Package org.openscience.cdk

Examples of org.openscience.cdk.AtomContainerSet

431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
        // Smiles reading
        if (cor.accepts(IAtomContainerSet.class) && chemModel==null) {
            // try to read a Molecule set
            try {
                IAtomContainerSet som = (AtomContainerSet) cor.read(new AtomContainerSet());
                chemModel = new ChemModel();
                chemModel.setMoleculeSet(som);
                if (chemModel == null) {
                    error = "The object chemModel was empty unexpectedly!";
                }
            } catch (Exception exception) {
                error = "Error while reading file: " + exception.getMessage();
                exception.printStackTrace();
            }
        }

        // MDLV3000 reading
        if (cor.accepts(IAtomContainer.class) && chemModel==null) {
            // try to read a Molecule
                IAtomContainer mol = (AtomContainer) cor.read(new AtomContainer());
                if(mol!=null )
                    try{
                        IAtomContainerSet newSet = new AtomContainerSet();
                        newSet.addAtomContainer(mol);
                        chemModel = new ChemModel();
                        chemModel.setMoleculeSet(newSet);
                        if (chemModel == null) {
                            error = "The object chemModel was empty unexpectedly!";
                        }
View Full Code Here
513
514
515
516
517
518
519
520
521
522
523
        if (molecule == null) return;

        IChemModel chemModel = chemPaintPanel.getChemModel();
        IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
        if (moleculeSet == null) {
            moleculeSet = new AtomContainerSet();
        }
       
        // On copy & paste on top of an existing drawn structure, prevent the
        // pasted section to be drawn exactly on top or to far away from the
        // original by shifting it to a fixed position next to it.
View Full Code Here
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
     * @throws CDKException InChI could not be generated
     */
    public static IChemModel readInChI(URL url) throws CDKException {
        IChemModel chemModel = new ChemModel();
        try {
            IAtomContainerSet moleculeSet = new AtomContainerSet();
            chemModel.setMoleculeSet(moleculeSet);

            BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
            String line;
            while ((line = in.readLine()) != null) {
                if (line.toLowerCase().startsWith("inchi=")) {
                    moleculeSet.addAtomContainer(parseInChI(line));
                }
            }
            in.close();
        } catch (Exception e) {

View Full Code Here
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
     */
    public static IChemModel readInChI(URL url) throws CDKException {

        IChemModel chemModel = new ChemModel();
        try {
            IAtomContainerSet moleculeSet = new AtomContainerSet();
            chemModel.setMoleculeSet(moleculeSet);
            StdInChIParser parser = new StdInChIParser();

            BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
            String line;
            while ((line = in.readLine()) != null)
            {
                if (line.toLowerCase().startsWith("inchi=")) {
                    IAtomContainer atc = parser.parseInchi(line);
                    moleculeSet.addAtomContainer(atc);
                }
            }
            in.close();
           
           
View Full Code Here
TOP

Related Classes of org.openscience.cdk.AtomContainerSet

  • org.openscience.jchempaint.application.JChemPaint
  • org.openscience.jchempaint.inchi.InChITool
  • org.openscience.jchempaint.inchi.StdInChIReader
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.