* Adds missing options docstring
* Always be cleaning
* Fix typos in RGroupDecomposition module
* Update documentation on configuring doxygen
* Was a step that I couldn't find reference to besides in the Makefile
* Undo american spelling of labelling
* British spelling appears more consistent
* Fix style of RGroupDecompositionParameters parameter
* Also fixes a typo
* Remove unintentional use of docstring
* Was assigning documentation about the parameters to the
RGroupDecomposition
* Remove empty string
* Apply suggestions from code review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Changed linux build from source docs to use miniconda
- closer to the azure builds
- uses conda-forge
- consolidated all dependencies into one command
- removed two cmake flags causing warnings that were not in the azure builds
* readability
* Switch to miniforge installers
* Parsing SCSR
* add scsrol to mol
* removed bad include file
* loosen distGeom test slightly
* add wrap test for SCSRMol
* Add test for scsr in python
* tests added for scsr and strict parsing removed
* remove extra stuff
* More fully specified use of SCSRMol for PR CI build
* Added flags for SCSR expansion to not include any leaving groups
* Added MolFromScsrParams to Wrap for python
* added SCSRMol destructor
* Added two tests for RNA macromols, and fixed a bug they revealed
* Added new tests abd expected files
* changes as per PR review
* SCSR Chnages for leaving groups
* fixed testScsr.py
* hydrogen bond treatment
* in SCSR expand, allow Hbond to be autoatically detected
* changes as per code review
* Adding new test file
* chages for SCSR contructors, destructors for CI build
* fixed pyton for SCSR hydrogen bond modes, and added tests
* Added new test files
* fixed edge case for SCSR
* fix checksum for inchi
* consistent capitalization of SCSR throughout
* switch to enum class
* make things shorter
* simplify
* get rid of the ATTCHORD class
* New section for SCSR in RDKit_book
* addeed section to RDKit_Book
* SCSRMol is no longer exposed in Python
* fix leak in MolFromSCSRFile()
light refactoring
* expose MolFromSCSRFile() to python
make the MolFromSCSR functions work with default args
a bit more testing
* removed C++ access to SCSRMol
* CXMsiles now ouputs hbonds, fix to template matching, and a few other things
* Addl fix for bad aromaticity in Hbond rings
* Test files needed
* Test files needed
* try to fix a CI build errors
* CI error fix
* Added missing test file
* CMake version - for CI build
* remove full file compoarison from macromol test file
* accidental change to debug restored to release
* Code review changes
* As per PR review
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Use distances on all valid paths rather than just shortest distance.
* Optimise BondPaths.
* Optimise BondPaths.
* Hash coded for the bond paths.
* Faster find all paths.
* Build in gcc working.
* Comment.
* Remove debugging code.
* Update GettingStartedInPython.rst.
* Now need to split the clique and keep the largest fragment.
Lots of warnings about how slow this is.
Split out long tests.
* Back out a lot of changes. Remove the distance check with singleLargestFrag when building modular product.
* Tidy code.
Update docstrings.
Add explanation to GettingStartedInPython.rst.
* Fix single fragment test.
* Response to review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* refactor the code to determine whether or not an atom is in brackets
* move the definition of isMetal to QueryOps
* atoms bound to metals in SMILES should always be in square brackets
Implementation and some test updates
needs confirmation that all of tests run
* basic tests pass
* java tests pass
* update js tests
* doc updates
* Update Code/GraphMol/catch_graphmol.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Update Code/GraphMol/SmilesParse/test.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* finish fixing tests
* bump yaehmop version to allow compilation to work
---------
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Expand on Explicit Valence Error - Partial Sanitization recipe, including adding molecular structures for the unsanitized and partially-sanitized iterations
* Format `argument=value`
* Fix typo in formatting
* Update label to *Original* Source
* Correct rdqueries import, and formatting of testoutput blocks
* Print out hybridization create doctests
* test fork commit
test complete, remove file
squashed test
* add skeleton file
* outline of the Python dev section
* add if not developer
* Update GettingStartedWithContributing.md
* strcuture things a bit more
* add summary of blog post
* update dev instructions
* update for devs
* Add example on how to add unit tests
* add style section
* added github issues and discussion
* add style example image
* update for devs
* add hyperlinks
* Move CodingStandards to GettingStartedWithContributing
Also updated the supported C++ version to C++17. I put in g++ 8.0 as a
rough guess of a version expected to support this standard.
* add initial git pull steps
* add how to check for bugs
* added how to contribute code
* Add a section on how to run tests
* Update "running tests" section
Fix a MD syntax error and add a paragraph encouraging people to run the tests! :-)
* add pullreq
* add pull_req2
* Add links to new GettingStartedWithContributing.md
* add missing image files
* update what and how section
* update how to pull req
* Update GettingStartedWithContributing.md
* update running tests
* tweak formatting
* start docs contribs
* typo fixes
* add rst overview
* move image to correct location, update python and C++ sections
* add how to do Python bindings
* Add batch 1 of Greg's suggested changes
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* add Greg changes
* Revert "add Greg changes"
This reverts commit 3f7d8eed6c.
* make Greg's (actual) changes
---------
Co-authored-by: mikey <m.k.blakey@icloud.com>
Co-authored-by: martin-sicho <sicho.martin@gmail.com>
Co-authored-by: dehaenw <66372095+dehaenw@users.noreply.github.com>
Co-authored-by: Franz Waibl <waiblfranz@gmail.com>
Co-authored-by: Rasmus Mejborg Borup <borup@eduroam-hci-dock-1-081.intern.ethz.ch>
Co-authored-by: Ivan Tubert-Brohman <Ivan.Tubert-Brohman@schrodinger.com>
Co-authored-by: Ivan Tubert-Brohman <ivan.tubert@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* doc updates
* add rdShapeAlign to the docs
* fix shape docs
* let's not add too much here, revert deprecation
* cleanup the python book
* more book cleanups
* bring in sphinx.napoleon so that we can use the numpy docstrings
* fix a typo
* Update rdkit.ML.rst
* Add "Include a Bond Index" recipe and image
* Add testoutput so doctest passes
* Use addBondIndices. Follow template of recipe "Include an Atom Index".
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* test changes
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* Merge branch 'master' into pr/specialQueries
* changes from previous PR
* Iclude false chiral
* rigorous enhnced stereo canoncalization
* Added more tests and clenup
* removed commented out code
* corrected init of SmilesWriteParams
* added MolFileStereoChem.h to the header files
* Renamed Rxn parser to MrvBlockToChemicalReaction
* To make catch2 work, and match the checksum
* Fixed Structchecker errors
* fix CI for DetermineBonds catch test
* error in catch_test for CI
* Allow custom smileWriteParams in GetMolLayers
* misnamed entry point
* ReactionFromMrvString change name
* remove adding writeParams to GetMolLayers
* make rigorous enhanced stereo the default, and fix tests
* only one abs group no longer needs Rigorous Enhanced treatment
* changed string_view to string in catch test
* Canonicalize Enhnaced Stereo only resturne unique smiles
* Now allows or and and groups together
* internal routines inside detail scope
* fix test error
* changed string back to string_view and fixed a CHECK
* Fixes for PR review tests
* Fix RDKit_Book.rst failure on build test
* fix xqm sql test
* updated expected files for cxsmiles_test
* Fixed removal of atom attrs
* Fixed tests after merge of master
* More efficient version of Stereo Groups Canonicalization
* Fixes for ctests
* removed debug code
* readded cipLabel test
* fix generalizedSubstruct/catch_tests.cpp error
* hueristics to improve speed
* Rationaized control of abs groups
* removed unused routine
* added rigorous stereo group treatment to test
* some suggested changes
* Changes per PR review and removed some changes to smiles
* Fixed CI errors
* changes per PR review
* more PR review vhanges and cleanup
* Fixed PSql PKL change
* changes as per PR review
* Restored error type for bad mols for canonicalizeStereoGroups and added a test
* Merge master and fix test in MolDraw2D
* Fix for randomize test error and other PR review comments
* Removed unsued variable to fix mac CI
* do not force aromatization in canonicalizeStereoGroups
* changes as per PR review
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* first try
* do over with @greglandrum: fix atomPairs, lower SP angle force constant.
* change test file for 'update parameters from JSON':'ETKDGv2'
* adapt length to fix
* remove overwritten random seed
* adapt test files to changes
* adapt amide test, check with Greg
* fix python tests and remove unused imports
* proposal for new test molecule
* remove double comparison, increase threshold. Check with greg
* remove TODO comments
* remove debugging statements
* same code for both since they are doing the same
* format docstring to make more readable
* remove todo comments
* add indentation to angle param
* adapt doctest to newly generated conformers
* fix test to pass with fewer failures and move mol to mol file for less cluttered test.
* a bit of modernization
* remove cerrs and format correcly
* reverted test to old behavior
* use insert and make force field contribs exception safe
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* 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>
* basic code to convert dative to single if we aren't outputting dative to the SMILES
add forms of GetAtomSmiles() and GetBondSmiles() that take SmilesWriteParams
* dative/coordinate bond support when writing CXSMILES
* expose all of that to Python
* remove usage of _doIsoSmiles property
add params to smarts writers
* allow disabling dative bonds in SMARTS
* typo
* add support to the reaction writers
* support params for SMARTS
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
* changes for CIP test errors
* Updated internal doc to match what it does
* changes per PR review
* removed cout statements in tests
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* deprecations for the 2024.09 release
* update doctests
* Fixes#7402
* get tests passing when the cairo build is not there
* fix a problem in the tests
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Include macrocycles in atropisomer calculation
Previously, atropisomeric bonds were sanitized away if they were part of a "ring bond", which happens in macrocyclic systems.
None of the existing test cases fail if that sanitization check is removed.
The sanitization step is removed to support biaryls that are part of a larger macrocyclic system.
A set of test cases is included that cover potential macrocyclic atropisomeric systems
* Remove unmentioned files
* Keep ring check, and narrow it to when bond is in as many rings as atoms
* exclude atropisomer bonds if in rings < 8 atoms
Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>
* Clarify macrocycle behavior in RDKit book
* fix typo
---------
Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>
* Add Double Cubic Lattice Volume (DCLV).
Method to compute the solvent accessible surface area and volume, van der Waals volume, compactness and packing density of a protein. Implemented from: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander and Michael Scharf, "The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", Journal of Computational Chemistry, Vol. 16, No. 3, pp. 273-284, 1995.
* refactor
* DCLV is no longer a configuration option
* add to the docs
* standalone test has been removed
* reduce use of pointers as args
* DCLV to catch_tests
* update python wrapper
* add copyright statements
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* update cookbook, draw molecule atomic indices
By default, RDKit 2023.09.3 does not explicitly displays atom index 0.
* describe absence of atom index zero in the formula
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* fix a float comparison in a test
* make ETKDGv3 (i.e. v2 of the torsion parameters) the default.
This should have been done a long time ago.
* change default for onlyHeavyAtomsForRMS too
* release notes update
* - added gen_rdkit_stubs Python module to generate rdkit-stubs
- added patch_rdkit_docstrings Python module to patch existing C++ sources to fix docstrings missing self parameter and add named parameters taken from C++ signatures where possible
- added rdkit-stubs/CMakeLists.txt to build rdkit-stubs as part of the RDKit build
- added an option to CMakeLists.txt to enable building rdkit-stubs as part of the RDKit build (defaults to OFF)
* fixed CMakeLists.txt, rdkit-stubs/CMakeLists.txt and a doctest
* - added missing cmp_func parameter
- fixed case with overloads with optional parameters
- do not trim params if expected_param_count == -1
- add dummy parameter names if we could not find any
- keep into account member functions when making up parameter names
- address __init__ and make_constructor __init__ functions
- fix incorrectly assigned staticmethods
* patched sources
* address residual few remarks
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* 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
Made the following changes
* removed RDK_USE_BOOST_REGEX cmake option and its references
* removed usage of RDKIT_USE_BOOST_REGEX macro
* removed install instructions related to boost regex
