* First pass at port
Mostly auto-converted using claude sonnet 4
Things are a bit slower in this initial port. Here's some timing data for molecules from SMILES (no coords) and from SDF (with coords)
# MASTER
## smiles
read: 50000 mols.
9.260000s wall, 8.650000s user + 0.600000s system = 9.250000s CPU (99.9%)
serialize
3.060000s wall, 2.400000s user + 0.660000s system = 3.060000s CPU (100.0%)
deserialize
1.350000s wall, 1.250000s user + 0.090000s system = 1.340000s CPU (99.3%)
## SDF
read: 50000 mols.
9.340000s wall, 8.930000s user + 0.400000s system = 9.330000s CPU (99.9%)
serialize
6.630000s wall, 5.960000s user + 0.680000s system = 6.640000s CPU (100.2%)
deserialize
1.450000s wall, 1.450000s user + 0.000000s system = 1.450000s CPU (100.0%)
# Boost::JSON
## smiles
read: 50000 mols.
9.250000s wall, 8.830000s user + 0.420000s system = 9.250000s CPU (100.0%)
serialize
4.770000s wall, 4.410000s user + 0.350000s system = 4.760000s CPU (99.8%)
deserialize
2.320000s wall, 2.100000s user + 0.230000s system = 2.330000s CPU (100.4%)
## SDF
read: 50000 mols.
9.500000s wall, 9.100000s user + 0.400000s system = 9.500000s CPU (100.0%)
serialize
8.760000s wall, 8.330000s user + 0.420000s system = 8.750000s CPU (99.9%)
deserialize
2.540000s wall, 2.330000s user + 0.210000s system = 2.540000s CPU (100.0%)
* some json parser optimization
* around the edges
* optimizations for the writer
* hopefully get things compiling
* convert the MinimalLib stuff to use boost::json
Again, a lot of the lifting here was done using Claude Sonnet 4 in VS Code Copilot
* fix Windows DLL build
* response to review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* better not to blindly accept suggestions
* fix the problems in MinimalLib
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: = <=>
- implement get_v2Kmolblock() in MinimalLib
- add the possibility to specify the MDL version preference as a get_molblock() forceMDLVersion JSON parameter, which is ignored by get_v3Kmolblock() and get_v2Kmolblock()
- changes in response to review
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - When depictions are made using the useMolBlockWedging flag, make sure that kekulization is done after original wedging has been applied to reduce the odds that bond wedges are placed on double bonds
- Refactored MinimalLib code to avoid code duplication
- get_molblock() should reapplyMolBlockWedging on a copy of the passed molecule rather than on the original
- Added unit tests
* Update Code/MinimalLib/jswrapper.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* - fix#7157
- add the assignCIPLabels flag to MinimalLib's mol_from_input()
- added cffi and JS tests
- refactored process_details(), process_mol_details() and process_rxn_details() to take a struct reference as parameter rather than a long list of parameters
- this also allowed to get rid of one of the ugly GET_JSON macros
- exposed panelWidth, panelHeight and noFreetype (the latter is useful for testing)
- made width and height to default to -1 in mol_to_svg since we now support flexicanvas
* added a bunch of assignments I'd forgotten in the deprecated process_mol_details() overload
* MSVC does not like inner functions
* updated docstrings
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
