Examples with InvalidSmilesException org.openscience.cdk.exception.InvalidSmilesException used on opensource projects

Example 6 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class FamilyDB method init.

public void init(MonomersDB monoDB) {
    Map<String, List<Monomer>> clusters = new HashMap<>();
    for (Monomer mono : monoDB.getObjects()) {
        String smiles = null;
        try {
            smiles = SmilesConverter.conv.toCanonicalSmiles(mono.getSmiles());
        } catch (InvalidSmilesException e) {
            System.err.println("Impossible to parse " + mono.getName() + " id:" + mono.getId());
            System.err.println(mono.getSmiles());
            continue;
        }
        List<Monomer> cluster = clusters.containsKey(smiles) ? clusters.get(smiles) : new ArrayList<Monomer>();
        cluster.add(mono);
        clusters.put(smiles, cluster);
    }
    for (String smiles : clusters.keySet()) {
        Family family = new Family();
        for (Monomer mono : clusters.get(smiles)) {
            family.addMonomer(mono);
            this.addObject(mono.getCode(), family);
        }
    }
}

Example 7 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class ParsePDBe method main.

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    File directory = new File("/mnt/data/PDBe/mmcif");
    Map<String, JSONObject> names = new HashMap<>();
    JSONArray poly = new JSONArray();
    JSONArray mono = new JSONArray();
    JSONArray nonpoly = new JSONArray();
    for (File molfile : directory.listFiles()) {
        try {
            BufferedReader br = new BufferedReader(new FileReader(molfile));
            JSONObject jso = new JSONObject();
            String line;
            while ((line = br.readLine()) != null) {
                if (line.startsWith("_chem_comp.pdbx_subcomponent_list")) {
                    if (line.contains("?")) {
                        mono.add(jso);
                        jso.put("desc", jso.get("name"));
                        jso.put("name", jso.get("id"));
                    } else {
                        // Graph spliting
                        String[] split = line.split("\"")[1].split(" ");
                        JSONObject graph = new JSONObject();
                        JSONArray v = new JSONArray();
                        graph.put("V", v);
                        JSONArray e = new JSONArray();
                        graph.put("E", e);
                        for (int i = 0; i < split.length; i++) {
                            v.add(split[i]);
                            if (i > 0) {
                                JSONArray bond = new JSONArray();
                                bond.add(i - 1);
                                bond.add(i);
                                e.add(bond);
                            }
                        }
                        jso.put("graph", graph);
                        // Add in polymers
                        poly.add(jso);
                    }
                } else if (line.startsWith("_chem_comp.id")) {
                    System.out.println(line);
                    line = line.replaceAll("_chem_comp.id", "");
                    line = line.replaceAll(" ", "").replaceAll("\t", "");
                    jso.put("id", line);
                    names.put(line, jso);
                } else if (line.startsWith("_chem_comp.name")) {
                    System.out.println(line);
                    line = line.replaceAll("_chem_comp.name", "");
                    line = line.replaceAll(" ", "").replaceAll("\t", "");
                    jso.put("name", line);
                    jso.put("desc", line);
                } else if (jso.containsKey("id") && line.startsWith((String) jso.get("id")) && line.contains("SMILES") && line.contains("ACDLabs")) {
                    System.out.println(line);
                    if (line.contains("\"")) {
                        String[] split = line.split("\"");
                        line = split[split.length - 2];
                    } else {
                        String[] split = line.split(" ");
                        line = split[split.length - 1];
                    }
                    try {
                        IMolecule mol = SmilesConverter.conv.transform(line);
                        if (ConnectivityChecker.isConnected(mol)) {
                            StructureDiagramGenerator sdg = new StructureDiagramGenerator(mol);
                            sdg.generateCoordinates();
                            jso.put("smiles", line);
                        }
                    } catch (InvalidSmilesException e) {
                    } catch (CDKException e) {
                    } catch (IllegalArgumentException e) {
                    }
                } else if (jso.containsKey("id") && line.startsWith((String) jso.get("id")) && line.contains("SMILES") && !jso.containsKey("smiles")) {
                    if (line.contains("\"")) {
                        String[] split = line.split("\"");
                        if (split.length > 1)
                            line = split[1];
                    } else {
                        String[] split = line.split(" ");
                        line = split[split.length - 1];
                    }
                    try {
                        IMolecule mol = SmilesConverter.conv.transform(line);
                        if (ConnectivityChecker.isConnected(mol)) {
                            StructureDiagramGenerator sdg = new StructureDiagramGenerator(mol);
                            sdg.generateCoordinates();
                            jso.put("smiles", line);
                        }
                    } catch (InvalidSmilesException e) {
                    } catch (CDKException e) {
                    } catch (IllegalArgumentException e) {
                    }
                } else if (line.startsWith("_chem_comp.type")) {
                    if (line.contains("NON-POLYMER"))
                        nonpoly.add(jso);
                }
            }
            if (!jso.containsKey("smiles") || jso.get("smiles") == null) {
                poly.remove(jso);
                mono.remove(jso);
                nonpoly.remove(jso);
                names.remove(jso);
                System.err.println(jso.toJSONString());
            }
            System.out.println();
            br.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    HashSet<String> needed = new HashSet<>();
    for (Object o : poly) {
        JSONObject p = (JSONObject) o;
        JSONObject graph = (JSONObject) p.get("graph");
        JSONArray v = (JSONArray) graph.get("V");
        for (Object o2 : v) {
            String name = (String) o2;
            needed.add(name);
        }
    }
    JSONArray minMonos = new JSONArray();
    for (String name : needed) {
        if (names.containsKey(name)) {
            minMonos.add(names.get(name));
            System.out.println(name + " added");
        } else {
            System.err.println("Impossible to add " + name);
        }
    }
    System.out.println(poly.size());
    System.out.println(mono.size());
    System.out.println(nonpoly.size());
    System.out.flush();
    // Save files
    try {
        BufferedWriter bw = new BufferedWriter(new FileWriter("data/pdbe_monos.json"));
        bw.write(nonpoly.toJSONString());
        bw.close();
        bw = new BufferedWriter(new FileWriter("data/pdbe_polys.json"));
        bw.write(poly.toJSONString());
        bw.close();
        bw = new BufferedWriter(new FileWriter("data/pdbe_monos_extended.json"));
        bw.write(mono.toJSONString());
        bw.close();
        bw = new BufferedWriter(new FileWriter("data/pdbe_monos_min.json"));
        bw.write(minMonos.toJSONString());
        bw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 8 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class PlanarityTest method main.

public static void main(String[] args) {
    String pepDBname = "datas/peptides.csv";
    // Loading databases
    PolymersJsonLoader pcl = new PolymersJsonLoader(new MonomersDB());
    PolymersDB pepDB = pcl.loadFile(pepDBname);
    // Tools
    Planarity pt = new Planarity();
    for (Polymer pep : pepDB.getObjects()) {
        System.out.println(pep.getName() + " : ");
        IMolecule mol = null;
        try {
            mol = SmilesConverter.conv.transform(pep.getSmiles());
        } catch (InvalidSmilesException e) {
            System.err.println("Impossible to parse " + pep.getName() + " id:" + pep.getId());
            continue;
        }
        SimpleGraph g = MoleculeGraphs.getMoleculeGraph(mol);
        System.out.println("planar : " + pt.isPlanar(g) + "\n");
    }
}

Example 9 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class PolymersTreeWidths method main.

public static void main(String[] args) {
    if (args.length < 1) {
        System.err.println("Command line : java main.PeptidesTreeWidths <peptidesFile> [outfile]");
        System.exit(-1);
    }
    // Parse arguments
    String pepDBname = args[0];
    BufferedWriter bw = null;
    if (args.length > 1) {
        File out = new File(args[1]);
        if (out.exists())
            out.delete();
        try {
            bw = new BufferedWriter(new FileWriter(out));
            bw.write("peptide;treewidth\n");
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    // Loading databases
    MonomersDB monoDB = new MonomersDB();
    PolymersJsonLoader pcl = new PolymersJsonLoader(monoDB);
    PolymersDB pepDB = pcl.loadFile(pepDBname);
    // Tools for treewidth
    MolTreeWidth mtw = new MolTreeWidth();
    for (Polymer pep : pepDB.getObjects()) {
        int tw;
        try {
            tw = mtw.calculateTreeWidth(SmilesConverter.conv.transform(pep.getSmiles()));
        } catch (InvalidSmilesException e) {
            System.err.println("Impossible to parse " + pep.getName() + " id:" + pep.getId());
            continue;
        }
        if (args.length > 1) {
            try {
                bw.write(pep.getName() + ";" + tw + "\n");
            } catch (IOException e) {
                e.printStackTrace();
            }
        } else {
            System.out.println(pep.getName() + " : " + tw);
        }
    }
    if (args.length > 1) {
        try {
            bw.close();
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
}

Example 10 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class SmilesConverter method transform.

public Molecule transform(String smiles, boolean addHydrogens, boolean calculateCoordinate, boolean expliciteHydrogens) throws InvalidSmilesException {
    Molecule imol = null;
    try {
        imol = new Molecule(sp.parseSmiles(smiles));
        // Add hydrogens
        if (addHydrogens) {
            CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(imol.getBuilder());
            try {
                adder.addImplicitHydrogens(imol);
                if (expliciteHydrogens)
                    AtomContainerManipulator.convertImplicitToExplicitHydrogens(imol);
            } catch (CDKException e) {
                e.printStackTrace();
            }
        } else {
            for (IAtom a : imol.atoms()) a.setImplicitHydrogenCount(0);
            if (!expliciteHydrogens)
                imol = new Molecule(AtomContainerManipulator.removeHydrogens(imol));
        }
        if (calculateCoordinate) {
            StructureDiagramGenerator sdg = new StructureDiagramGenerator(imol);
            try {
                sdg.generateCoordinates();
            } catch (CDKException e) {
                System.err.println(smiles);
                e.printStackTrace();
            }
            imol = new Molecule(sdg.getMolecule());
        }
    } catch (InvalidSmilesException e) {
        throw e;
    }
    return imol;
}