[Git][java-team/libbeam-java][master] 4 commits: New upstream version 1.3.7
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Thu Nov 7 06:25:03 GMT 2024
Andrius Merkys pushed to branch master at Debian Java Maintainers / libbeam-java
Commits:
d33fd3c0 by Andrius Merkys at 2024-11-07T01:15:54-05:00
New upstream version 1.3.7
- - - - -
f2f2ac37 by Andrius Merkys at 2024-11-07T01:15:59-05:00
Update upstream source from tag 'upstream/1.3.7'
Update to upstream version '1.3.7'
with Debian dir 9ca2511728bcad1c49f0da363a931451282d59c7
- - - - -
a00bc8d8 by Andrius Merkys at 2024-11-07T01:18:25-05:00
Reduce boilerplate.
- - - - -
736af863 by Andrius Merkys at 2024-11-07T01:18:50-05:00
Update changelog for 1.3.7-1 release
- - - - -
16 changed files:
- core/pom.xml
- core/src/main/java/uk/ac/ebi/beam/Bond.java
- core/src/main/java/uk/ac/ebi/beam/Element.java
- core/src/main/java/uk/ac/ebi/beam/Generator.java
- core/src/main/java/uk/ac/ebi/beam/Localise.java
- core/src/test/java/uk/ac/ebi/beam/GraphTest.java
- core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
- − debian/README.source
- debian/changelog
- − debian/maven.cleanIgnoreRules
- − debian/maven.properties
- − debian/maven.publishedRules
- debian/maven.rules
- 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>1.3.6</version>
+ <version>1.3.7</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
core/src/main/java/uk/ac/ebi/beam/Bond.java
=====================================
@@ -34,7 +34,9 @@ package uk.ac.ebi.beam;
* valid undirected and directed bond types and {@link #DOT}. Opposed to the
* other types, {@link #DOT} indicates that two atoms are not connected. <br>
*
- * <table summary="" style="font-family: Courier, monospace;"> <tr><th>{@link
+ * <table style="font-family: Courier, monospace;"> <caption>
+ * Bond Types
+ * </caption><tr><th>{@link
* Bond}</th><th>{@link #token()}</th><th>{@link #order()}</th><th>{@link
* #inverse()}</th></tr> <tr><td>{@link #DOT}</td><td>.</td><td>0</td><td></td></tr>
* <tr><td>{@link #IMPLICIT}</td><td></td><td>undefined (2 or
=====================================
core/src/main/java/uk/ac/ebi/beam/Element.java
=====================================
@@ -41,7 +41,7 @@ import java.util.Map;
/**
* Enumeration of valid OpenSMILES elements.
*
- * <h1>Organic subsets</h1> Several of the elements belong to the organic
+ * <h2>Organic subsets</h2> Several of the elements belong to the organic
* subset. Atoms of an organic element type can be written just as their symbol
* (see. <a href="http://www.opensmiles.org/opensmiles.html#orgsbst">Organic
* Subset, OpenSMILES Specification</a>).
@@ -52,7 +52,7 @@ import java.util.Map;
* #Sulfur}</li> <li>{@link #Chlorine}</li> <li>{@link #Bromine}</li> <li>{@link
* #Iodine}</li> </ul>
*
- * <h1>Usage</h1>
+ * <h2>Usage</h2>
*
* Elements can be created by either using the value directly or by looking up
* it's symbol. If the element may be aromatic the lower-case symbol can also be
=====================================
core/src/main/java/uk/ac/ebi/beam/Generator.java
=====================================
@@ -439,8 +439,22 @@ final class Generator {
.toLowerCase(Locale.ENGLISH)
: atom.element()
.symbol());
- if (c != Configuration.UNKNOWN)
- sb.append(c.shorthand().symbol());
+ if (c != Configuration.UNKNOWN) {
+ switch (c.type()) {
+ case SquarePlanar:
+ sb.append(g.degree(idx) == 4 ? c.shorthand().symbol() : c.symbol());
+ break;
+ case TrigonalBipyramidal:
+ sb.append(g.degree(idx) == 5 ? c.shorthand().symbol() : c.symbol());
+ break;
+ case Octahedral:
+ sb.append(g.degree(idx) == 6 ? c.shorthand().symbol() : c.symbol());
+ break;
+ default:
+ sb.append(c.shorthand().symbol());
+ break;
+ }
+ }
if (atom.hydrogens() > 0 && !hExpand)
sb.append(Element.Hydrogen.symbol());
if (atom.hydrogens() > 1 && !hExpand)
=====================================
core/src/main/java/uk/ac/ebi/beam/Localise.java
=====================================
@@ -192,7 +192,7 @@ final class Localise {
case Boron:
return (q == 0) && deg == 3;
case Carbon:
- return (q == 1 || q == -1) && deg == 3;
+ return ((q == 1 || q == -1) && deg == 3) || (q == 0 && deg == 4);
case Silicon:
case Germanium:
return q < 0;
=====================================
core/src/test/java/uk/ac/ebi/beam/GraphTest.java
=====================================
@@ -546,9 +546,28 @@ public class GraphTest {
Assert.assertThat(g.topologyOf(3).configuration(), is(Configuration.AL2));
}
+ @Test public void testDegenerateOctahedral1() throws Exception {
+ assertThat(Graph.fromSmiles("N[Co at OH1]N").toSmiles(),
+ containsString("N[Co at OH1]N"));
+ }
+
+ @Test public void testDegenerateOctahedral2() throws IOException {
+ Graph g = Graph.fromSmiles("O=[V at OH25](Cl)(Cl)(F)F");
+ assertThat(g.toSmiles(),
+ containsString("O=[V at OH25](Cl)(Cl)(F)F"));
+ }
+
+ @Test public void testDegenerateOctahedral3() throws IOException {
+ Graph g = Graph.fromSmiles("O=[V at OH25]12(F)F.Cl1.Cl2");
+ assertThat(g.toSmiles(),
+ containsString("O=[V at OH25](F)(F)(Cl)Cl"));
+ }
+
@Test public void nofail() throws IOException {
Graph g = Graph.fromSmiles("CCCO[P at H]1(OC[C@@H]2[C@@H](O1)[C@@]([C@@H](O2)n3cnc4c3nc(nc4OCC)N)(C)F)O CHEMBL1630021");
assertThat(g.toSmiles(),
CoreMatchers.is("CCCO[PH]1(OC[C@@H]2[C@@H](O1)[C@@]([C@@H](O2)n3cnc4c3nc(nc4OCC)N)(C)F)O"));
}
+
+
}
=====================================
core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
=====================================
@@ -360,6 +360,14 @@ public class LocaliseTest {
test("c1cc(c([n+]c1)N)[N+](=O)[O-]",
"C1=CC(=C([N+]=C1)N)[N+](=O)[O-]");
}
+
+ @Test public void acyclicValence() throws Exception {
+ test("[cH3]cc", "[CH3]C=C");
+ test("[cH2+][cH2-]", "[CH2+][CH2-]");
+ test("[cH+][cH-]", "[CH+]=[CH-]");
+ test("[nH2]cc", "[NH2]C=C");
+ test("[oH]cc", "[OH]C=C");
+ }
@Test public void smallRingTest_5() throws Exception {
Graph g = Graph.fromSmiles("C1CCCC1");
=====================================
debian/README.source deleted
=====================================
@@ -1,9 +0,0 @@
-Information about libbeam-java
-------------------------------
-
-This package was debianized using the mh_make command
-from the maven-debian-helper package.
-
-The build system uses Maven but prevents it from downloading
-anything from the Internet, making the build compliant with
-the Debian policy.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libbeam-java (1.3.7-1) unstable; urgency=medium
+
+ * New upstream version 1.3.7
+ * Reduce boilerplate.
+
+ -- Andrius Merkys <merkys at debian.org> Thu, 07 Nov 2024 01:18:46 -0500
+
libbeam-java (1.3.6-1) unstable; urgency=medium
* New upstream version 1.3.6
=====================================
debian/maven.cleanIgnoreRules deleted
=====================================
@@ -1 +0,0 @@
-
=====================================
debian/maven.properties deleted
=====================================
@@ -1,4 +0,0 @@
-# Include here properties to pass to Maven during the build.
-# For example:
-# maven.test.skip=true
-# project.build.sourceEncoding=UTF-8
=====================================
debian/maven.publishedRules deleted
=====================================
@@ -1 +0,0 @@
-
=====================================
debian/maven.rules
=====================================
@@ -1,4 +1,3 @@
-
junit junit jar s/.*/4.x/ * *
uk.ac.ebi.beam beam-core jar s/.*/debian/ * *
uk.ac.ebi.beam beam-exec jar s/.*/debian/ * *
=====================================
exec/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.6</version>
+ <version>1.3.7</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>1.3.6</version>
+ <version>1.3.7</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>1.3.6</version>
+ <version>1.3.7</version>
<modules>
<module>core</module>
<module>func</module>
@@ -96,7 +96,7 @@
<version>1.6.13</version>
<extensions>true</extensions>
<configuration>
- <serverId>ossrh</serverId>
+ <serverId>ossrh-beam</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
@@ -104,7 +104,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
- <version>1.6</version>
+ <version>3.2.4</version>
<executions>
<execution>
<id>sign-artifacts</id>
@@ -126,7 +126,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
- <version>3.2.1</version>
+ <version>3.3.1</version>
<executions>
<execution>
<id>attach-sources</id>
View it on GitLab: https://salsa.debian.org/java-team/libbeam-java/-/compare/91a5ce3afe5fb0854fc3ed5d42e192165af06a9b...736af8637d05a8f25a28b9ed47813da33898195e
--
View it on GitLab: https://salsa.debian.org/java-team/libbeam-java/-/compare/91a5ce3afe5fb0854fc3ed5d42e192165af06a9b...736af8637d05a8f25a28b9ed47813da33898195e
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