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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
* (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 com.actelion.research.chem.conf;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.RingCollection;
import com.actelion.research.chem.StereoMolecule;
public class BondAngleSet {
private static float TO_RADIAN = (float)Math.PI/180;
private final StereoMolecule mMol;
private final BondLengthSet mBondLengthSet;
private final float[][][] mBondAngle;
private final int[] mDefinedAngleCount,mTinyRingSizeSum;
private final float[] mDefinedAngleSum;
/**
* Calculates and caches a list of bond angle estimates for any two neighbours
* of any atom of the molecule.
* Internally it requires a valid BondLengthSet of this molecule,
* which can be passed if there is already one available. Otherwise,
* one is created internally.
* @param mol
* @param set null or a valid BondLengthSet of the molecule
*/
public BondAngleSet(final StereoMolecule mol, final BondLengthSet set) {
// initialize bond angle arrays
mBondLengthSet = (set == null) ? new BondLengthSet(mol) : set;
mMol = mol;
mBondAngle = new float[mMol.getAtoms()][][];
for (int atom=0; atom 4) {
for (int i=1; i 0))) {
if (connAtoms > 2) {
float angle;
if (mDefinedAngleCount[atom] == 1) {
if (mMol.getAtomicNo(atom) <= 14) // up to Si
angle = (2f * (float)Math.PI - mDefinedAngleSum[atom]) / 2.0f;
else
angle = calculateRemainingTetrahedralAngle(mDefinedAngleSum[atom]);
}
else {
// mDefinedAngleCount==2: we assume two annelated aromatic rings
// (and not spiro, which theoretically might be possible with e.g. sulphur)
angle = 2f * (float)Math.PI - mDefinedAngleSum[atom];
if (connAtoms > 3) {
// strange case with P,S,Se,etc sharing two/three annelated flat rings and additional substituent(s) sticking out of plane
if (mDefinedAngleCount[atom] == 2) { // we need to find the third angle in the plane
boolean[] isMissingIndex = new boolean[mMol.getAllConnAtoms(atom)];
for (int i=1; i 10) ? 109.47f * (float)Math.PI/180.0f
: (mMol.getAtomPi(atom) == 2) ? (float)Math.PI
: mMol.isFlatNitrogen(atom) ? 120.00f * (float)Math.PI/180.0f
: (mMol.getAtomPi(atom) == 0) ? 109.47f * (float)Math.PI/180.0f
: 120.00f * (float)Math.PI/180.0f;
for (int i=1; i Math.abs(maxForce)) {
maxForce = force;
maxForceIndex = i;
}
}
float factor = (float)Math.exp(-5*(float)cycle/cycles);
direction[maxForceIndex] += factor * maxForce;
}
for (int i=0; i 2*Math.PI)
angle -= 2*Math.PI;
setBondAngle(ringAtom[i], ringBond[im1], ringBond[i], angle);
}
/* double sx = 0.0;
double sy = 0.0;
System.out.println("------------------");
for (int i=0; i 2*Math.PI)
angle -= 2*Math.PI;
System.out.println("optAngle:"+optAngle[i]+"; angle("+i+"):"+com.actelion.research.util.DoubleFormat.toString(angle));
sx += mBondLengthSet.getLength(ringBond[i]) * Math.sin(direction[i]);
sy += mBondLengthSet.getLength(ringBond[i]) * Math.cos(direction[i]);
}
System.out.println("dsx:"+com.actelion.research.util.DoubleFormat.toString(sx));
System.out.println("dsy:"+com.actelion.research.util.DoubleFormat.toString(sy));
*/ }
private int getRingStrainClass(int atom) {
// the ring strain class of an atom is the sorted list
// of non-zero tinyRingSizeSums of all attached bonds
boolean[] handled = new boolean[mMol.getConnAtoms(atom)];
int strainClass = 0;
for (int i=0; i