Code

Add LON net#62

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lipelopesoliveira merged 61 commits intomasterlipelopesoliveira/pyCOFBuilder:masterfrom Implement_3D_netslipelopesoliveira/pyCOFBuilder:Implement_3D_netsCopy head branch name to clipboardFeb 8, 2025

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Commits

Commits on Jun 8, 2024

• Add LON net

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• Fix positioning of the BB on LON net

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Commits on Jun 9, 2024

• Update position of vertices on LON_A net

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Commits on Jun 22, 2024

• Merge branch 'master' into Implement_3D_nets

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Commits on Jul 1, 2024

• Fix ChemJson and read_gjf

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Commits on Sep 3, 2024

• Merge branch 'master' into Implement_3D_nets

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Commits on Dec 28, 2024

• Add PRZN2

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Commits on Dec 29, 2024

• Add the method to calculate the sizes of the building block

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Commits on Feb 1, 2025

• Refactor read_gjf to remove unused cell matrix extraction and update author name retrieval method

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• Bump version to 0.0.8.8 and update CHANGELOG for new features and bugfixes

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• Refactor save_csv function to improve readability and efficiency

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• Fix docstring for save_csv function to correct parameter type for 'head'

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• Refactor IO_Tools module for improved code quality and readability; update save_csv and read_xyz function signatures and error handling

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• Enhance read_xyz and read_gjf functions to support extended xyz format and improve error handling; update return values to include cell matrix

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• Enhance read_cif function to support optional use of ASE and Pymatgen libraries for reading CIF files; improve error handling and return values

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• Refactor save_xsf function to keep consistency

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• Refactor save_xsf function to use list for file content accumulation and improve file writing method

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• Refactor save_pqr function to improve parameter naming, enhance file writing method, and streamline atom handling

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• Refactor save_pqr and save_pdb functions to improve parameter naming, enhance file writing method, and streamline atom handling

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• Refactor save_gjf function to improve parameter naming, enhance file writing method, and streamline atom handling

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• Refactor save_xyz function to improve parameter naming, enhance file writing method, and streamline atom handling

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• Refactor save_turbomole function to improve parameter naming, enhance file writing method, and streamline atom handling

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• Refactor save_vasp function to improve parameter naming, enhance file writing method, and streamline atom handling

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• Refactor save_qe function to improve parameter naming and enhance code readability

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• Refactor read functions to improve parameter naming and enhance return value clarity

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• Add save_cif function to export CIF files with enhanced parameters and structure

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• Refactor save_chemjson function to improve parameter naming and enhance code clarity; remove unused conversion functions.

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• Refactor save_chemjson function to improve clarity; remove unused create_empty_CJSON and create_structure_CJSON functions

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• Add functionality to save molecular dictionary as a JSON file; include type ignore comments for cellpar_to_cell function calls

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• Replace print statement with warnings.warn in read_cif function for better error handling

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  cda3a0c

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• Enhance read_cif function: add P1 symmetry check, improve charge retrieval, and update structure parsing method

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• Update requirements and enhance basic tests: add pytest and pytest-cov, refactor test cases for clarity and structure

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• Refactor IO_Tools module for improved code quality; add unit tests for IO_Tools and Tools modules

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• Fix read_xyz function: update cellMatrix initialization to zeros and correct charge label in output; add comprehensive tests for read_xyz functionality

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• Add test data files for CH4 and RIO_13 structures; include CIF, PDB, and GJF formats

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• Fix read_cif function: add type ignore comment for cellMatrix initialization to suppress linting warnings

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• Refactor cjson and framework modules: update cell matrix handling and add save_labels option; remove obsolete test files

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• Merge branch 'master' into Implement_3D_nets

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• Fix bond types to comply with CCDC conventions

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• Add LON, LON-A, FXT, and FXT-A nets to the changelog

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Commits on Feb 2, 2025

• Update .gitignore to exclude additional Python cache files in tests directory

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• Add geometry module with functions for distance, angles, and shape validation

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• Enhance distance function documentation

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• Configure VSCode settings for pytest testing framework

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• Fix a bug on the saving of building blocks where the folder is created even if save_bb is False

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• Update changelog

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• Fix out_path keyword of Framework class

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• Update changelog

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• Update changelog and improve building block positioning calculations

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• Update CHANGELOG

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• Update CHANGELOG and modify LON network description in Framework class

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• Update CHANGELOG and raise NotImplementedError for unimplemented networks in Framework class

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Commits on Feb 6, 2025

• Add the LON_A edges position, angle and align_v

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• Refactor edge definitions in topology.py for improved readability

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• Implement LON_A structure creation with detailed docstring and connectivity checks

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Commits on Feb 8, 2025

• Enhance documentation and formatting in topology.py for clarity on net definitions and edge properties

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  5d0d7e3

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• Update CHANGELOG to clarify default behavior of building blocks saving

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• Update LON_A structure parameters and refine method signatures for clarity

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  947ea1f

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• Fix the LON_A atom positioning

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• Remove redundant CIF export statements from Framework class

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• Piblish the 0.0.8.8 on pip

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