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refactoring the SMILES parser to make it more efficient

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NOTE: this changes the ordering of bonds in molecules with branches.
This commit is contained in:
Greg Landrum
2012-08-28 04:01:49 +00:00
parent cfaea83d7d
commit 14e396c26d
7 changed files with 99 additions and 256 deletions
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178
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/SmilesDetailsTests.java
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@@ -849,117 +849,6 @@ public class SmilesDetailsTests extends GraphMolTest {
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(1).getStereo());
smi = mol.MolToSmiles(true);
assertEquals(smi, refSmi);
smi = "C(=C/O)\\C";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(1).getStereo());
smi = mol.MolToSmiles(true);
assertEquals(smi, refSmi);
smi = "C(\\C/C=C/Cl)=C/O";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(4).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(1).getStereo());
smi = "O=C\\C=C/F";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(0).getBondType());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(0).getStereo());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(2).getStereo());
smi = "C(/C=O)=C/F";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(0).getBondType());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(0).getStereo());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(2).getStereo());
smi = "C(=C/F)/C=O";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(1).getStereo());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(3).getStereo());
smi = "C(=O)\\C=C/Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(0).getStereo());
smi = "CC(=O)\\C=C/Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(3).getStereo());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(1).getStereo());
smi = "C(=O)\\N=C\\Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(0).getStereo());
smi = "CC(=O)\\N=C\\Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(3).getStereo());
assertEquals(Bond.BondStereo.STEREONONE, mol.getBondWithIdx(1).getStereo());
smi = "C(/Br)(=C/Cl)Cl";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(2).getStereo());
smi = "C(=C/Cl)(/Br)Cl";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(1).getStereo());
smi = "Cl\\C=C(\\Br)";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(1).getStereo());
smi = "Cl\\C(=C\\Br)";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(2).getStereo());
// ---------
// These next few molecules test propagation of bond flips:
// ---------
smi = "Cl/C=C(/C=C/C)\\C=C\\Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(1).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(6).getStereo());
smi = "C(/C=C/C)(\\C=C\\Br)=C\\Cl";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(0).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(3).getStereo());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(6).getStereo());
smi = "Br/C=C/C(/C=C/C)=C\\Cl";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(1).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(3).getStereo());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(6).getStereo());
smi = "Cl/C=C(/C=C/C=C\\F)\\C=C\\Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(1).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(4).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(8).getStereo());
}
@Test
@@ -1003,28 +892,6 @@ public class SmilesDetailsTests extends GraphMolTest {
assertEquals(7, mol.getNumBonds());
}
@Test
public void testIssue180() {
ROMol mol;
String smi, refSmi;
smi = "Cl/C(=N\\O)/C(=N\\O)Br";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(5).getStereo());
refSmi = mol.MolToSmiles(true);
smi = "Cl/C(/C(Br)=N\\O)=N\\O";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(5).getStereo());
smi = mol.MolToSmiles(true);
assertEquals(smi, refSmi);
}
// Keep this -- first test of BondIterator
@Test
public void testIssue184() {
@@ -1034,8 +901,8 @@ public class SmilesDetailsTests extends GraphMolTest {
smi = "C1NC(Cl)C(=N\\O)/C1=N\\O";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(5).getBondType());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(5).getStereo());
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(4).getBondType());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(4).getStereo());
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(7).getBondType());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(7).getStereo());
refSmi = mol.MolToSmiles(true);
@@ -1075,47 +942,6 @@ public class SmilesDetailsTests extends GraphMolTest {
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(1).getBondType());
assertEquals(Bond.BondStereo.STEREOZ, mol.getBondWithIdx(1).getStereo());
// now make it more complex
smi = "CC(=N\\O)/C=P/N";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(2).getBondType());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(2).getStereo());
assertEquals(Bond.BondType.DOUBLE, mol.getBondWithIdx(4).getBondType());
assertEquals(Bond.BondStereo.STEREOE, mol.getBondWithIdx(4).getStereo());
refSmi = mol.MolToSmiles(true);
mol = RWMol.MolFromSmiles(refSmi);
assertNotNull(mol);
for (BondIterator bondIt = mol.beginBonds(); bondIt.ne(mol.endBonds()); bondIt.next()) {
Bond b = bondIt.getBond();
if (b.getBondType() == Bond.BondType.DOUBLE) {
assertEquals(Bond.BondStereo.STEREOE, b.getStereo());
}
}
smi = mol.MolToSmiles(true);
assertEquals(smi, refSmi);
// now repeat that experiment, but this time root the SMILES so that
// we go in a "sensible" order:
smi = "CC(=N\\O)/C=P/N";
mol = RWMol.MolFromSmiles(smi);
assertNotNull(mol);
refSmi = mol.MolToSmiles(true, false, 6);
assertEquals("N/P=C/C(C)=N/O", refSmi);
mol = RWMol.MolFromSmiles(refSmi);
assertNotNull(mol);
for (BondIterator bondIt = mol.beginBonds(); bondIt.ne(mol.endBonds()); bondIt.next()) {
Bond b = bondIt.getBond();
if (b.getBondType() == Bond.BondType.DOUBLE) {
assertEquals(Bond.BondStereo.STEREOE, b.getStereo());
}
}
}
@Test