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Release_2021_03
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16 Commits

Author SHA1 Message Date
David Cosgrove
ba261bd68b Coordinates from coordgen are not centered around the origin (#3058) 
* automaticaally move coordGen coords to 0,0.

* Fixed no-centre if coordMap passed, and better tranform method.

* Reomoved extraneous line.

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
 2020-04-02 08:32:09 +02:00
Ric
6224a42516 Build warnings revisited (#2318) 
* unused vars in bison parser cleanup

* initialization order in TopologicalTorsionGenerator

* unused params in SLN bison

* sln flex unused params

* throwing destructor in TDTWriter

* signed comparison in substructmethods

* unused input param in smiles/smarts bison

* unused ms param in sln bison

* signed comparison in FingerprintGenerator

* store return of fscanf in StructCheckerOptions

* unreferenced var in catch

* uninitialized value in FileParserUtils

* avoid override overload warning in MolDraw2DSVG

* non-final overrides in Validate.h

* unused static var in Avalon

* unused vars in catch blocks

* make AvalonTools avalonSimilarityBits & avalonSSSBits const int

* assert fscanf result in StructCheckerOptions
 2019-03-08 16:42:54 +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
Paolo Tosco
f7c888844d moved test.h from RDBoost to RDGeneral for consistency with export.h (#2074) 2018-10-11 17:35:23 -04:00
Greg Landrum
f4cc148406 Fixes #1908 (#1912) 
* Fixes #1908

* cleanup
 2018-06-14 18:40:10 -04:00
Paolo Tosco
c08ea49bda - enable building DLLs on Windows (#1861) 
* - enable building DLLs on Windows

* - export.h and test.h are now auto-generated by CMake
 2018-05-16 08:42:41 +02:00
Paolo Tosco
c8deb705e7 There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral (#1673) 
* - there is no need to enforce that (i, j) and (k, l) be bonded
  when setting a i, j, k, l dihedral

* - added unit tests for PR #1673
 2017-12-21 05:45:24 +01:00
Greg Landrum
7c0bb0b743 clang-tidy output 2017-04-22 17:09:24 +02:00
Greg Landrum
fb2c546948 Fix/github1262 (#1265) 
* fix for calculation of prinicipal moments of inertia

* fix a typo
update expected values

* PMI and NPR tests working

* cleanup some of the other descriptors and tests

* Test against Moments.py descriptors

* add new tests from Brian

* remove some warnings
 2017-01-22 05:49:52 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Brian Kelley
210f2951e0 Silences warnings in tests 2015-10-18 21:20:11 -04:00
ptosco
865175104b - added getters/setters for bond lengths, angles, dihedrals 
in the MolTransforms namespace:

  * getBondLength(conf, iAtomId, jAtomId)
                 (only in this case, atoms need not be covalently bonded)
  * setBondLength(conf, iAtomId, jAtomId, value)
  * getAngleRad(conf, iAtomId, jAtomId, kAtomId)
  * setAngleRad(conf, iAtomId, jAtomId, kAtomId, value)
  * getAngleDeg(conf, iAtomId, jAtomId, kAtomId)
  * setAngleDeg(conf, iAtomId, jAtomId, kAtomId, value)
  * getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
  * getDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)

- added the corresponding Python wrappers in rdMolTransforms
  (same prototype as C++; as usual all Python methods
  have an uppercase initial)

- added relevant C++/Python tests
 2013-10-15 11:59:08 +02:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
5d03333c22 setup svn keywords (should have done this before import... grn) 2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00