org.openscience.cdk.fingerprint.HybridizationFingerprinter Maven / Gradle / Ivy
/* Copyright (C) 2002-2007 Christoph Steinbeck
* 2009-2011 Egon Willighagen
*
* 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.fingerprint;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.tools.periodictable.PeriodicTable;
/**
* Generates a fingerprint for a given {@link IAtomContainer}. Fingerprints are
* one-dimensional bit arrays, where bits are set according to a the occurrence
* of a particular structural feature (See for example the Daylight inc. theory
* manual for more information). Fingerprints allow for a fast screening step to
* exclude candidates for a substructure search in a database. They are also a
* means for determining the similarity of chemical structures.
*
* A fingerprint is generated for an AtomContainer with this code:
* Molecule molecule = new Molecule();
* IFingerprinter fingerprinter =
* new HybridizationFingerprinter();
* BitSet fingerprint = fingerprinter.getFingerprint(molecule);
* fingerprint.size(); // returns 1024 by default
* fingerprint.length(); // returns the highest set bit
*
*
* The FingerPrinter assumes that hydrogens are explicitly given!
* Furthermore, if pseudo atoms or atoms with malformed symbols are present,
* their atomic number is taken as one more than the last element currently
* supported in {@link PeriodicTable}.
*
*
Unlike the {@link Fingerprinter}, this fingerprinter does not take into
* account aromaticity. Instead, it takes into account SP2
* {@link Hybridization}.
*
* @cdk.keyword fingerprint
* @cdk.keyword similarity
* @cdk.module standard
* @cdk.githash
*/
public class HybridizationFingerprinter extends Fingerprinter implements IFingerprinter {
/**
* Creates a fingerprint generator of length DEFAULT_SIZE
* and with a search depth of DEFAULT_SEARCH_DEPTH.
*/
public HybridizationFingerprinter() {
this(DEFAULT_SIZE, DEFAULT_SEARCH_DEPTH);
}
public HybridizationFingerprinter(int size) {
this(size, DEFAULT_SEARCH_DEPTH);
}
/**
* Constructs a fingerprint generator that creates fingerprints of
* the given size, using a generation algorithm with the given search
* depth.
*
* @param size The desired size of the fingerprint
* @param searchDepth The desired depth of search
*/
public HybridizationFingerprinter(int size, int searchDepth) {
super(size, searchDepth);
}
/**
* Gets the bond Symbol attribute of the Fingerprinter class.
*
* @return The bondSymbol value
*/
protected String getBondSymbol(IBond bond) {
String bondSymbol = "";
if (bond.getOrder() == IBond.Order.SINGLE) {
if (isSP2Bond(bond)) {
bondSymbol = ":";
} else {
bondSymbol = "-";
}
} else if (bond.getOrder() == IBond.Order.DOUBLE) {
if (isSP2Bond(bond)) {
bondSymbol = ":";
} else {
bondSymbol = "=";
}
} else if (bond.getOrder() == IBond.Order.TRIPLE) {
bondSymbol = "#";
} else if (bond.getOrder() == IBond.Order.QUADRUPLE) {
bondSymbol = "*";
}
return bondSymbol;
}
/**
* Returns true if the bond binds two atoms, and both atoms are SP2.
*/
private boolean isSP2Bond(IBond bond) {
return bond.getAtomCount() == 2 && bond.getBegin().getHybridization() == Hybridization.SP2
&& bond.getEnd().getHybridization() == Hybridization.SP2;
}
}