Jonathan Bisson 56170a455d Add support for Marvin files (#6575) ...

* Add support for Marvin files

* And MRV lib to the Java wrapper

* And MRV lib to the Java wrapper

* Removed use of void * in MarvinParser.cpp and MarvinParser.h

* Changes as per code review from Greg

* Changes for PR review - many virtual methods

* changes as per Jonathan's comments

* some suggested changes

* PR review changes and fixed unit tests

* after merge, changes to make it run

* More PR review changes

* removed unneeded std::move()s · rdkit/rdkit@b4b8b9a · GitHub

* More PR review changes

* fix a compile error

* more defensive programming

* reorder

* final? PR review updates

* Erata

---------

Co-authored-by: Tad Hurst <tad.hurst@collaborativedrug.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>

2023-09-01 04:50:34 +02:00

..

test_data

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

Atom.cpp

Optimize GetPropsFromDict: use tags for conversion (#6355)

2023-05-25 09:50:08 -04:00

Bond.cpp

Optimize GetPropsFromDict: use tags for conversion (#6355)

2023-05-25 09:50:08 -04:00

Chirality.cpp

Initial support for non-tetrahedral stereochemistry (#5084)

2022-05-20 09:07:16 +02:00

ChiralityOps.cpp

New version of AssignStereochemistry (#5442)

2022-09-06 12:53:02 +02:00

CMakeLists.txt

Add support for Marvin files (#6575)

2023-09-01 04:50:34 +02:00

CompressedSDMolSupplier.cpp

Improve MaeMolSupplier API (#6053)

2023-02-08 04:31:51 +01:00

Conformer.cpp

Optimize GetPropsFromDict: use tags for conversion (#6355)

2023-05-25 09:50:08 -04:00

ContextManagers.h

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

EditableMol.cpp

fixed AddBond documentation (#4142)

2021-05-18 13:19:31 +02:00

ForwardSDMolSupplier.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

MaeMolSupplier.cpp

Improve MaeMolSupplier API (#6053)

2023-02-08 04:31:51 +01:00

MaeWriter.cpp

Drop the s_m_color_rgb property from MaeWriter (#6511)

2023-07-14 07:53:42 +02:00

Mol.cpp

Add atom and bond property parameters to substruct matching (#6453)

2023-06-15 05:08:48 +02:00

MolBundle.cpp

Add support for generalized substructure searching (#6443)

2023-06-22 10:54:35 +02:00

MolOps.cpp

Fix some build warnings (#6618)

2023-08-11 06:04:55 +02:00

MolSupplier.h

Improve MaeMolSupplier API (#6053)

2023-02-08 04:31:51 +01:00

MonomerInfo.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

MultithreadedMolSupplier.h

[GSoC-2020] Generalized and Multithreaded File Reader (#3363)

2020-10-09 04:31:05 +02:00

MultithreadedSDMolSupplier.cpp

Fixes #5210 (#5408)

2022-07-11 11:20:03 +02:00

MultithreadedSmilesMolSupplier.cpp

Fixes #5210 (#5408)

2022-07-11 11:20:03 +02:00

PDBWriter.cpp

Start a Maestro file (.mae) writer. (#6069)

2023-02-17 11:53:17 +01:00

props.hpp

switch from boost::any to std::any (#6662)

2023-08-25 17:55:33 +02:00

Queries.cpp

expose two missing queryatom types to python (#6158)

2023-03-05 05:56:37 +01:00

rdchem.cpp

Fixes #6208 (#6419)

2023-06-03 04:59:16 +02:00

rdchem.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

rdmolfiles.cpp

Add support for Marvin files (#6575)

2023-09-01 04:50:34 +02:00

rdmolfiles.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

rdmolops.cpp

Updated code for chirality perception (#3324)

2020-09-02 15:00:29 +02:00

rdmolops.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

rdqueries.cpp

Remove extra calls to python::register_exception_translator

2016-03-01 06:36:54 +01:00

rdTrajectory.cpp

- added miising Code/GraphMol/Wrap/rdTrajectory.cpp

2016-05-11 19:56:32 +01:00

ResonanceMolSupplier.cpp

run clang_format (#5676)

2022-11-01 04:14:26 +01:00

RingInfo.cpp

- Changed all unsigned to unsigned int for clarity (#6646)

2023-08-25 06:09:19 +02:00

rough_test.py

switch from boost::any to std::any (#6662)

2023-08-25 17:55:33 +02:00

SDMolSupplier.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

SDWriter.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

seqs.hpp

Fixes #6208 (#6419)

2023-06-03 04:59:16 +02:00

SmilesMolSupplier.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

SmilesWriter.cpp

Start a Maestro file (.mae) writer. (#6069)

2023-02-17 11:53:17 +01:00

StereoGroup.cpp

Fix bug in StereoGroup wrapper (#6619)

2023-08-11 20:30:24 +02:00

SubstanceGroup.cpp

Optimize GetPropsFromDict: use tags for conversion (#6355)

2023-05-25 09:50:08 -04:00

substructmethods.h

- Changed all unsigned to unsigned int for clarity (#6646)

2023-08-25 06:09:19 +02:00

Table.cpp

run clang_format (#5676)

2022-11-01 04:14:26 +01:00

TDTMolSupplier.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

TDTWriter.cpp

Support context managers for mol Suppliers and Writers (#3704)

2021-01-11 05:52:57 +01:00

test_cdxml.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testConformer.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testMultithreadedMolSupplier.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testPropertyLists.py

Optimize GetPropsFromDict: use tags for conversion (#6355)

2023-05-25 09:50:08 -04:00

testSGroups.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testThreads.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

testTrajectory.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

Trajectory.cpp

Fix a few broken docstrings (#6480)

2023-06-23 13:47:51 +02:00