* first pass at adding a SubstructMatchParameter struct
* start moving the rest of the backend to use the parameters
* backend at least mostly moved over
* add aromaticMatchesConjugated
add tests
* switch over the MolBundle too
Add templates to reduce duplicated code
* support older compilers
let's see if it works...
* add SubstructMatchParameters to Python wrapper
* remove some deprecations and warnings
* damn compilers
* parameter support for bundles in python wrapper
* add the parameters to the java wrappers
* response to review
* Implementation of SGroups
* remove sample files test
* update gitignore with test outputs
* fix RevisionModifier
* re-enable tests
* backup commit; things seem to work so far
* some refactoring; obvious s group tests pass now
* more refactoring
* everything now out of the public API
* not sure why this was still in there
* rename functions; all tests now pass
* remove getNextFreeSGroupId; readd comment in copy SGroups
* clang-format
* squash-merge current master
* squash merge master
* Address comments on PR
- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
* Fixes#2225
* A bit of extra cleanup
* forgotten file
* Make this thread safe and add support for v3K mol blocks
* add the file
* update expected results
* add documents translated into Japanese
* add conf.py
* change links to images
* change Translation_into Japanese to Translation_into_Japanese
* move japanese translation to Book_jp
* update image paths
* makefile and config
* remove Book/Translation_into_Japanese
* Add check of returned string from InChI helper functions and convert to NULL when blank string is returned (a valid InChI string or InChI key will never be blank).
* Since MolInchi() and MolInchiKey() will never return a NULL pointer, I have removed the check for NULL.
Hopefully the intent of the code is now clearer.
* removed unused and outdated file rdkit/Chem/PeriodicTable.py
* rm rdkit/Chem/UnitTestPeriodicTable.py
* rm UnitTestPeriodicTable from the unit tests list
* rm ref to PeriodicTable in rdkit/Chem/__init__.py
* MolSurf.py was still using Chem.PeriodicTable
* remove reference to Chem.PeriodicTable
* The Labute ASA contributions should use Rb0
* rm PeriodicTable from rdkit/Chem/GraphDescriptors.py
* rm names of unused params in Code/GraphMol/Fingerprints/AtomPairGenerator.cpp
* correct some compilation warnings
mostly unused parameters and one unsigned Vs signed comparison
* Do not allow PandasTools to overwrite pandas settings
When PandasTools is used, setting global pandas variables like
'display.max_rows' or 'display.max_columns' have no effect. For example,
executing the following code results in printing ten rows although
'display.max_rows' is set to 5:
import pandas as pd
from rdkit.Chem import PandasTools
PandasTools.RenderImagesInAllDataFrames()
pd.set_option('display.max_rows', 5)
pd.DataFrame(['some text'] * 10)
Solve this problem by using pandas' default HTML rendering method instead
of the DataFrameFormatter. Additionally, remove all unnecessary
'pd.set_option' calls.
* Set max_colwidth only temporarily
Setting pandas option 'display.max_colwith' only during the generation of
HTML avoids breaking unit tests.
* Set max_columns in unit tests
Some unit tests fail, because 'display.max_columns' is not set by
PandasTools anymore. Set this variable in the context of the particular
test cases to infinity in order to avoid truncating of data frames.
* move _embedPoints over to use EmbedArgs structure
* move _embedWithExpTorsions over
* a few pointer cleanups
* step by step
* more
* wrap the ETKDG paramaters into a struct
* fix a typo
* additional cleanup
* more
* simplify the embedargs struct
* pass embedParams instead of having them in embedargs
* a bit more cleanup
* response to code review
* Skip compound if smiles conversion fails
If something is wrong with one of the structures in an sdf, smiles cannot be generated and Chem.PandasToolsLoadSDF will throw an error and stops processing the file. Here I propose skipping the compound and continue processing the sdf.
* add None when smiles coversion fails
Now the smiles is set None, rather than skipping the compound (as suggested by @greglandrum)
* improved logging
Now using logging.warning, as suggested by @bp-kelley
* unlikely to work
* try using system boost
also disable mac builds for the moment
* yeah, can't use system boost; use conda instead
* typo
* switch to boost 1.67.0
1.65.1 causes failures with testEnumeration on linux
* oops
* re-enable mac builds
* trying to add shape tversky
* alpha and beta no defaults, added more tverskyIndex tests to testGrid
* added python function ShapeTverskyIndex to call tverskyMolShapes
* rebasing
* add python test for ShapeTverskyIndex
* changing to aassertAlmostEqual in testShapeHelpers
* 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
* Issue #2108: Read Enhanced Stereochemistry from Python
This wraps enhanced stereochemistry data for an ROMol for use
in Python and includes a test that demonstrates access.
* Adds test for potential memory management problems
(also fixes incorrect class name and bad docstring)
* Corrected file reading idiom and object lifetime test logic
