A new executable module for beam command line utils.

exec/make-stub.sh

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+#!/bin/bash
+
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+# Builds self contained unix executable
+cat ${DIR}/src/main/resources/stub.sh ${DIR}/target/beam.jar > ${DIR}/target/beam && chmod +x ${DIR}/target/beam
+cp ${DIR}/target/beam /usr/local/bin/beam

exec/pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  ~ Copyright (c) 2015. NextMove Software Ltd
+  -->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>beam</artifactId>
+        <groupId>uk.ac.ebi.beam</groupId>
+        <version>0.9-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>beam-exec</artifactId>
+
+    <dependencies>
+        <dependency>
+            <groupId>uk.ac.ebi.beam</groupId>
+            <artifactId>beam-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>uk.ac.ebi.beam</groupId>
+            <artifactId>beam-func</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>net.sf.jopt-simple</groupId>
+            <artifactId>jopt-simple</artifactId>
+            <version>4.8</version>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>beam</id>
+                        <configuration>
+                            <archive>
+                                <manifest>
+                                    <mainClass>uk.ac.ebi.beam.Main</mainClass>
+                                </manifest>
+                            </archive>
+                            <finalName>beam</finalName>
+                            <appendAssemblyId>false</appendAssemblyId>
+                            <descriptorRefs>
+                                <descriptorRef>jar-with-dependencies</descriptorRef>
+                            </descriptorRefs>
+                        </configuration>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>

exec/src/main/java/uk/ac/ebi/beam/Anonymise.java

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+/*
+ * Copyright (c) 2015. John May
+ */
+
+package uk.ac.ebi.beam;
+
+import joptsimple.OptionSet;
+
+/**
+ * Anonymise SMILES input to all '*' atoms. Bond orders can optionally be emitted.
+ */
+public final class Anonymise extends FunctorCmdLnModule {
+
+    private final Atom UNKN_ATOM = AtomImpl.AliphaticSubset.Unknown;
+
+    public Anonymise() {
+        super("anon");
+        super.optparser.accepts("bo", "keep bond orders");
+    }
+
+    @Override
+    Functor createFunctor(OptionSet optionSet) {
+        final boolean bondorders = optionSet.has("bo");
+        return new Functor() {
+            @Override
+            String map(String str) throws InvalidSmilesException {
+
+                Graph g = Graph.fromSmiles(str);
+
+                if (bondorders)
+                    g = g.kekule();
+
+                final GraphBuilder gb = GraphBuilder.create(g.order());
+
+                for (int v = 0; v < g.order(); v++) {
+                    gb.add(UNKN_ATOM);
+                    for (Edge e : g.edges(v)) {
+                        if (e.other(v) < v) {
+                            if (bondorders)
+                                gb.add(new Edge(v, e.other(v), bondForOrder(e.bond().order())));
+                            else
+                                gb.add(new Edge(v, e.other(v), Bond.IMPLICIT));
+                        }
+                    }
+                }
+
+                return gb.build().toSmiles() + suffixedId(str);
+            }
+        };
+    }
+
+    private Bond bondForOrder(int ord) {
+        switch (ord) {
+            case 1:
+                return Bond.IMPLICIT;
+            case 2:
+                return Bond.DOUBLE;
+            case 3:
+                return Bond.TRIPLE;
+            case 4:
+                return Bond.QUADRUPLE;
+            default:
+                return Bond.IMPLICIT;
+        }
+    }
+}

exec/src/main/java/uk/ac/ebi/beam/Aromatise.java

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+/*
+ * Copyright (c) 2015. John May
+ */
+
+package uk.ac.ebi.beam;
+
+import joptsimple.OptionSet;
+
+/**
+ * Simple module simply Kekulises then emits and normalised
+ * (by beam's model) aromatic form of the SMILES.
+ */
+public final class Aromatise extends FunctorCmdLnModule {
+
+    public Aromatise() {
+        super("arom");
+    }
+
+    @Override
+    Functor createFunctor(OptionSet optionSet) {
+        return new Functor() {
+            @Override
+            String map(String str) throws InvalidSmilesException {
+                return Graph.fromSmiles(str).kekule().aromatic().toSmiles() + suffixedId(str);
+            }
+        };
+    }
+}

exec/src/main/java/uk/ac/ebi/beam/CmdLnModule.java

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+/*
+ * Copyright (c) 2015. John May
+ */
+
+package uk.ac.ebi.beam;
+
+/**
+ * A plugable command line module providing functionality
+ * from the primary dispatch {@link Main}. Modules should
+ * be implemented and added to an SPI
+ * (META-INF/services/uk.ac.ebi.beam.CmdLnModule).
+ *
+ * @see <a href="https://docs.oracle.com/javase/tutorial/ext/basics/spi.html">SPI</a>
+ */
+public interface CmdLnModule {
+
+    /**
+     * The module name is a concise, often abbreviated, description
+     * of the module function. It is used to reference the
+     * functionality from the primary dispatch:
+     * <pre>{@code $ beam {module.name} {module.args}}</pre>
+     *
+     * @return module name
+     */
+    String name();
+
+    /**
+     * Displays the usage/help for this module.
+     *
+     * @return help info
+     */
+    String getHelpInfo();
+
+    /**
+     * Executes the module with the specified arguments. The
+     * arguments do not include the module name.
+     *
+     * @param args command line arguments
+     */
+    void exec(String[] args);
+}