@@ -54,6 +54,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IPseudoAtom; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; +import org.openscience.cdk.io.setting.BooleanIOSetting; +import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @@ -77,6 +79,8 @@ public class MDLWriter extends DefaultChemObjectWriter { private final static LoggingTool logger = new LoggingTool(MDLWriter.class); + private BooleanIOSetting forceWriteAs2DCoords; + private BufferedWriter writer; /** @@ -91,6 +95,7 @@ public class MDLWriter extends DefaultChemObjectWriter { } else { writer = new BufferedWriter(out); } + initIOSettings(); } /** @@ -155,6 +160,7 @@ public class MDLWriter extends DefaultChemObjectWriter { * @see #accepts(Class) */ public void write(IChemObject object) throws CDKException { + customizeJob(); try { if (object instanceof IChemFile) { writeChemFile((IChemFile)object); @@ -238,7 +244,7 @@ public class MDLWriter extends DefaultChemObjectWriter { for (int f = 0; f < container.getAtomCount(); f++) { IAtom atom = container.getAtom(f); line = ""; - if (atom.getPoint3d() != null) { + if (atom.getPoint3d() != null && !forceWriteAs2DCoords.isSet()) { line += formatMDLFloat((float) atom.getPoint3d().x); line += formatMDLFloat((float) atom.getPoint3d().y); line += formatMDLFloat((float) atom.getPoint3d().z) + " "; @@ -415,6 +421,25 @@ public class MDLWriter extends DefaultChemObjectWriter { return s; } + private void initIOSettings() { + forceWriteAs2DCoords = new BooleanIOSetting( + "ForceWriteAs2DCoordinates", + IOSetting.LOW, + "Should coordinates always be written as 2D?", + "false" + ); + } + + public void customizeJob() { + fireIOSettingQuestion(forceWriteAs2DCoords); + } + + public IOSetting[] getIOSettings() { + IOSetting[] settings = new IOSetting[1]; + settings[0] = forceWriteAs2DCoords; + return settings; + } + } src/main/org/openscience/cdk/io/MDLWriter.java 56852f8bd541bb84412e50cf451e0bfc881d7e82 Egon Willighagen egonw@users.sourceforge.net http://github.com/egonw/cdk/commit/0e6aa2cf14df67eb89c91a3a41131ed18f3b05d2 0e6aa2cf14df67eb89c91a3a41131ed18f3b05d2 2009-11-01T06:55:22-08:00 2009-06-11T11:24:38-07:00 Added writer IO option to force writing of 2D coordinates if 3D coordinates are present too, which now are preferably outputted. Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> 4be0dc49c5897a0604e2eb2822d28d0cd7709974 Rajarshi Guha rajarshi.guha@gmail.com