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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;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* Given a molecule with bond-based double bond configurations - add directional labels to edges
* which do not have it assigned. For example the molecule {@code NC(/C)=C\C} has no directional
* label between the nitrogen and the carbon. Applying this procedure will 'fill-in' missing
* directional information on the edge - {@code N/C(/C)=C\C}.
*
* If required the directional labels in conjugated systems may be adjusted to allow for
* full-specification. Attempting to assign a directional label to the central carbon of {@code
* F/C=C(/F)C(/F)=C/F} creates a conflict. This conflict will be resolved by flipping the labels on
* the second double-bond - {@code F/C=C(/F)\C(\F)=C\F}.
*
* @author John May
*/
final class AddDirectionalLabels
extends AbstractFunction {
enum Status {
COMPLETED,
WAITING,
INVALID
}
/**
* Transform all implicit up/down to their explicit type. 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)
throws InvalidSmilesException {
List doublebonds = new ArrayList<>();
// change edges (only changed added to replacement)
for (int u = 0; u < g.order(); u++) {
final int d = g.degree(u);
for (int j = 0; j < d; ++j) {
final Edge e = g.edgeAt(u, j);
int v = e.other(u);
if (v > u && e.bond() == Bond.DOUBLE) {
if (g.degree(u) < 2 || g.degree(v) < 2)
continue;
if (g.degree(u) + g.degree(v) > 4)
doublebonds.add(e);
}
}
}
if (doublebonds.isEmpty())
return g;
final Set remain = new HashSet<>(doublebonds);
final Map replacements = new HashMap<>();
boolean altered;
final Set completed = new HashSet<>();
do {
altered = false;
for (final Edge e : remain) {
Status status = replaceImplWithExpl(g, e, replacements);
if (status != Status.WAITING) {
completed.add(e);
altered = true;
}
}
remain.removeAll(completed);
completed.clear();
} while (altered && !remain.isEmpty());
// completed bonds, we can't do anything
if (remain.size() == doublebonds.size())
return g;
// cleanup any remaining edges that have 'dangling' directional labels
for (Edge e : remain) {
int u = e.either();
int v = e.other(u);
final int d = g.degree(u);
for (int j = 0; j < d; ++j) {
final Edge f = g.edgeAt(u, j);
if (isDirectional(f, replacements) && safeToClean(g, f.other(u), replacements)) {
replacements.put(f,
new Edge(u, f.other(u), Bond.IMPLICIT));
}
}
final int d2 = g.degree(v);
for (int j = 0; j < d2; ++j) {
final Edge f = g.edgeAt(v, j);
if (isDirectional(f, replacements) && safeToClean(g, f.other(v), replacements))
replacements.put(f,
new Edge(v, f.other(v), Bond.IMPLICIT));
}
}
Graph h = new Graph(g.order());
h.addFlags(g.getFlags(0xffffffff));
// copy atom/topology information this is unchanged
for (int u = 0; u < g.order(); u++) {
h.addAtom(g.atom(u));
h.addTopology(g.topologyOf(u));
}
// append the edges, replacing any which need to be changed
for (int u = 0; u < g.order(); u++) {
final int d = g.degree(u);
for (int j = 0; j < d; ++j) {
Edge e = g.edgeAt(u, j);
if (e.other(u) < u) {
Edge replacement = replacements.get(e);
if (replacement != null)
e = replacement;
h.addEdge(e);
}
}
}
return h.sort(new Graph.CanOrderFirst());
}
private boolean isDirectional(Edge f, Map replacements) {
if (f.bond().directional())
return true;
Edge g = replacements.get(f);
return g != null && g.bond().directional();
}
boolean safeToClean(Graph g, int v, Map replacements) {
final int d = g.degree(v);
for (int j = 0; j < d; ++j) {
final Edge e = g.edgeAt(v, j);
if (e.bond().order() == 2) {
int w = e.other(v);
final int d2 = g.degree(w);
for (int j2 = 0; j2 < d2; ++j2) {
final Edge f = g.edgeAt(w, j2);
if (isDirectional(f, replacements))
return false;
}
}
}
return true;
}
/**
* Given a double bond edge traverse the neighbors of both endpoints and accumulate any explicit
* replacements in the 'acc' accumulator.
*
* @param g the chemical graph
* @param e a edge in the graph ('double bond type')
* @param acc accumulator for new edges
* @throws InvalidSmilesException thrown if the edge could not be converted
*/
private Status replaceImplWithExpl(Graph g,
Edge e,
Map acc)
throws InvalidSmilesException {
int u = e.either(), v = e.other(u);
Status ustat = replaceImplWithExpl(g, e, u, acc);
Status vstat = replaceImplWithExpl(g, e, v, acc);
if (ustat == vstat)
return ustat;
else if (ustat == Status.INVALID && vstat != Status.WAITING)
return Status.INVALID;
else if (vstat == Status.INVALID && ustat != Status.WAITING)
return Status.INVALID;
else
return Status.WAITING;
}
/**
* Given a double bond edge traverse the neighbors of one of the endpoints and accumulate any
* explicit replacements in the 'acc' accumulator.
*
* @param g the chemical graph
* @param e a edge in the graph ('double bond type')
* @param u a endpoint of the edge 'e'
* @param acc accumulator for new edges
* @return does the edge 'e' need to be reconsidered later
* @throws InvalidSmilesException thrown if the edge could not be converted
*/
private Status replaceImplWithExpl(Graph g,
Edge e,
int u,
Map acc)
throws InvalidSmilesException {
Edge implicit = null;
Edge explicit = null;
for (Edge f : g.edges(u)) {
final Edge f2 = acc.containsKey(f) ? acc.get(f) : f;
switch (f2.bond(u)) {
case SINGLE:
case IMPLICIT:
case IMPLICIT_AROMATIC:
if (implicit != null)
return Status.WAITING;
implicit = f;
break;
case DOUBLE:
case DOUBLE_AROMATIC:
if (!f.equals(e))
return Status.COMPLETED;
break;
case UP:
case DOWN:
if (explicit != null) {
if (acc.containsKey(explicit))
explicit = acc.get(explicit);
// original bonds are invalid
if ((f.bond() == Bond.UP || f.bond() == Bond.DOWN) && explicit.bond(u).inverse() != f.bond(u)) {
return Status.INVALID;
}
if (explicit.bond(u).inverse() != f2.bond(u)) {
acc.put(f, f2.inverse());
BitSet visited = new BitSet();
visited.set(u);
invertExistingDirectionalLabels(g, visited, acc, f2
.other(u));
}
return Status.COMPLETED;
}
explicit = f;
break;
}
}
// no implicit don't do anything
if (implicit == null)
return Status.COMPLETED;
// no explicit bond we might get one in future...?
if (explicit == null)
return Status.WAITING;
if (acc.containsKey(explicit))
explicit = acc.get(explicit);
int v = implicit.other(u);
Edge existing = acc.put(implicit, new Edge(u,
v,
explicit.bond(u)
.inverse()));
if (existing != null && existing.bond(u) != explicit.bond(u).inverse()) {
throw new InvalidSmilesException("unable to assign explict type for " + implicit);
}
return Status.COMPLETED;
}
private void invertExistingDirectionalLabels(Graph g,
BitSet visited,
Map replacement,
int u) {
visited.set(u);
if (g.topologyOf(u) == null)
return;
for (Edge e : g.edges(u)) {
int v = e.other(u);
if (!visited.get(v)) {
Edge f = replacement.get(e);
if (f != null && f.bond().directional()) {
replacement.put(e,
f.inverse());
}
else if (e.bond().directional()) {
replacement.put(e,
e.inverse());
}
invertExistingDirectionalLabels(g, visited, replacement, v);
}
}
}
}
