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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.coords.CoordinateInventor;
import java.util.ArrayList;
public class MarkushStructure implements java.io.Serializable {
static final long serialVersionUID = 0x20080515;
private static final int MAX_RGROUP_DEPTH = 5;
private ArrayList mCoreList;
private ArrayList mRGroupList;
private StereoMolecule[][] mSubstituent;
private int mCoreIndex;
private int[] mSubstituentCount,mSubstituentIndex;
private int[][] mCoreRGroup;
private int[][][] mSubstituentRGroup;
public MarkushStructure() {
mCoreList = new ArrayList();
mRGroupList = new ArrayList();
}
public MarkushStructure(StereoMolecule[] fragment, int coreCount) {
this();
if (fragment != null) {
for (int i=0; i rGroupList = new ArrayList();
for (int atom=0; atom= mRGroupList.size())
throw new Exception("Not all used R-groups are defined.");
String warning = null;
if (rGroupCount < mRGroupList.size())
warning = "One or more defined R-group(s) are unreferenced.";
mSubstituent = new StereoMolecule[mRGroupList.size()][];
mSubstituentRGroup = new int[mRGroupList.size()][][];
for (int i=0; i rGroupList = new ArrayList();
for (int atom=0; atom 1) {
if (mSubstituentIndex[rGroup]+1 < mSubstituentCount[rGroup]) {
mSubstituentIndex[rGroup]++;
incrementCoreIndex = false;
break;
}
else {
mSubstituentIndex[rGroup] = 0;
}
}
}
if (incrementCoreIndex)
mCoreIndex++;
return mol;
}
private int getRGroupIndex(int atomicNo) {
if (atomicNo < 129 || atomicNo > 144)
return -1;
return (atomicNo >= 142) ? atomicNo - 142 : atomicNo - 126;
}
private StereoMolecule createCurrentEnumeration() {
StereoMolecule mol = new StereoMolecule();
mol.addMolecule(mCoreList.get(mCoreIndex));
for (int atom=0; atom