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// Copyright (C) 2020 Gareth Jones, Glysade LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
package org.RDKit;
import static org.junit.Assert.*;
import java.util.ArrayList;
import java.util.List;
import org.junit.*;
public class QueryAtomTest extends GraphMolTest {
@Test
public void testChemdrawBlock() {
// smiles c1[nH]ccc1
// Chemdraw will convert explicit hydrogens in aromatic compounds to query hydrogen count
String block = String.join("\n",
"ChemDraw05012418152D",
"",
"0 0 0 0 0 0 V3000",
"M V30 BEGIN CTAB",
"M V30 COUNTS 5 5 0 0 0",
"M V30 BEGIN ATOM",
"M V30 1 C - 0.652854 - 0.050688 0.000000 0",
"M V30 2 C - 0.240354 0.663783 0.000000 0",
"M V30 3 C 0.566618 0.492256 0.000000 0",
"M V30 4 C 0.652854 - 0.328225 0.000000 0",
"M V30 5 N - 0.100821 - 0.663783 0.000000 0 HCOUNT = 1",
"M V30 END ATOM",
"M V30 BEGIN BOND",
"M V30 1 4 1 2",
"M V30 2 4 2 3",
"M V30 3 4 3 4",
"M V30 4 4 4 5",
"M V30 5 4 1 5",
"M V30 END BOND",
"M V30 END CTAB",
"M END",
"");
RWMol mol = RWMol.MolFromMolBlock(block, false);
assertNotNull(mol);
assertEquals(5, mol.getNumAtoms());
Atom queryAtom = mol.getAtomWithIdx(4);
assertTrue(queryAtom.hasQuery());
String smarts = queryAtom.AtomGetSmarts();
String expected = "[#7&h{1-}]";
assertEquals(expected, smarts);
String description = queryAtom.describeQuery();
expected = "AtomAnd\n AtomAtomicNum 7 = val\n less_AtomImplicitHCount 1 <= \n";
assertEquals(expected, description);
String molSmiles = mol.MolToSmiles();
Atom atom = new Atom(7);
atom.setNumExplicitHs(1);
mol.replaceAtom(4, atom);
mol.clearComputedProps(true);
mol.sanitizeMol();
atom = mol.getAtomWithIdx(4);
assertEquals(7, atom.getAtomicNum());
assertEquals(1, atom.getNumExplicitHs());
molSmiles = mol.MolToSmiles();
assertEquals("c1cc[nH]c1", molSmiles);
}
@Test
public void testReplaceQuerySimple() {
RWMol query = RWMol.MolFromSmiles("c1[nH]ccc1");
Atom nitrogen = query.getAtomWithIdx(2);
long imp = nitrogen.getNumImplicitHs();
assertEquals(1, imp);
Atom queryAtom = RDKFuncs.replaceAtomWithQueryAtom(query, nitrogen);
queryAtom.ExpandQuery(RDKFuncs.ExplicitDegreeEqualsQueryAtom(3));
RWMol mol1 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
assertTrue(mol1.hasSubstructMatch(query));
RWMol mol2 = RWMol.MolFromSmiles("c1[nH]ccc1");
assertFalse(mol2.hasSubstructMatch(query));
}
@Test
public void testExpandQuerySimple() {
RWMol query = RWMol.MolFromSmarts("c1nccc1");
RWMol mol1 = RWMol.MolFromSmiles("c1[nH]ccc1");
assertTrue(mol1.hasSubstructMatch(query));
Atom atom = query.getAtomWithIdx(0);
assertTrue(atom.hasQuery());
QueryAtom queryAtom = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
atom.ExpandQuery(queryAtom, CompositeQueryType.COMPOSITE_AND);
assertFalse(mol1.hasSubstructMatch(query));
RWMol mol2 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
assertTrue(mol2.hasSubstructMatch(query));
}
// adapted from Python tests
private int[] GetAtomIdxsMatchingQuery(ROMol mol, QueryAtom qa) {
List<Integer> indices = new ArrayList<Integer>();
for (int i =0; i< mol.getNumAtoms(); i++) {
Atom atom = mol.getAtomWithIdx(i);
if (qa.MatchAtom(atom)) {
indices.add(i);
}
}
int[] arr = new int[indices.size()];
for (int i=0; i<arr.length; i++) {
arr[i] = indices.get(i);
}
return arr;
}
@Test
public void testQueryAtoms() {
RWMol m = RWMol.MolFromSmiles("c1nc(C)n(CC)c1");
QueryAtom qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
int[] matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {2, 4}, matches);
qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true));
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {4}, matches);
qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true),
CompositeQueryType.COMPOSITE_OR);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1, 2, 4}, matches);
qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true),
CompositeQueryType.COMPOSITE_XOR);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1, 2}, matches);
qa = RDKFuncs.ExplicitDegreeGreaterQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {2, 4}, matches);
qa = RDKFuncs.ExplicitDegreeLessQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {3, 6}, matches);
m = RWMol.MolFromSmiles("N[CH][CH]");
qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(0);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1, 2}, matches);
qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(1);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {2}, matches);
m = RWMol.MolFromSmiles("F[C@H](Cl)C");
qa = RDKFuncs.HasChiralTagQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1}, matches);
qa = RDKFuncs.MissingChiralTagQueryAtom();
assertArrayEquals(new int[] {1}, matches);
m = RWMol.MolFromSmiles("F[CH](Cl)C");
qa = RDKFuncs.HasChiralTagQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {}, matches);
qa = RDKFuncs.MissingChiralTagQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1}, matches);
m = RWMol.MolFromSmiles("CNCON");
qa = RDKFuncs.NumHeteroatomNeighborsEqualsQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {2}, matches);
qa = RDKFuncs.NumHeteroatomNeighborsGreaterQueryAtom(0);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {0, 2, 3, 4}, matches);
m = RWMol.MolFromSmiles("CC12CCN(CC1)C2");
qa = RDKFuncs.IsBridgeheadQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1, 4}, matches);
m = RWMol.MolFromSmiles("OCCOC");
qa = RDKFuncs.NonHydrogenDegreeEqualsQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
assertArrayEquals(new int[] {1, 2, 3}, matches);
}
private int[] GetBondIdxsMatchingQuery(ROMol mol, QueryBond qa) {
List<Integer> indices = new ArrayList<Integer>();
for (int i =0; i< mol.getNumBonds(); i++) {
Bond atom = mol.getBondWithIdx(i);
if (qa.MatchBond(atom)) {
indices.add(i);
}
}
int[] arr = new int[indices.size()];
for (int i=0; i<arr.length; i++) {
arr[i] = indices.get(i);
}
return arr;
}
@Test
public void TestBondPropQueries() {
RWMol m = RWMol.MolFromSmiles("CCCCCCCCCCCCCC");
Bond_Vect bonds = m.getBonds();
bonds.get(0).setProp("hah", "hah");
bonds.get(1).setIntProp("bar", 1);
bonds.get(2).setIntProp("bar", 2);
bonds.get(3).setBoolProp("baz", true);
bonds.get(4).setBoolProp("baz", false);
bonds.get(5).setProp("boo", "hoo");
bonds.get(6).setProp("boo", "-urns");
bonds.get(7).setDoubleProp("boot", 1.0);
bonds.get(8).setDoubleProp("boot", 4.0);
bonds.get(9).setDoubleProp("number", 4.0);
bonds.get(10).setIntProp("number", 4);
QueryBond qb = RDKFuncs.HasIntPropWithValueQueryBond("bar", 1);
int[] matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {1}, matches);
qb = RDKFuncs.HasIntPropWithValueQueryBond("bar", 2);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {2}, matches);
qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz", true);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {3}, matches);
qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz", false);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {4}, matches);
qb = RDKFuncs.HasStringPropWithValueQueryBond("boo", "hoo");
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {5}, matches);
qb = RDKFuncs.HasStringPropWithValueQueryBond("boo", "-urns");
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {6}, matches);
qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot", 1.0);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {7}, matches);
qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot", 4.0);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {8}, matches);
qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot", 1.0, false, 3.0);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {7, 8}, matches);
qb = RDKFuncs.HasIntPropWithValueQueryBond("number", 4);
matches = GetBondIdxsMatchingQuery(m, qb);
assertArrayEquals(new int[] {10}, matches);
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.RascalMCESTest");
}
}
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