* Expose tautomer scoring functions to python
* Add more tests/documentation
* Rename getDefaultTautomerSubstructs to getDefaultTautomerScoreSubstructs
* Remove ROMOL_SPTR
* Add full custom scoring function example
* Run clang format
* Use proper BOOST_PYTHON_FUNCTION_OVERLOADS
* Use default copy constructor
* change valence model to use isolobal analogy
Remove support for five-coordinate C+ and, by analogy, five-coordinate N+2
Removes support for charge states that take atoms past the end of the periodic table
i.e. [Lv-4] is no longer supported
* update the tests for that
* remove valence state of 6 for Al
* fix representation of phosphate in the mol2 parser
this is a correction of what was done during #5973
* cleanup the exceptions for P, S, As, and Se
* drop valence states:
Si 6, P 7, As 7
* a couple of additional changes from #7397
* update java tests
* fix an inconsistency: Rb now supports valence -1
* documentation
* - replace operator[] with at() for bounds check
- extract some code into a function to avoid duplication
- use TAB as separator throughout in the periodic table data for consistency
* removing the .at() usage
We know that these vectors aren't empty, so there's no need for the bounds check.
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Add a 'force' option to MolStandardize::Uncharger
* update comment
* add more test cases exercising MolStandardize::Uncharger
* fix the neutralization of surplus negative charges
* changes in response to review
* Add a test case for MolStandardize::Uncharger
* refactor the neutralization of negative charges in MolStandardize::Uncharger
* initial addition of MT support to MolStandardize
* do the other inplace functions
* add mt ops to python wrappers
including tests
* release the GIL
* remove exploratory code added during dev
* make normalizer thread safe
* refactor some repeated code
* reionizer and uncharger and normalizer can now operate in place
* add removeUnmatchedAtoms argument to in-place version of runReactant
When set to false atoms which are not explicitly removed by the reaction are preserved
* Fix a case where transforms were incorrectly updating atomic numbers
* add more inplace operations to MolStandardize
* support those in the Python layer
* support inplace for the rest of the python wrappers
* move a few more functions over to the inplace code
* Swap to using a data structure for default normalization parameters
* bring the default fragment data into the code too
* cleanup
* add reionizer parameters via data
change fragment parse failures to ValueErrorExceptions
* tautomer parameters in the code
* got a little over-enthusiastic in that last cleanup
* use boost::flyweight to cache normalization and charge data params
* a bit more cleanup
* support reading params from JSON
* fragments from JSON
single-call for fragment removal
* add a one-liner for the canonical tautomer
* quick refactor
* Fixes#4115
* complete the parents
* docs
* move the definitions to a namespace and make them const
* see if switching to c++14 fixes the CI compile problems with g++ 5.5
* somewhat uglier way of solving the initalizer list problem
* Make MetalDisconnector more robust against metallorganics
* - fixed misbehavior with radicals
- added tests
- code cleanup
* - fixed MetalDisconnector with dative bonds
- removed pointless test
* fixed issue #2965
* added test case for issue #2965
* fixed formatting and added comment.
* update
* General Reader files
* removed dependency on boost filesystems
* removed class
* clang-format
* added-comments
* further-cleanup
* added clang-formatting
* braces-for-if-else
* changed error messages, added option for windows file path
* fixed getFileName function
* cleanup
* option for filename without path
* further-cleanup
* added tests for determineFileFormat
* cleanup, const arguments for validate function
* init
* cleanup
* cleanup
* clang-format does not work for CMake
* added RDK_TEST_MULTITHREADED option
* add-flag
* cleanup
* Delete ConcurrentQueue.h
This PR deals with the Generalized File Reader.
* Delete testConcurrentQueue.cpp
This PR deals with the Generalized File Reader.
* no change
* concurrent queue
* print values
* Single Producer Multiple Consumer works
* cleanup
* Producer Consumer Example
* update queue methods and tests
* cleanup
* test
* fixed tests
* cleanup, updated tests
* Delete ProducerConsumer.h
* Delete testProducerConsumer.cpp
* cleanup
* futher cleanup
* changes based on feedback
* make queue non copyable
* psuedocode
* possible implementation
* untested implementation
* change class to typename
* basic-setup
* need to fix segfault
* need to fix blocking
* need to fix blocking
* need to fix blocking
* fix indentation
* one possibility
* without lambda function
* possible fix with some test cases
* performance tests
* added support for record id and item text
* cleanup
* cleanup
* fixed memory leak and added methods with tests for getting last id and item text
* cleanup
* added more test cases with different smi files
* cleanup
* SD mol supplier
* modified the parsing for SDMolSupplier
* cleanup
* cleanup
* new file for testing
* added support for reading molecule properties with tests
* thread-safe logging and exception handling
* cleanup
* without thread safe logging
* cleanup
* cleanup, modified MultithreadedSmilesMolSupplier
* cleanup, made reader and writer functions private
* move O2.sdf
* basic python wrapper with tests
* cleanup, added new methods for python wrappers
* made changes suggested by Andrew
* file and compression formats are case-insensitive
* cannot open files with gzstream
* cleanup
* possible fix for opening compressed streams (SMILES)
* removed seekg() and tellg() methods from multithreadeded suppliers
* cleanup
* test cases for python wrappers
* some wrapper cleanup
* cleanup, removed unused functions
* update the MT tests so that they actually do some work
also includes some cleanup here
* cleanup
* remove iterator_next header include
* added support for multithreaded readers
* use getNumThreadsToUse for multithreaded suppliers
* fixed documentation for multithreaded python wrappers
* commented performance test
* first draft of final evaluation report
* removed inline variables
* first draft getting started in python
* fixed typos in getting started in python
* fixed typos
* fix documentation tests
* fixed documentation tests
* added links to important files and PR
* added perfomance results
* first version of wrappers with compressed streams
* getting rid of streambuf stream method
* modified General File Reader
* make this work when building in non-threads mode
* rename a test
* rename a function in the python API
* rearrange the python test a bit
* disable the stream-based constructors in Python
* mark the multithreaded classes as experimental
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* This commit fixes the bug "segmenation fault/core dump when chargeParent is run with skip_standardize set to true" mentioned in #2970
* Fixed memory leaks in MolStandardize and deleted variables which aren't required
* modify the uncharger to be use a canonical atom ordering
* add doCanonical cleanup parameter
make canonical ordering the default
document the change
* Add neutralization of additonal negative groups (not just acids).
This may not be the right thing to do.
* expose the new parameter to python
* changes in response to review
* add SKIP_IF_ALL_MATCH argument to FragmentRemover
Refactor FragmentRemover::remove() to make it more efficient
* implement and test SKIP_IF_ALL_MATCH
* expose the extra option to Python
* add info to logger
