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https://github.com/rdkit/rdkit.git
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Expose reading/writing PNG metadata to CFFI and MinimalLib (#8381)
* get SynthonSpace.cpp to build also when RDK_USE_BOOST_SERIALIZATION is not defined * test should not fail when RDK_USE_BOOST_SERIALIZATION is not defined * - expose reading/writing PNG metadata to CFFI and MinimalLib - add relevant CFFI and MinimalLib unit tests - add RDK_USE_BOOST_PROGRAM_OPTIONS CMake option - enable using standalone zlib in the absence of boost::iostreams for parsing PNG files - enable linking against maeparser in the absence of boost::iostreams also on Windows - enable building RDKit in the absence of boost::program_options * add check for boost::program_options * change size_t into std::uint64_t in SearchResults for consistency with doTheSearch() which uses std::uint64_t * change size_t into std::uint64_t in SearchResults for consistency with SynthonSpaceSearcher::doTheSearch() * set CMake policy to allow YAeHMOP to require a version which is not actually supported * reverted External/YAeHMOP/CMakeLists.txt to master version * check if Windows build will work * fix build * configure zlib install location * build zlib dependency * include zlib header directory * explicitly set PropertyFlags.AllProps so the test does not fail on static builds --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>
This commit is contained in:
Paolo Tosco
GitHub
@@ -2809,6 +2809,21 @@ function captureStdoutStderr(stdoutCallback, optStderrCallback) {
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};
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}
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function captureStdoutStderr(stdoutCallback, optStderrCallback) {
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if (!stdoutCallback) {
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return null;
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}
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const stderrCallback = optStderrCallback || stdoutCallback;
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const origStdoutWrite = process.stdout.write;
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const origStderrWrite = process.stderr.write;
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process.stdout.write = (chunk) => stdoutCallback(chunk);
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process.stderr.write = (chunk) => stderrCallback(chunk);
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return () => {
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process.stdout.write = origStdoutWrite;
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process.stderr.write = origStderrWrite;
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};
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}
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function test_capture_logs() {
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const PENTAVALENT_CARBON = 'CC(C)(C)(C)C';
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const PENTAVALENT_CARBON_VALENCE_ERROR = 'Explicit valence for atom # 1 C, 5, is greater than permitted';
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@@ -3756,6 +3771,398 @@ M END
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mol.delete();
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}
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function test_png_metadata() {
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const PNG_COLCHICINE_NO_METADATA = "/../../GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
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const PNG_COLCHICINE_WITH_METADATA = "/../../GraphMol/FileParsers/test_data/colchicine.png";
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const PNG_PENICILLIN_METADATA = "penicillin_metadata.png";
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const PNG_PENICILLIN_AMOXICILLIN_METADATA = "penicillin_amoxicillin_metadata.png";
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const PNG_COLCHICINE_AMOXICILLIN_METADATA = "colchicine_amoxicillin_metadata.png";
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const BENZYLPENICILLIN_SMI = "CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)Cc3ccccc3)C(=O)O)C";
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const BENZYLPENICILLIN_CAN_SMI = "CC1(C)S[C@@H]2[C@H](NC(=O)Cc3ccccc3)C(=O)N2[C@H]1C(=O)O";
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const AMOXICILLIN_SMI = "O=C(O)[C@@H]2N3C(=O)[C@@H](NC(=O)[C@@H](c1ccc(O)cc1)N)[C@H]3SC2(C)C";
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const AMOXICILLIN_CAN_SMI = "CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccc(O)cc3)C(=O)N2[C@H]1C(=O)O";
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let mol;
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let mols;
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let molSan;
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const png_no_metadata_buf = fs.readFileSync(__dirname + PNG_COLCHICINE_NO_METADATA);
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const png_no_metadata_blob = new Uint8Array(png_no_metadata_buf.length);
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const png_no_metadata_blob2 = new Uint8Array(png_no_metadata_buf.length);
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png_no_metadata_buf.copy(png_no_metadata_blob);
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png_no_metadata_buf.copy(png_no_metadata_blob2);
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const png_with_metadata_buf = fs.readFileSync(__dirname + PNG_COLCHICINE_WITH_METADATA);
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const png_with_metadata_blob = new Uint8Array(png_with_metadata_buf.length);
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png_with_metadata_buf.copy(png_with_metadata_blob);
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assert(!RDKitModule.get_mol_from_png_blob(png_no_metadata_blob));
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assert(!RDKitModule.get_mols_from_png_blob(png_no_metadata_blob));
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let penicillin = RDKitModule.get_mol(BENZYLPENICILLIN_SMI);
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assert(penicillin);
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assert(penicillin.set_new_coords());
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let png_penicillin_metadata_blob = penicillin.add_to_png_blob(png_no_metadata_blob,
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"{\"includePkl\":false,\"includeSmiles\":true,\"includeMol\":true}");
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penicillin.delete();
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assert(png_penicillin_metadata_blob);
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fs.writeFileSync(PNG_PENICILLIN_METADATA, png_penicillin_metadata_blob);
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penicillin = RDKitModule.get_mol_from_png_blob(png_penicillin_metadata_blob);
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assert(penicillin);
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assert.equal(penicillin.has_coords(), 2);
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penicillin.delete();
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RDKitModule.enable_logging()
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mol = RDKitModule.get_mol_from_png_blob(png_with_metadata_blob);
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assert(mol);
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assert.equal(mol.has_coords(), 2);
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mol.delete();
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mols = RDKitModule.get_mols_from_png_blob(png_with_metadata_blob);
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assert(!mols);
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mols = RDKitModule.get_mols_from_png_blob(png_with_metadata_blob,
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JSON.stringify({ includePkl: true, includeSmiles: true }));
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assert(!mols);
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mols = RDKitModule.get_mols_from_png_blob(
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png_with_metadata_blob, JSON.stringify({ includeSmiles: true }));
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assert(mols);
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assert.equal(mols.size(), 1);
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mol = mols.next();
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assert.equal(mol.has_coords(), 2);
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mol.delete();
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mols.delete();
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assert(!RDKitModule.get_mol_from_png_blob(png_penicillin_metadata_blob,
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"{\"includePkl\":true,\"includeSmiles\":false,\"includeMol\":false}"));
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penicillin = RDKitModule.get_mol_from_png_blob(png_penicillin_metadata_blob,
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"{\"includePkl\":false,\"includeSmiles\":false,\"includeMol\":true,\"sanitize\":false,\"removeHs\":false,\"assignStereo\":false,\"fastFindRings\":false}");
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assert(penicillin);
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assert.equal(penicillin.has_coords(), 2);
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smi = penicillin.get_smiles();
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assert.notEqual(smi, BENZYLPENICILLIN_CAN_SMI);
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molSan = RDKitModule.get_mol(smi)
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assert.equal(molSan.get_smiles(), BENZYLPENICILLIN_CAN_SMI);
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molSan.delete();
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penicillin.delete();
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assert(!RDKitModule.get_mol_from_png_blob(png_no_metadata_blob2));
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penicillin = RDKitModule.get_mol(BENZYLPENICILLIN_SMI);
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assert(penicillin);
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let amoxicillin = RDKitModule.get_mol(AMOXICILLIN_SMI);
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assert(amoxicillin);
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assert(amoxicillin.set_new_coords());
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png_penicillin_metadata_blob = penicillin.add_to_png_blob(png_no_metadata_blob2,
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"{\"includePkl\":false,\"includeMol\":true,\"CX_ALL_BUT_COORDS\":true}");
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assert(png_penicillin_metadata_blob);
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let png_penicillin_amoxicillin_metadata_blob = amoxicillin.add_to_png_blob(png_penicillin_metadata_blob,
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"{\"includePkl\":false,\"includeMol\":true,\"CX_ALL_BUT_COORDS\":true}");
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assert(png_penicillin_amoxicillin_metadata_blob);
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fs.writeFileSync(PNG_PENICILLIN_AMOXICILLIN_METADATA, png_penicillin_amoxicillin_metadata_blob);
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mol = RDKitModule.get_mol_from_png_blob(png_penicillin_amoxicillin_metadata_blob,
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"{\"sanitize\":false,\"removeHs\":false,\"assignStereo\":false,\"fastFindRings\":false}");
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assert(mol);
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assert(!mol.has_coords());
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smi = mol.get_smiles();
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assert.equal(smi, BENZYLPENICILLIN_CAN_SMI);
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mol.delete();
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assert(!RDKitModule.get_mol_from_png_blob(png_penicillin_amoxicillin_metadata_blob,
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"{\"includePkl\":false,\"includeSmiles\":false,\"includeMol\":false}"));
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mol = RDKitModule.get_mol_from_png_blob(png_penicillin_amoxicillin_metadata_blob,
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"{\"includePkl\":true,\"includeSmiles\":false,\"includeMol\":true}");
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assert(mol);
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assert.equal(mol.has_coords(), 2);
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smi = mol.get_smiles();
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assert.equal(smi, BENZYLPENICILLIN_CAN_SMI);
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mol.delete();
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mols = RDKitModule.get_mols_from_png_blob(png_penicillin_amoxicillin_metadata_blob);
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assert(!mols);
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mols = RDKitModule.get_mols_from_png_blob(
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png_penicillin_amoxicillin_metadata_blob, JSON.stringify({ includeSmiles: true }));
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assert(mols);
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assert.equal(mols.size(), 2);
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mol = mols.at(0);
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assert(!mol.has_coords());
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smi = mol.get_smiles();
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assert.equal(smi, BENZYLPENICILLIN_CAN_SMI);
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assert(mol.get_morgan_fp());
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mol.delete();
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mol = mols.at(1);
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assert(!mol.has_coords());
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smi = mol.get_smiles();
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assert.equal(smi, AMOXICILLIN_CAN_SMI);
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assert(mol.get_morgan_fp());
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mol.delete();
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mols.delete();
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mols = RDKitModule.get_mols_from_png_blob(png_penicillin_amoxicillin_metadata_blob, JSON.stringify({
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includePkl: false, includeMol: true, sanitize: false, removeHs: false, assignStereo: false, fastFindRings: false
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}));
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assert(mols);
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assert.equal(mols.size(), 2);
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mol = mols.at(0);
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assert(mol.has_coords());
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smi = mol.get_smiles();
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assert.notEqual(smi, BENZYLPENICILLIN_CAN_SMI);
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molSan = RDKitModule.get_mol(smi)
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assert.equal(molSan.get_smiles(), BENZYLPENICILLIN_CAN_SMI);
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molSan.delete();
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mol.delete();
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mol = mols.at(1);
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assert(mol.has_coords());
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smi = mol.get_smiles();
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assert.notEqual(smi, AMOXICILLIN_CAN_SMI);
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molSan = RDKitModule.get_mol(smi)
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assert.equal(molSan.get_smiles(), AMOXICILLIN_CAN_SMI);
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molSan.delete();
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mol.delete();
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mols.delete();
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let png_colchicine_amoxicillin_metadata_blob = amoxicillin.add_to_png_blob(
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png_with_metadata_blob, JSON.stringify({ includeMol: true, CX_ALL_BUT_COORDS:true }));
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assert(png_colchicine_amoxicillin_metadata_blob);
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fs.writeFileSync(PNG_COLCHICINE_AMOXICILLIN_METADATA, png_colchicine_amoxicillin_metadata_blob);
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mols = RDKitModule.get_mols_from_png_blob(png_colchicine_amoxicillin_metadata_blob,
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"{\"includePkl\":false,\"includeMol\":true}");
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assert.equal(mols.size(), 1);
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mol = mols.at(0);
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assert.equal(mol.has_coords(), 2);
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mol.delete();
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mols.delete();
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mols = RDKitModule.get_mols_from_png_blob(png_colchicine_amoxicillin_metadata_blob,
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"{\"includeSmiles\":true}");
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assert.equal(mols.size(), 2);
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assert.equal(mols.at(0).has_coords(), 2);
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assert(!mols.at(1).has_coords());
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mols.delete();
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penicillin.delete();
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amoxicillin.delete();
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const colchicine = RDKitModule.get_mol('COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2');
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assert(colchicine);
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png_no_metadata_buf.copy(png_no_metadata_blob);
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let png_colchicine_metadata_blob;
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png_colchicine_metadata_blob = colchicine.add_to_png_blob(png_no_metadata_blob);
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mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
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assert(mol);
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assert.equal(mol.get_num_atoms(), 29);
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assert(!mol.has_coords());
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mol.delete();
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// use SMILES
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png_colchicine_metadata_blob = colchicine.add_to_png_blob(png_no_metadata_blob,
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JSON.stringify({ includePkl: false }));
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mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
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assert(mol);
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assert.equal(mol.get_num_atoms(), 29);
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assert(!mol.has_coords());
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mol.delete();
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// use MOL
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png_colchicine_metadata_blob = colchicine.add_to_png_blob(png_no_metadata_blob,
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JSON.stringify({ includePkl: false, includeSmiles: false, includeMol: true }));
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mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
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assert(mol);
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assert.equal(mol.get_num_atoms(), 29);
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assert.equal(mol.has_coords(), 2);
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mol.delete();
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// use PKL
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colchicine.set_new_coords();
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assert.equal(colchicine.has_coords(), 2);
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const PROPERTY_NAME = 'property';
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const PROPERTY_VALUE = 'value';
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colchicine.set_prop(PROPERTY_NAME, PROPERTY_VALUE);
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png_colchicine_metadata_blob = colchicine.add_to_png_blob(png_no_metadata_blob, JSON.stringify({
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includePkl: true, includeSmiles: false, includeMol: false, propertyFlags: { NoProps: true }
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}));
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mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
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assert(mol);
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assert.equal(mol.get_num_atoms(), 29);
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assert.equal(mol.has_coords(), 2);
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assert(!mol.has_prop(PROPERTY_NAME));
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mol.delete();
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png_colchicine_metadata_blob = colchicine.add_to_png_blob(png_no_metadata_blob, JSON.stringify({
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includePkl: true, includeSmiles: false, includeMol: false, propertyFlags: { AllProps: true }
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}));
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mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
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assert(mol);
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assert.equal(mol.get_num_atoms(), 29);
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assert.equal(mol.has_coords(), 2);
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assert(mol.has_prop(PROPERTY_NAME));
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assert(mol.get_prop(PROPERTY_NAME) == PROPERTY_VALUE);
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mol.delete();
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png_colchicine_metadata_blob = colchicine.add_to_png_blob(png_no_metadata_blob, JSON.stringify({
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includePkl: false, includeSmiles: true, includeMol: false,
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propertyFlags: { NoProps: true }, CX_ALL_BUT_COORDS: true
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}));
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mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
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assert(mol);
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assert.equal(mol.get_num_atoms(), 29);
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assert(!mol.has_coords());
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assert(!mol.has_prop(PROPERTY_NAME));
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mol.delete();
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// use original wedging
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const colchicineUnusualWedging = RDKitModule.get_mol(`
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RDKit 2D
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29 31 0 0 0 0 0 0 0 0999 V2000
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6.4602 1.0300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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5.3062 1.9883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
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3.8993 1.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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2.7453 2.4262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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1.3384 1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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1.0856 0.4273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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2.2396 -0.5309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
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1.9868 -2.0094 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.1408 -2.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.6465 -0.0106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.8005 -0.9688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.5477 -2.4474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.2280 -0.2968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.1857 -1.7387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.6836 -2.9611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.1813 -3.0436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.7569 -4.4288 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.2442 -4.6230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.1797 -1.9240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.6215 -2.3378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.9268 -0.4455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.6132 0.2787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.0269 1.7205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.5055 1.9733 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-4.0258 3.3802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-5.5043 3.6330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.0675 4.5342 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.1576 2.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.3401 3.0254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0
|
||||
2 3 1 0
|
||||
3 4 2 0
|
||||
4 5 1 0
|
||||
5 6 2 0
|
||||
6 7 1 0
|
||||
7 8 1 0
|
||||
8 9 1 0
|
||||
7 10 2 0
|
||||
10 11 1 0
|
||||
11 12 1 0
|
||||
6 13 1 0
|
||||
13 14 2 0
|
||||
14 15 1 0
|
||||
15 16 2 0
|
||||
16 17 1 0
|
||||
17 18 1 0
|
||||
16 19 1 0
|
||||
19 20 2 0
|
||||
19 21 1 0
|
||||
21 22 2 0
|
||||
23 22 1 1
|
||||
23 24 1 0
|
||||
24 25 1 0
|
||||
25 26 1 0
|
||||
25 27 2 0
|
||||
23 28 1 0
|
||||
28 29 1 0
|
||||
10 3 1 0
|
||||
22 13 1 0
|
||||
29 5 1 0
|
||||
M END
|
||||
`);
|
||||
assert(colchicineUnusualWedging);
|
||||
assert.equal(colchicineUnusualWedging.has_coords(), 2);
|
||||
assert(colchicineUnusualWedging.get_cxsmiles().includes('wU:22.24|'));
|
||||
assert(colchicineUnusualWedging.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionTrue' })).includes('wU:22.23|'));
|
||||
png_colchicine_metadata_blob = colchicineUnusualWedging.add_to_png_blob(png_no_metadata_blob, JSON.stringify({
|
||||
includePkl: true, includeSmiles: true, includeMol: true,
|
||||
propertyFlags: { AtomProps: true, BondProps: true }
|
||||
}));
|
||||
mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
|
||||
// the mol is restored from pickle, so it will retain
|
||||
// original molblock wedging
|
||||
assert(mol);
|
||||
assert.equal(mol.get_num_atoms(), 29);
|
||||
assert.equal(mol.has_coords(), 2);
|
||||
assert(mol.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionTrue' })).includes('wU:22.23|'));
|
||||
assert(mol.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionClear' })).includes('wU:22.24|'));
|
||||
assert(mol.get_molblock().includes(' 23 24 1 1'));
|
||||
assert(mol.get_molblock(JSON.stringify({ useMolBlockWedging: true })).includes(' 23 22 1 1'));
|
||||
mol.delete();
|
||||
// the mol is restored from CXSMILES, so it will not retain
|
||||
// original molblock wedging, as it was not stored in the CXSMILES string
|
||||
png_colchicine_metadata_blob = colchicineUnusualWedging.add_to_png_blob(png_no_metadata_blob, JSON.stringify({
|
||||
includePkl: false, includeSmiles: true, includeMol: true,
|
||||
propertyFlags: { AtomProps: true, BondProps: true }
|
||||
}));
|
||||
mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
|
||||
assert(mol);
|
||||
assert.equal(mol.get_num_atoms(), 29);
|
||||
assert.equal(mol.has_coords(), 2);
|
||||
assert(mol.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionTrue' })).includes('wU:22.24|'));
|
||||
assert(mol.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionClear' })).includes('wU:22.24|'));
|
||||
assert(mol.get_molblock().includes(' 23 24 1 1'));
|
||||
assert(mol.get_molblock(JSON.stringify({ useMolBlockWedging: true })).includes(' 23 24 1 1'));
|
||||
mol.delete();
|
||||
// the mol is restored from CXSMILES, but restoreBondDirOption was set
|
||||
// to 'RestoreBondDirOptionTrue', so it will not retain
|
||||
// original molblock wedging, as it was stored in the CXSMILES string
|
||||
png_colchicine_metadata_blob = colchicineUnusualWedging.add_to_png_blob(png_no_metadata_blob, JSON.stringify({
|
||||
includePkl: false, includeSmiles: true, includeMol: true,
|
||||
propertyFlags: { AtomProps: true, BondProps: true },
|
||||
restoreBondDirOption: 'RestoreBondDirOptionTrue'
|
||||
}));
|
||||
mol = RDKitModule.get_mol_from_png_blob(png_colchicine_metadata_blob);
|
||||
assert(mol);
|
||||
assert.equal(mol.get_num_atoms(), 29);
|
||||
assert.equal(mol.has_coords(), 2);
|
||||
assert(mol.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionTrue' })).includes('wU:22.23|'));
|
||||
assert(mol.get_cxsmiles(JSON.stringify({ CX_ALL: true, restoreBondDirOption: 'RestoreBondDirOptionClear' })).includes('wU:22.24|'));
|
||||
assert(mol.get_molblock().includes(' 23 22 1 1'));
|
||||
assert(mol.get_molblock(JSON.stringify({ useMolBlockWedging: true })).includes(' 23 22 1 1'));
|
||||
mol.delete();
|
||||
colchicineUnusualWedging.delete();
|
||||
}
|
||||
|
||||
function test_combine_with() {
|
||||
{
|
||||
var mol = RDKitModule.get_mol("CC");
|
||||
assert(mol);
|
||||
var other = RDKitModule.get_mol("NCC");
|
||||
assert(other);
|
||||
assert(!mol.combine_with(other));
|
||||
assert.equal(mol.get_num_atoms(), 5);
|
||||
assert(mol.get_smiles() === "CC.CCN");
|
||||
mol.delete();
|
||||
other.delete();
|
||||
}
|
||||
{
|
||||
var mol = RDKitModule.get_mol("C1CC1 |(0.866025,0,;-0.433013,0.75,;-0.433013,-0.75,)|");
|
||||
var mol_copy = RDKitModule.get_mol_copy(mol);
|
||||
assert(mol);
|
||||
var other = RDKitModule.get_mol("C1CNC1 |(-1.06066,0,;0,-1.06066,;1.06066,0,;0,1.06066,)|");
|
||||
assert(other);
|
||||
assert(!mol.combine_with(other, JSON.stringify({offset: [4.0, 0.0, 0.0]})));
|
||||
assert.equal(mol.get_num_atoms(), 7);
|
||||
assert(mol.get_smiles() === "C1CC1.C1CNC1");
|
||||
assert(mol.get_molblock().includes(" 4.0000"));
|
||||
mol.delete();
|
||||
assert(!mol_copy.combine_with(other, JSON.stringify({offset: [9.0, 0.0, 0.0]})));
|
||||
assert.equal(mol_copy.get_num_atoms(), 7);
|
||||
assert(mol_copy.get_smiles() === "C1CC1.C1CNC1");
|
||||
assert(mol_copy.get_molblock().includes(" 9.0000"));
|
||||
mol_copy.delete();
|
||||
other.delete();
|
||||
}
|
||||
}
|
||||
|
||||
function test_get_coords() {
|
||||
{
|
||||
var mol = RDKitModule.get_mol("C1CC1 |(0.866025,0,;-0.433013,0.75,;-0.433013,-0.75,)|");
|
||||
assert(mol);
|
||||
assert.equal(mol.has_coords(), 2);
|
||||
var pos = mol.get_coords();
|
||||
assert(Array.isArray(pos));
|
||||
assert(pos.length === mol.get_num_atoms());
|
||||
assert(pos.every((xyz) => Array.isArray(xyz) && xyz.length === 3 && xyz.every((c) => typeof c === "number")));
|
||||
assert(JSON.stringify(pos) === "[[0.866025,0,0],[-0.433013,0.75,0],[-0.433013,-0.75,0]]");
|
||||
mol.delete();
|
||||
}
|
||||
{
|
||||
var mol = RDKitModule.get_mol("C1CC1");
|
||||
assert(mol);
|
||||
assert(!mol.has_coords());
|
||||
var pos = mol.get_coords();
|
||||
assert(Array.isArray(pos));
|
||||
assert(!pos.length);
|
||||
mol.delete();
|
||||
}
|
||||
}
|
||||
|
||||
initRDKitModule().then(function(instance) {
|
||||
var done = {};
|
||||
const waitAllTestsFinished = () => {
|
||||
@@ -3850,8 +4257,11 @@ initRDKitModule().then(function(instance) {
|
||||
test_pickle();
|
||||
test_remove_hs_details();
|
||||
test_get_mol_remove_hs();
|
||||
test_png_metadata();
|
||||
test_combine_with();
|
||||
test_get_coords();
|
||||
|
||||
waitAllTestsFinished().then(() =>
|
||||
console.log("Tests finished successfully")
|
||||
);
|
||||
});
|
||||
});
|
||||
|
||||
Reference in New Issue
Block a user