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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.util.ArrayList;
public class RingCollection {
public static final int MAX_SMALL_RING_SIZE = 7;
// public static final int MAX_LARGE_RING_SIZE = 24; // disabled ring size limit, because atom ring flags must be
// reliable, e.g. for substituent detection. TLS 20130613
private static final int MODE_SMALL_RINGS = 1;
private static final int MODE_LARGE_RINGS = 2;
private static final int MODE_AROMATICITY = 4;
public static final int MODE_SMALL_RINGS_ONLY = MODE_SMALL_RINGS;
public static final int MODE_SMALL_AND_LARGE_RINGS = MODE_SMALL_RINGS
| MODE_LARGE_RINGS;
public static final int MODE_SMALL_RINGS_AND_AROMATICITY = MODE_SMALL_RINGS
| MODE_AROMATICITY;
public static final int MODE_SMALL_AND_LARGE_RINGS_AND_AROMATICITY = MODE_SMALL_RINGS
| MODE_LARGE_RINGS
| MODE_AROMATICITY;
private ExtendedMolecule mMol;
private ArrayList mRingAtomSet;
private ArrayList mRingBondSet;
private int[] mAtomRingSize;
private int[] mBondRingSize;
private int[] mHeteroPosition;
private boolean[] mAromaticityHandled;
private boolean[] mIsAromatic;
private boolean[] mIsDelocalized;
/**
* Generates the complete set of small rings, which contains all rings
* up to 7 members.
If mode includes LARGE_RINGS, then it determines
* for every atom and bond the size of the smallest ring, which they are
* a member of.
If mode includes AROMATICITY then every small ring
* is checked, whether it is aromatic.
* @param mol
* @param mode one of the public MODE_ options
*/
public RingCollection(ExtendedMolecule mol, int mode) {
mMol = mol;
mRingAtomSet = new ArrayList();
mRingBondSet = new ArrayList();
mAtomRingSize = new int[mMol.getAtoms()];
mBondRingSize = new int[mMol.getBonds()];
mMol.ensureHelperArrays(ExtendedMolecule.cHelperNeighbours);
boolean[] isConfirmedChainAtom = new boolean[mMol.getAtoms()];
boolean[] isConfirmedChainBond = new boolean[mMol.getBonds()];
boolean found;
do { // detect atoms of side chains as non-ring-atoms
found = false;
for (int atom=0; atom highest) {
// if run out of atoms look for new base atom of other fragment
for (int atom=0; atom MAX_LARGE_RING_SIZE)
// return null; // disabled ring size limit, TLS 20130613
for (int i=0; i 1) && candidate == atom1) {
int ringAtom[] = new int[graphLevel[graphAtom[current]]];
int atom = graphAtom[current];
for (int j=0; j MAX_SMALL_RING_SIZE)
return;
for (int i=0; i 1) && candidate == atom1) {
int ringAtom[] = new int[graphLevel[graphAtom[current]]];
int atom = graphAtom[current];
for (int j=0; j ringAtom[i]) {
lowAtom = ringAtom[i];
lowIndex = i;
}
}
int sortedRing[] = new int[ringAtoms];
int leftIndex = (lowIndex > 0) ? lowIndex - 1 : ringAtoms - 1;
int rightIndex = (lowIndex < ringAtoms - 1) ? lowIndex + 1 : 0;
boolean inverse = (ringAtom[leftIndex] < ringAtom[rightIndex]);
for (int i=0; i= ringSize)
index -= ringSize;
while (index < 0)
index += ringSize;
return index;
}
/**
* Returns the position of the electron pair providing hetero atom
* or carbenium atom in case of 5-membered, respective 7-membered
* aromatic ring.
* @param ringNo
* @return position index referring to ringAtom array
*/
public int getHeteroPosition(int ringNo) {
return mHeteroPosition[ringNo];
}
public boolean isAtomMember(int ringNo, int atom) {
int[] ringAtom = mRingAtomSet.get(ringNo);
for (int i=0; i ringSize)
mAtomRingSize[ringAtom[i]] = ringSize;
for (int i=0; i ringSize)
mBondRingSize[ringBond[i]] = ringSize;
}
private int[] getRingBonds(int[] ringAtom) {
int ringAtoms = ringAtom.length;
int ringBond[] = new int[ringAtoms];
for (int i=0; i= 5 && ringBond.length <= 7) {
for (int i=0; i 0) {
annelatedRing[ringMembership[bond] >>> 16]
[ringMembership[bond] & 0x7FFF] = ring;
annelatedRing[ring][i] = (ringMembership[bond] >>> 16);
}
else {
ringMembership[bond] = (ring << 16) + 0x8000 + i;
}
}
}
}
}
int ringsHandled = 0;
int lastRingsHandled = -1;
while (ringsHandled > lastRingsHandled) {
lastRingsHandled = ringsHandled;
for (int ring=0; ring 1
|| mMol.getBondType(ringBond[i]) == Molecule.cBondTypeDelocalized)
bondSequence |= 1;
else {
int annelated = annelatedRing[ringNo][i];
if (annelated != -1) {
if (mAromaticityHandled[annelated]) {
if (mIsAromatic[annelated]) {
bondSequence |= 1;
if (!mIsDelocalized[annelated])
aromaticButNotDelocalizedSequence |= 1;
}
}
else {
unhandledAnnelatedRingFound = true;
}
}
}
}
boolean hasDelocalizationLeak = false;
switch (ringBonds) {
case 5:
final int[] cSequence5Ring = {
10, // 01010
5, // 00101
18, // 10010
9, // 01001
20 }; // 01010
hasDelocalizationLeak = true;
for (int heteroPosition=0; heteroPosition<5; heteroPosition++) {
if ((bondSequence & cSequence5Ring[heteroPosition]) == cSequence5Ring[heteroPosition]) {
switch (mMol.getAtomicNo(ringAtom[heteroPosition])) {
case 6:
if (mMol.getAtomCharge(ringAtom[heteroPosition]) == -1) {
mIsAromatic[ringNo] = true;
mHeteroPosition[ringNo] = heteroPosition;
if ((aromaticButNotDelocalizedSequence & cSequence5Ring[heteroPosition]) == 0)
hasDelocalizationLeak = false;
}
break;
case 7:
if (mMol.getAtomCharge(ringAtom[heteroPosition]) <= 0) {
mIsAromatic[ringNo] = true;
mHeteroPosition[ringNo] = heteroPosition;
}
break;
case 8:
mIsAromatic[ringNo] = true;
mHeteroPosition[ringNo] = heteroPosition;
break;
case 16:
if (mMol.getConnAtoms(ringAtom[heteroPosition]) == 2) {
mIsAromatic[ringNo] = true;
mHeteroPosition[ringNo] = heteroPosition;
}
break;
}
}
}
break;
case 6:
hasDelocalizationLeak = true;
if ((bondSequence & 21) == 21) { // 010101
mIsAromatic[ringNo] = true;
if ((aromaticButNotDelocalizedSequence & 21) == 0)
hasDelocalizationLeak = false;
}
if ((bondSequence & 42) == 42) { // 101010
mIsAromatic[ringNo] = true;
if ((aromaticButNotDelocalizedSequence & 42) == 0)
hasDelocalizationLeak = false;
}
break;
case 7:
final int[] cSequence7Ring = {
42, // 0101010
21, // 0010101
74, // 1001010
37, // 0100101
82, // 1010010
41, // 0101001
84 };// 1010100
hasDelocalizationLeak = true;
for (int carbeniumPosition=0; carbeniumPosition<7; carbeniumPosition++) {
if ((bondSequence & cSequence7Ring[carbeniumPosition]) == cSequence7Ring[carbeniumPosition]) {
if ((mMol.getAtomicNo(ringAtom[carbeniumPosition]) == 6
&& mMol.getAtomCharge(ringAtom[carbeniumPosition]) == 1)
|| (mMol.getAtomicNo(ringAtom[carbeniumPosition]) == 5
&& mMol.getAtomCharge(ringAtom[carbeniumPosition]) == 0)) {
mIsAromatic[ringNo] = true;
mHeteroPosition[ringNo] = carbeniumPosition;
if ((aromaticButNotDelocalizedSequence & cSequence7Ring[carbeniumPosition]) == 0)
hasDelocalizationLeak = false;
}
}
}
break;
}
if (mIsAromatic[ringNo] && !hasDelocalizationLeak)
mIsDelocalized[ringNo] = true;
if (mIsAromatic[ringNo])
return true;
return !unhandledAnnelatedRingFound;
}
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