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Low memory path traversal.
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@johnmay
johnmay committed Apr 8, 2017
1 parent cd59c82 commit 87dd91f
Showing 1 changed file with 107 additions and 33 deletions.
140 changes: 107 additions & 33 deletions base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java
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Expand Up @@ -35,10 +35,12 @@
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import java.util.ArrayList;
import java.util.BitSet;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Random;
Expand Down Expand Up @@ -186,29 +188,105 @@ private IBond findBond(List<IBond> bonds, IAtom beg, IAtom end) {
return null;
}

private String encodePath(IAtomContainer mol, Map<IAtom, List<IBond>> cache, List<IAtom> path) {
StringBuilder sb = new StringBuilder();

IAtom prev = path.get(0);
sb.append(getAtomSymbol(prev));
for (int i = 1; i < path.size(); i++) {
final IAtom next = path.get(i);
private String encodePath(IAtomContainer mol, Map<IAtom, List<IBond>> cache, List<IAtom> path, StringBuilder buffer) {
buffer.setLength(0);
IAtom prev = path.get(path.size()-1);
buffer.append(getAtomSymbol(prev));
for (int i = path.size()-2; i >= 0; i--) {
final IAtom next = path.get(i);
List<IBond> bonds = cache.get(prev);

if (bonds == null) {
bonds = mol.getConnectedBondsList(prev);
cache.put(prev, bonds);
}

IBond bond = findBond(bonds, next, prev);
IBond bond = findBond(bonds, next, prev);
if (bond == null)
throw new IllegalStateException("FATAL - Atoms in patch were connected?");
sb.append(getBondSymbol(bond));
sb.append(getAtomSymbol(next));
buffer.append(getBondSymbol(bond));
buffer.append(getAtomSymbol(next));
prev = next;
}
return buffer.toString();
}

private static final class State {
private int numPaths = 0;
private Random rand = new Random();
private BitSet fp;
private IAtomContainer mol;
private Set<IAtom> visited = new HashSet<>();
private List<IAtom> apath = new ArrayList<>();
private List<IBond> bpath = new ArrayList<>();
private final int maxDepth;
private final int fpsize;
private Map<IAtom,List<IBond>> cache = new IdentityHashMap<>();
public StringBuilder buffer = new StringBuilder();

public State(IAtomContainer mol, BitSet fp, int fpsize, int maxDepth) {
this.mol = mol;
this.fp = fp;
this.fpsize = fpsize;
this.maxDepth = maxDepth;
}

List<IBond> getBonds(IAtom atom) {
List<IBond> bonds = cache.get(atom);
if (bonds == null) {
bonds = mol.getConnectedBondsList(atom);
cache.put(atom, bonds);
}
return bonds;
}

return sb.toString();
boolean visit(IAtom a) {
return visited.add(a);
}

boolean unvisit(IAtom a) {
return visited.remove(a);
}

void push(IAtom atom, IBond bond) {
apath.add(atom);
if (bond != null)
bpath.add(bond);
}

void pop() {
if (!apath.isEmpty())
apath.remove(apath.size()-1);
if (!bpath.isEmpty())
bpath.remove(bpath.size()-1);
}

void addHash(int x) {
numPaths++;
rand.setSeed(x);
// XXX: fp.set(x % size); would work just as well but would encode a
// different bit
fp.set(rand.nextInt(fpsize));
}
}

private void traversePaths(State state, IAtom beg, IBond prev) throws CDKException {
state.push(beg, prev);
state.addHash(encodeUniquePath(state.mol, state.cache, state.apath, state.buffer));
if (state.numPaths > pathLimit)
throw new CDKException("To many paths!");
if (state.apath.size() < state.maxDepth) {
for (IBond bond : state.getBonds(beg)) {
if (bond == prev)
continue;
final IAtom nbr = bond.getConnectedAtom(beg);
if (state.visit(nbr)) {
traversePaths(state, nbr, prev);
state.unvisit(nbr); // traverse all paths
}
}
}
state.pop();
}

/**
Expand All @@ -228,11 +306,11 @@ protected int[] findPathes(IAtomContainer container, int searchDepth) throws CDK
Set<Integer> hashes = new HashSet<>();

Map<IAtom, List<IBond>> cache = new HashMap<>();

StringBuilder buffer = new StringBuilder();
for (IAtom startAtom : container.atoms()) {
List<List<IAtom>> p = PathTools.getLimitedPathsOfLengthUpto(container, startAtom, searchDepth, pathLimit);
for (List<IAtom> path : p) {
hashes.add(encodePath(container, cache, path).hashCode());
hashes.add(encodeUniquePath(container, cache, path, buffer));
}
}

Expand All @@ -245,27 +323,23 @@ protected int[] findPathes(IAtomContainer container, int searchDepth) throws CDK
}

protected void encodePaths(IAtomContainer mol, int depth, BitSet fp, int size) throws CDKException {

Random rand = new Random();

Map<IAtom, List<IBond>> cache = new HashMap<>();

for (IAtom startAtom : mol.atoms()) {
List<List<IAtom>> p = PathTools.getLimitedPathsOfLengthUpto(mol, startAtom, depth, pathLimit);
for (List<IAtom> path : p) {
final int x = encodeUniquePath(mol, cache, path);
rand.setSeed(x);
// XXX: fp.set(x % size); would work just as well but would encode a
// different bit
fp.set(rand.nextInt(size));
}
State state = new State(mol, fp, size, depth+1);
for (IAtom atom : mol.atoms()) {
state.numPaths = 0;
state.visit(atom);
traversePaths(state, atom, null);
state.unvisit(atom);
}
}

private int encodeUniquePath(IAtomContainer container, Map<IAtom, List<IBond>> cache, List<IAtom> path) {
String forward = encodePath(container, cache, path);
private int encodeUniquePath(IAtomContainer container, Map<IAtom, List<IBond>> cache, List<IAtom> path, StringBuilder buffer) {
int hash = 0;
if (path.size() == 1)
return getAtomSymbol(path.get(0)).hashCode();
String forward = encodePath(container, cache, path, buffer);
Collections.reverse(path);
String reverse = encodePath(container, cache, path, buffer);
Collections.reverse(path);
String reverse = encodePath(container, cache, path);

final int x;
if (reverse.compareTo(forward) < 0)
Expand All @@ -276,9 +350,9 @@ private int encodeUniquePath(IAtomContainer container, Map<IAtom, List<IBond>> c
}

private String getAtomSymbol(IAtom atom) {
if (atom instanceof IPseudoAtom ||
atom.getAtomicNumber() == null ||
atom.getAtomicNumber() == 0) {
if (atom.getAtomicNumber() == null ||
atom.getAtomicNumber() == 0 ||
atom instanceof IPseudoAtom){
return "*";
} else {
// XXX: backwards compatibility
Expand Down

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