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/*
* Copyright (c) 2013, European Bioinformatics Institute (EMBL-EBI)
* 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.
*
* 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.
*
* The views and conclusions contained in the software and documentation are those
* of the authors and should not be interpreted as representing official policies,
* either expressed or implied, of the FreeBSD Project.
*/
package uk.ac.ebi.beam;
/**
* Convert a chemical graph with implicit edge labels to one with explicit
* single or aromatic edge labels.
*
* @author John May
*/
final class ImplicitToExplicit extends AbstractFunction {
/**
* Transform all implicit to explicit bonds. The original graph is
* unmodified
*
* @param g a chemical graph
* @return new chemical graph but with all explicit bonds
*/
public Graph apply(final Graph g) {
Graph h = new Graph(g.order());
// copy atom/topology information
for (int u = 0; u < g.order(); u++) {
h.addAtom(g.atom(u));
h.addTopology(g.topologyOf(u));
}
// apply edges
for (int u = 0; u < g.order(); u++) {
for (final Edge e : g.edges(u)) {
if (e.other(u) > u)
h.addEdge(toExplicitEdge(g, e));
}
}
return h;
}
/**
* Given a chemical graph and an edge in that graph, return the explicit
* form of that edge. Neither the graph or the edge is modified, if the edge
* is already explicit then 'e' is returned.
*
* @param g chemical graph
* @param e an edge of g
* @return the edge with specified explicit bond type
*/
static Edge toExplicitEdge(final Graph g, final Edge e) {
final int u = e.either(), v = e.other(u);
if (e.bond() == Bond.IMPLICIT) {
return new Edge(u, v,
type(g.atom(u),
g.atom(v)));
}
return e;
}
/**
* Given two atoms which are implicitly connected determine the explicit
* bond type. The type is 'aromatic' if both atoms are aromatic, if either
* or both atoms are non-aromatic then the bond type is 'single'.
*
* @param u an atom
* @param v another atom (connected to u)
* @return the bond type
*/
static Bond type(Atom u, Atom v) {
return u.aromatic() && v.aromatic() ? Bond.AROMATIC : Bond.SINGLE;
}
}
