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Enable using JSSubstructLibrary without pattern fps (#6431)

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* - enable using JSSubstructLibrary with no fp by passing num_bits 0
- get rid of dynamic_cast which never looks great
- add unit tests for no-fingerprint JSSubstructLibrary

* change in response to review

---------

Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
2023-06-07 06:41:45 +02:00
committed by GitHub
parent 96c8279207
commit f9f23a569c
2 changed files with 125 additions and 92 deletions
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164
Code/MinimalLib/tests/tests.js
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@@ -385,87 +385,101 @@ function test_abbreviations() {
function test_substruct_library(done) {
done.test_substruct_library = false;
var smiReader = readline.createInterface({
input: fs.createReadStream(__dirname + '/../../GraphMol/test_data/compounds.smi')
});
var query = RDKitModule.get_qmol('C1CCCCN1');
var nonExistingQuery = RDKitModule.get_mol('O=C(O)C(c1ccc(cc1)CCN4CCC(c2nc3ccccc3n2CCOCC)CC4)(C)C');
var sslib = new RDKitModule.SubstructLibrary();
assert.equal(sslib.count_matches(query), 0);
assert.equal(sslib.get_matches(query), JSON.stringify([]));
assert.equal(sslib.get_matches_as_uint32array(query).length, 0);
// var t0 = performance.now()
// console.log('Started adding trusted SMILES');
var matches = [];
var expectedMatches = [39, 64, 80, 127, 128, 234, 240];
var i = 0;
const numBitOptions = [-1, 0];
var patternFpArray = [];
var trustedSmiArray = []
smiReader.on('line', (smi) => {
sslib.add_trusted_smiles(smi);
var mol = RDKitModule.get_mol(smi);
var res = JSON.parse(mol.get_substruct_match(query));
if (res.atoms) {
matches.push(i);
}
++i;
mol.delete();
});
smiReader.on('close', () => {
// var t1 = performance.now();
// console.log('Finished adding trusted SMILES took ' + (t1 - t0) / 1000 + ' seconds');
for (var i = 0; i < sslib.size(); ++i) {
trustedSmiArray.push(sslib.get_trusted_smiles(i));
var fp = sslib.get_pattern_fp_as_uint8array(i);
patternFpArray.push(fp);
}
assert.equal(trustedSmiArray.length, sslib.size());
assert.equal(patternFpArray.length, sslib.size());
assert.equal(trustedSmiArray.length, patternFpArray.length);
var sslib2 = new RDKitModule.SubstructLibrary();
for (var i = 0; i < sslib.size(); ++i) {
sslib2.add_trusted_smiles_and_pattern_fp(trustedSmiArray[i], patternFpArray[i]);
}
assert.equal(sslib.size(), sslib2.size());
numBitOptions.forEach((numBits, optIdx) => {
var smiReader = readline.createInterface({
input: fs.createReadStream(__dirname + '/../../GraphMol/test_data/compounds.smi')
});
var sslib = numBits < 0 ? new RDKitModule.SubstructLibrary() : new RDKitModule.SubstructLibrary(numBits);
assert.equal(sslib.count_matches(query), 0);
assert.equal(sslib.get_matches(query), JSON.stringify([]));
assert.equal(sslib.get_matches_as_uint32array(query).length, 0);
// var t0 = performance.now()
// console.log('Started adding trusted SMILES');
var matches = [];
var expectedMatches = [39, 64, 80, 127, 128, 234, 240];
var i = 0;
var trustedSmiArray = []
smiReader.on('line', (smi) => {
sslib.add_trusted_smiles(smi);
var mol = RDKitModule.get_mol(smi);
var res = JSON.parse(mol.get_substruct_match(query));
if (res.atoms) {
matches.push(i);
}
++i;
mol.delete();
});
smiReader.on('close', () => {
// var t1 = performance.now();
// console.log('Finished adding trusted SMILES took ' + (t1 - t0) / 1000 + ' seconds');
for (var i = 0; i < sslib.size(); ++i) {
trustedSmiArray.push(sslib.get_trusted_smiles(i));
let excRaised = false;
try {
var fp = sslib.get_pattern_fp_as_uint8array(i);
patternFpArray.push(fp);
} catch (e) {
// this is expected to fail when numBits === 0
excRaised = true;
}
assert((excRaised && numBits === 0) || (!excRaised && numBits !== 0));
}
assert.equal(trustedSmiArray.length, sslib.size());
assert.equal(patternFpArray.length, sslib.size());
assert.equal(trustedSmiArray.length, patternFpArray.length);
var sslib2 = new RDKitModule.SubstructLibrary();
for (var i = 0; i < sslib.size(); ++i) {
sslib2.add_trusted_smiles_and_pattern_fp(trustedSmiArray[i], patternFpArray[i]);
}
assert.equal(sslib.size(), sslib2.size());
{
assert.equal(sslib.count_matches(query, false), 7);
var sslibMatches = sslib.get_matches(query);
assert.equal(sslibMatches, JSON.stringify(expectedMatches));
var sslibMatchesUInt32Array = sslib.get_matches_as_uint32array(query);
assert.equal(sslibMatchesUInt32Array.length, expectedMatches.length);
for (var i = 0; i < expectedMatches.length; ++i) {
assert.equal(sslibMatchesUInt32Array[i], expectedMatches[i]);
assert.equal(sslib.count_matches(query, false), 7);
var sslibMatches = sslib.get_matches(query);
assert.equal(sslibMatches, JSON.stringify(expectedMatches));
assert.equal(sslibMatches, JSON.stringify(matches));
var sslibMatchesUInt32Array = sslib.get_matches_as_uint32array(query);
assert.equal(sslibMatchesUInt32Array.length, expectedMatches.length);
for (var i = 0; i < expectedMatches.length; ++i) {
assert.equal(sslibMatchesUInt32Array[i], expectedMatches[i]);
}
}
}
{
assert.equal(sslib.count_matches(nonExistingQuery, false), 0);
var sslibMatches = sslib.get_matches(nonExistingQuery);
assert.equal(sslibMatches, JSON.stringify([]));
var sslibMatchesUInt32Array = sslib.get_matches_as_uint32array(nonExistingQuery);
assert.equal(sslibMatchesUInt32Array.length, 0);
}
{
assert.equal(sslib2.count_matches(query, false), 7);
var sslib2Matches = sslib2.get_matches(query);
assert.equal(sslib2Matches, JSON.stringify(expectedMatches));
var sslib2MatchesUInt32Array = sslib2.get_matches_as_uint32array(query);
assert.equal(sslib2MatchesUInt32Array.length, expectedMatches.length);
for (var i = 0; i < expectedMatches.length; ++i) {
assert.equal(sslib2MatchesUInt32Array[i], expectedMatches[i]);
{
assert.equal(sslib.count_matches(nonExistingQuery, false), 0);
var sslibMatches = sslib.get_matches(nonExistingQuery);
assert.equal(sslibMatches, JSON.stringify([]));
var sslibMatchesUInt32Array = sslib.get_matches_as_uint32array(nonExistingQuery);
assert.equal(sslibMatchesUInt32Array.length, 0);
}
}
{
assert.equal(sslib2.count_matches(nonExistingQuery, false), 0);
var sslib2Matches = sslib2.get_matches(nonExistingQuery);
assert.equal(sslib2Matches, JSON.stringify([]));
var sslib2MatchesUInt32Array = sslib2.get_matches_as_uint32array(nonExistingQuery);
assert.equal(sslib2MatchesUInt32Array.length, 0);
}
done.test_substruct_library = true;
query.delete();
nonExistingQuery.delete();
sslib.delete();
sslib2.delete();
{
assert.equal(sslib2.count_matches(query, false), 7);
var sslib2Matches = sslib2.get_matches(query);
assert.equal(sslib2Matches, JSON.stringify(expectedMatches));
assert.equal(sslib2Matches, JSON.stringify(matches));
var sslib2MatchesUInt32Array = sslib2.get_matches_as_uint32array(query);
assert.equal(sslib2MatchesUInt32Array.length, expectedMatches.length);
for (var i = 0; i < expectedMatches.length; ++i) {
assert.equal(sslib2MatchesUInt32Array[i], expectedMatches[i]);
}
}
{
assert.equal(sslib2.count_matches(nonExistingQuery, false), 0);
var sslib2Matches = sslib2.get_matches(nonExistingQuery);
assert.equal(sslib2Matches, JSON.stringify([]));
var sslib2MatchesUInt32Array = sslib2.get_matches_as_uint32array(nonExistingQuery);
assert.equal(sslib2MatchesUInt32Array.length, 0);
}
sslib.delete();
sslib2.delete();
if (optIdx === numBitOptions.length - 1) {
done.test_substruct_library = true;
query.delete();
nonExistingQuery.delete();
}
});
});
}