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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.
*
* @author Thomas Sander
*/
package com.actelion.research.chem;
import java.io.*;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.Locale;
public class MolfileCreator {
private static final float TARGET_AVBL = 1.5f;
private StringBuilder mBuilder;
private DecimalFormat mDoubleFormat;
/**
* This creates a new molfile version 2 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 MolfileCreator(ExtendedMolecule mol) {
this(mol, true);
}
/**
* This creates a new molfile version 2 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 MolfileCreator(ExtendedMolecule mol, boolean allowScaling) {
this(mol, allowScaling, new StringBuilder(32768));
}
/**
* This creates a new molfile version 2 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 MolfileCreator(ExtendedMolecule mol, boolean allowScaling, StringBuilder builder) {
this(mol, allowScaling, 0.0, builder);
}
/**
* This creates a new molfile version 2 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 scalingFactor is given, then the molecule is scaled accordingly independent of the average bond length.
* If a StringBuilder is given, then the molfile will be appended to that.
* @param mol
* @param allowScaling if false, then no scaling is performed
* @param scalingFactor if not 0.0 then the molecule is scaled by this factor
* @param builder null or StringBuilder to append to
*/
public MolfileCreator(ExtendedMolecule mol, boolean allowScaling, double scalingFactor, StringBuilder builder) {
mDoubleFormat = new DecimalFormat("0.0000", new DecimalFormatSymbols(Locale.ENGLISH)); //English local ('.' for the dot)
final String nl = System.lineSeparator();
mol.ensureHelperArrays(Molecule.cHelperParities);
boolean isRacemic = true;
for (int atom=0; atom 3.0f)
grafac = TARGET_AVBL / avbl;
}
else { // make the minimum distance between any two atoms twice as long as TARGET_AVBL
double minDistance = Double.MAX_VALUE;
for (int atom1=1; atom1 distance)
minDistance = distance;
}
}
grafac = 2.0f * TARGET_AVBL / minDistance;
}
}
}
for (int atom=0; atom= 129 && mol.getAtomicNo(atom) <= 144) || mol.getAtomicNo(atom) == 154)
mBuilder.append(" R# ");
else {
String atomLabel = mol.getAtomLabel(atom);
mBuilder.append(" "+atomLabel);
if (atomLabel.length() == 1)
mBuilder.append(" ");
else if (atomLabel.length() == 2)
mBuilder.append(" ");
}
mBuilder.append(" 0 0 0"); // massDif, charge, parity
long hydrogenFlags = Molecule.cAtomQFHydrogen & mol.getAtomQueryFeatures(atom);
if (hydrogenFlags == 0)
mBuilder.append(" 0");
else if (hydrogenFlags == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen))
mBuilder.append(" 3"); // at least 2 hydrogens
else if (hydrogenFlags == Molecule.cAtomQFNot0Hydrogen)
mBuilder.append(" 2"); // at least 1 hydrogens
else if (hydrogenFlags == (Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mBuilder.append(" 1"); // no hydrogens
else if (hydrogenFlags == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mBuilder.append(" 2"); // use at least 1 hydrogens as closest match for exactly one
mBuilder.append(((mol.getAtomQueryFeatures(atom) & Molecule.cAtomQFMatchStereo) != 0) ? " 1" : " 0");
int valence = mol.getAtomAbnormalValence(atom);
if (valence == -1)
mBuilder.append(" 0");
else if (valence == 0)
mBuilder.append(" 15");
else
appendThreeDigitInt(valence);
mBuilder.append(" 0 0 0");
appendThreeDigitInt(mol.getAtomMapNo(atom));
mBuilder.append(" 0 0"+nl);
}
for (int bond=0; bond= 129 && mol.getAtomicNo(atom) <= 144) || mol.getAtomicNo(atom) == 154)
no++;
if (no != 0) {
int count = 0;
for (int atom=0; atom= 129 && atomicNo <= 144) || atomicNo == 154) {
if (count == 0) {
mBuilder.append("M RGP");
appendThreeDigitInt(Math.min(8, no));
}
mBuilder.append(" ");
appendThreeDigitInt(atom + 1);
mBuilder.append(" ");
appendThreeDigitInt(atomicNo == 154 ? 0 : atomicNo >= 142 ? atomicNo - 141 : atomicNo - 125);
no--;
if (++count == 8 || no == 0) {
count = 0;
mBuilder.append(nl);
}
}
}
}
if (mol.isFragment()) {
no = 0;
for (int atom=0; atom 999) {
mBuilder.append(" ?");
return;
}
boolean digitFound = false;
for (int i=0; i<3; i++) {
int theChar = data / 100;
if (theChar==0) {
if (i==2 || digitFound)
mBuilder.append((char)'0');
else
mBuilder.append((char)' ');
}
else {
mBuilder.append((char)('0' + theChar));
digitFound = true;
}
data = 10 * (data % 100);
}
}
private void appendTenDigitDouble(double theDouble) {
String val = mDoubleFormat.format(theDouble);
for(int i=val.length(); i<10; i++) mBuilder.append(' ');
mBuilder.append(val);
}
}