Canonical label その3

各原子に割り当てられた素数の積と
並び替えらた原子の中間順位を出力してみます。

/* inv_label_EC.java */
import java.io.*;

import org.openscience.cdk.interfaces.*;

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

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesGenerator;

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

import org.openscience.cdk.tools.periodictable.PeriodicTable;

import org.openscience.cdk.CDKConstants;

import java.util.*;


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

            System.err.println("inv_label <sd-file>");

            System.exit(1);

        }

        FileInputStream fis = null;

        IteratingMDLReader isr = null;

        try{

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

            isr = new IteratingMDLReader(fis, DefaultChemObjectBuilder.getInstance() );

        } catch (Exception e) {

            e.printStackTrace();

        }
        while( isr.hasNext() ){

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

            String id = (String)imol.getProperty("cdk:Title");
            ArrayList vect = new ArrayList();

            try {

                AtomContainerManipulator acm = new AtomContainerManipulator();

                IAtomContainer atoms = acm.removeHydrogens(imol);

                vect = createInvarLabel(atoms);
                System.out.printf("%s", id);

                for (int i = 0 ; i < vect.size() ; i++){

                    System.out.printf(" %s", atoms.getAtom(i).getSymbol() );

                }

                System.out.print("\n");

                for (int i = 0 ; i < vect.size() ; i++){

                    System.out.printf(" %s",

                                      atoms.getAtom(i).getProperty("InvariancePair"));

                }

                System.out.print("\n");
                step3(vect, atoms);
            }catch (Exception e1) {

                e1.printStackTrace();

            }

        }

    }
    private static void primeProduct(ArrayList v, IAtomContainer atomContainer) {

        Iterator it = v.iterator();

        Iterator n;

        InvPair inv;

        IAtom a;

        long summ;

        while (it.hasNext()) {

            inv = (InvPair) it.next();

            List neighbour = atomContainer.getConnectedAtomsList(inv.getAtom());

            n = neighbour.iterator();

            summ = 1;

            while (n.hasNext()) {

                a = (IAtom) n.next();

                int next = ( (InvPair)a.getProperty(InvPair.INVARIANCE_PAIR)).getPrime();

                summ = summ * next;

            }

            inv.setLast(inv.getCurr());

            inv.setCurr(summ);

        }

    }
    private static void sortArrayList(ArrayList v) {

        Collections.sort(v, new Comparator() {

                public int compare(Object o1, Object o2) {

                    return (int) ( ( (InvPair) o1).getCurr() - ( (InvPair)o2).getCurr());

                }

            });

        Collections.sort(v, new Comparator() {

                public int compare(Object o1, Object o2) {

                    return (int) ( ( (InvPair) o1).getLast() - ( (InvPair)o2).getLast());

                }

            });

    }
    private static void rankArrayList(ArrayList v) {

        int num = 1;

        int[] temp = new int[v.size()];

        InvPair last = (InvPair) v.get(0);

        Iterator it = v.iterator();

        InvPair curr;

        for (int x = 0; it.hasNext(); x++) {

            curr = (InvPair) it.next();

            if (!last.equals(curr)) {

                num++;

            }

            temp[x] = num;

            last = curr;

        }

        it = v.iterator();

        for (int x = 0; it.hasNext(); x++) {

            curr = (InvPair) it.next();

            curr.setCurr(temp[x]);

            curr.setPrime();

        }

    }
    private static boolean isInvPart(ArrayList v) {

        if ( ( (InvPair) v.get(v.size()-1)).getCurr() == v.size())

            return true;

        Iterator it = v.iterator();

        InvPair curr;

        while (it.hasNext()) {

            curr = (InvPair) it.next();

            if (curr.getCurr() != curr.getLast())

                return false;

        }

        return true;

    }
    private static void breakTies(ArrayList v) {

        Iterator it = v.iterator();

        InvPair curr;

        InvPair last = null;

        int tie = 0;

        boolean found = false;

        for (int x = 0; it.hasNext(); x++) {

            curr = (InvPair) it.next();

            curr.setCurr(curr.getCurr() * 2);

            curr.setPrime();

            if (x != 0 && !found && curr.getCurr() == last.getCurr()) {

                tie = x - 1;

                found = true;

            }

            last = curr;

        }

        curr = (InvPair) v.get(tie);

        curr.setCurr(curr.getCurr() - 1);

        curr.setPrime();

    }
    private static ArrayList createInvarLabel(IAtomContainer ac) {

        StringBuffer inv;

        ArrayList vect = new ArrayList();

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

            IAtom a = ac.getAtom(i);

            inv = new StringBuffer();

            Integer ddd = a.getImplicitHydrogenCount();
            // 1. Num connections (incl H)

            inv.append( ac.getConnectedAtomsList(a).size() +

                        (a.getImplicitHydrogenCount() == CDKConstants.UNSET ?

                         0 : a.getImplicitHydrogenCount()) );

            // 2. Num of non H bonds

            //System.out.printf(" %d\n", ac.getConnectedAtomsList(a).size() );

            inv.append( String.format("%02d",

                                      ac.getConnectedAtomsList(a).size()) );

            // 3. Atomic num

            inv.append( String.format("%02d",

                                      PeriodicTable.getAtomicNumber(a.getSymbol()) ) );

            // 4. Sign of charge

            Integer fcharge = a.getFormalCharge();

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

            if (fcharge < 0){

                inv.append(1);

            } else {

                inv.append(0);

            }

            // 5. Absolute charge

            inv.append( (int)Math.abs( (a.getFormalCharge() ==

                                CDKConstants.UNSET ? 0.0 : a.getFormalCharge()) ) );

            // 6. Hydrogen count

            inv.append( (a.getImplicitHydrogenCount() == CDKConstants.UNSET ?

                         0 : a.getImplicitHydrogenCount()));
            vect.add(new InvPair(Long.parseLong(inv.toString()), a));

        }

        return vect;

    }

}