* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* first round of cleanups based on PVS-studio suggestions
* a couple more
* a few more cleanups
* another round of cleanups
* undo one of those cleanups
we want the integer rounding behavior here
* add a comment to make that clear
* Fix for filter catalog PRECONDITION redundancy
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
FilterCatalogs give RDKit the ability to screen out or reject
undesirable molecules based on various criteria. Supplied
with RDKIt are the following filter sets:
* PAINS - Pan assay interference patterns.
These are separated into three sets PAINS_A, PAINS_B and PAINS_C.
Reference: Baell JB, Holloway GA. New Substructure Filters for
Removal of Pan Assay Interference Compounds (PAINS)
from Screening Libraries and for Their Exclusion in
Bioassays.
J Med Chem 53 (2010) 2719Ð40. doi:10.1021/jm901137j.
* BRENK - filters unwanted functionality due to potential tox reasons
or unfavorable pharmacokinetics.
Reference: Brenk R et al. Lessons Learnt from Assembling Screening
Libraries for Drug Discovery for Neglected Diseases.
ChemMedChem 3 (2008) 435-444. doi:10.1002/cmdc.200700139.
* NIH - annotated compounds with problematic functional groups
Reference: Doveston R, et al. A Unified Lead-oriented Synthesis of
over Fifty Molecular Scaffolds. Org Biomol Chem 13
(2014) 859Ð65.
doi:10.1039/C4OB02287D.
Reference: Jadhav A, et al. Quantitative Analyses of Aggregation,
Autofluorescence, and Reactivity Artifacts in a Screen
for Inhibitors of a Thiol Protease.
J Med Chem 53 (2009) 37Ð51. doi:10.1021/jm901070c.
* ZINC - Filtering based on drug-likeness and unwanted functional
groups
Reference: http://blaster.docking.org/filtering/
The following is C++ and Python examples of how to filter molecules.
[C++]
#include <GraphMol/FilterCatalog.h>
using namespace RDKit;
SmilesMolSupplier suppl(…);
// setup the desired catalogs
FilterCatalogParams params;
params.addCatalog(FilterCatalogParams::PAINS_A);
params.addCatalog(FilterCatalogParams::PAINS_B);
params.addCatalog(FilterCatalogParams::PAINS_C);
// create the catalog
FilterCatalog catalog(params);
unique_ptr<ROMol> mol; // automatically cleans up after us
int count = 0;
while(!suppl.atEnd()){
mol.reset(suppl.next());
TEST_ASSERT(mol.get());
// Does a PAINS filter hit?
if (catalog.hasMatch(*mol)) {
std::cerr << "Warning: molecule failed filter " << std::endl;
}
// More detailed data by retrieving the catalog entry
const FilterCatalogEntry *entry = catalog.getFirstMatch(*mol);
if (entry) {
std::cerr << "Warning: molecule failed filter: reason " <<
entry->getDescription() << std::endl;
// get the matched substructure atoms for visualization
std::vector<FilterMatch> matches;
if (entry->getFilterMatches(*mol, matches)) {
for(std::vector<FilterMatch>::const_iterator it = matches.begin();
it != matches.end(); ++it) {
// Get the SmartsMatcherBase that matched
const FilterMatch & fm = (*it);
boost::shared_ptr<SmartsMatcherBase> matchingFilter = \
fm.filterMatch;
// Get the matching atom indices
const MatchVectType &vect = fm.atomPairs;
for (MatchVectType::const_iterator it=vect.begin();
it != vect.end(); ++it) {
int atomIdx = it->second;
}
}
}
}
count ++;
} // end while
Python API
import sys
from rdkit.Chem import FilterCatalog
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_A)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_B)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_C)
catalog = FilterCatalog.FilterCatalog(params)
...
for mol in mols:
if catalog.HasMatch(mol):
print("Warning: molecule failed filter", file=sys.stderr)
# more detailed
entry = catalog.GetFirstMatch(mol)
if entry:
print("Warning: molecule failed filter: reason %s"%(
entry.GetDescription()), file=sys.stderr)
# get to the atoms involved in the substructure
# there ma be many matching filters here...
for filterMatch in entry.getFilterMatches(mol):
filter = filterMatch.filterMatch
# get a description of the matching filter
print(filter)
for queryAtomIdx, atomIdx in filterMatch.atomPairs:
# do something with the substructure matches
Advanced
FilterCatalogs are fully serializable and can be stored for later use.
To serialize a catalog, use the catalog.Serialize() method.
std::string pickle = catalog.Serialize();
To unserialize, send the resulting string into the constructor
FilterCatalog catalog(pickle);
The underlying matchers can be arbitrarily complicated and new
ones with more complicated semantics can be created. The default
matching objects are:
SmartsMatcher - match a smarts pattern or query molecule with a minimum
and maximum count
ExclusionList - returns false if any of the supplied matches exist
And - combine two matchers
Or - true if any of two matchers are true
Not - invert the match (note that this can have confusing semantics
when dealing with substructure matches)
Entries can be added at any time to a catalog:
ExclusionList excludedList;
excludedList.addPattern(SmartsMatcher("Pattern 1", smarts));
excludedList.addPattern(SmartsMatcher("Pattern 2", smarts2));
A FilterCatalog supports a few different types of matching. One is
a traditional rejection filter where if a substructure exists in
the target molecule, the molecule is rejected.
These types of queries can indicate the substructure that triggered
the rejection through the FilterCatalogEntry::GetMatch(mol)
function.
The FilterCatalog also supports acceptance filters, that are
designed to indicate which molecules are ok. These have
to be transformed into rejection filters or simply wrapped in a
Not( acceptanceFilter ) when entered into the catalog. For example,
from Zinc:
carbons [#6] 40
means that we have a maximum of 40 carbon atoms. We can write this by
converting the max count to a min count (i.e. the pattern is triggered
when the molecule has mincount atoms);
const unsigned int minCount = 40+1;
SmartsMatcher( "Too many carbons", "[#6"], minCount );
This can be properly substructure searched.
Or we can wrap this in a not:
const unsigned int minCount = 0;
const unsigned int maxCount = 40;
Not( SmartsMatcher( "ok number of carbons", "[#6]", minCount, maxCount) );
Note: Wrapping in a Not loses the ability to highlight the rejecting
pattern when visualizing the molecule.
the horrible cross-library exception handling mess on linux. This may well break things on windows, which
might want these things static. Regardless, even as it is, this should be considered experimental
- Remove requirement that boost be in $RDBASE/External on windows (the BOOSTHOME environment variable is now required)
- fix dependencies
This builds on windows in debug mode now and most tests pass. There's a problem with PySVD in debug mode and for some reason the rdAlignments wrapper test fails; but these don't seem super important.
https://sourceforge.net/tracker/index.php?func=detail&aid=1485703&group_id=160139&atid=814650
