com.actelion.research.chem.CanonizerMesoHelper Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Show all versions of openchemlib Show documentation
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
*/
// 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 TreeSet<>();
// 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 mesoFragmentList) {
MesoFragmentMembers members = tryFindMesoFragment(atom1, atom2);
if (members != null && members.hasStereoCenters(mIsStereoCenter))
mesoFragmentList.add(members);
}
/**
* Tries to find a symmetry plane starting from symmetrical atom1 and atom2.
* Stops atom matching at non-ring single bonds, thus locates and assigns one meso fragment.
* @param atom1
* @param atom2
* @return a MesoFragmentMembers object, if a meso fragment was found
*/
private MesoFragmentMembers tryFindMesoFragment(int atom1, int atom2) {
int[] graphAtom = new int[mMol.getAtoms()];
int[] matchAtom = new int[mMol.getAtoms()];
boolean[] isOrthogonal = new boolean[mMol.getAtoms()];
boolean[] hasOrthogonality = new boolean[mMol.getAtoms()];
MesoFragmentBranch[] branch = new MesoFragmentBranch[mMol.getAtoms()];
MesoFragmentMembers members = new MesoFragmentMembers(mMol.getAtoms());
graphAtom[0] = atom1;
matchAtom[atom1] = atom2;
matchAtom[atom2] = -2; // -2 := on mirror side
members.add(atom1);
members.add(atom2);
int current = 0;
int highest = 0;
while (current <= highest) {
int currentAtom = graphAtom[current];
// if currentAtom is in mirror plane
if (matchAtom[currentAtom] == currentAtom) {
for (int i=0; i 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 members;
}
/*
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) {
int[] candidate = new int[mMol.getConnAtoms(parentOfMirrorAtom)];
int index = 0;
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 boolean[] isMember;
public int[] memberAtom;
public MesoFragmentMembers(int atoms) {
isMember = new boolean[atoms];
}
public void add(int atom) {
isMember[atom] = true;
}
private void consolidate() {
int count = 0;
for (boolean is:isMember)
if (is)
count++;
memberAtom = new int[count];
count = 0;
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