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/*
* 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.
*
*/
// This class handles the meso detection for the Canonizer class.
package com.actelion.research.chem;
import java.util.*;
public class CanonizerMesoHelper {
private static final int REMOVE_ESR_GROUP = 1;
private static final int SWAP_ESR_GROUPS = 2;
private ExtendedMolecule mMol;
private int[] mCanRankWithoutStereo;
private byte[] mTHParity;
private byte[] mEZParity;
private byte[] mTHESRType;
private byte[] mTHESRGroup;
// private byte[] mEZESRType;
// private byte[] mEZESRGroup;
private int[][] mMesoFragmentAtom;
private boolean[] mIsStereoCenter; // based on meso ranking
private boolean[] mIsMesoFragmentMember;
private boolean[] mTHParityRoundIsOdd;
private boolean[] mEZParityRoundIsOdd;
private boolean[] mTHESRTypeNeedsNormalization;
private ArrayList mESRGroupNormalizationInfoList;
protected CanonizerMesoHelper(ExtendedMolecule mol,
int[] canRankWithoutStereo,
boolean[] isStereoCenter,
byte[] thParity,
byte[] ezParity,
byte[] thESRType,
byte[] thESRGroup,
byte[] ezESRType,
byte[] ezESRGroup,
boolean[] thParityRoundIsOdd,
boolean[] ezParityRoundIsOdd,
boolean[] esrTypeNeedsNormalization) {
mMol = mol;
mCanRankWithoutStereo = canRankWithoutStereo;
mIsStereoCenter = isStereoCenter;
mTHParity = thParity;
mEZParity = ezParity;
mTHESRType = thESRType;
mTHESRGroup = thESRGroup;
// mEZESRType = ezESRType;
// mEZESRGroup = ezESRGroup;
mTHParityRoundIsOdd = thParityRoundIsOdd;
mEZParityRoundIsOdd = ezParityRoundIsOdd;
mTHESRTypeNeedsNormalization = esrTypeNeedsNormalization;
findMesoFragments();
}
protected boolean isMeso() {
// Must be called with mTHParities and mEZParities
// freshly calculated after ESR pre-normalization.
boolean meso = true;
for (int atom=0; atom mesoFragmentList = new ArrayList();
// Detect mirror planes by finding a seed atom (an atom with
// at least 2 neighbours sharing the same canRankWithoutStereo)
// or seed bond (a bond connecting to atoms sharing the same
// canRankWithoutStereo).
for (int seedAtom=0; seedAtom 2) {
for (int i=1; i=0; i--) {
int[] atomList = mesoFragmentList.get(i);
boolean found = false;
for (int j=0; j() {
public int compare(int[] a1, int[] a2) {
if (a1.length != a2.length)
return (a1.length < a2.length) ? -1 : 1;
for (int i=0; i mesoFragmentList) {
if (atomMask == null)
return;
int count = 0;
for (int atom=0; atom 2) {
boolean found = false;
for (int j=1; j"+matchAtom[atom]+",p:"+mTHParity[matchAtom[atom]]+",o:"+mTHParityRoundIsOdd[matchAtom[atom]]);
}
System.out.print("graphAtom:");
for (int j=0; j<=highest; j++)
System.out.print(" "+graphAtom[j]);
System.out.println();
*/
return isFragmentMember;
}
/*
private void printFragmentMsg(String msg, int atom1, int atom2, int current, int highest, int[] graphAtom, int[] matchAtom, boolean[] isOrthogonal, boolean[] hasOrthogonality) {
System.out.println("##fragmentMessage:"+msg+" atom1:"+atom1+" atom2:"+atom2+" current:"+current+" highest:"+highest);
System.out.print("graphAtom:");
for (int j=0; j 2)
|| (mMol.getAtomicNo(atom) == 16 && mMol.getConnAtoms(atom) > 2);
}
/**
* temporarilly
* @param atom
* @param parentOfMirrorAtom
* @param isFragmentMember
* @return
*/
private int findMirrorAtom(int atom, int parentOfMirrorAtom, boolean[] isFragmentMember) {
for (int i=0; i();
for (int fragment=0; fragment 0) {
// put temporarily all fragment's ABS atoms int new group of esrType OR
if (containsABS) {
putABSAtomsIntoESRGroup(fragment, matrix.newESRGroup(Molecule.cESRTypeOr), Molecule.cESRTypeOr);
orCount++;
}
// after stereo ranking convert lowest ranking group of esrType into ABS atoms
mESRGroupNormalizationInfoList.add(new ESRGroupNormalizationInfo(fragment,
REMOVE_ESR_GROUP, -1, -1));
}
else if (andCount > 0) {
// put temporarily all fragment's ABS atoms int new group of esrType AND
if (containsABS)
putABSAtomsIntoESRGroup(fragment, matrix.newESRGroup(Molecule.cESRTypeAnd), Molecule.cESRTypeAnd);
// after stereo ranking convert lowest ranking group of esrType into ABS atoms
mESRGroupNormalizationInfoList.add(new ESRGroupNormalizationInfo(fragment,
REMOVE_ESR_GROUP, -1, -1));
}
else if (containsABS) {
putABSAtomsIntoESRGroup(fragment, matrix.newESRGroup(Molecule.cESRTypeAnd), Molecule.cESRTypeAnd);
// after stereo ranking convert lowest ranking group of esrType into ABS atoms
mESRGroupNormalizationInfoList.add(new ESRGroupNormalizationInfo(fragment,
REMOVE_ESR_GROUP, -1, -1));
}
}
else if (dependentGroupCount == 1) {
// IF we have ABS atoms
// 1.) Swapping ESR roles of ABS atoms and dependent group atoms
// doesn't change the molecule. Therefore select one of these
// two representations in a normalized way.
// ELSE
// 1.) Groups are independent from the rest of the molecule, so
// give them independent group numbers.
// 2.) We can convert one of the groups into ABS atoms without
// changing the molecule.
// ENDIF
if (containsTypeABSParity1Or2(fragment)) {
int group = matrix.getDependentGroup(fragment);
int type = matrix.getDependentType(fragment);
mESRGroupNormalizationInfoList.add(new ESRGroupNormalizationInfo(fragment,
SWAP_ESR_GROUPS, group, type));
}
else {
matrix.cutTiesOfIndependentGroups(fragment);
mESRGroupNormalizationInfoList.add(new ESRGroupNormalizationInfo(fragment,
REMOVE_ESR_GROUP, -1, -1));
}
}
}
}
}
private boolean containsTypeABSParity1Or2(int fragment) {
for (int i=0; i=0; i--) {
boolean done = false;
ESRGroupNormalizationInfo info = mESRGroupNormalizationInfoList.get(i);
if (info.action == SWAP_ESR_GROUPS) {
done = normalizeESRGroupSwapping(info.fragment, info.group, info.type, canRank);
}
else if (info.action == REMOVE_ESR_GROUP) {
done = removeESRGroupFromFragment(info.fragment, canRank);
}
if (done) {
mESRGroupNormalizationInfoList.remove(info);
for (int j=0; j is a dependent group
// -2 -> is free group, i.e. is neither member of an ABS atoms
// containing fragment nor of the outside area
// -1 -> is member of outside area
// >=0 -> fragment# with ABS atoms to which all group atoms belong
for (int group=0; group= -1) {
int[] chainMemberLevel = new int[mGroupCount];
if (extendAnchorChain(chainMemberLevel, anchorGroup)) {
for (int group=0; group mCanRankWithoutStereo[atom] + ((esrType == Molecule.cESRTypeAnd) ? 0x10000 : 0)) {
minRank = mCanRankWithoutStereo[atom] + ((esrType == Molecule.cESRTypeAnd) ? 0x10000 : 0);
minGroup = esrGroup;
minType = esrType;
minGroupIndex = cycle[i];
}
}
}
}
}
for (int atom=0; atom {
public int compare(int[] o1, int[] o2) {
if (o1 == null) // put null arrays at the end of the list values
return (o2 == null) ? 0 : 1;
if (o2 == null)
return -1;
int count = Math.min(o1.length, o2.length);
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy