gilleain

package biojava;

import java.util.ArrayList;
import java.util.List;

import javax.vecmath.Point3d;

import org.biojava.bio.structure.Atom;
import org.biojava.bio.structure.Chain;
import org.biojava.bio.structure.Group;

gilleain

var iter = cdk.createMoleculeIterator("/tmp/C10H16_filtered.sdf");
var substructure = cdk.fromSMILES("C1CCCCC1");
var filepath = "/tmp/matches.sdf";
var molList = cdk.createMoleculeList();

while (iter.hasNext()) {
	var mol = cdk.create(iter.next());
	if (cdk.subStructureMatches(mol, substructure)) {
		molList.add(mol);
	}

gilleain

def EnumPartitions(m, n):
    P = {(0, 0) : 1}
    for i in range(1, m + 1):
        P[(i, 0)] = 0
    for i in range(1, m + 1):
        for j in range(1, min(i, n) + 1):
            if i < 2 * j:
                P[(i, j)] = P[(i - 1, j - 1)]
            else:
                P[(i, j)] = P[(i - 1, j - 1)] + P[(i - j, j)]

gilleain

def bin(x, count=8):
    return map(lambda y: (x>>y)&1, range(count-1, -1, -1))

def pvrSequenceToMatrix(X):
    return [bin(x, len(X)) for x in X]
        
def generateAllPVRSequences(xs, X, l, n, m):
    if l == n:
        xs.append(X)
    else:

gilleain

  public static IChemObjectBuilder builder = 
        NoNotificationChemObjectBuilder.getInstance();
    
    public IMolecule makeCHXFragment(int hCount) {
        IMolecule mol = builder.newMolecule();
        mol.addAtom(builder.newAtom("C"));
        mol.getAtom(0).setHydrogenCount(hCount);
        return mol;
    }
    

gilleain

package tmp;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

public class Model {
    
    public Map<String, Class> parameterTypes;
    

gilleain

package tmp;

import java.util.HashMap;
import java.util.Map;
import java.util.Set;

public class BaseGenerator implements IGenerator {
    
    public Map<String, Class> parameterTypes;
    

gilleain

package tmp;

public class MyGenerator extends BaseGenerator {
    
    public static final String BOND_DISTANCE = "BondDistance";
    
    public MyGenerator() {
        super.register(BOND_DISTANCE, Double.class, 5.0);
    }

gilleain

package test;

import java.util.ArrayList;
import java.util.List;

import tmp.IGenerator;
import tmp.Model;
import tmp.MyGenerator;

import static tmp.MyGenerator.BOND_DISTANCE;

gilleain

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;

import signature.chemistry.Molecule.BondOrder;


/**
 * Adapts a CDK IAtomContainer class to a signature.chemistry.Molecule class,