水素結合ドナー

前回のコードを改造して、
ドナー（水素を供与する側の原子）の数も同時に数えてみましょう。
定義は、アクセプターより単純です。

• 酸素もしくは窒素原子のうち、水素原子に隣接し、しかも負電荷を帯びていないもの

ID, アクセプター数、ドナー数をタブ区切りで出力してみます。

/* HBAccDon.java */
import java.io.*;

import org.openscience.cdk.io.iterator.IteratingSMILESReader;

import org.openscience.cdk.interfaces.IMolecule;

import org.openscience.cdk.interfaces.IAtom;

import org.openscience.cdk.interfaces.IAtomContainer;

import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import org.openscience.cdk.CDKConstants;

import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;


class HBAccDon {

    public static void main(String args[]){
        if(args.length!=1){

            System.err.println("HBAccDon <smiles-file>");

            System.exit(1);

        }

        FileInputStream fis = null;

        IteratingSMILESReader isr = null;

        try{

            fis = new FileInputStream(new File(args[0]));

            isr = new IteratingSMILESReader(fis);

        } catch (Exception e) {

            e.printStackTrace();

        }
        while( isr.hasNext() ){    // Read a file line by line

            IMolecule imol = (IMolecule)isr.next();

            String id = (String)imol.getProperty("cdk:Title");  // The 2nd column
            int hBondAcceptors = 0;

            IAtomContainer ac;

            try {
                ac = (IAtomContainer) imol.clone();

                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);

                CDKHueckelAromaticityDetector.detectAromaticity(ac);
                atomloop:

                for (int atomIndex = 0; atomIndex < ac.getAtomCount(); atomIndex++) {

                    // looking for suitable nitrogen atoms

                    if (ac.getAtom(atomIndex).getSymbol().equals("N") &&

                        ac.getAtom(atomIndex).getFormalCharge() <= 0) {

                        // excluding nitrogens that are adjacent to an oxygen

                        java.util.List neighbours =

                            ac.getConnectedAtomsList(ac.getAtom(atomIndex));

                        for (Object neighbour : neighbours)

                            if (((IAtom) neighbour).getSymbol().equals("O"))

                                continue atomloop;

                        hBondAcceptors++;

                    }

                    // looking for suitable oxygen atoms

                    if (ac.getAtom(atomIndex).getSymbol().equals("O") &&

                        ac.getAtom(atomIndex).getFormalCharge() <= 0) {

                        //excluding oxygens that are adjacent to a nitrogen or to an aromatic carbon
                        java.util.List neighbours = ac.getConnectedAtomsList(ac.getAtom(atomIndex));

                        for (Object neighbour : neighbours)

                            if (((IAtom) neighbour).getSymbol().equals("N") ||

                                (((IAtom) neighbour).getSymbol().equals("C")

                                 && ((IAtom) neighbour ).getFlag(CDKConstants.ISAROMATIC)))
                                continue atomloop;

                        hBondAcceptors++;

                    }

                }
                int hBondDonors = 0;

                atomloop2:

                for (int atomIndex = 0; atomIndex < ac.getAtomCount(); atomIndex++) {

                    IAtom atom = (IAtom) ac.getAtom(atomIndex);

                    // checking for O and N atoms where the formal charge is >= 0

                    if ( (atom.getSymbol().equals("O") || atom.getSymbol().equals("N"))

                         && atom.getFormalCharge() >= 0) {

                        // implicit hydrogens

                        Integer implicitH = atom.getHydrogenCount();

                        if (implicitH == CDKConstants.UNSET) implicitH = 0;

                        if (implicitH > 0) {

                            hBondDonors++;

                            continue atomloop2;

                        }

                        // explicit hydrogens

                        java.util.List neighbours = ac.getConnectedAtomsList(atom);

                        for (Object neighbour : neighbours) {

                            if (((IAtom) neighbour).getSymbol().equals("H")) {

                                hBondDonors++;

                                continue atomloop2;

                            }

                        }

                    }

                }
                System.out.printf("%s\t%d\t%d\n", id, hBondAcceptors, hBondDonors);

            } catch (Exception e1) {

                e1.printStackTrace();

            }

        }

    }

}