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/*
* 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
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*
* @author Thomas Sander
*/
package org.openmolecules.chem.conf.gen;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.*;
import java.util.Random;
/**
* A RotatableBond knows the two rigid fragments within a molecule
* that are connected by this bond. It also knows about possible torsion
* states with associated likelyhoods, which are taken from COD statistics
* and modified to account for collisions due to bulky groups in the molecule.
* It knows the smaller half of the molecule and rotate the smaller half to
* a given torsion angle.
*/
public class RotatableBond {
private static final double ANGLE_TOLERANCE = 0.001f; // limit for considering bonds as parallel
// For every optimum torsion we check for collisions and in case we try, whether left or right
// range ends are substantially better.
private static final double ACCEPTABLE_CENTER_STRAIN = 0.05f; // if we have less strain than this we don't check whether range edges improve strain
private static final double NECESSARY_EDGE_STRAIN_IMPROVEMENT = 0.02f; // necessary strain improvement to use edge torsion rather than center torsion
private static final double MAXIMUM_CENTER_STRAIN = 0.2f; // if center torsion is above this limit we refuse that torsion
// If no acceptable torsion remains after checking and attempting to use range edge values,
// we try to modify the least bad torsion stepwise until it is acceptable.
private static final int ESCAPE_ANGLE = 8; // degrees to rotate the rotatable bond to escape collisions
private static final int ESCAPE_STEPS = 4; // how often we apply this rotation trying to solve the collision
private static final double MIN_ESCAPE_GAIN_PER_STEP = 0.05;
private static final short[] SIXTY_DEGREE_TORSION = { 0, 60, 120, 180, 240, 300};
private static final short[] SIXTY_DEGREE_FREQUENCY = { 17, 17, 17, 17, 17, 17};
private static final short[][] SIXTY_DEGREE_RANGE = { {-20,20},{40,80},{100,140},{160,200},{220,260},{280,320}};
private RigidFragment mFragment1,mFragment2;
private Random mRandom;
private int mRotationCenter,mBond,mFragmentNo1,mFragmentNo2;
private boolean mBondAtomsInFragmentOrder;
private float mBondRelevance;
private short[] mTorsion;
private short[] mFrequency;
private short[][] mTorsionRange;
private double[] mLikelyhood; // considering directly connected rigid fragments (frequency and collision strain)
private int[] mTorsionAtom,mRearAtom,mSmallerSideAtomList;
public RotatableBond(StereoMolecule mol, int bond, int[] fragmentNo, int[] disconnectedFragmentNo,
int disconnectedFragmentSize, RigidFragment[] fragment, Random random) {
this(mol, bond, fragmentNo, disconnectedFragmentNo, disconnectedFragmentSize, fragment, random, false);
}
public RotatableBond(StereoMolecule mol, int bond, int[] fragmentNo, int[] disconnectedFragmentNo,
int disconnectedFragmentSize, RigidFragment[] fragment, Random random, boolean use60degreeSteps) {
mBond = bond;
mRandom = random;
mTorsionAtom = new int[4];
mRearAtom = new int[2];
TorsionDetail detail = new TorsionDetail();
if (TorsionDB.getTorsionID(mol, bond, mTorsionAtom, detail) != null) {
mRearAtom[0] = detail.getRearAtom(0);
mRearAtom[1] = detail.getRearAtom(1);
}
else {
predictAtomSequence(mol);
}
mFragmentNo1 = fragmentNo[mTorsionAtom[1]];
mFragmentNo2 = fragmentNo[mTorsionAtom[2]];
mFragment1 = fragment[mFragmentNo1];
mFragment2 = fragment[mFragmentNo2];
mBondAtomsInFragmentOrder = (fragmentNo[mol.getBondAtom(0, bond)] == mFragmentNo1);
if (use60degreeSteps) {
mTorsion = SIXTY_DEGREE_TORSION;
mFrequency = SIXTY_DEGREE_FREQUENCY;
mTorsionRange = SIXTY_DEGREE_RANGE;
}
else {
mTorsion = TorsionDB.getTorsions(detail.getID());
if (mTorsion == null) {
TorsionPrediction prediction = new TorsionPrediction(mol, mTorsionAtom);
mTorsion = prediction.getTorsions();
mFrequency = prediction.getTorsionFrequencies();
mTorsionRange = prediction.getTorsionRanges();
} else {
mFrequency = TorsionDB.getTorsionFrequencies(detail.getID());
mTorsionRange = TorsionDB.getTorsionRanges(detail.getID());
}
}
removeIllegalTorsions(mol);
removeEquivalentTorsions(mol);
mLikelyhood = new double[mTorsion.length];
findSmallerSideAtomList(mol, disconnectedFragmentNo, disconnectedFragmentSize);
}
public RigidFragment getFragment(int i) {
return (i == 0) ? mFragment1 : mFragment2;
}
public int getFragmentNo(int i) {
return (i == 0) ? mFragmentNo1 : mFragmentNo2;
}
private void predictAtomSequence(StereoMolecule mol) {
for (int i=0; i<2; i++) {
int centralAtom = mol.getBondAtom(i, mBond);
int rearAtom = mol.getBondAtom(1-i, mBond);
// walk along sp-chains to first sp2 or sp3 atom
while (mol.getAtomPi(centralAtom) == 2
&& mol.getConnAtoms(centralAtom) == 2
&& mol.getAtomicNo(centralAtom) < 10) {
for (int j=0; j<2; j++) {
int connAtom = mol.getConnAtom(centralAtom, j);
if (connAtom != rearAtom) {
rearAtom = centralAtom;
centralAtom = connAtom;
break;
}
}
}
mTorsionAtom[i+1] = centralAtom;
mRearAtom[i] = rearAtom;
}
// A TorsionPrediction does not distinguish hetero atoms from carbons a positions 0 and 3.
// Therefore we can treat two sp2 neighbors as equivalent when predicting torsions.
if (mol.getAtomPi(mTorsionAtom[1]) == 0 && mol.getConnAtoms(mTorsionAtom[1]) == 3) {
mTorsionAtom[0] = -1;
}
else {
for (int i=0; i disconnectedFragmentSize-alkyneAtoms-memberCount) {
memberCount = disconnectedFragmentSize-alkyneAtoms-memberCount;
invert = true;
}
// if invert, then flag all linear alkyne atoms to be avoided
if (invert && alkyneAtoms != 0) {
int spAtom = mRearAtom[0];
int backAtom = mTorsionAtom[1];
while (mol.getAtomPi(spAtom) == 2
&& mol.getConnAtoms(spAtom) == 2
&& mol.getAtomicNo(spAtom) < 10) {
isMember[spAtom] = true;
for (int j=0; j<2; j++) {
int connAtom = mol.getConnAtom(spAtom, j);
if (connAtom != backAtom) {
backAtom = spAtom;
spAtom = connAtom;
break;
}
}
}
}
int memberNo = 0;
int fragmentNo = disconnectedFragmentNo[mTorsionAtom[1]];
mSmallerSideAtomList = new int[memberCount];
for (int atom=0; atom mFragment2.getCoreSize()) ? mFragment1 : mFragment2;
int largerFragmentNo = (mFragment1.getCoreSize() > mFragment2.getCoreSize()) ? mFragmentNo1 : mFragmentNo2;
isAttached[largerFragmentNo] = true;
int fragmentConformer = (fragmentPermutation == null) ? 0 : fragmentPermutation[largerFragmentNo];
for (int i=0; i Math.PI / 2) ?
froot.subC(fragment.getExtendedCoordinates(fragmentConformer, i))
: fragment.getExtendedCoordinates(fragmentConformer, i).subC(froot);
}
}
else {
Coordinates rotationAxis;
if (alpha < Math.PI - ANGLE_TOLERANCE) { // normal case, just rotate around the plane orthogonal
rotationAxis = uv.cross(fuv);
}
else { // special case both axes anti-parallel: for cross-product we need any vector being different from uv
if (Math.abs(uv.x) >= Math.abs(uv.y) && Math.abs(uv.x) >= Math.abs(uv.z))
rotationAxis = new Coordinates(-(uv.y + uv.z) / uv.x, 1.0, 1.0);
else if (Math.abs(uv.y) >= Math.abs(uv.x) && Math.abs(uv.y) >= Math.abs(uv.z))
rotationAxis = new Coordinates(1.0, -(uv.x + uv.z) / uv.y, 1.0);
else
rotationAxis = new Coordinates(1.0, 1.0, -(uv.x + uv.y) / uv.z);
}
double[][] m = getRotationMatrix(rotationAxis.unit(), alpha);
for (int i=0; i 1)
|| (mFragment2.getConformerCount() > 1);
//System.out.print("connectFragments() original torsions:"); for (int t=0; t NECESSARY_EDGE_STRAIN_IMPROVEMENT) {
if (isFirstAlternative) {
mTorsion[t] = mTorsionRange[t][r];
mFrequency[t] = (short)((mFrequency[t]+1) / 2);
double relativeStrain = rangeStrain / MAXIMUM_CENTER_STRAIN;
mLikelyhood[t] = mFrequency[t] * (1f - relativeStrain * relativeStrain);
usedStrain = rangeStrain;
torsionEdgeUsed = r+1;
isFirstAlternative = false;
}
else {
double relativeStrain = rangeStrain / MAXIMUM_CENTER_STRAIN;
insertTorsion(t, r, relativeStrain);
if (mLikelyhood[t+1] > mLikelyhood[t]) {
usedStrain = rangeStrain;
torsionEdgeUsed = r+1;
}
t++;
}
foundAlternative = true;
}
}
if (!foundAlternative /* && strain < MAXIMUM_CENTER_STRAIN really bad ones should get a negative likelyhood */) {
double relativeStrain = centerStrain / MAXIMUM_CENTER_STRAIN;
mLikelyhood[t] = mFrequency[t] * (1f - relativeStrain * relativeStrain);
}
}
if (mLikelyhood[bestTorsionIndex] < mLikelyhood[t]) {
bestTorsionIndex = t;
bestTorsionEdgeUsed = torsionEdgeUsed;
bestTorsionStrain = usedStrain; // this is the strain with the highest likelyhood (not necessarily the lowest strain)
}
}
double totalLikelyhood = 0f;
for (int t=0; t 0f)
totalLikelyhood += mLikelyhood[t];
// make sure, we have at least one torsion with positive likelyhood, because only those are considered later
if (mLikelyhood[bestTorsionIndex] <= 0f) {
mLikelyhood[bestTorsionIndex] = 1.0f;
int angle = bestTorsionEdgeUsed == 1 ? -ESCAPE_ANGLE
: bestTorsionEdgeUsed == 2 ? ESCAPE_ANGLE
: (mRandom.nextDouble() < 0.5) ? -ESCAPE_ANGLE : ESCAPE_ANGLE;
for (int step=1; step<=ESCAPE_STEPS; step++) {
currentTorsion = (short)(mTorsion[bestTorsionIndex]+angle*step);
double[][] m = getRotationMatrix(uv, Math.PI * currentTorsion / 180 - startTorsion);
for (int i=0; i 0f)
count++;
short[] newTorsion = new short[count];
short[] newFrequency = new short[count];
double[] newLikelyhood = new double[count];
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy