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Dev/substructlibrary docs (#1620)

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* Adds substruct library documentation

* Adds testing of (fixed) documentation code

* Fixes typos and emphasizes the speed of trusted smiles

* Removes colons from parameters in docstrings, was causing warnings
This commit is contained in:
Brian Kelley
2017-11-22 03:05:28 -05:00
committed by Greg Landrum
parent 03e351e68b
commit 1bef493512
3 changed files with 133 additions and 6 deletions
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61
Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp
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@@ -184,7 +184,65 @@ void test4() {
TEST_ASSERT(res.size() == 40);
delete query;
BOOST_LOG(rdErrorLog) << " Done (stereo options)" << std::endl;
BOOST_LOG(rdErrorLog) << " Done (trusted smiles)" << std::endl;
}
/// Tests the code in the docs
// to make sure it compiles.
void docTest() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing C++ docs" << std::endl;
ROMol *q = SmartsToMol("C-1-C-C-O-C(-[O])(-[N])1");
ROMol *m = SmilesToMol("C1CCO[C@@](N)(O)1");
ROMol &query = *q;
ROMol &mol = *m;
{
SubstructLibrary lib;
lib.addMol(mol);
std::vector<unsigned int> results = lib.getMatches(query);
for (std::vector<unsigned int>::const_iterator matchIndex = results.begin();
matchIndex != results.end(); ++matchIndex) {
boost::shared_ptr<ROMol> match = lib.getMol(*matchIndex);
}
}
{
boost::shared_ptr<CachedTrustedSmilesMolHolder> molHolder =
boost::make_shared<CachedTrustedSmilesMolHolder>();
boost::shared_ptr<PatternHolder> patternHolder =
boost::make_shared<PatternHolder>();
SubstructLibrary lib(molHolder, patternHolder);
lib.addMol(mol);
}
{
boost::shared_ptr<CachedTrustedSmilesMolHolder> molHolder =
boost::make_shared<CachedTrustedSmilesMolHolder>();
boost::shared_ptr<PatternHolder> patternHolder =
boost::make_shared<PatternHolder>();
// the PatternHolder instance is able to make fingerprints.
// These, of course, can be read from a file. For demonstration
// purposes we construct them here.
const std::string trustedSmiles = "c1ccccc1";
ROMol *m = SmilesToMol(trustedSmiles);
const ExplicitBitVect *bitVector = patternHolder->makeFingerprint(*m);
// The trusted smiles and bitVector can be read from any source.
// This is the fastest way to load a substruct library.
molHolder->addSmiles(trustedSmiles);
patternHolder->addFingerprint(*bitVector);
SubstructLibrary lib(molHolder, patternHolder);
delete m;
delete bitVector;
}
delete q;
delete m;
BOOST_LOG(rdErrorLog) << " Done (C++ doc tests)" << std::endl;
}
int main(int argc, char *argv[]) {
@@ -193,6 +251,7 @@ int main(int argc, char *argv[]) {
test2();
test3();
test4();
docTest();
#endif
return 0;
}