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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;
public class AromaticityResolver {
ExtendedMolecule mMol;
private boolean mAllHydrogensAreExplicit;
private boolean[] mIsDelocalizedAtom,mIsDelocalizedBond;
private int mAromaticAtoms,mAromaticBonds,mPiElectronsAdded;
/**
* Creates a new AromaticityResolver for molecule mol.
* @param mol
*/
public AromaticityResolver(ExtendedMolecule mol) {
mMol = mol;
}
/**
* This method promotes all necessary bonds of the defined delocalized part of the molecule
* from single to double bonds in order to create a valid delocalized system
* of conjugated single and double bonds.
* The delocalized part of the molecule may be defined by passing an array
* to isAromaticBond that has all bonds flagged, which are part of a delocalized area.
* In this case these bonds are assumed to have bond type cBondTypeSingle.
* Alternatively, one may pass null and indicate affected bonds with bond type cBondTypeDelocalized.
* Non-cyclic atom chains defined to be delocalized are treated depending
* on whether we have a molecule or a query fragment. For fragments the respective bond
* types will be set to cBondTypeDelocalized; for molecules the chain will
* have alternating single and double bonds starting with double at a non-ring end.
* @return true if all bonds of the delocalized area could be consistently converted.
*/
public boolean locateDelocalizedDoubleBonds(boolean[] isAromaticBond) {
return locateDelocalizedDoubleBonds(isAromaticBond, false, false);
}
/**
* This method promotes all necessary bonds of the defined delocalized part of the molecule
* from single to double bonds in order to create a valid delocalized system
* of conjugated single and double bonds.
* The delocalized part of the molecule may be defined by passing an array
* to isAromaticBond that has all bonds flagged, which are part of a delocalized area.
* In this case these bonds are assumed to have bond type cBondTypeSingle.
* Alternatively, one may pass null and indicate affected bonds with bond type cBondTypeDelocalized.
* Non-cyclic atom chains defined to be delocalized are treated depending
* on whether we have a molecule or a query fragment. For fragments the respective bond
* types will be set to cBondTypeDelocalized; for molecules the chain will
* have alternating single and double bonds starting with double at a non-ring end.
* @param isAromaticBond if null, then bond type cBondTypeDelocalized is used to indicate delocalized bonds
* @param mayChangeAtomCharges true if input molecule doesn't carry atom charges and these may be added to achieve aromaticity
* @param allHydrogensAreExplicit true this method can rely on all hydrogens being explicitly present
* @return true if all bonds of the delocalized area could be consistently converted.
*/
public boolean locateDelocalizedDoubleBonds(boolean[] isAromaticBond, boolean mayChangeAtomCharges, boolean allHydrogensAreExplicit) {
mMol.ensureHelperArrays(Molecule.cHelperNeighbours);
if (isAromaticBond != null) {
mIsDelocalizedBond = isAromaticBond;
}
else {
mIsDelocalizedBond = new boolean[mMol.getBonds()];
for (int bond=0; bond 1)
return true;
return false;
}
private int getNextOuterDelocalizedConnIndex(int atom, int previousAtom, int[] sharedDelocalizedRingCount) {
for (int i=0; i 0))
protectAtom(atom);
}
private void protectAtom(int atom) {
if (mIsDelocalizedAtom[atom]) {
mIsDelocalizedAtom[atom] = false;
mAromaticAtoms--;
}
for (int i=0; i 1) { // bridgehead atom
if (!checkAtomTypePi1(atom, false)) {
possible = false;
break;
}
}
else { // non-bridgehead in 5- or 7-membered ring
int priority = (ringSize == 5) ?
checkAtomTypeLeak5(atom, false) : checkAtomTypeLeak7(atom, false);
if (!checkAtomTypePi1(atom, false)) {
if (leakPriority == 10) {
possible = false;
break;
}
leakAtom = atom;
leakPriority = 20; // MAX
}
else if (leakPriority < priority) {
leakPriority = priority;
leakAtom = atom;
}
}
}
if (possible) {
for (int atom : ringSet.getRingAtoms(ring)) {
if (atom == leakAtom) {
if (ringSize == 5)
checkAtomTypeLeak5(atom, true); // 5-membered
else
checkAtomTypeLeak7(atom, true); // 3- or 7-membered
protectAtom(atom);
}
else {
checkAtomTypePi1(atom, true);
}
}
}
}
}
}
// From here locate delocalized strings of atoms, which are not member
// of an aromatic ring. Protect preferred atoms and add obvious atom charges.
// count for every atom the number of delocalized bonds attached
int[] delocalizedNeighbourCount = new int[mMol.getAtoms()];
boolean[] hasMetalLigandBond = new boolean[mMol.getAtoms()];
for (int bond=0; bond 0) {
checkAtomTypeLeakNonRing(maxAtom, true);
protectAtom(maxAtom);
}
}
}
}
}
}
/**
* Checks, whether the atom is compatible with an aromatic atom of the type
* that carries one half of a delocalized double bond.
* @param atom
* @param correctCharge if true then may add a charge to make the atom compatible
* @return
*/
private boolean checkAtomTypePi1(int atom, boolean correctCharge) {
int atomicNo = mMol.getAtomicNo(atom);
if ((atomicNo >=5 && atomicNo <= 8)
|| atomicNo == 15 || atomicNo == 16 || atomicNo == 33 || atomicNo == 34) { // P,S,As,Se
int freeValence = mMol.getFreeValence(atom);
if (freeValence == 1 || freeValence == 2) // we allow one more free valence, because the atom may have a missing charge
return true;
if (mMol.getAtomCharge(atom) == 0) {
if ((atomicNo == 15 || atomicNo == 33) && freeValence == 3) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return true;
}
if ((atomicNo == 16 || atomicNo == 34) && freeValence == 4) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return true;
}
if (atomicNo == 5 && freeValence == 0) {
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return true;
}
if ((atomicNo == 7 || atomicNo == 8) && freeValence == 0) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return true;
}
}
}
return false;
}
/**
* Checks, whether the atom is compatible with that aromatic atom of
* a 5-membered ring that supplies the additional electron pair.
* @param atom
* @param correctCharge if true then may add a charge to make the atom compatible
* @return 0 (not compatible) or priority to be used (higher numbers have higher priority)
*/
private int checkAtomTypeLeak5(int atom, boolean correctCharge) {
if (mMol.getAtomicNo(atom) == 7) {
if (mMol.getAllConnAtoms(atom) == 3)
return 6;
else if (mMol.getConnAtoms(atom) == 2)
return 4;
}
else if (mMol.getAtomicNo(atom) == 8) {
return 10;
}
else if (mMol.getAtomicNo(atom) == 15 || mMol.getAtomicNo(atom) == 33) {
if (mMol.getConnAtoms(atom) == 3)
return 8;
}
else if (mMol.getAtomicNo(atom) == 16 || mMol.getAtomicNo(atom) == 34) {
if (mMol.getConnAtoms(atom) == 2)
return 12;
}
else if (mMol.getAtomicNo(atom) == 6) {
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return (mMol.getAllConnAtoms(atom) != mMol.getAllConnAtomsPlusMetalBonds(atom)) ? 2 : 3;
}
return 0;
}
/**
* Checks, whether the atom is compatible with that aromatic atom of
* a 3- or 7-membered ring that supplies the empty orbital.
* @param atom
* @param correctCharge if true then may add a charge to make the atom compatible
* @return 0 (not compatible) or priority to be used (higher numbers have higher priority)
*/
private int checkAtomTypeLeak7(int atom, boolean correctCharge) {
if (mAllHydrogensAreExplicit) {
if (mMol.getAllConnAtoms(atom) != 3)
return 0;
}
else {
if (mMol.getAllConnAtoms(atom) > 3)
return 0;
}
if (mMol.getAtomicNo(atom) == 6) {
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return 2;
}
if (mMol.getAtomicNo(atom) == 5) {
return 4;
}
return 0;
}
/**
* Checks, whether the atom is compatible with the (typically charged) atom
* in a delocalized chain of an odd number of atoms that does not carry a pi bond.
* @param atom
* @param correctCharge if true then may add a charge to make the atom compatible
* @return 0 (not compatible) or priority to be used (higher numbers have higher priority)
*/
private int checkAtomTypeLeakNonRing(int atom, boolean correctCharge) {
if (mMol.getAtomCharge(atom) != 0)
return 0;
if (mAllHydrogensAreExplicit) {
if (mMol.getAtomicNo(atom) == 5) {
if (mMol.getOccupiedValence(atom) != 2)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return 1;
}
if (mMol.getAtomicNo(atom) == 7) {
if (mMol.getOccupiedValence(atom) != 2)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 6 : 3;
}
if (mMol.getAtomicNo(atom) == 8) {
if (mMol.getOccupiedValence(atom) != 1)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 7 : 4;
}
if (mMol.getAtomicNo(atom) == 16) {
if (mMol.getOccupiedValence(atom) != 1)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 5 : 2;
}
if (mMol.getAtomicNo(atom) == 34) {
if (mMol.getOccupiedValence(atom) != 1)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 4 : 1;
}
}
else {
if (mMol.getAtomicNo(atom) == 5) {
if (mMol.getOccupiedValence(atom) > 2)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, 1);
return 1;
}
if (mMol.getAtomicNo(atom) == 7) {
if (mMol.getOccupiedValence(atom) > 2)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 5 : 3;
}
if (mMol.getAtomicNo(atom) == 8) {
if (mMol.getOccupiedValence(atom) > 1)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 7 : 4;
}
if (mMol.getAtomicNo(atom) == 16) {
if (mMol.getOccupiedValence(atom) > 1)
return 0;
if (correctCharge)
mMol.setAtomCharge(atom, -1);
return hasMetalNeighbour(atom) ? 5 : 2;
}
}
return 0;
}
private boolean hasMetalNeighbour(int atom) {
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy