org.openscience.cdk.aromaticity.PiBondModel Maven / Gradle / Ivy
/*
* Copyright (c) 2013 European Bioinformatics Institute (EMBL-EBI)
* John May
*
* 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 U
*/
package org.openscience.cdk.aromaticity;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.ringsearch.RingSearch;
import static org.openscience.cdk.interfaces.IBond.Order.DOUBLE;
/**
* A simple aromatic model which only allows cyclic pi-bonds to contribute to an
* aromatic system. Lone pairs are not considered and as such molecules like
* furan and pyrrole are non-aromatic. This model is suitable for storing
* aromaticity in the MDL/Mol2 file formats.
*
* @author John May
* @cdk.module standard
*/
final class PiBondModel extends ElectronDonation {
/**{@inheritDoc} */
@Override
int[] contribution(IAtomContainer container, RingSearch ringSearch) {
int n = container.getAtomCount();
int[] electrons = new int[n];
int[] piBonds = new int[n];
// count number of cyclic pi bonds
for (IBond bond : container.bonds()) {
int u = container.indexOf(bond.getBegin());
int v = container.indexOf(bond.getEnd());
if (bond.getOrder() == DOUBLE && ringSearch.cyclic(u, v)) {
piBonds[u]++;
piBonds[v]++;
}
}
// any atom which is adjacent to one (and only one) cyclic
// pi bond contributes 1 electron
for (int i = 0; i < n; i++) {
electrons[i] = piBonds[i] == 1 ? 1 : -1;
}
return electrons;
}
}
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