7 Commits

Author SHA1 Message Date
Greg Landrum
ec31bea97b clang-tidy-7 pass (#2408) 2019-04-16 12:05:47 -04:00
Paolo Tosco
42544b928b - enable building FreeSASA under Windows (#2402)
- enable setting probeRadius as SASAOpts
2019-04-15 12:55:20 +01:00
Ric
a6b26253ff Fix (most of) mem problems (#2123)
* 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
2018-10-29 14:33:26 +00:00
Greg Landrum
9d5dbac2e3 switch to using a specific freesasa version (#1619)
* switch to using a release version on linux (windows still needs to be looked at)

* finish that

* switch to a local copy of the test file
2017-11-15 06:36:33 +01:00
Greg Landrum
1efa8e696e another clang-format run 2017-10-12 06:42:15 +02:00
Greg Landrum
f94e277856 another pass of clang modernize 2017-10-12 06:35:51 +02:00
Brian Kelley
210935a92c Adds FreeSASA adapter (#1565)
* Adds FreeSASA adapter

* Uses windows branch when necessary

* Oops inverted windows and unix builds

* Fixes windows source build

* Adds downloading message

* Updates FreeSASA to final API

* Adds python API

* Finished queryatom API

* Changes d_alg to algorithm (and d_classifier) exposes to python adds docs/tests

* Adds FATAL_ERROR to MSVC builds, removes from appveyor
2017-09-25 08:57:14 +02:00