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Add tautomer query to the substructlibrary (#3808)

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* Fixes #3797

* [WIP] Add tautomer queries to the substruct library

* Add TautomerQuery to CMake

* Add missing TautomerQuery functions, python wrapper and tests

* Add python wrappers for Substruct Library Tautomer Queries

* Explictly label non-const pattern function now that we have both

* Use boost::shared_ptr not std::shared_ptr

* Fix java builds

* One more try to fix java builds

* Fix Java Tests

* Run clang format

* Reenable tests

* Fix annoyingly stupid bug and annoying commit of debug code

* Fix documentation

* reenable ifdef threadsafe check

* Throw warning and perform tautomer search instead of bailing with incorrect fingerprints

* Simplfy api with templates

* Fix SubstructLibrary java issues

* minor API cleanup

* simplify the SWIG wrappers

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
This commit is contained in:
Brian Kelley
2021-03-04 22:56:20 -05:00
committed by GitHub
parent e21e2c2af6
commit c8aa10c80f
13 changed files with 643 additions and 273 deletions
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75
Code/JavaWrappers/gmwrapper/src-test/org/RDKit/SubstructLibraryTests.java
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@@ -57,6 +57,7 @@ public class SubstructLibraryTests extends GraphMolTest {
// fpholder - can we create it...
PatternHolder ph = new PatternHolder();
TautomerPatternHolder tph = new TautomerPatternHolder();
// Now lets make some molecules
mol = RWMol.MolFromSmiles("c1ccccc1");
@@ -139,7 +140,10 @@ public class SubstructLibraryTests extends GraphMolTest {
matches = lib.getMatches(mol);
assertEquals(1, matches.size());
assertEquals(1, lib.countMatches(mol));
assertTrue(lib.hasMatch(mol));
if(lib.canSerialize()) {
byte pickle[] = lib.Serialize();
assertTrue(pickle != null);
@@ -148,6 +152,8 @@ public class SubstructLibraryTests extends GraphMolTest {
assertEquals(lib.size(), 1);
matches = lib.getMatches(mol);
assertEquals(1, matches.size());
assertEquals(1, lib.countMatches(mol));
assertTrue(lib.hasMatch(mol));
}
// cached smiles mol holder
@@ -237,6 +243,75 @@ public class SubstructLibraryTests extends GraphMolTest {
assertEquals(1, matches.size());
}
@Test
public void test4Basics() {
MolHolder mh = new MolHolder();
TautomerPatternHolder pat = new TautomerPatternHolder();
assertEquals(0, mh.size());
CachedMolHolder cmh = new CachedMolHolder();
assertEquals(0, cmh.size());
CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
assertEquals(0, csmh.size());
CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
assertEquals(0, ctsmh.size());
mol = RWMol.MolFromSmiles("c1ccccc1");
TautomerQuery tautomerQuery = TautomerQuery.fromMol(mol);
// mol holder
SubstructLibrary lib = new SubstructLibrary(mh, pat);
lib.addMol(mol);
UInt_Vect matches = lib.getMatches(mol);
assertEquals(1, matches.size());
matches = lib.getMatches(tautomerQuery);
assertEquals(1, matches.size());
assertEquals(1, lib.countMatches(mol));
assertEquals(1, lib.countMatches(tautomerQuery));
// cached mol holder
try {
lib = new SubstructLibrary(cmh, pat);
lib.addMol(mol);
assertTrue(false); // shouldn't get here can't share patternholder and addmol
} catch(Exception e) {
// ok to get here
}
cmh = new CachedMolHolder();
pat = new TautomerPatternHolder();
lib = new SubstructLibrary(cmh, pat);
lib.addMol(mol);
matches = lib.getMatches(mol);
assertEquals(1, matches.size());
matches = lib.getMatches(tautomerQuery);
assertEquals(1, matches.size());
assertEquals(1, lib.countMatches(mol));
assertEquals(1, lib.countMatches(tautomerQuery));
// cached smiles mol holder
pat = new TautomerPatternHolder();
lib = new SubstructLibrary(csmh, pat);
lib.addMol(mol);
matches = lib.getMatches(mol);
assertEquals(1, matches.size());
matches = lib.getMatches(tautomerQuery);
assertEquals(1, matches.size());
assertEquals(1, lib.countMatches(mol));
assertEquals(1, lib.countMatches(tautomerQuery));
// cached trusted smiles mol holder
pat = new TautomerPatternHolder();
lib = new SubstructLibrary(ctsmh, pat);
lib.addMol(mol);
matches = lib.getMatches(mol);
assertEquals(1, matches.size());
matches = lib.getMatches(tautomerQuery);
assertEquals(1, matches.size());
assertEquals(1, lib.countMatches(mol));
assertEquals(1, lib.countMatches(tautomerQuery));
}
public static void main(String args[]) {