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[Cdk-commits] SF.net SVN: cdk: [6053] trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java
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From: <to...@us...> - 2006-04-20 16:09:14
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Revision: 6053 Author: tohel Date: 2006-04-20 09:09:01 -0700 (Thu, 20 Apr 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6053&view=rev Log Message: ----------- the MDLWriter now handles AtomContainers, too Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java Modified: trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java 2006-04-20 15:58:27 UTC (rev 6052) +++ trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java 2006-04-20 16:09:01 UTC (rev 6053) @@ -201,13 +201,13 @@ writeSetOfMolecules((ISetOfMolecules)object); } else if (object instanceof IChemFile) { writeChemFile((IChemFile)object); - } else if (object instanceof IMolecule) { + } else if (object instanceof IMolecule || object instanceof IAtomContainer) { try{ - boolean[] isVisible=new boolean[((IMolecule)object).getAtomCount()]; + boolean[] isVisible=new boolean[((IAtomContainer)object).getAtomCount()]; for(int i=0;i<isVisible.length;i++){ isVisible[i]=true; } - writeMolecule((IMolecule)object,isVisible); + writeMolecule((IAtomContainer)object,isVisible); } catch (Exception ex) { logger.error(ex.getMessage()); @@ -215,7 +215,7 @@ throw new CDKException("Exception while writing MDL file: " + ex.getMessage(), ex); } } else { - throw new CDKException("Only supported is writing of ChemFile, SetOfMolecules and Molecule objects."); + throw new CDKException("Only supported is writing of ChemFile, SetOfMolecules, AtomContainer and Molecule objects."); } } @@ -277,7 +277,7 @@ * @param molecule Molecule that is written to an OutputStream * @param isVisible Should a certain atom be written to mdl? */ - public void writeMolecule(IMolecule molecule, boolean[] isVisible) throws Exception { + public void writeMolecule(IAtomContainer container, boolean[] isVisible) throws Exception { String line = ""; // taking care of the $$$$ signs: // we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule @@ -287,7 +287,7 @@ } // write header block // lines get shortened to 80 chars, that's in the spec - String title = (String)molecule.getProperty(CDKConstants.TITLE); + String title = (String)container.getProperty(CDKConstants.TITLE); if (title == null) title = ""; if(title.length()>80) title=title.substring(0,80); @@ -309,7 +309,7 @@ ); writer.write('\n'); - String comment = (String)molecule.getProperty(CDKConstants.REMARK); + String comment = (String)container.getProperty(CDKConstants.REMARK); if (comment == null) comment = ""; if(comment.length()>80) comment=comment.substring(0,80); @@ -323,20 +323,20 @@ } line += formatMDLInt(upToWhichAtom, 3); int numberOfBonds=0; - if(upToWhichAtom<molecule.getAtomCount()){ - for(int i=0;i<molecule.getBondCount();i++){ - if(isVisible[molecule.getAtomNumber(molecule.getBondAt(i).getAtoms()[0])] && isVisible[molecule.getAtomNumber(molecule.getBondAt(i).getAtoms()[1])]) + if(upToWhichAtom<container.getAtomCount()){ + for(int i=0;i<container.getBondCount();i++){ + if(isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(i).getAtoms()[1])]) numberOfBonds++; } }else{ - numberOfBonds=molecule.getBondCount(); + numberOfBonds=container.getBondCount(); } line += formatMDLInt(numberOfBonds, 3); line += " 0 0 0 0 0 0 0 0999 V2000\n"; writer.write(line); // write Atom block - IAtom[] atoms = molecule.getAtoms(); + IAtom[] atoms = container.getAtoms(); for (int f = 0; f < atoms.length; f++) { if(isVisible[f]){ IAtom atom = atoms[f]; @@ -356,10 +356,10 @@ line += formatMDLFloat((float)0.0); line += formatMDLFloat((float)0.0) + " "; } - if(molecule.getAtomAt(f) instanceof IPseudoAtom) - line += formatMDLString(((IPseudoAtom) molecule.getAtomAt(f)).getLabel(), 3); + if(container.getAtomAt(f) instanceof IPseudoAtom) + line += formatMDLString(((IPseudoAtom) container.getAtomAt(f)).getLabel(), 3); else - line += formatMDLString(molecule.getAtomAt(f).getSymbol(), 3); + line += formatMDLString(container.getAtomAt(f).getSymbol(), 3); line += " 0 0 0 0 0 0 0 0 0 0 0 0"; writer.write(line); writer.newLine(); @@ -367,9 +367,9 @@ } // write Bond block - IBond[] bonds = molecule.getBonds(); + IBond[] bonds = container.getBonds(); for (int g = 0; g < bonds.length; g++) { - if(upToWhichAtom==molecule.getAtomCount() || (isVisible[molecule.getAtomNumber(molecule.getBondAt(g).getAtoms()[0])] && isVisible[molecule.getAtomNumber(molecule.getBondAt(g).getAtoms()[1])])){ + if(upToWhichAtom==container.getAtomCount() || (isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[0])] && isVisible[container.getAtomNumber(container.getBondAt(g).getAtoms()[1])])){ IBond bond = bonds[g]; if (bond.getAtoms().length != 2) { logger.warn("Skipping bond with more/less than two atoms: " + bond); @@ -377,11 +377,11 @@ if (bond.getStereo() == CDKConstants.STEREO_BOND_UP_INV || bond.getStereo() == CDKConstants.STEREO_BOND_DOWN_INV) { // turn around atom coding to correct for inv stereo - line = formatMDLInt(molecule.getAtomNumber(bond.getAtomAt(1)) + 1,3); - line += formatMDLInt(molecule.getAtomNumber(bond.getAtomAt(0)) + 1,3); + line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1,3); + line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1,3); } else { - line = formatMDLInt(molecule.getAtomNumber(bond.getAtomAt(0)) + 1,3); - line += formatMDLInt(molecule.getAtomNumber(bond.getAtomAt(1)) + 1,3); + line = formatMDLInt(container.getAtomNumber(bond.getAtomAt(0)) + 1,3); + line += formatMDLInt(container.getAtomNumber(bond.getAtomAt(1)) + 1,3); } line += formatMDLInt((int)bond.getOrder(),3); line += " "; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |