency = new short[2];
mFrequency[0] = 10;
mFrequency[1] = 90;
}
else {
mTorsion = new short[6];
mTorsion[0] = 0;
mTorsion[1] = 50;
mTorsion[2] = 130;
mTorsion[3] = 180;
mTorsion[4] = 230;
mTorsion[5] = 310;
mTorsionRange = new short[6][2];
mTorsionRange[0][0] = -15;
mTorsionRange[0][1] = 15;
mTorsionRange[1][0] = 35;
mTorsionRange[1][1] = 65;
mTorsionRange[2][0] = 115;
mTorsionRange[2][1] = 145;
mTorsionRange[3][0] = 165;
mTorsionRange[3][1] = 195;
mTorsionRange[4][0] = 215;
mTorsionRange[4][1] = 245;
mTorsionRange[5][0] = 295;
mTorsionRange[5][1] = 325;
mFrequency = new short[6];
mFrequency[0] = 40;
mFrequency[1] = 5;
mFrequency[2] = 5;
mFrequency[3] = 40;
mFrequency[4] = 5;
mFrequency[5] = 5;
}
}
else {
mTorsion = new short[1];
mTorsion[0] = 180;
mTorsionRange = new short[1][2];
mTorsionRange[0][0] = 165;
mTorsionRange[0][1] = 195;
mFrequency = new short[1];
mFrequency[0] = 100;
}
}
public short[] getTorsions() {
return mTorsion;
}
public short[] getTorsionFrequencies() {
return mFrequency;
}
public short[][] getTorsionRanges() {
return mTorsionRange;
}
}