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Commit 2f8a82f5 authored by Andrius Merkys's avatar Andrius Merkys
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New upstream version 1.3.6

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core/pom.xml
+ 1
− 1
View file @ 2f8a82f5
......@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
<version>1.3.5</version>
<version>1.3.6</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......
core/src/main/java/uk/ac/ebi/beam/Bond.java
+ 28
− 0
View file @ 2f8a82f5
......@@ -106,6 +106,34 @@ public enum Bond {
return UP;
}
@Override boolean directional() {
return true;
}
},
/**
* This is an internal quirk to allow the aromaticity of input to be preserved when
* we kekulize. The up/down bonds may be between aromatic atoms:
* {@code O=c1cccc\c1=C/C} Since the double bond is exo, the / \ must be aromatic.
*/
UP_AROMATIC("/", 1) {
@Override public Bond inverse() {
return DOWN_AROMATIC;
}
@Override boolean directional() {
return true;
}
},
/**
* This is an internal quirk to allow the aromaticity of input to be preserved when
* we kekulize. The up/down bonds may be between aromatic atoms:
* {@code O=c1cccc\c1=C/C} Since the double bond is exo, the / \ must be aromatic.
*/
DOWN_AROMATIC("\\", 1) {
@Override public Bond inverse() {
return UP_AROMATIC;
}
@Override boolean directional() {
return true;
}
......
core/src/main/java/uk/ac/ebi/beam/Localise.java
+ 14
− 0
View file @ 2f8a82f5
......@@ -95,6 +95,20 @@ final class Localise {
int v = e.other(u);
if (v < u) {
switch (e.bond()) {
case UP:
case UP_AROMATIC:
if (aromatic.get(u) && aromatic.get(v))
e.bond(Bond.UP_AROMATIC);
else
e.bond(Bond.UP);
break;
case DOWN:
case DOWN_AROMATIC:
if (aromatic.get(u) && aromatic.get(v))
e.bond(Bond.DOWN_AROMATIC);
else
e.bond(Bond.DOWN);
break;
case SINGLE:
if (aromatic.get(u) && aromatic.get(v)) {
e.bond(Bond.SINGLE);
......
core/src/main/java/uk/ac/ebi/beam/Parser.java
+ 150
− 82
View file @ 2f8a82f5
......@@ -46,26 +46,38 @@ import static java.util.Map.Entry;
*/
final class Parser {
/** Keep track of branching. */
/**
* Keep track of branching.
*/
private final IntStack stack = new IntStack(10);
/** Molecule being loaded. */
/**
* Molecule being loaded.
*/
private final Graph g;
/** Keep track of ring information. */
/**
* Keep track of ring information.
*/
private RingBond[] rings = new RingBond[10];
/** Local arrangement for ring openings. */
/**
* Local arrangement for ring openings.
*/
private Map<Integer, LocalArrangement> arrangement
= new HashMap<Integer, LocalArrangement>(5);
private Map<Integer, Configuration> configurations
= new HashMap<Integer, Configuration>(5);
/** Current bond. */
/**
* Current bond.
*/
private Bond bond = Bond.IMPLICIT;
/** Current configuration. */
/**
* Current configuration.
*/
private Configuration configuration = Configuration.UNKNOWN;
......@@ -76,16 +88,20 @@ final class Parser {
*/
private Set<Integer> start = new TreeSet<Integer>();
/** Number of open rings - all rings should be closed. */
/**
* Number of open rings - all rings should be closed.
*/
private int openRings = 0;
/** Strict parsing. */
/**
* Strict parsing.
*/
private final boolean strict;
private BitSet checkDirectionalBonds = new BitSet();
private int lastBondPos = -1;
private Map<Edge,Integer> bondStrPos = new HashMap<>();
private Map<Edge, Integer> bondStrPos = new HashMap<>();
private List<String> warnings = new ArrayList<>();
......@@ -116,7 +132,7 @@ final class Parser {
int nArom = 0;
for (Edge e : g.edges(i)) {
if (e.bond() == Bond.AROMATIC ||
e.bond() == Bond.IMPLICIT && g.atom(e.other(i)).aromatic())
e.bond() == Bond.IMPLICIT && g.atom(e.other(i)).aromatic())
nArom++;
}
if (nArom >= 2) {
......@@ -124,13 +140,13 @@ final class Parser {
g.setAtom(i, AtomImpl.AromaticSubset.Any);
else
g.setAtom(i,
new AtomImpl.BracketAtom(-1,
Element.Unknown,
atom.label(),
atom.hydrogens(),
atom.charge(),
atom.atomClass(),
true));
new AtomImpl.BracketAtom(-1,
Element.Unknown,
atom.label(),
atom.hydrogens(),
atom.charge(),
atom.atomClass(),
true));
}
}
}
......@@ -190,6 +206,7 @@ final class Parser {
// create topologies (stereo configurations)
for (Entry<Integer, Configuration> e : configurations.entrySet()) {
addTopology(e.getKey(),
e.getValue(),
Topology.toExplicit(g, e.getKey(), e.getValue()));
}
......@@ -244,8 +261,8 @@ final class Parser {
offset2 = bondStrPos.get(e);
}
String errorPos = InvalidSmilesException.display(buffer,
offset1-buffer.length(),
offset2-buffer.length());
offset1 - buffer.length(),
offset2 - buffer.length());
if (strict)
throw new InvalidSmilesException("Ignored invalid Cis/Trans specification: " + errorPos);
else
......@@ -261,8 +278,8 @@ final class Parser {
offset2 = bondStrPos.get(e);
}
String errorPos = InvalidSmilesException.display(buffer,
offset1-buffer.length(),
offset2-buffer.length());
offset1 - buffer.length(),
offset2 - buffer.length());
if (strict)
throw new InvalidSmilesException("Ignored invalid Cis/Trans specification: " + errorPos);
else
......@@ -311,22 +328,25 @@ final class Parser {
return new int[]{prevEnd1, prevEnd2};
}
/** Access the local edges in order. */
/**
* Access the local edges in order.
*/
private List<Edge> getLocalEdges(int end) {
return getEdges(arrangement.get(end), end);
}
/**
* Complicated process to get correct Allene neighbors.
*
* @param focus the focus (central cumualted atom)
* @return the carrier list
*/
public int[] getAlleneCarriers(int focus) {
int[] carriers = new int[4];
int i = 0;
int[] ends = findExtendedTetrahedralEnds(focus);
int beg = ends[0];
int end = ends[1];
int i = 0;
int[] ends = findExtendedTetrahedralEnds(focus);
int beg = ends[0];
int end = ends[1];
boolean begh = g.implHCount(beg) == 1;
boolean endh = g.implHCount(end) == 1;
List<Edge> begEdges = new ArrayList<>(getLocalEdges(beg));
......@@ -372,52 +392,56 @@ final class Parser {
* @param c explicit configuration of that vertex
* @see Topology#toExplicit(Graph, int, Configuration)
*/
private void addTopology(int u, Configuration c) throws
InvalidSmilesException {
private void addTopology(int u, Configuration input, Configuration c) throws
InvalidSmilesException {
// stereo on ring closure - use local arrangement
if (arrangement.containsKey(u)) {
int[] us = arrangement.get(u).toArray();
List<Edge> es = getLocalEdges(u);
if (c.type() == Configuration.Type.Tetrahedral)
if (c.type() == Configuration.Type.Tetrahedral) {
us = insertThImplicitRef(u, us); // XXX: temp fix
else if (c.type() == Configuration.Type.DoubleBond)
} else if (c.type() == Configuration.Type.DoubleBond) {
us = insertDbImplicitRef(u, us); // XXX: temp fix
else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
} else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
g.addFlags(Graph.HAS_EXT_STRO);
if ((us = getAlleneCarriers(u)) == null) {
if (strict)
throw new InvalidSmilesException("Invalid Allene stereo");
else
warnings.add("Ignored invalid Allene stereochemistry");
return;
if (strict)
throw new InvalidSmilesException("Invalid Allene stereo");
else
warnings.add("Ignored invalid Allene stereochemistry");
return;
}
} else if (input.type() == Configuration.Type.SquarePlanar) {
us = insertMultipleImplicitRefs(u, us, 4);
} else if (input.type() == Configuration.Type.TrigonalBipyramidal) {
us = insertMultipleImplicitRefs(u, us, 5);
} else if (input.type() == Configuration.Type.Octahedral) {
us = insertMultipleImplicitRefs(u, us, 6);
} else if (c.type() == Configuration.Type.SquarePlanar &&
us.length != 4) {
if (strict)
throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
else
warnings.add("SquarePlanar without 4 explicit neighbours");
return;
if (strict)
throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
else
warnings.add("SquarePlanar without 4 explicit neighbours");
return;
} else if (c.type() == Configuration.Type.TrigonalBipyramidal &&
us.length != 5) {
if (strict)
throw new InvalidSmilesException("SquarePlanar without 5 explicit neighbours");
else
warnings.add("SquarePlanar without 5 explicit neighbours");
return;
if (strict)
throw new InvalidSmilesException("TrigonalBipyramidal without 5 explicit neighbours");
else
warnings.add("SquarePlanar without 5 explicit neighbours");
return;
} else if (c.type() == Configuration.Type.Octahedral &&
us.length != 6) {
if (strict)
throw new InvalidSmilesException("SquarePlanar without 6 explicit neighbours");
else
warnings.add("SquarePlanar without 6 explicit neighbours");
return;
if (strict)
throw new InvalidSmilesException("Octahedral without 6 explicit neighbours");
else
warnings.add("SquarePlanar without 6 explicit neighbours");
return;
}
g.addTopology(Topology.create(u, us, es, c));
}
else {
} else {
int[] us = new int[g.degree(u)];
List<Edge> es = g.edges(u);
for (int i = 0; i < us.length; i++)
......@@ -425,35 +449,78 @@ final class Parser {
if (c.type() == Configuration.Type.Tetrahedral) {
us = insertThImplicitRef(u, us); // XXX: temp fix
}
else if (c.type() == Configuration.Type.DoubleBond) {
} else if (c.type() == Configuration.Type.DoubleBond) {
us = insertDbImplicitRef(u, us); // XXX: temp fix
}
else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
} else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
g.addFlags(Graph.HAS_EXT_STRO);
if ((us = getAlleneCarriers(u)) == null)
return;
} else if (input.type() == Configuration.Type.SquarePlanar) {
us = insertMultipleImplicitRefs(u, us, 4);
} else if (input.type() == Configuration.Type.TrigonalBipyramidal) {
us = insertMultipleImplicitRefs(u, us, 5);
} else if (input.type() == Configuration.Type.Octahedral) {
us = insertMultipleImplicitRefs(u, us, 6);
} else if (c.type() == Configuration.Type.SquarePlanar &&
us.length != 4) {
if (strict)
throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
else
warnings.add("SquarePlanar without 4 explicit neighbours");
return;
} else if (c.type() == Configuration.Type.TrigonalBipyramidal &&
us.length != 5) {
if (strict)
throw new InvalidSmilesException("TrigonalBipyramidal without 5 explicit neighbours");
else
warnings.add("SquarePlanar without 5 explicit neighbours");
return;
} else if (c.type() == Configuration.Type.Octahedral &&
us.length != 6) {
if (strict)
throw new InvalidSmilesException("Octahedral without 6 explicit neighbours");
else
warnings.add("SquarePlanar without 6 explicit neighbours");
return;
}
g.addTopology(Topology.create(u, us, es, c));
}
}
// XXX: temporary fix for correcting configurations
private int[] insertThImplicitRef(int u, int[] vs) throws
InvalidSmilesException {
InvalidSmilesException {
if (vs.length == 4)
return vs;
if (vs.length != 3)
throw new InvalidSmilesException("Invaid number of verticies for TH1/TH2 stereo chemistry");
throw new InvalidSmilesException("Invalid number of vertices for TH1/TH2 stereo chemistry");
if (start.contains(u))
return new int[]{u, vs[0], vs[1], vs[2]};
else
return new int[]{vs[0], u, vs[1], vs[2]};
}
private int[] insertMultipleImplicitRefs(int u, int[] vs, int n) throws
InvalidSmilesException {
if (vs.length == n)
return vs;
if (vs.length <= 1)
throw new InvalidSmilesException("Cannot have <= 1 vertices for high-order stereo chemistry");
int cnt = n - vs.length;
int srcIdx = 0;
int dstIdx = 0;
int[] padded = new int[n];
if (!start.contains(u))
padded[dstIdx++] = vs[srcIdx++];
while (cnt-- > 0)
padded[dstIdx++] = u;
while (srcIdx < vs.length)
padded[dstIdx++] = vs[srcIdx++];
return padded;
}
// XXX: temporary fix for correcting configurations
private int[] insertDbImplicitRef(int u, int[] vs) throws
InvalidSmilesException {
InvalidSmilesException {
if (vs.length == 3)
return vs;
if (vs.length != 2)
......@@ -484,8 +551,7 @@ final class Parser {
g.addEdge(e);
if (arrangement.containsKey(u))
arrangement.get(u).add(v);
}
else {
} else {
start.add(v); // start of a new run
}
}
......@@ -507,7 +573,7 @@ final class Parser {
* @throws InvalidSmilesException invalid grammar
*/
private void readSmiles(final CharBuffer buffer) throws
InvalidSmilesException {
InvalidSmilesException {
// primary dispatch
while (buffer.hasRemaining()) {
char c = buffer.get();
......@@ -733,7 +799,7 @@ final class Parser {
* specification.
*/
Atom readBracketAtom(final CharBuffer buffer) throws
InvalidSmilesException {
InvalidSmilesException {
int start = buffer.position;
boolean arbitraryLabel = false;
......@@ -770,8 +836,7 @@ final class Parser {
if (!arbitraryLabel && !buffer.getIf(']')) {
if (strict) {
throw InvalidSmilesException.invalidBracketAtom(buffer);
}
else {
} else {
arbitraryLabel = true;
}
}
......@@ -852,10 +917,10 @@ final class Parser {
private static int readCharge(int acc, final CharBuffer buffer) {
if (buffer.getIf('+'))
return buffer.nextIsDigit() ? acc + buffer.getNumber()
: readCharge(acc + 1, buffer);
: readCharge(acc + 1, buffer);
if (buffer.getIf('-'))
return buffer.nextIsDigit() ? acc - buffer.getNumber()
: readCharge(acc - 1, buffer);
: readCharge(acc - 1, buffer);
return acc;
}
......@@ -988,7 +1053,7 @@ final class Parser {
* Decide the bond to use for a ring bond. The bond symbol can be present on
* either or both bonded atoms. This method takes those bonds, chooses the
* correct one or reports an error if there is a conflict.
*
* <p>
* Equivalent SMILES:
* <blockquote><pre>
* C=1CCCCC=1
......@@ -996,9 +1061,9 @@ final class Parser {
* C1CCCCC=1
* </pre></blockquote>
*
* @param a a bond
* @param b other bond
* @param pos the position in the string of bond a
* @param a a bond
* @param b other bond
* @param pos the position in the string of bond a
* @param buffer the buffer and it's current position
* @return the bond to use for this edge
* @throws InvalidSmilesException ring bonds did not match
......@@ -1013,11 +1078,11 @@ final class Parser {
if (strict || a.inverse() != b)
throw new InvalidSmilesException("Ring closure bonds did not match, '" + a + "'!='" + b + "':" +
InvalidSmilesException.display(buffer,
pos-buffer.position,
lastBondPos-buffer.position));
pos - buffer.position,
lastBondPos - buffer.position));
warnings.add("Ignored invalid Cis/Trans on ring closure, should flip:" +
InvalidSmilesException.display(buffer, pos-buffer.position,
lastBondPos-buffer.position));
InvalidSmilesException.display(buffer, pos - buffer.position,
lastBondPos - buffer.position));
return Bond.IMPLICIT;
}
......@@ -1035,6 +1100,7 @@ final class Parser {
/**
* Access any warning messages from parsing the SMILES.
*
* @return the warnings.
*/
public Collection<? extends String> getWarnings() {
......@@ -1046,9 +1112,9 @@ final class Parser {
* specify the bond type.
*/
private static final class RingBond {
int u;
int u;
Bond bond;
int pos;
int pos;
private RingBond(int u, Bond bond, int pos) {
this.u = u;
......@@ -1070,9 +1136,11 @@ final class Parser {
private static final class LocalArrangement {
int[] vs;
int n;
int n;
/** New local arrangement. */
/**
* New local arrangement.
*/
private LocalArrangement() {
this.vs = new int[4];
}
......
exec/pom.xml
+ 1
− 1
View file @ 2f8a82f5
......@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
<version>1.3.5</version>
<version>1.3.6</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......
func/pom.xml
+ 1
− 1
View file @ 2f8a82f5
......@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
<version>1.3.5</version>
<version>1.3.6</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......
func/src/main/java/uk/ac/ebi/beam/AddDirectionalLabels.java
+ 3
− 1
View file @ 2f8a82f5
......@@ -246,14 +246,16 @@ final class AddDirectionalLabels
return Status.COMPLETED;
break;
case UP:
case UP_AROMATIC:
case DOWN:
case DOWN_AROMATIC:
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)) {
if ((f.bond().directional()) && explicit.bond(u).inverse() != f.bond(u)) {
return Status.INVALID;
}
......
func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java
+ 3
− 3
View file @ 2f8a82f5
......@@ -182,7 +182,7 @@ final class NormaliseDirectionalLabels
if (first == null)
return;
if (ordering[first.other(u)] < ordering[u]) {
if (first.bond(u) == Bond.UP)
if (first.bond(u) == Bond.UP || first.bond(u) == Bond.UP_AROMATIC)
invertExistingDirectionalLabels(g,
u,
new BitSet(),
......@@ -198,7 +198,7 @@ final class NormaliseDirectionalLabels
u);
}
else {
if (first.bond(u) == Bond.DOWN)
if (first.bond(u) == Bond.DOWN || first.bond(u) == Bond.DOWN_AROMATIC)
invertExistingDirectionalLabels(g,
u,
new BitSet(),
......@@ -220,7 +220,7 @@ final class NormaliseDirectionalLabels
final int d = g.degree(u);
for (int j = 0; j < d; ++j) {
final Edge f = g.edgeAt(u, j);
if (f.bond() == Bond.UP || f.bond() == Bond.DOWN) {
if (f.bond().directional()) {
if (first == null || ordering[f.other(u)] < ordering[first.other(u)])
first = f;
}
......
func/src/main/java/uk/ac/ebi/beam/RemoveUpDownBonds.java
+ 2
− 0
View file @ 2f8a82f5
......@@ -162,6 +162,8 @@ final class RemoveUpDownBonds extends AbstractFunction<Graph,Graph> {
break;
case UP:
case DOWN:
case UP_AROMATIC:
case DOWN_AROMATIC:
edges.add(f);
break;
}
......
func/src/main/java/uk/ac/ebi/beam/ToTrigonalTopology.java
+ 3
− 4
View file @ 2f8a82f5
......@@ -63,8 +63,7 @@ final class ToTrigonalTopology extends AbstractFunction<Graph,Graph> {
// change edges (only changed added to replacement)
for (int u = 0; u < g.order(); u++) {
for (final Edge e : g.edges(u)) {
if (e.other(u) > u && e.bond() == Bond.UP || e
.bond() == Bond.DOWN) {
if (e.other(u) > u && e.bond().directional()) {
replacements.put(e,
new Edge(u, e.other(u), Bond.IMPLICIT));
}
......@@ -181,11 +180,11 @@ final class ToTrigonalTopology extends AbstractFunction<Graph,Graph> {
}
static boolean isUp(Bond b) {
return b == Bond.UP;
return b == Bond.UP || b == Bond.UP_AROMATIC;
}
static boolean isDown(Bond b) {
return b == Bond.DOWN;
return b == Bond.DOWN || b == Bond.DOWN_AROMATIC;
}
private List<Edge> doubleBondLabelledEdges(Graph g) {
......
pom.xml
+ 14
− 6
View file @ 2f8a82f5
......@@ -7,7 +7,7 @@
<description>SMILES parsing and generation library for cheminformatics</description>
<url>http://www.github.com/johnmay/beam/</url>
<packaging>pom</packaging>
<version>1.3.5</version>
<version>1.3.6</version>
<modules>
<module>core</module>
<module>func</module>
......@@ -93,8 +93,8 @@
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.3</version>
<extensions>false</extensions>
<version>1.6.13</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
......@@ -104,7 +104,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.5</version>
<version>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
......@@ -112,13 +112,21 @@
<goals>
<goal>sign</goal>
</goals>
<configuration>
<executable>gpg</executable>
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
<passphrase>${gpg.passphrase}</passphrase>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
<version>3.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
......@@ -131,7 +139,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9.1</version>
<version>3.3.1</version>
<executions>
<execution>
<id>attach-javadocs</id>
......
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