[Git][java-team/libbeam-java][upstream] New upstream version 1.3.8
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Fri Jan 10 10:21:11 GMT 2025
Andrius Merkys pushed to branch upstream at Debian Java Maintainers / libbeam-java
Commits:
cac9e0c4 by Andrius Merkys at 2025-01-10T04:41:54-05:00
New upstream version 1.3.8
- - - - -
6 changed files:
- core/pom.xml
- core/src/main/java/uk/ac/ebi/beam/GraphBuilder.java
- core/src/main/java/uk/ac/ebi/beam/Topology.java
- exec/pom.xml
- func/pom.xml
- pom.xml
Changes:
=====================================
core/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.7</version>
+ <version>1.3.8</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
core/src/main/java/uk/ac/ebi/beam/GraphBuilder.java
=====================================
@@ -32,8 +32,6 @@ package uk.ac.ebi.beam;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
-import java.util.Collections;
-import java.util.Comparator;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
@@ -195,13 +193,25 @@ public final class GraphBuilder {
* Start building a tetrahedral configuration.
*
* @param u the central atom
- * @return a {@link TetrahedralBuilder} to create the stereo-configuration
+ * @return a {@link AtomStereoBuilder} to create the stereo-configuration
* from
*/
public TetrahedralBuilder tetrahedral(int u) {
return new TetrahedralBuilder(this, u);
}
+ /**
+ * Start building an atom stereo configuration (tetrahedral/square planar/
+ * octahedral/trigonal bipyramidal).
+ *
+ * @param u the central atom
+ * @return a {@link AtomStereoBuilder} to create the stereo-configuration
+ * from
+ */
+ public AtomStereoBuilder atomStereo(int u, Configuration configuration) {
+ return new AtomStereoBuilder(this, u).config(configuration);
+ }
+
/** Start building the geometric configuration of the double bond 'u' / 'v'. */
public GeometricBuilder geometric(int u, int v) {
GeometricBuilder builder = new GeometricBuilder(this, u, v);
@@ -231,7 +241,7 @@ public final class GraphBuilder {
/**
* (internal) Add a topology to the chemical graph. The topologies should be
* created using one of the configuration builders (e.g. {@link
- * TetrahedralBuilder}).
+ * AtomStereoBuilder}).
*
* @param t the topology to add
*/
@@ -733,6 +743,119 @@ public final class GraphBuilder {
return gb;
}
}
+
+ /** @author John Mayfield */
+ public static final class AtomStereoBuilder {
+
+ /**
+ * Reference to the graph builder we came from - allows us to add the
+ * topology once the configuration as been built.
+ */
+ final GraphBuilder gb;
+
+ /** Central/Focus vertex. */
+ final int u;
+
+ /** The vertex we are looking from. */
+ int v;
+
+ /** The other neighbors */
+ int[] vs;
+
+ /** The configuration of the other neighbors */
+ Configuration config;
+
+ /**
+ * (internal) - constructor for starting to configure atom stereo.
+ *
+ * @param gb the graph builder (where we came from)
+ * @param u the vertex to
+ */
+ private AtomStereoBuilder(GraphBuilder gb,
+ int u) {
+ this.gb = gb;
+ this.u = u;
+ }
+
+ /**
+ * Indicate from which vertex the atom stereo. is being 'looked-at'.
+ *
+ * @param v the vertex from which we are looking from.
+ * @return tetrahedral builder for further configuration
+ */
+ public AtomStereoBuilder lookingFrom(int v) {
+ this.v = v;
+ return this;
+ }
+
+ /**
+ * Indicate the other neighbors of atom stereo (excluding the vertex we
+ * are looking from). There should be exactly 3 neighbors.
+ *
+ * @param vs the neighbors
+ * @return tetrahedral builder for further configuration
+ * @throws IllegalArgumentException when there was not exactly 3
+ * neighbors
+ */
+ public AtomStereoBuilder neighbors(int[] vs) {
+ this.vs = vs;
+ return this;
+ }
+
+ /**
+ * Indicate the other neighbors of atom stereo (excluding the vertex we
+ * are looking from).
+ *
+ * @param u a neighbor
+ * @param v another neighbor
+ * @param w another neighbor
+ * @return tetrahedral builder for further configuration
+ */
+ public AtomStereoBuilder neighbors(int u, int v, int w) {
+ return neighbors(new int[]{u, v, w});
+ }
+
+ /**
+ * Specify the winding of the {@link #neighbors(int, int, int)}.
+ *
+ * @param c configuration
+ * @return tetrahedral builder for further configuration
+ */
+ public AtomStereoBuilder config(Configuration c) {
+ this.config = c;
+ return this;
+ }
+
+ /**
+ * Finish configuring the atom stereo centre and add it to the graph.
+ *
+ * @return the graph-builder to add more atoms/bonds or stereo elements
+ * @throws IllegalArgumentException configuration was missing
+ */
+ public GraphBuilder build() {
+ if (config == null)
+ throw new IllegalArgumentException("no configuration defined");
+ if (vs == null)
+ throw new IllegalArgumentException("no neighbors defined");
+ Topology t = null;
+ if (config.type() == Configuration.Type.Tetrahedral) {
+ if (vs.length != 3) throw new IllegalArgumentException("incorrect neighbour count");
+ t = Topology.tetrahedral(u, new int[]{v, vs[0], vs[1], vs[2]}, config);
+ } else if (config.type() == Configuration.Type.SquarePlanar) {
+ if (vs.length != 3) throw new IllegalArgumentException("incorrect neighbour count");
+ t = Topology.squarePlanar(u, new int[]{v, vs[0], vs[1], vs[2]}, config);
+ } else if (config.type() == Configuration.Type.TrigonalBipyramidal) {
+ if (vs.length != 4) throw new IllegalArgumentException("incorrect neighbour count");
+ t = Topology.trigonalBipyramidal(u, new int[]{v, vs[0], vs[1], vs[2], vs[3]}, config);
+ } else if (config.type() == Configuration.Type.Octahedral) {
+ if (vs.length != 5) throw new IllegalArgumentException("incorrect neighbour count");
+ t = Topology.octahedral(u, new int[]{v, vs[0], vs[1], vs[2], vs[3], vs[4]}, config);
+ } else
+ throw new IllegalArgumentException("Unimplemented config type: " + config);
+ gb.topology(u, t);
+ return gb;
+ }
+ }
/** @author John May */
public static final class ExtendedTetrahedralBuilder {
=====================================
core/src/main/java/uk/ac/ebi/beam/Topology.java
=====================================
@@ -270,7 +270,7 @@ abstract class Topology {
}
}
- private static Topology trigonalBipyramidal(int u, int[] vs, Configuration c) {
+ static Topology trigonalBipyramidal(int u, int[] vs, Configuration c) {
if (Configuration.TB1.ordinal() <= c.ordinal() &&
Configuration.TB20.ordinal() >= c.ordinal()) {
int order = 1 + c.ordinal() - Configuration.TB1.ordinal();
@@ -279,7 +279,7 @@ abstract class Topology {
return null;
}
- private static Topology octahedral(int u, int[] vs, Configuration c) {
+ static Topology octahedral(int u, int[] vs, Configuration c) {
if (Configuration.OH1.ordinal() <= c.ordinal() &&
Configuration.OH30.ordinal() >= c.ordinal()) {
int order = 1 + c.ordinal() - Configuration.OH1.ordinal();
=====================================
exec/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.7</version>
+ <version>1.3.8</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
func/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.7</version>
+ <version>1.3.8</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
pom.xml
=====================================
@@ -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>1.3.7</version>
+ <version>1.3.8</version>
<modules>
<module>core</module>
<module>func</module>
View it on GitLab: https://salsa.debian.org/java-team/libbeam-java/-/commit/cac9e0c423bd516321b53fa196f5ec133ba9b61b
--
View it on GitLab: https://salsa.debian.org/java-team/libbeam-java/-/commit/cac9e0c423bd516321b53fa196f5ec133ba9b61b
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