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Feb 7, 2022
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Utility functions for determining the smallest ring size of an atom/b… #820

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149 changes: 149 additions & 0 deletions base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,11 @@
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.RingSearch;

import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Deque;
import java.util.List;

import static org.openscience.cdk.graph.GraphUtil.EdgeToBondMap;
Expand Down Expand Up @@ -410,6 +412,153 @@ public static CycleFinder allOrVertexShort() {
return or(all(), vertexShort());
}

/**
* Convenience method to determine the smallest ring size of every atom in
* the molecule. For each atom index the smallest ring size is set in the
* array, if 0 the atom is acyclic. If you just need to check a single atom
* is more efficient to call {@link #smallRingSize(IAtom, int)}.
*
* @param mol the molecule
* @param rsizes the array to be filled
* @see #smallRingSize(IAtom, int)
*/
public static void smallRingSizes(IAtomContainer mol, int[] rsizes)
{
int acount = mol.getAtomCount();
int marker = acount+1;
if (rsizes == null || acount > rsizes.length)
throw new IllegalArgumentException();
Arrays.fill(rsizes, 0, acount, marker);
Cycles cycles = Cycles.vertexShort(mol);
for (int[] path : cycles.paths()) {
int rsize = path.length-1;
for (int v : path) {
rsizes[v] = Math.min(rsize, rsizes[v]);
}
}
// replace temporary marker values with '0'
for (int i = 0; i < acount; i++) {
if (rsizes[i] == marker)
rsizes[i] = 0;
}
}

/**
* Determine the smallest ring size an atom belongs to. This method requires
* that {@link #markRingAtomsAndBonds(IAtomContainer)} has been called
* first to set the {@link IAtom#isInRing()} status of each atom/bond. If
* you need to check every atom in a molecule use
* {@link @see #smallRingSizes(IAtomContainer, int[])}.
*
* @param atom the atom
* @param max the max ring size
* @return the ring size, or 0 if the atom is not in a ring or is in a ring
* larger than 'max'
* @see #smallRingSizes(IAtomContainer, int[])
*/
public static int smallRingSize(IAtom atom, int max) {
if (!atom.isInRing())
return 0;
IAtomContainer mol = atom.getContainer();
int[] distTo = new int[mol.getAtomCount()];
Arrays.fill(distTo, 1 + distTo.length);
distTo[atom.getIndex()] = 0;
Deque<IAtom> queue = new ArrayDeque<>();
queue.add(atom);
int smallest = 1 + distTo.length;
while (!queue.isEmpty()) {
IAtom a = queue.poll();
int dist = 1 + distTo[a.getIndex()];
for (IBond b : a.bonds()) {
if (!b.isInRing())
continue;
IAtom nbr = b.getOther(a);
if (dist < distTo[nbr.getIndex()]) {
distTo[nbr.getIndex()] = dist;
queue.add(nbr);
} else if (dist != 2 + distTo[nbr.getIndex()]) {
int tmp = dist + distTo[nbr.getIndex()];
if (tmp < smallest)
smallest = tmp;
}
}
if (2 * dist > 1 + max)
break;
}
return smallest <= max ? smallest : 0;
}

/**
* Determine the smallest ring size an atom belongs to. This method requires
* that {@link #markRingAtomsAndBonds(IAtomContainer)} has been called
* first to set the {@link IAtom#isInRing()} status of each atom/bond. If
* you need to check every atom in a molecule use
* {@link @see #smallRingSizes(IAtomContainer, int[])}.
*
* @param atom the atom
* @return the ring size, or 0 if the atom is not in a ring
* @see #smallRingSizes(IAtomContainer, int[])
*/
public static int smallRingSize(IAtom atom) {
return smallRingSize(atom, atom.getContainer().getAtomCount());
}

/**
* Determine the smallest ring size an bond belongs to. This method requires
* that {@link #markRingAtomsAndBonds(IAtomContainer)} has been called
* first to set the {@link IBond#isInRing()} status of each atom/bond.
*
* @param bond the bond
* @param max the max ring size
* @return the ring size, or 0 if the bond is not in a ring or is in a ring
* larger than 'max'
*/
public static int smallRingSize(IBond bond, int max) {
if (!bond.isInRing())
return 0;
IAtomContainer mol = bond.getContainer();
int[] distTo = new int[mol.getAtomCount()];
Arrays.fill(distTo, 1 + distTo.length);
distTo[bond.getBegin().getIndex()] = 0;
distTo[bond.getEnd().getIndex()] = 0;
Deque<IAtom> queue = new ArrayDeque<>();
queue.add(bond.getBegin());
queue.add(bond.getEnd());
int smallest = 1 + distTo.length;
while (!queue.isEmpty()) {
IAtom a = queue.poll();
int dist = 1 + distTo[a.getIndex()];
for (IBond b : a.bonds()) {
if (b == bond || !b.isInRing())
continue;
IAtom nbr = b.getOther(a);
if (dist < distTo[nbr.getIndex()]) {
distTo[nbr.getIndex()] = dist;
queue.add(nbr);
} else if (dist != 2 + distTo[nbr.getIndex()]) {
int tmp = 1 + dist + distTo[nbr.getIndex()];
if (tmp < smallest)
smallest = tmp;
}
}
if (2 * dist > 1 + max)
break;
}
return smallest <= max ? smallest : 0;
}

/**
* Determine the smallest ring size an bond belongs to. This method requires
* that {@link #markRingAtomsAndBonds(IAtomContainer)} has been called
* first to set the {@link IBond#isInRing()} status of each atom/bond.
*
* @param bond the bond
* @return the ring size, or 0 if the bond is not in a ring or is in a ring
* larger than 'max'
*/
public static int smallRingSize(IBond bond) {
return smallRingSize(bond, bond.getContainer().getAtomCount());
}

/**
* Find and mark all cyclic atoms and bonds in the provided molecule.
Expand Down
136 changes: 136 additions & 0 deletions base/test-core/src/test/java/org/openscience/cdk/graph/CyclesTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,18 +2,23 @@

import org.junit.Test;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.TestMoleculeFactory;

import java.util.Arrays;
import java.util.Iterator;

import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.CoreMatchers.not;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.openscience.cdk.templates.TestMoleculeFactory.makeAnthracene;
import static org.openscience.cdk.templates.TestMoleculeFactory.makeBicycloRings;
Expand Down Expand Up @@ -265,4 +270,135 @@ private IAtomContainer fullerene() throws Exception {
static void checkSize(Cycles cs, int nCycles) {
assertThat(cs.numberOfCycles(), is(nCycles));
}

private static IAtomContainer loadSmiles(String smi) throws InvalidSmilesException {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles(smi);
return mol;
}

private static void assertRingSizes(String smi, int ... expected) throws InvalidSmilesException {
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles(smi);
Cycles.markRingAtomsAndBonds(mol);
int[] actual = new int[mol.getAtomCount()];
Cycles.smallRingSizes(mol, actual);
assertThat(Arrays.toString(actual), actual, is(expected));
}

@Test
public void testSmallRings() throws InvalidSmilesException {
assertRingSizes("C1CCCCC1", 6, 6, 6, 6, 6, 6);
assertRingSizes("C1CCCC1", 5, 5, 5, 5, 5);
// spiro
assertRingSizes("C1CCCCC11CCCC1", 6, 6, 6, 6, 6, 5, 5, 5, 5, 5);
// fused
assertRingSizes("CCC12CCC2CCCC1", 0, 0, 4, 4, 4, 4, 6, 6, 6, 6);
assertRingSizes("[nH]1ccc2c1cccc2", 5, 5, 5, 5, 5, 6, 6, 6, 6);
// compound
assertRingSizes("Clc4cccc(N3CCN(CCCCOc2ccc1c(NC(=O)CC1)c2)CC3)c4Cl",
0, 6, 6, 6, 6, 6, 6, 6, 6, 6, 0, 0, 0, 0, 0, 6, 6, 6, 6, 6, 6, 6, 0, 6, 6, 6, 6, 6, 6, 0);
}

@Test
public void testSmallRing_atom_simple() throws InvalidSmilesException {
IAtomContainer mol = loadSmiles("C1CCCCC1");
Cycles.markRingAtomsAndBonds(mol); // required
assertEquals(6,Cycles.smallRingSize(mol.getAtom(0)));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(2)));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(5)));

assertEquals(0,Cycles.smallRingSize(mol.getAtom(0), 4));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(2), 4));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(5), 4));

assertEquals(6,Cycles.smallRingSize(mol.getAtom(0), 6));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(2), 6));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(5), 6));

assertEquals(6,Cycles.smallRingSize(mol.getAtom(0), 7));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(2), 7));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(5), 7));
}

@Test
public void testSmallRing_atom_acyclic() throws InvalidSmilesException {
IAtomContainer mol = loadSmiles("CCCC");
Cycles.markRingAtomsAndBonds(mol); // required
assertEquals(0,Cycles.smallRingSize(mol.getAtom(0)));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(1)));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(2)));
}

@Test
public void testSmallRing_atom_indole() throws InvalidSmilesException {
IAtomContainer mol = loadSmiles("[nH]1ccc2c1cccc2");
Cycles.markRingAtomsAndBonds(mol); // required
assertEquals(5,Cycles.smallRingSize(mol.getAtom(0)));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(1)));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(2)));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(3)));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(4)));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(5)));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(6)));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(7)));
assertEquals(6,Cycles.smallRingSize(mol.getAtom(8)));
}

@Test
public void testSmallRing_atom_indole_lim() throws InvalidSmilesException {
IAtomContainer mol = loadSmiles("[nH]1ccc2c1cccc2");
Cycles.markRingAtomsAndBonds(mol); // required
assertEquals(5,Cycles.smallRingSize(mol.getAtom(0), 5));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(1), 5));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(2), 5));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(3), 5));
assertEquals(5,Cycles.smallRingSize(mol.getAtom(4), 5));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(5), 5));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(6), 5));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(7), 5));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(8), 5));
// limit = 4
assertEquals(0,Cycles.smallRingSize(mol.getAtom(0), 4));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(1), 4));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(2), 4));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(3), 4));
assertEquals(0,Cycles.smallRingSize(mol.getAtom(4), 4));
}

@Test
public void testSmallRing_bond_indole() throws InvalidSmilesException {
IAtomContainer mol = loadSmiles("[nH]1ccc2c1cccc2");
Cycles.markRingAtomsAndBonds(mol); // required
assertEquals(5,Cycles.smallRingSize(mol.getBond(0)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(1)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(2)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(3)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(4)));
assertEquals(6,Cycles.smallRingSize(mol.getBond(5)));
assertEquals(6,Cycles.smallRingSize(mol.getBond(6)));
assertEquals(6,Cycles.smallRingSize(mol.getBond(7)));
assertEquals(6,Cycles.smallRingSize(mol.getBond(8)));
}

@Test
public void testSmallRing_bond_spiro() throws InvalidSmilesException {
IAtomContainer mol = loadSmiles("C1CCCC11CCC1");
Cycles.markRingAtomsAndBonds(mol); // required
assertEquals(5,Cycles.smallRingSize(mol.getBond(0)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(1)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(2)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(3)));
assertEquals(5,Cycles.smallRingSize(mol.getBond(4)));
assertEquals(4,Cycles.smallRingSize(mol.getBond(5)));
assertEquals(4,Cycles.smallRingSize(mol.getBond(6)));
assertEquals(4,Cycles.smallRingSize(mol.getBond(7)));
assertEquals(4,Cycles.smallRingSize(mol.getBond(8)));
// limit=4
assertEquals(0,Cycles.smallRingSize(mol.getBond(3),4));
assertEquals(4,Cycles.smallRingSize(mol.getBond(7),4));
// limit=3
assertEquals(0,Cycles.smallRingSize(mol.getBond(3),3));
assertEquals(0,Cycles.smallRingSize(mol.getBond(7),3));
}
}