Added support for the smiles and sdf generator.

tool/structgen/src/test/java/org/openscience/cdk/structgen/maygen/MaygenCLI.java

@@ -27,8 +27,6 @@
 import org.apache.commons.cli.ParseException;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
-import org.openscience.cdk.tools.ILoggingTool;
-import org.openscience.cdk.tools.LoggingToolFactory;
 
 import java.io.File;
 import java.io.IOException;
@@ -70,10 +68,17 @@ public boolean parseArgs(String[] args) throws ParseException {
                     maygen.setConsumer(new SmiOutputConsumer(getFileDir(cmd)));
                 }
                 if (cmd.hasOption("sdf") || cmd.hasOption(SDF_COORD)) {
-                    SdfOutputConsumer sdfout = new SdfOutputConsumer(getFileDir(cmd));
-                    if (cmd.hasOption(SDF_COORD))
-                        sdfout.setCoordinates(true);
-                    maygen.setConsumer(sdfout);
+                    if (cmd.hasOption("smi")) {
+                        SdfAndSmiOutputConsumer sdfAndSmiOut = new SdfAndSmiOutputConsumer(getFileDir(cmd));
+                        if (cmd.hasOption(SDF_COORD))
+                            sdfAndSmiOut.setCoordinates(true);
+                        maygen.setConsumer(sdfAndSmiOut);
+                    } else{
+                        SdfOutputConsumer sdfout = new SdfOutputConsumer(getFileDir(cmd));
+                        if (cmd.hasOption(SDF_COORD))
+                            sdfout.setCoordinates(true);
+                        maygen.setConsumer(sdfout);
+                    }
                 }
 
                 if (cmd.hasOption("verbose")) {

tool/structgen/src/test/java/org/openscience/cdk/structgen/maygen/SdfAndSmiOutputConsumer.java

@@ -0,0 +1,132 @@
+/*
+ * Copyright (c) 2021 Mehmet Aziz Yirik <mehmetazizyirik@outlook.com> <0000-0001-7520-7215@orcid.org>
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.openscience.cdk.structgen.maygen;
+
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.io.MDLV2000Writer;
+import org.openscience.cdk.io.SDFWriter;
+import org.openscience.cdk.layout.StructureDiagramGenerator;
+import org.openscience.cdk.smiles.SmiFlavor;
+import org.openscience.cdk.smiles.SmilesGenerator;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+import java.nio.charset.StandardCharsets;
+
+final class SdfAndSmiOutputConsumer implements Maygen.Consumer {
+
+    private final ILoggingTool logger = LoggingToolFactory.createLoggingTool(SdfAndSmiOutputConsumer.class);
+
+    private BufferedWriter wtr;
+    private SDFWriter sdfw;
+    private final SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default);
+    private final File dir;
+    private boolean coordinates;
+
+    public SdfAndSmiOutputConsumer(File dir) {
+        this.dir = dir;
+        if (dir == null) {
+            sdfw = new SDFWriter(System.out);
+            wtr = new BufferedWriter(new OutputStreamWriter(System.out,
+                    StandardCharsets.UTF_8));
+        } else {
+            dir.mkdirs();
+        }
+        setupOptions();
+    }
+
+    public SdfAndSmiOutputConsumer(Writer writer) {
+        this.dir = null;
+        sdfw = new SDFWriter(writer);
+        wtr = new BufferedWriter(writer);
+        setupOptions();
+    }
+
+    @Override
+    public void configure(String name) {
+        if (dir != null) {
+            if (sdfw != null) {
+                try {
+                    sdfw.close();
+                } catch (IOException e) {
+                    logger.error(e.getMessage());
+                }
+            }
+            if (wtr != null) {
+                try {
+                    wtr.close();
+                } catch (IOException e) {
+                    logger.error(e);
+                }
+            }
+            try {
+                sdfw = new SDFWriter(new FileOutputStream(new File(dir, name + ".sdf")));
+                wtr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new File(dir, name + ".smi")),
+                        StandardCharsets.UTF_8));
+                setupOptions();
+            } catch (FileNotFoundException e) {
+                logger.error(e.getMessage());
+            }
+        }
+    }
+
+    private void setupOptions() {
+        if (sdfw == null)
+            return;
+        try {
+            sdfw.getSetting(MDLV2000Writer.OptProgramName)
+                .setSetting("MAYGEN");
+            sdfw.getSetting(MDLV2000Writer.OptWriteDefaultProperties)
+                .setSetting("false");
+        } catch (CDKException e) {
+            logger.error(e);
+        }
+    }
+
+    @Override
+    public void consume(IAtomContainer mol) {
+        try {
+            if (coordinates)
+                new StructureDiagramGenerator().generateCoordinates(mol);
+            sdfw.write(mol);
+            String smi = smigen.create(mol);
+            wtr.write(smi + "\n");
+        } catch (CDKException | IOException e) {
+            logger.error(e);
+        }
+    }
+
+    @Override
+    public void close() throws IOException {
+        sdfw.close();
+        wtr.close();
+    }
+
+    public void setCoordinates(boolean b) {
+        this.coordinates = b;
+    }
+}