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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.
*
*/
package com.actelion.research.chem;
import com.actelion.research.chem.reaction.Reaction;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class IsomericSmilesCreator {
private StereoMolecule mMol;
private Canonizer mCanonizer;
private String mSmiles;
private boolean mIncludeMapping;
private int[] mAtomRank;
private int[] mClosureNumber;
private int[] mSmilesIndex;
private int[] mClosureBuffer;
private int[][] mKnownTHCountInESRGroup;
private List mGraphAtomList;
private boolean[] mAtomUsed;
private boolean[] mBondUsed;
private boolean[] mClosureOpened;
private boolean[] mPseudoStereoGroupInversion;
private boolean[] mPseudoStereoGroupInitialized;
public static String createReactionSmiles(Reaction rxn) {
StringBuilder sb = new StringBuilder();
for (int i=0; i');
for (int i=0; i');
for (int i=0; i();
int atom = findUnusedStartAtom();
while (atom != -1) {
int graphIndex = mGraphAtomList.size();
addToGraph(new SmilesAtom(atom, -1, false, false), graphIndex);
if (mMol.getConnAtoms(atom) != 0) {
addHighestRankingChain(graphIndex, false);
while (graphIndex < mGraphAtomList.size() - 1) {
while (hasUnusedNeighborAtom(mGraphAtomList.get(graphIndex).atom))
addHighestRankingChain(graphIndex, true);
graphIndex++;
}
}
// we may have multiple unconnected fragments
atom = findUnusedStartAtom();
}
// assign a smiles position index to every atom (needed for stereo assignment)
mSmilesIndex = new int[mMol.getAtoms()];
int index = 0;
for (SmilesAtom smilesAtom:mGraphAtomList)
mSmilesIndex[smilesAtom.atom] = index++;
}
private void findRingClosures() {
boolean[] closureNumberUsed = new boolean[mMol.getBonds()];
mClosureNumber = new int[mMol.getBonds()];
for (SmilesAtom smilesAtom:mGraphAtomList) {
for (int i=0; i rank) {
startRank = rank;
startAtom = atom;
}
}
}
return startAtom;
}
private boolean hasUnusedNeighborAtom(int atom) {
for (int i=0; i 1)
builder.append(hCount);
}
}
if (charge != 0) {
builder.append(charge > 0 ? '+' : '-');
if (Math.abs(charge) > 1)
builder.append(Math.abs(charge));
}
if (mapNo != 0) {
builder.append(':');
builder.append(mapNo);
}
if (useBrackets)
builder.append(']');
appendClosureBonds(smilesAtom, builder);
if (smilesAtom.isSideChainEnd)
builder.append(')');
}
/**
* Don't store nitrogen parities in SMILES unless we have a quarternary nitrogen.
* Some software packages seem to have promblems when decoding parities on nitrogen atoms.
* @param atom
* @return
*/
private boolean qualifiesForAtomParity(int atom) {
return (mMol.getAtomParity(atom) == Molecule.cAtomParity1
|| mMol.getAtomParity(atom) == Molecule.cAtomParity2)
&& !isSingleKnownStereoCenterInESRGroup(atom)
&& (mMol.getAtomicNo(atom) != 7 || mMol.getAtomCharge(atom) > 0);
}
private boolean isSingleKnownStereoCenterInESRGroup(int atom) {
int type = mMol.getAtomESRType(atom) - 1;
return type == -1 ? false : mKnownTHCountInESRGroup[type][mMol.getAtomESRGroup(atom)] <= 1;
}
private void appendClosureBonds(SmilesAtom smilesAtom, StringBuilder builder) {
int closureCount = 0;
for (int i=0; i> 20);
if (!mClosureOpened[bond]) {
mClosureOpened[bond] = true;
appendBondOrderSymbol(bond, builder);
}
if (closureNumber > 9)
builder.append('%');
builder.append(closureNumber);
}
}
}
private void appendBondOrderSymbol(SmilesAtom smilesAtom, StringBuilder builder) {
if (smilesAtom.ezHalfParity != 0) {
builder.append(smilesAtom.ezHalfParity == 1 ? '/' : '\\');
return;
}
appendBondOrderSymbol(mMol.getBond(smilesAtom.atom, smilesAtom.parent), builder);
}
private void appendBondOrderSymbol(int bond, StringBuilder builder) {
if (!mMol.isAromaticBond(bond)) {
int order = mMol.getBondType(bond) & Molecule.cBondTypeMaskSimple;
if (order == Molecule.cBondTypeSingle) {
if (mMol.isAromaticAtom(mMol.getBondAtom(0, bond))
&& mMol.isAromaticAtom(mMol.getBondAtom(1, bond)))
builder.append('-');
} else if (order == Molecule.cBondTypeDouble)
builder.append('=');
else if (order == Molecule.cBondTypeTriple)
builder.append('#');
// else if (order == Molecule.cBondTypeQuadruple) // not supported by Molecule
// builder.append('$');
}
}
private String getAtomParitySymbol(int atom, int parent) {
boolean inversion = false;
if (mMol.getAtomPi(atom) != 0
&& mMol.getConnAtoms(atom) == 2
&& mMol.getConnBondOrder(atom,0) == 2
&& mMol.getConnBondOrder(atom,1) == 2) { // allene parities
for (int i=0; i neighborRank[1])
inversion = !inversion;
if (neighborRank[0] > neighborRank[2])
inversion = !inversion;
if (neighborRank[1] > neighborRank[2])
inversion = !inversion;
if (neighborAtom[0] > neighborAtom[1])
inversion = !inversion;
if (neighborAtom[0] > neighborAtom[2])
inversion = !inversion;
if (neighborAtom[1] > neighborAtom[2])
inversion = !inversion;
for (int i=0; i<3; i++)
if (parent > neighborAtom[i])
inversion = !inversion;
}
boolean isClockwise = ((mMol.getAtomParity(atom) == Molecule.cAtomParity1) ^ inversion);
if (mMol.isAtomParityPseudo(atom)) {
int group = mCanonizer.getPseudoTHGroup(atom);
if (!mPseudoStereoGroupInitialized[group]) {
mPseudoStereoGroupInitialized[group] = true;
mPseudoStereoGroupInversion[group] = isClockwise;
}
if (mPseudoStereoGroupInversion[group])
isClockwise = !isClockwise;
}
return isClockwise ? "@@" : "@";
}
/**
* @param atom for which to return a neighbor's smiles rank
* @param neighborIndex index for getConnAtoms() to get neighbor atom and bond
* @return neighbor's position rank in smiles from a perspective of atom using closure digit positions for closure neighbors
*/
private int getSmilesRank(int atom, int neighborIndex) {
int bond = mMol.getConnBond(atom, neighborIndex);
if (mClosureNumber[bond] != 0) {
// if neighbor is attached via a closure digit, then the rank is based primarily on atom's position
// in the smiles and secondary on the count of other closures at atom that precede this closure
int rank = 8 * mSmilesIndex[atom] + 1;
for (int i=0; i= 5 && atomicNo <= 9) // B,C,N,O,F
|| (atomicNo >= 15 && atomicNo <= 17) // P,S,Cl
|| atomicNo == 35 // Br
|| atomicNo == 53; // I
}
}
class SmilesAtom {
public int atom,parent,ezHalfParity;
public boolean isSideChainStart,isSideChainEnd;
public SmilesAtom(int atom, int parent, boolean isSideChainStart, boolean isSideChainEnd) {
this.atom = atom;
this.parent = parent;
this.isSideChainStart = isSideChainStart;
this.isSideChainEnd = isSideChainEnd;
}
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