com.actelion.research.chem.SimpleCanonizer 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.
*
*/
package com.actelion.research.chem;
@Deprecated // use Canonizer with mode NEGLECT_ANY_STEREO_INFORMATION instead
public class SimpleCanonizer {
private static final int cIDCodeVersion3 = 9;
// productive version since May 2006 based on the molfile version 3
// being compatible with MDL's "Enhanced Stereo Representation"
private ExtendedMolecule mMol;
private int mCanRank[];
private long mCanBaseValue[];
private boolean mGraphGenerated;
private int mGraphRings;
private int mGraphAtom[];
private int mGraphBond[];
private int mGraphFrom[];
private int mGraphClosure[];
public static final int MAX_ATOM_BITS = 8;
private String mIDCode,mCoordinates;
private StringBuffer mEncodingBuffer;
private int mEncodingBitsAvail,mEncodingTempData;
private boolean mZCoordinatesAvailable;
public SimpleCanonizer(ExtendedMolecule mol) {
mMol = mol;
mMol.ensureHelperArrays(Molecule.cHelperRings);
for (int atom=0; atom 1)
break;
}
for (int atom=0; atomj; k--)
connRank[k] = connRank[k-1];
connRank[j] = rank;
}
mCanBaseValue[atom] = 0;
for (int i=0; i mCanBaseValue[atom])
lowest = mCanBaseValue[atom];
if (lowest != 0x7fffffffffffffffL) {
canRank++;
for (int atom=0; atom mCanRank[startAtom])
startAtom = atom;
boolean atomHandled[] = new boolean[mMol.getAtoms()];
boolean bondHandled[] = new boolean[mMol.getBonds()];
int newAtomNo[] = new int[mMol.getAtoms()];
mGraphAtom = new int[mMol.getAtoms()];
mGraphFrom = new int[mMol.getAtoms()];
mGraphBond = new int[mMol.getBonds()];
mGraphAtom[0] = startAtom;
atomHandled[startAtom] = true;
int atomsWithoutParents = 1; // the startatom has no parent
int firstUnhandled = 0;
int firstUnused = 1;
int graphBonds = 0;
while (firstUnhandled < mMol.getAtoms()) {
if (firstUnhandled < firstUnused) { // attach neighbours in rank order to unhandled
while (true) {
int highestRankingConnAtom = 0;
int highestRankingConnBond = 0;
int highestRank = -1;
for (int i=0; i highestRank) {
highestRankingConnAtom = connAtom;
highestRankingConnBond = mMol.getConnBond(mGraphAtom[firstUnhandled],i);
highestRank = mCanRank[connAtom];
}
}
if (highestRank == -1)
break;
newAtomNo[highestRankingConnAtom] = firstUnused;
mGraphFrom[firstUnused] = firstUnhandled;
mGraphAtom[firstUnused++] = highestRankingConnAtom;
mGraphBond[graphBonds++] = highestRankingConnBond;
atomHandled[highestRankingConnAtom] = true;
bondHandled[highestRankingConnBond] = true;
}
firstUnhandled++;
}
else {
int highestRankingAtom = 0;
int highestRank = -1;
for (int atom=0; atom highestRank) {
highestRankingAtom = atom;
highestRank = mCanRank[atom];
}
}
atomsWithoutParents++;
newAtomNo[highestRankingAtom] = firstUnused;
mGraphFrom[firstUnused] = -1; // no parent atom in graph tree
mGraphAtom[firstUnused++] = highestRankingAtom;
atomHandled[highestRankingAtom] = true;
}
}
mGraphClosure = new int[2 * (mMol.getBonds() - graphBonds)];
mGraphRings = 0;
while (true) { // add ring closure bonds (those with lowest new atom numbers first)
int lowAtomNo1 = mMol.getMaxAtoms();
int lowAtomNo2 = mMol.getMaxAtoms();
int lowBond = -1;
for (int bond=0; bond 0) {
encodeBits(1, 1); // more data to come
encodeBits(8, 4); // 8 = datatype 'AtomList'
encodeBits(count, nbits);
for (int atom=0; atom> Molecule.cAtomRadicalStateShift, 2);
}
}
}
if (mMol.isFragment()) { // more QueryFeatures and fragment specific properties
isSecondFeatureBlock |= addAtomQueryFeatures(22, isSecondFeatureBlock, nbits, Molecule.cAtomQFFlatNitrogen, 1, -1);
isSecondFeatureBlock |= addBondQueryFeatures(23, isSecondFeatureBlock, nbits, Molecule.cBondQFMatchStereo, 1, -1);
isSecondFeatureBlock |= addBondQueryFeatures(24, isSecondFeatureBlock, nbits,
Molecule.cBondQFAromState,
Molecule.cBondQFAromStateBits,
Molecule.cBondQFAromStateShift);
}
boolean[] isAromaticSPBond = getAromaticSPBonds();
if (isAromaticSPBond != null) {
count = 0;
for (int bond=0; bond 15) {
ensureSecondFeatureBlock(isSecondFeatureBlock);
codeNo -= 16;
}
encodeBits(1, 1); // more data to come
encodeBits(codeNo, 4); // datatype
encodeBits(count, nbits);
for (int atom=0; atom> qfShift, qfBits);
}
}
return true;
}
private boolean addBondQueryFeatures(int codeNo, boolean isSecondFeatureBlock, int nbits, int qfMask, int qfBits, int qfShift) {
int count = 0;
for (int bond=0; bond 15) {
ensureSecondFeatureBlock(isSecondFeatureBlock);
codeNo -= 16;
}
encodeBits(1, 1); // more data to come
encodeBits(codeNo, 4); // datatype
encodeBits(count, nbits);
for (int bond=0; bond> qfShift, qfBits);
}
}
return true;
}
private boolean[] getAromaticSPBonds() {
boolean[] isAromaticSPBond = null;
for (int bond=0; bond