* Fixes#2057
docs still need to be updated
* docs update
* Update getting started doc.
This still needs to have the doctests run and should probably be
proofread and tweaked
* some doc updates
* change in response to review
* Adding the RDK_BUILD_RPATH_SUPPORT build flag to specify that RDKit
should link its shared libraries using -rpath. This allows the C++
shared libraries to be loaded from python without needing
LD_LIBRARY_PATH to be set.
This assumes the user has specified CMAKE_INSTALL_PREFIX to be the
place the RDKit will be installed to as this will use absolute paths
with -rpath. More work will need to be done by any user wishing to
make rpath work with relative paths from $ORIGIN.
* Allow the catch source code to be populated directly by un-taring the source code into the proper location.
* Fix 2D/3D interpretation of V2000 ctabs
* Remove debugging statements
* Apply fix to V3000 molblock
* Add 3D pretending to be 2D test case
* Fix for review comments.
* Set drawing label for the "extra" atoms by setting atomic number
* first pass at drawing multiple morgan bits
* get this working with the RDKit FP too
* Fix memory leak in Dict operator=
* Reenable old tests
* Don't overwrite nonPodData until the last moment
* Fix previous bug. Need to check other._hasNonPodData, not our own
* short test file for MolVS standardize_sm
* short test file for MolVS fragment
* short test file for MolVS metals
* short test file for MolVS normalize
* short test file for MolVS reionize
* short test file for MolVS tautomer
* short test file for MolVS validate
* long test file for MolVS standardize smiles
* long test file for MolVS fragment
* long test file for MolVS metals
* long test file for MolVS normalize
* long test file for MolVS reionize
* long test file for MolVS tautomer
* long test file for MolVS validate
* Unit tests for MolVS steps
* dropping support for Python2
* molvs/__init__.py
* molvs/charge.py
* molvs/errors.py
* molvs/fragment.py
* molvs/metal.py
* molvs/normalize.py
* molvs/resonance.py
* molvs/standardize.py
* molvs/tautomer.py
* molvs/utils.py
* molvs/validate.py
* molvs/validations.py
* molvs/cli.py
* adapted and renamed molvs/cli.py to work within $RDBASE/Contrib/MolVS/
* setup MolStandardize directories, source with empty cleanup function, header, CMake files
* corrections to empty source, header and test1.cpp
* adding empty functions and initializers to MolStandardize
* empty Metal source, header and added test
* added most of Metal.cpp functionality and made some more tests
* empty functions and initializers to Normalize
* empty functions and initializers to Validate
* added most code for RDKitDefault mode, along with some tests
* restructure for abstract base class ValidateMethod
* written in isNoneValidation for MolVSValidation
* took out isNoneValidation, put in noAtomValidation, neutralValidation, isotopeValidation for MolVSValidation
* added in AllowedAtoms
* added in disallowedAtoms
* corrections to Validate
* added code for FragmentRemover
* extended fragment functionality to include choose largest fragment, added in tests for fragment catalog, fragment remover. Also added fragmentValidation method in MolStandardize
* added another test to testValidate test_fragment
* corrections to fragment
* corrections to Metal
* added code for Normalize
* added normalize member function to MolStandardize and added tests
* added multi fragment functionality to Normalize.cpp and additional tests
* TransformCatalog
* tests for Normalize.cpp
* first bit of cleanup
* added most of Charge functionality and some tests
* some corrections to Charge.cpp and some more tests to testCharge.cpp
* corrections to Charge.cpp
* start of Tautomer Enumerate with some tests
* added BondType option to Tautomer Enumeration
* correcting for some memory leakage
* a few alterations to formatting
* sorting out some memory leaks
* sorting out some memory leaks
* some corrections for PCS test set
* redo tests with updated RDKit
* fixing memory leak
* more fixes after 100kPCS set testing
* using tab as delimiter in CSVs rather than comma
* tutorial for MolStandardize
* still working on Tautomer enumeration
* deleted some empty tests
* starting writing tautomer canonicalize
* rename test_data -> data (the source still needs to be updated)
* automatic source reformatting
* adjust to directory rename
* move the fragment catalog test into the MolStandardize directory
do not create separate library for FragmentCatalog
* stop building separate libraries for the catalogs
* move the CleanupParameters into the MolStandardize namespace
* first pass at python wrapper
* move the py module to the correct dir;
add some python tests;
add standardizeSmiles to python wrapper
* disabling the compareMolVSTest since that requires command line arguments to run
* get this building on windows
* put the python lib in the right place
* further work on python wrapper for rdMolStandardize
* added get and set functions to Metal and wrapped them
* added get and set functions to Metal and wrapped them
* changed construstor of Reionizer class and input args for reionize, wrapped this default
* overload Reionizer constructor so user can input own AcidBaseFile from python
* added Uncharger class to Charge and added test for Uncharger
* wrapped Fragment, fixed some memory leakage, changed some args and return types, added some tests
* wrapped Normalized and changed how Normalizer class is initiated
* changing MolVSValidation structure so user can choose which MolVS submethod they want
* starting to write Wrap for Validate
* now it compiles with Wrap/Validate.cpp
* a couple refactorings around validate
* move the validate code into the rdMolStandardize module
* make sure a valid pointer is returned for standardizeSmiles
* rdMolStandardize.MolVSValidation done and tests added
* half way through AllowedAtomsValidation
* finished AllowedAtomsValidation and DisallowedAtomsValidation
* moved charge, fragment, metal, normalize into the rdMolStandardize module
* changed tutorial to use wrapped code
* added copyrights
* added copyrights
* move the data files
* modify source files to adjust to the move
* added validateSmiles functionality
* removed std::cout
* redid some of the 100k PCS tests
* working on the tutorial
* adding some documentation
* deleting some comment lines
* some changes after pull review
* More changes after pull review
* start of trying to make java wrap
* remove some warnings, add some questions
* additional warning removals, a bit more reporting
* some test cleanups
* enable testing of the java code
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
* add SVG parsing to python
re-enable the moldraw2d tests
* A couple of fixes connected to #2029
* handle problems parsing atom/bond SMILES
* wrap the whole thing in the <metadata> tag
* patch a memory allocation problem in the maeparser v1.0.0 (#2044)
* add atoms
* add bonds
* backup
* Fixes#2029
* Get metadata working for drawMolecules()
* add to python wrapper
const correctness
* also connected to #2029: make sure bond direction also ends up in the output
* initial version of an SVG->ROMol parser
this is in the wrong place, but I wanted to make sure it actually works
* move svg parser to a more reasonable location
there is still some work to be done here
* add conformer parsing
* add basic fingerprint bit rendering code
This was inspired by/adapted from the CheTo code from Nadine
* add some tests
* add documentation
add option to control which example of the bit is used
* Fixes: #1988
This just handles the atomic number part. Still need to think about the bond types
* update the tests
This includes adding UnitTestSaltRemover.py to the list of tests to be run
* fix bug from interacting PRs
* Fixes#1990
makes sure we don't destroy a double bond's StereoAtoms just because a bond connected to one of its atoms is removed
* change in response to review
* not done... nossir
* this works for molecules
* works
* update the .cmake files for the smiles parser
* do the same thing for smarts
* add to the python wrappers
