com.actelion.research.chem.MolfileV3Creator 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;
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(StereoMolecule mol) {
this(mol, true);
}
/**
* This creates a new molfile version 3 from the given molecule.
* If allowScaling==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 allowScaling
*/
public MolfileV3Creator(StereoMolecule mol, boolean allowScaling) {
this(mol, allowScaling, 0.0, new StringBuilder(32768));
}
/**
* This creates a new molfile version 3 from the given molecule.
* If allowScaling==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 allowScaling
* @param builder null or StringBuilder to append to
*/
public MolfileV3Creator(StereoMolecule mol, boolean allowScaling, StringBuilder builder) {
this(mol, allowScaling, 0.0, builder);
}
/**
* This creates a new molfile version 3 from the given molecule.
* If allowScaling==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 allowScaling
* @param builder null or StringBuilder to append to
*/
public MolfileV3Creator(StereoMolecule mol, boolean allowScaling, double scalingFactor, StringBuilder builder) {
mol.ensureHelperArrays(Molecule.cHelperParities);
final String nl = System.lineSeparator();
mMolfile = (builder == null) ? new StringBuilder() : builder;
String name = (mol.getName() != null) ? mol.getName() : "";
mMolfile.append(name + nl);
mMolfile.append("Actelion Java MolfileCreator 2.0"+nl+nl);
mMolfile.append(" 0 0 0 0 0 0 0 V3000"+nl);
mScalingFactor = 1.0;
boolean hasCoordinates = hasCoordinates(mol);
if (hasCoordinates) {
if (scalingFactor != 0)
mScalingFactor = scalingFactor;
else if (allowScaling)
mScalingFactor = calculateScalingFactor(mol);
}
writeBody(mol, hasCoordinates);
mMolfile.append("M END"+nl);
}
private static boolean hasCoordinates(StereoMolecule mol) {
if (mol.getAllAtoms() == 1)
return true; // we can only assume
for(int atom=1; atom 3.0)
scalingFactor = 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;
}
}
scalingFactor = 2.0 * TARGET_AVBL / Math.max(TARGET_AVBL / 2, minDistance);
}
return scalingFactor;
}
/**
* @param mol
* @param scalingFactor
* @return a CTAB V3 with scaled atom coordinates
*/
public static String writeCTAB(StereoMolecule mol, double scalingFactor) {
MolfileV3Creator mf = new MolfileV3Creator();
mf.mScalingFactor = scalingFactor;
mol.ensureHelperArrays(Molecule.cHelperParities);
mf.writeBody(mol, true);
return mf.getMolfile();
}
/**
* @param mol
* @param hasCoordinates
* @return a CTAB V3 without any coordinate scaling
*/
private static String writeCTAB(StereoMolecule 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(StereoMolecule mol, boolean hasCoordinates) {
final String nl = System.lineSeparator();
mMolfile.append("M V30 BEGIN CTAB"+nl);
mMolfile.append("M V30 COUNTS " + mol.getAllAtoms() + " " + mol.getAllBonds() + " 0 0 0"+nl);
mMolfile.append("M V30 BEGIN ATOM"+nl);
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 if((mol.getAtomicNo(atom) >= 129 && mol.getAtomicNo(atom) <= 144) || mol.getAtomicNo(atom) == 154) {
mMolfile.append(" R#");
}
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 atomicNo = mol.getAtomicNo(atom);
if ((atomicNo >= 129 && atomicNo <= 144) || atomicNo == 154) {
mMolfile.append(" RGROUPS=(1 " + (atomicNo == 154 ? 0 : atomicNo >= 142 ? atomicNo - 141 : atomicNo - 125) +")");
}
long 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
}
long 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");
}
}
long ringFeatures = mol.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingState;
if (ringFeatures != 0) {
if (ringFeatures == (Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds))
mMolfile.append(" RBCNT=-1");
else if (ringFeatures == Molecule.cAtomQFNotChain)
mMolfile.append(" RBCNT=2"); // any ring atom; there is no MDL equivalent
else if (ringFeatures == (Molecule.cAtomQFNotChain | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds))
mMolfile.append(" RBCNT=2");
else if (ringFeatures == (Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot4RingBonds))
mMolfile.append(" RBCNT=3");
else if (ringFeatures == (Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds))
mMolfile.append(" RBCNT=4");
}
mMolfile.append(nl);
}
mMolfile.append("M V30 END ATOM"+nl);
mMolfile.append("M V30 BEGIN BOND"+nl);
for (int bond=0; bond