* Fix parse error messages for bad characters
This updates the SMILES and SMARTS parser error messages to include the token
position for "bad" characters.
* copy generated files
* add test
* Try tab-separated before space-separated when reading synthon lines.
Fix bug in looking up reactions by name.
amino_acid.txt had a mixture of tab-separated and space-separated lines which is no longer allowed.
* Typo
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* get SynthonSpace.cpp to build also when RDK_USE_BOOST_SERIALIZATION is
not defined
* test should not fail when RDK_USE_BOOST_SERIALIZATION is not defined
* - expose reading/writing PNG metadata to CFFI and MinimalLib
- add relevant CFFI and MinimalLib unit tests
- add RDK_USE_BOOST_PROGRAM_OPTIONS CMake option
- enable using standalone zlib in the absence of boost::iostreams for parsing PNG files
- enable linking against maeparser in the absence of boost::iostreams also on Windows
- enable building RDKit in the absence of boost::program_options
* add check for boost::program_options
* change size_t into std::uint64_t in SearchResults for consistency with doTheSearch() which uses std::uint64_t
* change size_t into std::uint64_t in SearchResults for consistency with
SynthonSpaceSearcher::doTheSearch()
* set CMake policy to allow YAeHMOP to require a version which is not
actually supported
* reverted External/YAeHMOP/CMakeLists.txt to master version
* check if Windows build will work
* fix build
* configure zlib install location
* build zlib dependency
* include zlib header directory
* explicitly set PropertyFlags.AllProps so the test does not fail on
static builds
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* fix scsr parsing for non-template SUP groups
* Rempoved two tests not related to this PR
* Update Code/GraphMol/FileParsers/SCSRMolFileParser.cpp
added the constexpr as suggested
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* changed constrexpr to const for std:string
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* ChemDraw Document and read/write support for the RDKit
* Add missing test file
* Rev chemdraw version
* Rev chemdraw version
* Rev chemdraw version for g++11
* Update CMakeLists.txt
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Build chemdraw from an external CMake file
* Remove unused platform bigendian check
* Revert changes to constants, remove unused ones
* Keep the original constant names
* Remove __main__ section
* Use as much of the ChemDraw CMakeList as possible
* Skip installing expat
* Rev chemdraw version to fix windows issue
* Don't install expat, set the appropriate CHEMDRAW_BUILD definition
* resolve windows builds
* Fix minimal lib builds
* Move ChemDraw document to private header
* Move utility functions to ChemDraw namespace
* Move ChemDraw to v2 unique ptr api namespace
* Make class enum
* Switch to camelCase
* Response to review
* Move ChemDrawToDocument to ChemDraw namespace
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix typo
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add better documentation
* Rev chemdraw version
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* ChemDraw Document and read/write support for the RDKit
* Add missing test file
* Rev chemdraw version
* Rev chemdraw version
* Rev chemdraw version for g++11
* Update CMakeLists.txt
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Build chemdraw from an external CMake file
* Remove unused platform bigendian check
* Revert changes to constants, remove unused ones
* Keep the original constant names
* Remove __main__ section
* Use as much of the ChemDraw CMakeList as possible
* Skip installing expat
* Rev chemdraw version to fix windows issue
* Don't install expat, set the appropriate CHEMDRAW_BUILD definition
* resolve windows builds
* Fix minimal lib builds
* Move ChemDraw document to private header
* Move utility functions to ChemDraw namespace
* Move ChemDraw to v2 unique ptr api namespace
* Make class enum
* Switch to camelCase
* Response to review
* Move ChemDrawToDocument to ChemDraw namespace
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix typo
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add better documentation
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* feed dummy perpendicular point for cross product to prevent zero error in normalization during atropisomer chirality, fixes#8602
* remove debug log
* move test, and check that no bonds
* progress, passes tests, needs more optimization
* passes tests
* minor
* cleanup
set diagonal elements of matrix
* replace numeric consts with enum
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Fixes#8559
Also includes some minor refactoring of set14Bounds()
* apply the same change to the cis/trans trackers
* cleanup
---------
Co-authored-by: = <=>
* Adds a df_forceStop to stop readers and writers, clears out queues on destructor
* Propery implement close function, requires protected closeStreams
* changes from greg's version
* close() needs to be called in the derived destructors
* Close the writers before the reader to avoid deadlock
* Don't process trailing new lines
* Don't accept pushes if the queue is done
* Add mutex protecting d_threadCounter, remove unneeded forceStop checks
* Update Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add comment for the d_threadCounterMutex unlock
---------
Co-authored-by: = <=>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Basic transliteration and tests complete.
* Atropisomers for assigned only.
* Python wrapper.
* Tidy.
* Working with gcc.
* Tidy.
* Rename Python test file.
* Clear other atropisomer bond.
* Fiddle Windows export thing.
* Fiddle Windows export thing.
* Split namespace declaration.
* No export thing.
* More export things, and add it to CMakeLists.txt.
* Response to review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Count chiral atoms just counts tetrahedral atoms.
* Put an actual check in.
* Randomly fix some unconnected warnings.
* Curb my enthusiasm for std::cmp_less.
* Trigger Build
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Add getMolFrags test
confirm bond-only stereogroups are preserved during fragmenation
* Update molopstest.cpp
* Prevent deletion of stereogroups
Prevent removeAtomFromGroups from deleting stereogroups that have bonds but no atoms
* - avoid a large number of warnings when building MinimalLib with emscripten, which does not support SHARED
- fix indentation in CoordGen CMakeLists.txt
* disable RDK_USE_BOOST_STACKTRACE on emscripten platform
* revert change done by mistake
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* only exclude multiple double bonds from check if degree of center atom is 2
* clang-format
* add test for fix
* try fixing DLL build
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fix Widnows build as suggested by @greglandrum
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* apply root id correctly for each fragment
* add missing rootedAtAtom assignment
* add tests for rootedAtAtom with multiple fragments
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
