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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.coords;
import com.actelion.research.chem.*;
import java.util.*;
public class CoordinateInventor {
public static final int MODE_SKIP_DEFAULT_TEMPLATES = 1;
public static final int MODE_REMOVE_HYDROGEN = 2;
public static final int MODE_KEEP_MARKED_ATOM_COORDS = 4;
public static final int MODE_PREFER_MARKED_ATOM_COORDS = 8;
private static final int MODE_CONSIDER_MARKED_ATOMS = MODE_KEEP_MARKED_ATOM_COORDS | MODE_PREFER_MARKED_ATOM_COORDS;
public static final int MODE_DEFAULT = MODE_REMOVE_HYDROGEN;
private static final byte FLIP_AS_LAST_RESORT = 1;
private static final byte FLIP_POSSIBLE = 2;
private static final byte FLIP_PREFERRED = 3;
private static final int PREFERRED_FLIPS = 32;
private static final int POSSIBLE_FLIPS = 64;
private static final int LAST_RESORT_FLIPS = 128;
private static final int TOTAL_FLIPS = PREFERRED_FLIPS + POSSIBLE_FLIPS + LAST_RESORT_FLIPS;
private static volatile List sDefaultTemplateList;
private StereoMolecule mMol;
private long[] mFFP;
private Random mRandom;
private boolean[] mAtomHandled;
private boolean[] mBondHandled;
private boolean[] mAtomIsPartOfCustomTemplate;
private boolean mAbsoluteOrientationTemplateFound; // we just use the first matching template, which is set to define absolute orientation
private int[] mUnPairedCharge;
private int mMode;
private List mFragmentList;
private List mCustomTemplateList;
private static synchronized void buildDefaultTemplateList() {
if (sDefaultTemplateList == null)
sDefaultTemplateList = new InventorDefaultTemplateList();
}
/**
* Creates an CoordinateInventor, which removes unneeded hydrogen atoms
* and creates new atom coordinates for all(!) atoms.
* This constructor creates a CoordinateInventor that uses templates
* of the InventorDefaultTemplateList to create 3D-projection derived coordinates for
* polycyclic structures from these templates (adamantanes, cubane, etc.).
*/
public CoordinateInventor () {
this(MODE_DEFAULT);
}
/**
* Creates an CoordinateInventor, which removes unneeded hydrogens, if mode flags include
* MODE_REMOVE_HYDROGEN. If mode includes MODE_KEEP_MARKED_ATOM_COORDS, then marked atoms
* keep their coordinates. If mode includes MODE_PREFER_MARKED_ATOM_COORDS, then coordinates
* of marked atoms are changed only, if perfect coordinates are not possible without.
* Unless mode includes MODE_SKIP_DEFAULT_TEMPLATES, the CoordinateInventor uses templates
* of the InventorDefaultTemplateList to create 3D-projection derived coordinates for
* polycyclic structures from these templates (adamantanes, cubane, etc.).
* @param mode
*/
public CoordinateInventor (int mode) {
mMode = mode;
if ((mode & MODE_SKIP_DEFAULT_TEMPLATES) == 0 && sDefaultTemplateList == null)
buildDefaultTemplateList();
}
public void setRandomSeed(long seed) {
mRandom = new Random(seed);
}
/**
* A custom template list contains substructures with predefined atom coordinates.
* When such a list is provided, and if a molecules contains one of the list's substructures,
* then the matching atoms will receive the relative atom coordinates of the provided template,
* unless the substructure shares two or more atoms with another earlier found template or
* if mode is MODE_????_MARKED_ATOM_COORDS and the substructure match contains two or more
* non-marked (and therefore untouchable) atoms. If a template substructure contains an E- or Z-
* double bound, then the query feature 'match EZ-parity' should be set.
* @param templateList
*/
public void setCustomTemplateList(List templateList) {
mCustomTemplateList = templateList;
for (InventorTemplate template:templateList)
template.normalizeCoordinates();
}
/**
* Creates new atom 2D-coordinates for a molecule or a part of a molecule.
* Typically, the molecule has defined TH- and EZ-parities (even if unknown or none), which were not
* calculated, but taken from a SMILES or from an IDCode. In these cases setParitiesValid() should have
* been called to indicate that a parity calculation is not needed and even would destroy given parities.
* New coordinates will correctly reflect E/Z double bond parities, unless the double bond is in a small ring.
* If atom parities are available, this call is typically followed by calling mol.setStereoBondsFromParity();
* Unneeded explicit hydrogens are removed, if mode includes MODE_REMOVE_HYDROGEN.
* The relative orientation of all marked atoms is retained, if mode includes MODE_KEEP_MARKED_ATOM_COORDS.
* The relative orientation of all marked atoms is changed as last resort only, if mode includes MODE_PREFER_MARKED_ATOM_COORDS.
* If setTemplateList() was called, then any substructures matching any of the templates will be shown
* with the relative atom orientation provided with the template. If many molecule's coordinates are invented
* with templates, then you should also provide the molecules' fragment fingerprint to speed up template search
* using invent(mol, ffp).
* @param mol the molecule that gets new 2D coordinates in place
*/
public void invent(StereoMolecule mol) {
invent(mol, null);
}
/**
* Creates new atom 2D-coordinates for a molecule or a part of a molecule.
* Typically, the molecule has defined TH- and EZ-parities (even if unknown or none), which were not
* calculated, but taken from a SMILES or from an IDCode. In these cases setParitiesValid() should have
* been called to indicate that a parity calculation is not needed and even would destroy given parities.
* New coordinates will correctly reflect E/Z double bond parities, unless the double bond is in a small ring.
* If atom parities are available, this call is typically followed by calling mol.setStereoBondsFromParity();
* Unneeded explicit hydrogens are removed, if mode includes MODE_REMOVE_HYDROGEN.
* The relative orientation of all marked atoms is retained, if mode includes MODE_KEEP_MARKED_ATOM_COORDS.
* The relative orientation of all marked atoms is changed as last resort only, if mode includes MODE_PREFER_MARKED_ATOM_COORDS.
* If setTemplateList() was called, then any substructures matching any of the templates will be shown
* with the relative atom orientation provided with the template. If many molecule's coordinates are invented
* with templates, then you should also provide the molecules' fragment fingerprint to speed up template search.
* @param mol the molecule that gets new 2D coordinates in place
* @parem ffp null or fragment fingerprint of the molecule, which is used (if available) for faster template location
*/
public void invent(StereoMolecule mol, long[] ffp) {
boolean paritiesPresent = (mol.getHelperArrayStatus() & Molecule.cHelperParities) != 0;
int parityState = mol.getHelperArrayStatus() & Molecule.cHelperBitsStereo;
if (mRandom == null)
mRandom = new Random();
if ((mMode & MODE_REMOVE_HYDROGEN) != 0)
mol.removeExplicitHydrogens(false, false);
mMol = mol;
mMol.ensureHelperArrays(Molecule.cHelperRings);
mFFP = ffp;
mFragmentList = new ArrayList() {
@Override
public boolean add(InventorFragment f) {
for (InventorFragment ff:this)
if (ff.equals(f))
return false;
return super.add(f);
}
};
mAtomHandled = new boolean[mMol.getAllAtoms()];
mBondHandled = new boolean[mMol.getAllBonds()];
mUnPairedCharge = new int[mMol.getAllAtoms()];
for (int atom=0; atom templateList, int priority) {
boolean useFFP = (mFFP != null && templateList.size() != 0 && templateList.get(0).getFFP() != null);
SSSearcher searcher = null;
SSSearcherWithIndex searcherWithIndex = null;
if (useFFP) {
searcherWithIndex = new SSSearcherWithIndex();
searcherWithIndex.setMolecule(mMol, mFFP);
}
else {
searcher = new SSSearcher();
searcher.setMolecule(mMol);
}
boolean[] atomIsPartOfTemplate = new boolean[mMol.getAtoms()];
for (InventorTemplate template: templateList) {
ArrayList matchList = null;
StereoMolecule templateMol = template.getFragment();
if (useFFP) {
searcherWithIndex.setFragment(templateMol, template.getFFP());
if (searcherWithIndex.findFragmentInMolecule(SSSearcher.cCountModeOverlapping, SSSearcher.cDefaultMatchMode) != 0)
matchList = searcherWithIndex.getGraphMatcher().getMatchList();
}
else {
searcher.setFragment(templateMol);
if (searcher.findFragmentInMolecule(SSSearcher.cCountModeOverlapping, SSSearcher.cDefaultMatchMode) != 0)
matchList = searcher.getMatchList();
}
if (matchList != null) {
for (int[] match:matchList) {
int templateAtomCount = 0;
for (int atom:match)
if (atomIsPartOfTemplate[atom])
templateAtomCount++;
if (templateAtomCount <= 1) {
// we just use the first matching template that is supposed to keep its absolute orientation
boolean definesAbsoluteOrientation = template.keepAbsoluteOrientation();
if (mAbsoluteOrientationTemplateFound)
definesAbsoluteOrientation = false;
else
mAbsoluteOrientationTemplateFound = true;
InventorFragment fragment = new InventorFragment(mMol, match.length, definesAbsoluteOrientation);
for (int i=0; i 4) {
InventorFragment f = new InventorFragment(mMol, 1+mMol.getAllConnAtoms(atom), false);
f.mAtomX[mMol.getAllConnAtoms(atom)] = 0.0;
f.mAtomY[mMol.getAllConnAtoms(atom)] = 0.0;
f.mPriority[mMol.getAllConnAtoms(atom)] = 32;
f.mGlobalAtom[mMol.getAllConnAtoms(atom)] = atom;
mAtomHandled[atom] = true;
for (int i=0; i 2) {
InventorFragment f = new InventorFragment(mMol, members, false);
int count = 0;
for (int i=0; i 2)
break;
mAtomHandled[alleneAtom[last+1]] = true;
mBondHandled[mMol.getConnBond(alleneAtom[last], nextIndex)] = true;
last++;
} while (mMol.getAtomPi(alleneAtom[last]) == 2
&& mMol.getAllConnAtoms(alleneAtom[last]) == 2);
int members = mMol.getAllConnAtoms(alleneAtom[0])
+ mMol.getAllConnAtoms(alleneAtom[last])
+ last - 1;
InventorFragment f = new InventorFragment(mMol, members, false);
for (int j=0; j<=last; j++) {
f.mAtomX[j] = j;
f.mAtomY[j] = 0.0;
f.mPriority[j] = 64;
f.mGlobalAtom[j] = alleneAtom[j];
}
int current = last+1;
boolean found = false;
for (int j=0; j connAtom)
secondAtomCounts[i] = true;
f.mAtomX[count] = (i==0) ? -1.0 : 1.0;
f.mAtomY[count] = (neighbours==0) ? -Math.sin(Math.PI/3) : Math.sin(Math.PI/3);
f.mAtom[count++] = connAtom;
mAtomHandled[connAtom] = true;
mBondHandled[mMol.getConnBond(bondAtom[i], j)] = true;
neighbours++;
}
}
}
if ((bondParity == Molecule.cBondParityE) ^ (secondAtomCounts[0] ^ secondAtomCounts[1]))
for (int i=1; i longestChain.getChainLength())
longestChain = theChain;
}
}
if (longestChain == null)
break;
InventorFragment f = new InventorFragment(mMol, longestChain.getChainLength(), false);
for (int i=0; i= FIRST_RING_SIZE)
// printRingStats(f, ringAtom, ringBond);
int maxBit = (1 << f.size());
int bondEConstraint = 0;
int bondZConstraint = 0;
if (f.size() > 7) {
for (int i=0; i>>= 1;
bondZConstraint >>>= 1;
}
}
int ringIndex = f.size()-FIRST_RING_SIZE;
if (f.size() >= FIRST_RING_SIZE && f.size() <= LAST_RING_SIZE && cBondZList[ringIndex] != null) {
for (int zList=0; zList>>= 1;
}
// We choose the starting turn direction such that we end up
// with more right turns and, thus, close the ring in clockwise direction.
boolean wasRightTurn = (rightTurns > f.size() / 2); // create a ring that closes with right turns
for (int i=1; i>>= 1;
}
return;
}
if ((bondZList & 1) != 0)
bondZList |= maxBit;
bondZList >>>= 1;
}
}
}
}
// if not successful so far
createRegularRingFragment(f, bondEConstraint, bondZConstraint);
}
private int getLargeRingBondParity(int[] ringAtom, int[] ringBond, int index) {
int higherIndex = (index == ringAtom.length-1) ? 0 : index+1; // second ringAtom index
int lowerIndex = (index == 0) ? ringAtom.length-1 : index-1;
int highestIndex = (higherIndex == ringAtom.length-1) ? 0 : higherIndex+1;
if (mMol.getBondOrder(ringBond[index]) == 2) {
int bondParity = mMol.getBondParity(ringBond[index]);
if (bondParity == Molecule.cBondParityEor1
|| bondParity == Molecule.cBondParityZor2) {
// translate bond configuration from lowest atom index to ring members
if (isLowestIndexNeighbour(ringAtom[lowerIndex], ringAtom[index], ringAtom[higherIndex])
^ isLowestIndexNeighbour(ringAtom[highestIndex], ringAtom[higherIndex], ringAtom[index]))
bondParity = (bondParity == Molecule.cBondParityEor1) ?
Molecule.cBondParityZor2 : Molecule.cBondParityEor1;
return bondParity;
}
}
// If the bond is also a member of a small ring
if (mMol.isSmallRingBond(ringBond[index])) {
int sharedRing1 = mMol.getRingSet().getSharedRing(ringBond[lowerIndex], ringBond[index]);
int sharedRing2 = mMol.getRingSet().getSharedRing(ringBond[higherIndex], ringBond[index]);
// If more than one bond is shared by the large and the small ring,
// then the first and the last shared bond are E and the ones between Z.
if (sharedRing1 != -1 || sharedRing2 != -1)
return sharedRing1 == sharedRing2 ? Molecule.cBondParityZor2 : Molecule.cBondParityEor1;
// If only this one bond is shared, then we have a Z-configuration
return Molecule.cBondParityZor2;
}
return Molecule.cBondParityNone;
}
/**
* @param atom
* @param rootAtom
* @param excludeAtom
* @return whether atom has the lowest atom index of rootAtom's neighbours not considering excludeAtom
*/
private boolean isLowestIndexNeighbour(int atom, int rootAtom, int excludeAtom) {
for (int i=0; i>>= 1;
bondZConstraint >>>= 1;
}
System.out.println("ringSize:"+f.size()
+" E-list:"+Integer.toBinaryString(bondEConstraint)
+" Z-list:"+Integer.toBinaryString(bondZConstraint));
}*/
private InventorChain getSmallestRingFromBond(int bond) {
// find smallest ring of given bond
int atom1 = mMol.getBondAtom(0, bond);
int atom2 = mMol.getBondAtom(1, bond);
int graphAtom[] = new int[mMol.getAllAtoms()];
int graphBond[] = new int[mMol.getAllAtoms()];
int graphLevel[] = new int[mMol.getAllAtoms()];
int graphParent[] = new int[mMol.getAllAtoms()];
graphAtom[0] = atom1;
graphAtom[1] = atom2;
graphBond[1] = bond;
graphLevel[atom1] = 1;
graphLevel[atom2] = 2;
graphParent[0] = -1;
graphParent[1] = 0;
int current = 1;
int highest = 1;
while (current <= highest) {
for (int i=0; i 1) && candidate == atom1) {
InventorChain theRing = new InventorChain(graphLevel[graphAtom[current]]);
graphBond[0] = mMol.getConnBond(graphAtom[current], i);
int index = current;
for (int j=0; j 0) {
int handlePreferred = (commonAtoms == 1
&& getConnAtoms(f1, commonAtom) == 1
&& getConnAtoms(f2, commonAtom) == 1) ? 0 : 1;
int joinPriority;
if (maxF1Priority > maxF2Priority)
joinPriority = (handlePreferred << 24)
+ (maxF1Priority << 16)
+ (maxF2Priority << 8)
+ commonAtoms;
else
joinPriority = (handlePreferred << 24)
+ (maxF2Priority << 16)
+ (maxF1Priority << 8)
+ commonAtoms;
if (maxJoinPriority < joinPriority) {
maxJoinPriority = joinPriority;
maxCommonAtoms = commonAtoms;
// retain coordinates of fragment with highest priority atom
maxF1Priority = 0;
maxF2Priority = 0;
for (int k=0; k maxF2Priority) {
maxFragment1 = f1;
maxFragment2 = f2;
}
else {
maxFragment1 = f2;
maxFragment2 = f1;
}
}
}
}
}
if (maxJoinPriority == 0)
break;
if (maxCommonAtoms == maxFragment1.size())
mFragmentList.remove(maxFragment1);
else if (maxCommonAtoms == maxFragment2.size())
mFragmentList.remove(maxFragment2);
else
joinFragments(maxFragment1, maxFragment2, maxCommonAtoms);
}
}
private void joinFragments(InventorFragment f1, InventorFragment f2, int commonAtoms) {
int[] commonAtom = new int[commonAtoms];
int count = 0;
for (int i = 0; i Math.abs(getAngleDif(meanNeighbourAngleF1.mAngle, meanNeighbourAngleF2Flip.mAngle))) {
f2.rotate(meanX1, meanY1, meanAngleDif.mAngle);
}
else {
f2.flip(meanX1, meanY1, 0.0);
f2.rotate(meanX1, meanY1, meanAngleDifFlip.mAngle);
}
return getMergedFragment(f1, f2, commonAtoms);
}
private InventorFragment getMergedFragment(InventorFragment f1, InventorFragment f2, int commonAtoms) {
// merges all atoms of two fragments into a new one retaining original coordinates
InventorFragment f = new InventorFragment(mMol, f1.mGlobalAtom.length + f2.mGlobalAtom.length - commonAtoms, f1.mKeepMarkedAtoms | f2.mKeepMarkedAtoms);
int count = 0;
for (int i = 0; i0; i--) { // bubble sort
for (int j=0; j connAngle[j+1]) {
double tempAngle = connAngle[j];
connAngle[j] = connAngle[j+1];
connAngle[j+1] = tempAngle;
int tempAtom = connAtom[j];
connAtom[j] = connAtom[j+1];
connAtom[j+1] = tempAtom;
int tempBond = connBond[j];
connBond[j] = connBond[j+1];
connBond[j+1] = tempBond;
}
}
}
connAngle[connAngles] = connAngle[0] + 2 * Math.PI;
connAtom[connAngles] = connAtom[0];
connBond[connAngles] = connBond[0];
double maxAngleDif = -100.0;
int maxIndex = 0;
for (int i=0; i 2
&& mMol.isRingBond(connBond[i])
&& mMol.isRingBond(connBond[i+1])) {
int ringSize = getSmallestRingSize(connAtom[i], atom, connAtom[i+1]);
if (ringSize != 0)
angleDif -= 100.0 - ringSize;
}
if (maxAngleDif < angleDif) {
maxAngleDif = angleDif;
maxIndex = i;
}
}
return (connAngle[maxIndex] + connAngle[maxIndex+1]) / 2;
}
private double getAngleDif(double angle1, double angle2) {
double angleDif = angle1 - angle2;
while (angleDif < -Math.PI)
angleDif += 2 * Math.PI;
while (angleDif > Math.PI)
angleDif -= 2 * Math.PI;
return angleDif;
}
protected static InventorAngle getMeanAngle(InventorAngle[] angle, int noOfAngles) {
// adds noOfAngles vectors of length=1 with angles angle[i]
// and returns angle of sum-vector
// length of sum-vector is criteria for deviation
double sinSum = 0;
double cosSum = 0;
for (int i=0; i 0) ? Math.PI/2 : -Math.PI/2;
else {
meanAngle = Math.atan(sinSum/cosSum);
if (cosSum < 0)
meanAngle += Math.PI;
}
double length = Math.sqrt(sinSum * sinSum + cosSum * cosSum) / noOfAngles;
return new InventorAngle(meanAngle, length);
}
private int getConnAtoms(InventorFragment f, int atom) {
int connAtoms = 0;
for (int i=0; i 1)
&& (mMol.getConnAtoms(mMol.getBondAtom(1, bond)) > 1)
&& (mMol.getBondParity(bond) == Molecule.cBondParityEor1
|| mMol.getBondParity(bond) == Molecule.cBondParityZor2)) {
int[] minConnAtom = new int[2];
int[] bondAtom = new int[2];
for (int j=0; j<2; j++) {
minConnAtom[j] = mMol.getMaxAtoms();
bondAtom[j] = mMol.getBondAtom(j, bond);
for (int k=0; k connAtom)
minConnAtom[j] = connAtom;
}
}
double dbAngle = InventorAngle.getAngle(f.mAtomX[f.mGlobalToLocalAtom[bondAtom[0]]],
f.mAtomY[f.mGlobalToLocalAtom[bondAtom[0]]],
f.mAtomX[f.mGlobalToLocalAtom[bondAtom[1]]],
f.mAtomY[f.mGlobalToLocalAtom[bondAtom[1]]]);
double angle1 = InventorAngle.getAngle(f.mAtomX[f.mGlobalToLocalAtom[minConnAtom[0]]],
f.mAtomY[f.mGlobalToLocalAtom[minConnAtom[0]]],
f.mAtomX[f.mGlobalToLocalAtom[bondAtom[0]]],
f.mAtomY[f.mGlobalToLocalAtom[bondAtom[0]]]);
double angle2 = InventorAngle.getAngle(f.mAtomX[f.mGlobalToLocalAtom[bondAtom[1]]],
f.mAtomY[f.mGlobalToLocalAtom[bondAtom[1]]],
f.mAtomX[f.mGlobalToLocalAtom[minConnAtom[1]]],
f.mAtomY[f.mGlobalToLocalAtom[minConnAtom[1]]]);
if (((getAngleDif(dbAngle, angle1) < 0)
^ (getAngleDif(dbAngle, angle2) < 0))
^ (mMol.getBondParity(bond) == Molecule.cBondParityZor2)) {
f.flipOneSide(bond);
}
}
}
}
}
}
private void optimizeFragments() {
int[] atomSymRank = calculateAtomSymmetries();
byte[] bondFlipPriority = new byte[mMol.getAllBonds()];
locateFlipBonds(bondFlipPriority, atomSymRank);
for (int bond=0; bond collisionList = f.getCollisionList();
double minCollisionPanalty = f.getCollisionPanalty();
InventorFragment minCollisionFragment = new InventorFragment(f);
int lastBond = -1;
for (int flip=0; flip= FLIP_POSSIBLE)
availableBond[availableBonds++] = bondSequence[i];
}
else {
for (int i=1; i= FLIP_AS_LAST_RESORT)
availableBond[availableBonds++] = bondSequence[i];
}
if (availableBonds != 0) {
int theBond = availableBond[0];
if (availableBonds > 1) {
do { // don't rotate 2 times around same bond
theBond = availableBond[mRandom.nextInt(availableBonds)];
} while (theBond == lastBond);
}
if (theBond != lastBond) {
lastBond = theBond;
f.flipOneSide(theBond);
// getCollisionList() is necessary to update collision panalty
collisionList = f.getCollisionList();
if (minCollisionPanalty > f.getCollisionPanalty()) {
minCollisionPanalty = f.getCollisionPanalty();
minCollisionFragment = new InventorFragment(f);
}
}
}
}
mFragmentList.set(fragmentNo, minCollisionFragment);
// finished optimization by rotating around single bonds
// starting optimization by moving individual atoms
/*
double avbl = mMol.getAverageBondLength();
for (int i=0; i currentRank && theRank < nextAvailableRank)
nextAvailableRank = theRank;
}
currentRank = nextAvailableRank;
} while (nextAvailableRank != 9999);
}
}
private int[] getShortestConnection(int atom1, int atom2) {
int graphAtom[] = new int[mMol.getAllAtoms()];
int graphBond[] = new int[mMol.getAllAtoms()];
int graphLevel[] = new int[mMol.getAllAtoms()];
int graphParent[] = new int[mMol.getAllAtoms()];
graphAtom[0] = atom2;
graphLevel[atom2] = 1;
graphParent[0] = -1;
int current = 0;
int highest = 0;
while (current <= highest) {
for (int i=0; i 2) {
boolean symmetricEndFound = true;
int connSymRank = -1;
for (int j=0; jj; k--)
connRank[k] = connRank[k-1];
connRank[j] = rank;
}
int neighbours = mMol.getAllConnAtoms(atom);
baseValue[atom].init(atom);
baseValue[atom].add(atomBits, symRank[atom]);
baseValue[atom].add((maxConnAtoms - neighbours)*(atomBits + 1), 0);
for (int i=0; i associationList = createMetalBondAssociations();
while (associationList != null) {
FragmentAssociation association = getMaxPriorityAssociation(associationList);
joinAssociatedFragments(association, 1.2);
associationList = createMetalBondAssociations();
}
}
private void joinChargedFragments() {
FragmentAssociation association = createChargeAssociation();
while (association != null) {
joinAssociatedFragments(association, 1.5);
association = createChargeAssociation();
}
}
private void joinRemainingFragments() {
FragmentAssociation association = createDisconnectedAssociation();
while (association != null) {
joinAssociatedFragments(association, 1.8);
association = createDisconnectedAssociation();
}
}
private void joinAssociatedFragments(FragmentAssociation association, double minDistance) {
association.arrange(minDistance, (mMode & MODE_CONSIDER_MARKED_ATOMS) != 0);
InventorFragment mergedFragment = getMergedFragment(association.getFragment(0), association.getFragment(1), 0);
updateFragmentList(association.getFragment(0), association.getFragment(1), mergedFragment);
}
private FragmentAssociation getMaxPriorityAssociation(ArrayList associationList) {
int maxPriority = 0;
FragmentAssociation maxFA = null;
for (FragmentAssociation association:associationList) {
if (maxPriority < association.getPriority()) {
maxPriority = association.getPriority();
maxFA = association;
}
}
return maxFA;
}
private ArrayList createMetalBondAssociations() {
ArrayList associationList = null;
FragmentAssociation[][] fa = null;
for (int bond=0; bond f2) { // f1 must be the smaller one (and potentially the core fragment with fixed coords)
int temp = f1;
f1 = f2;
f2 = temp;
temp = atomIndex1;
atomIndex1 = atomIndex2;
atomIndex2 = temp;
}
if (fa == null)
fa = new FragmentAssociation[mFragmentList.size()][];
if (fa[f2] == null)
fa[f2] = new FragmentAssociation[f2];
if (fa[f2][f1] != null)
fa[f2][f1].add(atomIndex1, atomIndex2);
else {
fa[f2][f1] = new FragmentAssociation(mFragmentList.get(f1), mFragmentList.get(f2), atomIndex1, atomIndex2);
if (associationList == null)
associationList = new ArrayList();
associationList.add(fa[f2][f1]);
}
}
}
}
return associationList;
}
private FragmentAssociation createChargeAssociation() {
ArrayList negChargeList = new ArrayList();
ArrayList posChargeList = new ArrayList();
ArrayList chargeList = new ArrayList();
for (InventorFragment f:mFragmentList) {
int fragmentCharge = 0;
chargeList.clear();
for (int i=0; i() {
//@Override Annotation incompatible with 1.5
public int compare(InventorCharge o1, InventorCharge o2) {
int c1 = Math.abs(o1.charge);
int c2 = Math.abs(o2.charge);
return c1 < c2 ? -1 : c1 == c2 ? 0 : 1;
}
});
for (InventorCharge ic:chargeList) {
if (fragmentCharge * ic.charge > 0) { // charges have same sign
int charge = (Math.abs(fragmentCharge) >= Math.abs(ic.charge)) ? ic.charge : fragmentCharge;
fragmentCharge -= charge;
(charge < 0 ? negChargeList : posChargeList).add(new InventorCharge(f, ic.atom, charge));
if (fragmentCharge == 0)
break;
}
}
}
}
if (negChargeList.size() == 0 || posChargeList.size() == 0)
return null;
// with positive charges we have the large fragments first
Collections.sort(posChargeList, new Comparator() {
//@Override Annotation incompatible with 1.5
public int compare(InventorCharge o1, InventorCharge o2) {
int c1 = o1.fragment.size();
int c2 = o1.fragment.size();
return c1 < c2 ? 1 : c1 == c2 ? 0 : -1;
}
});
// with negative charges we have the small o1.fragments first
Collections.sort(negChargeList, new Comparator() {
//@Override Annotation incompatible with 1.5
public int compare(InventorCharge o1, InventorCharge o2) {
int c1 = o1.fragment.size();
int c2 = o1.fragment.size();
return c1 < c2 ? -1 : c1 == c2 ? 0 : 1;
}
});
// we combine preferably small with large
for (InventorCharge pc:posChargeList) {
for (InventorCharge nc : negChargeList) {
if (pc.charge == -nc.charge) {
mUnPairedCharge[pc.fragment.getGlobalAtom(pc.atom)] -= pc.charge;
mUnPairedCharge[nc.fragment.getGlobalAtom(nc.atom)] -= nc.charge;
return new FragmentAssociation(pc.fragment, nc.fragment, pc.atom, nc.atom);
}
}
}
for (InventorCharge pc:posChargeList) {
for (InventorCharge nc : negChargeList) {
if (pc.charge > -nc.charge) {
mUnPairedCharge[pc.fragment.getGlobalAtom(pc.atom)] += nc.charge;
mUnPairedCharge[nc.fragment.getGlobalAtom(nc.atom)] -= nc.charge;
return new FragmentAssociation(pc.fragment, nc.fragment, pc.atom, nc.atom);
}
}
}
for (InventorCharge pc:posChargeList) {
for (InventorCharge nc : negChargeList) {
if (pc.charge < -nc.charge) {
mUnPairedCharge[pc.fragment.getGlobalAtom(pc.atom)] -= pc.charge;
mUnPairedCharge[nc.fragment.getGlobalAtom(nc.atom)] += pc.charge;
return new FragmentAssociation(pc.fragment, nc.fragment, pc.atom, nc.atom);
}
}
}
return null;
}
private FragmentAssociation createDisconnectedAssociation() {
if (mFragmentList.size() < 2)
return null;
return new FragmentAssociation(mFragmentList.get(0), mFragmentList.get(1));
}
/* ingenious solution to whether we have a cyclic relationship between fragments and metal bond associations
private boolean isCyclic(FragmentAssociation[][] fa) {
for (int i=1; i