Examples with IAtom org.openscience.cdk.interfaces.IAtom used on opensource projects

Example 36 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class Extension method getSerial.

public String getSerial() {
    IAtom a0 = this.bond.getAtom(0);
    IAtom a1 = this.bond.getAtom(1);
    String name0 = a0.getFlag(CDKConstants.ISAROMATIC) ? a0.getSymbol().toLowerCase() : a0.getSymbol();
    String name1 = a1.getFlag(CDKConstants.ISAROMATIC) ? a1.getSymbol().toLowerCase() : a1.getSymbol();
    return name0 + "," + this.bond.getOrder().ordinal() + "," + name1 + "," + a0.getImplicitHydrogenCount() + "," + a1.getImplicitHydrogenCount();
}

Example 37 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class Extension method clone.

public Extension clone() {
    Extension ext = new Extension();
    IAtom a0 = null, a1 = null;
    try {
        a0 = (IAtom) this.bond.getAtom(0).clone();
        a1 = (IAtom) this.bond.getAtom(1).clone();
    } catch (CloneNotSupportedException e) {
        e.printStackTrace();
    }
    ext.bond = new Bond(a0, a1, this.bond.getOrder());
    return ext;
}

Example 38 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class Extension method match.

/**
 * Match "this" extension on the bond from the chemical object with or without strict rules
 * @param bond Bond to match
 * @param light False for strict matching, true for aromatic, bond degree and hydrogen approximation.
 * @return list of matches
 */
public List<BondMapping> match(IBond bond, MatchingType type) {
    List<BondMapping> mappings = new ArrayList<>();
    IAtom a0 = bond.getAtom(0);
    IAtom a1 = bond.getAtom(1);
    IAtom e0 = this.bond.getAtom(0);
    IAtom e1 = this.bond.getAtom(1);
    int h0 = a0.getImplicitHydrogenCount();
    int h1 = a1.getImplicitHydrogenCount();
    int eh0 = e0.getImplicitHydrogenCount();
    int eh1 = e1.getImplicitHydrogenCount();
    // Mapping in bond direction
    if (this.areSameAtoms(e0, e1, a0, a1))
        if (this.lightToStrongMatching(e0, e1, eh0, eh1, a0, a1, h0, h1, this.bond, bond)) {
            if (this.strongToExactMatching(eh0, eh1, h0, h1))
                mappings.add(new BondMapping(bond, this, a0, a1, eh0, eh1, MatchingType.EXACT));
            else if (type != MatchingType.EXACT)
                mappings.add(new BondMapping(bond, this, a0, a1, eh0, eh1, MatchingType.STRONG));
        } else if (type == MatchingType.LIGHT) {
            mappings.add(new BondMapping(bond, this, a0, a1, 0, 0, MatchingType.LIGHT));
        }
    // Reverse mapping
    if (this.areSameAtoms(e0, e1, a1, a0))
        if (this.lightToStrongMatching(e0, e1, eh0, eh1, a1, a0, h1, h0, this.bond, bond)) {
            if (this.strongToExactMatching(eh0, eh1, h1, h0))
                mappings.add(new BondMapping(bond, this, a1, a0, eh0, eh1, MatchingType.EXACT));
            else if (type != MatchingType.EXACT)
                mappings.add(new BondMapping(bond, this, a1, a0, eh0, eh1, MatchingType.STRONG));
        } else if (type == MatchingType.LIGHT) {
            mappings.add(new BondMapping(bond, this, a1, a0, 0, 0, MatchingType.LIGHT));
        }
    return mappings;
}

Example 39 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class HydrogenAdd method getFreeHydrogens.

/**
 * Transform mc parameter to correct parameters for arity calculation
 * @param mc
 * @return
 */
private int getFreeHydrogens(MappedChain mc) {
    int atomIdx = mc.getAtomsMapping().get(this.idx);
    IMolecule mol = mc.getChemObject().getMolecule();
    IAtom a = mol.getAtom(atomIdx);
    int mappedHydrogens = mc.getHydrogensMapping().get(atomIdx);
    int presentHydrogens = a.getImplicitHydrogenCount();
    return presentHydrogens - mappedHydrogens;
}

Example 40 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class MappedChain method addAllHydrogens.

/**
 * To add real hydrogens from the chemical object to the bloc mapping
 * @return new BlocMapping with hydrogens.
 */
public void addAllHydrogens() {
    // Create the list of extensions
    Chain b = this.bloc;
    while (b != null) {
        b.setSerial(null);
        Extension ext = b.getExt().clone();
        b.setExtension(ext);
        IAtom a0 = ext.getBond().getAtom(0);
        IAtom a1 = ext.getBond().getAtom(1);
        int hs = 0;
        int idx0 = this.atomsMapping.get(b.getAbsolutePosition1());
        hs = this.getChemObject().getMolecule().getAtom(idx0).getImplicitHydrogenCount();
        a0.setImplicitHydrogenCount(hs);
        this.hydrogensMapping.put(idx0, hs);
        int idx1 = this.atomsMapping.get(b.getAbsolutePosition2());
        hs = this.getChemObject().getMolecule().getAtom(idx1).getImplicitHydrogenCount();
        a1.setImplicitHydrogenCount(hs);
        this.hydrogensMapping.put(idx1, hs);
        if (a0.getAtomicNumber() == a1.getAtomicNumber() && a0.getFlag(CDKConstants.ISAROMATIC) == a1.getFlag(CDKConstants.ISAROMATIC) && a0.getImplicitHydrogenCount() == a1.getImplicitHydrogenCount() && b.getPosition1() > b.getPosition2()) {
            b.invertPositions();
        }
        b = b.getSubBlc();
    }
}