org.openscience.cdk.tools.SmilesValencyChecker Maven / Gradle / Ivy
/* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.tools;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* Small customization of ValencyHybridChecker suggested by Todd Martin
* specially tuned for SMILES parsing.
*
* @author Egon Willighagen
* @cdk.created 2004-06-12
* @cdk.keyword atom, valency
* @cdk.module valencycheck
* @cdk.githash
*/
public class SmilesValencyChecker implements IValencyChecker, IDeduceBondOrderTool {
private String atomTypeList = null;
protected AtomTypeFactory structgenATF;
protected static ILoggingTool logger = LoggingToolFactory.createLoggingTool(SmilesValencyChecker.class);
public SmilesValencyChecker() {
this("org/openscience/cdk/dict/data/cdk-atom-types.owl");
}
public SmilesValencyChecker(String atomTypeList) {
this.atomTypeList = atomTypeList;
logger.info("Using configuration file: ", atomTypeList);
}
/**
* Saturates a molecule by setting appropriate bond orders.
*
* @cdk.keyword bond order, calculation
*
* @cdk.created 2003-10-03
*/
@Override
public void saturate(IAtomContainer atomContainer) throws CDKException {
logger.info("Saturating atomContainer by adjusting bond orders...");
boolean allSaturated = allSaturated(atomContainer);
if (!allSaturated) {
logger.info("Saturating bond orders is needed...");
IBond[] bonds = new IBond[atomContainer.getBondCount()];
for (int i = 0; i < bonds.length; i++)
bonds[i] = atomContainer.getBond(i);
boolean succeeded = saturate(bonds, atomContainer);
if (!succeeded) {
throw new CDKException("Could not saturate this atomContainer!");
}
}
}
/**
* Saturates a set of Bonds in an AtomContainer.
*/
public boolean saturate(IBond[] bonds, IAtomContainer atomContainer) throws CDKException {
logger.debug("Saturating bond set of size: ", bonds.length);
boolean bondsAreFullySaturated = false;
if (bonds.length > 0) {
IBond bond = bonds[0];
// determine bonds left
int leftBondCount = bonds.length - 1;
IBond[] leftBonds = new IBond[leftBondCount];
System.arraycopy(bonds, 1, leftBonds, 0, leftBondCount);
// examine this bond
logger.debug("Examining this bond: ", bond);
if (isSaturated(bond, atomContainer)) {
logger.debug("OK, bond is saturated, now try to saturate remaining bonds (if needed)");
bondsAreFullySaturated = saturate(leftBonds, atomContainer);
} else if (isUnsaturated(bond, atomContainer)) {
logger.debug("Ok, this bond is unsaturated, and can be saturated");
// two options now:
// 1. saturate this one directly
// 2. saturate this one by saturating the rest
logger.debug("Option 1: Saturating this bond directly, then trying to saturate rest");
// considering organic bonds, the max order is 3, so increase twice
boolean bondOrderIncreased = saturateByIncreasingBondOrder(bond, atomContainer);
bondsAreFullySaturated = bondOrderIncreased && saturate(bonds, atomContainer);
if (bondsAreFullySaturated) {
logger.debug("Option 1: worked");
} else {
logger.debug("Option 1: failed. Trying option 2.");
logger.debug("Option 2: Saturing this bond by saturating the rest");
// revert the increase (if succeeded), then saturate the rest
if (bondOrderIncreased) unsaturateByDecreasingBondOrder(bond);
bondsAreFullySaturated = saturate(leftBonds, atomContainer) && isSaturated(bond, atomContainer);
if (!bondsAreFullySaturated) logger.debug("Option 2: failed");
}
} else {
logger.debug("Ok, this bond is unsaturated, but cannot be saturated");
// try recursing and see if that fixes things
bondsAreFullySaturated = saturate(leftBonds, atomContainer) && isSaturated(bond, atomContainer);
}
} else {
bondsAreFullySaturated = true; // empty is saturated by default
}
return bondsAreFullySaturated;
}
public boolean unsaturateByDecreasingBondOrder(IBond bond) {
if (bond.getOrder() != IBond.Order.SINGLE) {
bond.setOrder(BondManipulator.decreaseBondOrder(bond.getOrder()));
return true;
} else {
return false;
}
}
/**
* Returns whether a bond is unsaturated. A bond is unsaturated if
* all Atoms in the bond are unsaturated.
*/
public boolean isUnsaturated(IBond bond, IAtomContainer atomContainer) throws CDKException {
logger.debug("isBondUnsaturated?: ", bond);
IAtom[] atoms = BondManipulator.getAtomArray(bond);
boolean isUnsaturated = true;
for (int i = 0; i < atoms.length && isUnsaturated; i++) {
isUnsaturated = isUnsaturated && !isSaturated(atoms[i], atomContainer);
}
logger.debug("Bond is unsaturated?: ", isUnsaturated);
return isUnsaturated;
}
/**
* Tries to saturate a bond by increasing its bond orders by 1.0.
*
* @return true if the bond could be increased
*/
public boolean saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer) throws CDKException {
IAtom[] atoms = BondManipulator.getAtomArray(bond);
IAtom atom = atoms[0];
IAtom partner = atoms[1];
logger.debug(" saturating bond: ", atom.getSymbol(), "-", partner.getSymbol());
IAtomType[] atomTypes1 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(atom.getSymbol());
IAtomType[] atomTypes2 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(partner.getSymbol());
for (int atCounter1 = 0; atCounter1 < atomTypes1.length; atCounter1++) {
IAtomType aType1 = atomTypes1[atCounter1];
logger.debug(" condidering atom type: ", aType1);
if (couldMatchAtomType(atomContainer, atom, aType1)) {
logger.debug(" trying atom type: ", aType1);
for (int atCounter2 = 0; atCounter2 < atomTypes2.length; atCounter2++) {
IAtomType aType2 = atomTypes2[atCounter2];
logger.debug(" condidering partner type: ", aType1);
if (couldMatchAtomType(atomContainer, partner, atomTypes2[atCounter2])) {
logger.debug(" with atom type: ", aType2);
if (BondManipulator.isLowerOrder(bond.getOrder(), aType2.getMaxBondOrder())
&& BondManipulator.isLowerOrder(bond.getOrder(), aType1.getMaxBondOrder())) {
bond.setOrder(BondManipulator.increaseBondOrder(bond.getOrder()));
logger.debug("Bond order now ", bond.getOrder());
return true;
}
}
}
}
}
return false;
}
/**
* Returns whether a bond is saturated. A bond is saturated if
* both Atoms in the bond are saturated.
*/
public boolean isSaturated(IBond bond, IAtomContainer atomContainer) throws CDKException {
logger.debug("isBondSaturated?: ", bond);
IAtom[] atoms = BondManipulator.getAtomArray(bond);
boolean isSaturated = true;
for (int i = 0; i < atoms.length; i++) {
logger.debug("isSaturated(Bond, AC): atom I=", i);
isSaturated = isSaturated && isSaturated(atoms[i], atomContainer);
}
logger.debug("isSaturated(Bond, AC): result=", isSaturated);
return isSaturated;
}
/**
* Determines of all atoms on the AtomContainer are saturated.
*/
@Override
public boolean isSaturated(IAtomContainer container) throws CDKException {
return allSaturated(container);
}
public boolean allSaturated(IAtomContainer ac) throws CDKException {
logger.debug("Are all atoms saturated?");
for (int f = 0; f < ac.getAtomCount(); f++) {
if (!isSaturated(ac.getAtom(f), ac)) {
return false;
}
}
return true;
}
/**
* Determines if the atom can be of type AtomType. That is, it sees if this
* AtomType only differs in bond orders, or implicit hydrogen count.
*/
public boolean couldMatchAtomType(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, IAtomType type) {
logger.debug("couldMatchAtomType: ... matching atom ", atom, " vs ", type);
int hcount = atom.getImplicitHydrogenCount();
int charge = atom.getFormalCharge();
if (charge == type.getFormalCharge()) {
logger.debug("couldMatchAtomType: formal charge matches...");
// if (atom.getHybridization() == type.getHybridization()) {
// logger.debug("couldMatchAtomType: hybridization is OK...");
if (bondOrderSum + hcount <= type.getBondOrderSum()) {
logger.debug("couldMatchAtomType: bond order sum is OK...");
if (!BondManipulator.isHigherOrder(maxBondOrder, type.getMaxBondOrder())) {
logger.debug("couldMatchAtomType: max bond order is OK... We have a match!");
return true;
}
} else {
logger.debug("couldMatchAtomType: no match", "" + (bondOrderSum + hcount), " > ",
"" + type.getBondOrderSum());
}
// }
} else {
logger.debug("couldMatchAtomType: formal charge does NOT match...");
}
logger.debug("couldMatchAtomType: No Match");
return false;
}
/**
* Calculates the number of hydrogens that can be added to the given atom to fullfil
* the atom's valency. It will return 0 for PseudoAtoms, and for atoms for which it
* does not have an entry in the configuration file.
*/
public int calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder,
int neighbourCount) throws CDKException {
int missingHydrogens = 0;
if (atom instanceof IPseudoAtom) {
logger.debug("don't figure it out... it simply does not lack H's");
return 0;
}
logger.debug("Calculating number of missing hydrogen atoms");
// get default atom
IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
if (atomTypes.length == 0) {
logger.warn("Element not found in configuration file: ", atom);
return 0;
}
logger.debug("Found atomtypes: ", atomTypes.length);
for (int f = 0; f < atomTypes.length; f++) {
IAtomType type = atomTypes[f];
if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type)) {
logger.debug("This type matches: ", type);
int formalNeighbourCount = type.getFormalNeighbourCount();
if (type.getHybridization() == CDKConstants.UNSET) {
missingHydrogens = (int) (type.getBondOrderSum() - bondOrderSum);
} else if (type.getHybridization() == Hybridization.SP3) {
missingHydrogens = formalNeighbourCount - neighbourCount;
} else if (type.getHybridization() == Hybridization.SP2) {
missingHydrogens = formalNeighbourCount - neighbourCount;
} else if (type.getHybridization() == Hybridization.SP1) {
missingHydrogens = formalNeighbourCount - neighbourCount;
} else {
missingHydrogens = (int) (type.getBondOrderSum() - bondOrderSum);
}
break;
}
}
logger.debug("missing hydrogens: ", missingHydrogens);
return missingHydrogens;
}
/**
* Checks whether an Atom is saturated by comparing it with known AtomTypes.
* It returns true if the atom is an PseudoAtom and when the element is not in the list.
*/
@Override
public boolean isSaturated(IAtom atom, IAtomContainer container) throws CDKException {
if (atom instanceof IPseudoAtom) {
logger.debug("don't figure it out... it simply does not lack H's");
return true;
}
IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol());
if (atomTypes.length == 0) {
logger.warn("Missing entry in atom type list for ", atom.getSymbol());
return true;
}
double bondOrderSum = container.getBondOrderSum(atom);
IBond.Order maxBondOrder = container.getMaximumBondOrder(atom);
int hcount = atom.getImplicitHydrogenCount();
int charge = atom.getFormalCharge();
logger.debug("Checking saturation of atom ", atom.getSymbol());
logger.debug("bondOrderSum: ", bondOrderSum);
logger.debug("maxBondOrder: ", maxBondOrder);
logger.debug("hcount: ", hcount);
logger.debug("charge: ", charge);
boolean elementPlusChargeMatches = false;
for (int f = 0; f < atomTypes.length; f++) {
IAtomType type = atomTypes[f];
if (couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type)) {
if (bondOrderSum + hcount == type.getBondOrderSum()
&& !BondManipulator.isHigherOrder(maxBondOrder, type.getMaxBondOrder())) {
logger.debug("We have a match: ", type);
logger.debug("Atom is saturated: ", atom.getSymbol());
return true;
} else {
// ok, the element and charge matche, but unfulfilled
elementPlusChargeMatches = true;
}
} // else: formal charges don't match
}
if (elementPlusChargeMatches) {
logger.debug("No, atom is not saturated.");
return false;
}
// ok, the found atom was not in the list
logger.error("Could not find atom type!");
throw new CDKException("The atom with element " + atom.getSymbol() + " and charge " + charge + " is not found.");
}
public int calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container) throws CDKException {
return this.calculateNumberOfImplicitHydrogens(atom, container.getBondOrderSum(atom),
container.getMaximumBondOrder(atom), container.getConnectedAtomsCount(atom));
}
protected AtomTypeFactory getAtomTypeFactory(IChemObjectBuilder builder) throws CDKException {
if (structgenATF == null) {
try {
structgenATF = AtomTypeFactory.getInstance(atomTypeList, builder);
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Could not instantiate AtomTypeFactory!", exception);
}
}
return structgenATF;
}
/**
* Determines if the atom can be of type AtomType.
*/
public boolean couldMatchAtomType(IAtomContainer container, IAtom atom, IAtomType type) {
double bondOrderSum = container.getBondOrderSum(atom);
IBond.Order maxBondOrder = container.getMaximumBondOrder(atom);
return couldMatchAtomType(atom, bondOrderSum, maxBondOrder, type);
}
}
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