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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 java.io.IOException;
import java.io.Writer;
/**
* This class generates an MDL molfile version 3.0 from a StereoMolecule
* as described by MDL in 'CTFile Formats June 2005'.
* Since the MDL enhanced stereo recognition concept doesn't include
* support for axial chirality as bond property, we added object type 'BONDS'
* to the internal collection types STEABS,STERAC and STEREL, in order to
* properly encode ESR assignments of axial stereo bonds, e.g. BINAP kind of
* stereo bonds.
* @author sandert
*
*/
public class MolfileV3Creator
{
private StringBuilder mMolfile;
private static final double TARGET_AVBL = 1.5;
private static final double PRECISION_FACTOR = 10000;
private double mScalingFactor = 1.0;
/**
* This creates a new molfile version 3 from the given molecule.
* If the average bond length is smaller than 1.0 or larger than 3.0,
* then all coordinates are scaled to achieve an average bond length of 1.5.
* @param mol
*/
public MolfileV3Creator(ExtendedMolecule mol) {
this(mol, true);
}
/**
* This creates a new molfile version 3 from the given molecule.
* If scale==true and the average bond length is smaller than 1.0 or larger than 3.0,
* then all coordinates are scaled to achieve an average bond length of 1.5.
* @param mol
* @param scale
*/
public MolfileV3Creator(ExtendedMolecule mol, boolean scale) {
this(mol, scale, new StringBuilder(32768));
}
/**
* This creates a new molfile version 3 from the given molecule.
* If scale==true and the average bond length is smaller than 1.0 or larger than 3.0,
* then all coordinates are scaled to achieve an average bond length of 1.5.
* If a StringBuilder is given, then the molfile will be appended to that.
* @param mol
* @param scale
* @param builder null or StringBuilder to append to
*/
public MolfileV3Creator(ExtendedMolecule mol, boolean scale, StringBuilder builder) {
mol.ensureHelperArrays(Molecule.cHelperParities);
mMolfile = builder;
String name = (mol.getName() != null) ? mol.getName() : "";
mMolfile.append(name + "\n");
mMolfile.append("Actelion Java MolfileCreator 2.0\n\n");
mMolfile.append(" 0 0 0 0 0 0 0 V3000\n");
boolean hasCoordinates = (mol.getAllAtoms() == 1);
for(int atom=1; atom 3.0)
mScalingFactor = TARGET_AVBL / avbl;
}
else { // make the minimum distance between any two atoms twice as long as TARGET_AVBL
double minDistance = Float.MAX_VALUE;
for (int atom1=1; atom1 distance)
minDistance = distance;
}
}
mScalingFactor = 2.0 * TARGET_AVBL / minDistance;
}
}
writeBody(mol, hasCoordinates);
mMolfile.append("M END\n");
}
public static String writeCTAB(ExtendedMolecule mol, boolean hasCoordinates) {
MolfileV3Creator mf = new MolfileV3Creator();
mol.ensureHelperArrays(Molecule.cHelperParities);
mf.writeBody(mol, hasCoordinates);
return mf.getMolfile();
}
private MolfileV3Creator() {
mMolfile = new StringBuilder(32768);
}
private void writeBody(ExtendedMolecule mol, boolean hasCoordinates) {
mMolfile.append("M V30 BEGIN CTAB\n");
mMolfile.append("M V30 COUNTS " + mol.getAllAtoms() + " " + mol.getAllBonds() + " 0 0 0\n");
mMolfile.append("M V30 BEGIN ATOM\n");
for (int atom=0; atom 0) {
mMolfile.append(",");
}
String label = Molecule.cAtomLabel[atomList[i]];
switch (label.length()) {
case 1:
mMolfile.append(label);
break;
case 2:
mMolfile.append(label);
break;
case 3:
mMolfile.append(label);
break;
default:
mMolfile.append("?");
break;
}
}
mMolfile.append("]");
}
else if((mol.getAtomQueryFeatures(atom) & Molecule.cAtomQFAny) != 0) {
mMolfile.append(" A");
}
else {
mMolfile.append(" " + mol.getAtomLabel(atom));
}
if (hasCoordinates) {
mMolfile.append(" " + ((double)((int)(PRECISION_FACTOR * mScalingFactor * mol.getAtomX(atom))) / PRECISION_FACTOR));
mMolfile.append(" " + ((double)((int)(PRECISION_FACTOR * mScalingFactor * -mol.getAtomY(atom))) / PRECISION_FACTOR));
mMolfile.append(" " + ((double)((int)(PRECISION_FACTOR * mScalingFactor * -mol.getAtomZ(atom))) / PRECISION_FACTOR));
}
else {
mMolfile.append(" 0 0 0");
}
mMolfile.append(" " + mol.getAtomMapNo(atom));
if (mol.getAtomCharge(atom) != 0) {
mMolfile.append(" CHG=" + mol.getAtomCharge(atom));
}
if (mol.getAtomRadical(atom) != 0) {
mMolfile.append(" RAD=");
switch (mol.getAtomRadical(atom)) {
case Molecule.cAtomRadicalStateS:
mMolfile.append("1");
break;
case Molecule.cAtomRadicalStateD:
mMolfile.append("2");
break;
case Molecule.cAtomRadicalStateT:
mMolfile.append("3");
break;
}
}
if (mol.getAtomParity(atom) == Molecule.cAtomParity1
|| mol.getAtomParity(atom) == Molecule.cAtomParity2) {
mMolfile.append(" CFG=");
if (mol.getAtomParity(atom) == Molecule.cAtomParity1) {
mMolfile.append("1");
}
else {
mMolfile.append("2");
}
}
if (mol.getAtomMass(atom) != 0) {
mMolfile.append(" MASS=" + mol.getAtomMass(atom));
}
int valence = mol.getAtomAbnormalValence(atom);
if (valence != -1) {
mMolfile.append(" VAL=" + ((valence == 0) ? "-1" : valence));
}
int hydrogenFlags = Molecule.cAtomQFHydrogen & mol.getAtomQueryFeatures(atom);
if (hydrogenFlags == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen)) {
mMolfile.append(" HCOUNT=2"); // at least 2 hydrogens
}
else if(hydrogenFlags == Molecule.cAtomQFNot0Hydrogen) {
mMolfile.append(" HCOUNT=1"); // at least 1 hydrogens
}
else if(hydrogenFlags == (Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen)) {
mMolfile.append(" HCOUNT=-1"); // no hydrogens
}
else if(hydrogenFlags == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen)) {
mMolfile.append(" HCOUNT=1"); // use at least 1 hydrogens as closest match for exactly one
}
int substitution = mol.getAtomQueryFeatures(atom) & (Molecule.cAtomQFMoreNeighbours | Molecule.cAtomQFNoMoreNeighbours);
if (substitution != 0) {
if ((substitution & Molecule.cAtomQFMoreNeighbours) != 0) {
mMolfile.append(" SUBST=" + (mol.getAllConnAtoms(atom) + 1));
}
else {
mMolfile.append(" SUBST=-1");
}
}
int ringFeatures = mol.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingState;
if (ringFeatures != 0) {
switch(ringFeatures) {
case Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds:
mMolfile.append(" RBCNT=-1");
break;
case Molecule.cAtomQFNotChain:
mMolfile.append(" RBCNT=2"); // any ring atom; there is no MDL equivalent
break;
case Molecule.cAtomQFNotChain | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds:
mMolfile.append(" RBCNT=2");
break;
case Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot4RingBonds:
mMolfile.append(" RBCNT=3");
break;
case Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds:
mMolfile.append(" RBCNT=4");
break;
}
}
mMolfile.append("\n");
}
mMolfile.append("M V30 END ATOM\n");
mMolfile.append("M V30 BEGIN BOND\n");
for (int bond=0; bond © 2015 - 2025 Weber Informatics LLC | Privacy Policy