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NO_JIRA Open source clean up - #93
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… for PEP8 compliance. Changed any http links to https. Improved comments and docstrings for clarity.
| """ | ||
| This script will generate a generic Gaussian input file | ||
| Input: CSD Identifier as a string or .mol2 |
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trailing whitespace
| # Crystal structure file | ||
| crystal_1 = CrystalReader(crystal_id) | ||
| crystal = crystal_1[0] | ||
| except: |
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🚫 [flake8] <722> reported by reviewdog 🐶
do not use bare 'except'
| raise RuntimeError("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file") | ||
| else: | ||
| try: | ||
| # CSD refcode |
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🚫 [flake8] <115> reported by reviewdog 🐶
expected an indented block (comment)
| try: | ||
| # CSD refcode | ||
| crystal = CrystalReader('CSD').crystal(crystal_id) | ||
| except: |
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🚫 [flake8] <722> reported by reviewdog 🐶
do not use bare 'except'
| hkl = all_hkl[i] | ||
| rug_list = [] | ||
| # check rugosity of crystal plane at 0, 0.25, 0.5, and 0.75 offset from origin |
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trailing whitespace
| """ | ||
| This script will generate a generic Gaussian input file | ||
| Input: CSD Identifier as a string or .mol2 |
There was a problem hiding this comment.
trailing whitespace
| # Crystal structure file | ||
| crystal_1 = CrystalReader(crystal_id) | ||
| crystal = crystal_1[0] | ||
| except: |
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🚫 [flake8] <722> reported by reviewdog 🐶
do not use bare 'except'
| raise RuntimeError("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file") | ||
| else: | ||
| try: | ||
| # CSD refcode |
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🚫 [flake8] <115> reported by reviewdog 🐶
expected an indented block (comment)
| try: | ||
| # CSD refcode | ||
| crystal = CrystalReader('CSD').crystal(crystal_id) | ||
| except: |
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🚫 [flake8] <722> reported by reviewdog 🐶
do not use bare 'except'
| hkl = all_hkl[i] | ||
| rug_list = [] | ||
| # check rugosity of crystal plane at 0, 0.25, 0.5, and 0.75 offset from origin |
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trailing whitespace
| This is a short script to generate conformers with some rudimentary analysis for a single molecule. | ||
| There are also options to overlay the results to view in Hermes. | ||
| ### Example output showing what the user can expect to see: |
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[markdownlint]reported by reviewdog 🐶
MD001/heading-increment Heading levels should only increment by one level at a time [Expected: h2; Actual: h3]
| This is a short script to generate conformers with some rudimentary analysis for a single molecule. | ||
| There are also options to overlay the results to view in Hermes. | ||
| ### Example output showing what the user can expect to see: |
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[markdownlint]reported by reviewdog 🐶
MD026/no-trailing-punctuation Trailing punctuation in heading [Punctuation: ':']
| ### Example output showing what the user can expect to see: | ||
| ``` |
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[markdownlint]reported by reviewdog 🐶
MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
| Chris Ringrose - 22/11/24 | ||
| For feedback or to report any issues please contact support@ccdc.cam.ac.uk |
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[markdownlint]reported by reviewdog 🐶
MD046/code-block-style Code block style [Expected: fenced; Actual: indented]
| ## Instructions on Running | ||
| Script can be run with any multimolecule file e.g. sdf. |
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MD009/no-trailing-spaces Trailing spaces [Expected: 0 or 2; Actual: 1]
| ```cmd | ||
| python find_binding_conformation.py pdb_example.txt | ||
| ``` |
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[markdownlint]reported by reviewdog 🐶
MD031/blanks-around-fences Fenced code blocks should be surrounded by blank lines [Context: "```"]
| python find_binding_conformation.py pdb_example.txt | ||
| ``` | ||
| ## Author | ||
| ## Authors |
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[markdownlint]reported by reviewdog 🐶
MD022/blanks-around-headings Headings should be surrounded by blank lines [Expected: 1; Actual: 0; Above] [Context: "## Authors"]
| python find_binding_conformation.py pdb_example.txt | ||
| ``` | ||
| ## Author | ||
| ## Authors |
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MD022/blanks-around-headings Headings should be surrounded by blank lines [Expected: 1; Actual: 0; Below] [Context: "## Authors"]
| ``` | ||
| ## Author | ||
| ## Authors | ||
| _'Brandl, Giangreco, Higueruelo, Schaerfer and Sykes'_ |
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MD036/no-emphasis-as-heading Emphasis used instead of a heading [Context: "'Brandl, Giangreco, Higueruelo..."]
| ## Authors | ||
| _'Brandl, Giangreco, Higueruelo, Schaerfer and Sykes'_ | ||
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MD012/no-multiple-blanks Multiple consecutive blank lines [Expected: 1; Actual: 2]
| This is a short script to generate conformers with some rudimentary analysis for a single molecule. | ||
| There are also options to overlay the results to view in Hermes. | ||
| ### Example output showing what the user can expect to see: |
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[markdownlint-fix]reported by reviewdog 🐶
| ### Example output showing what the user can expect to see: | |
| ### Example output showing what the user can expect to see |
| ## Instructions on Running | ||
| Script can be run with any multimolecule file e.g. sdf. |
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| Script can be run with any multimolecule file e.g. sdf. | |
| Script can be run with any multimolecule file e.g. sdf. |
| * -h, --help; Show this help message and exit | ||
| * -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on | ||
| molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from |
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| * -h, --help; Show this help message and exit | |
| * -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on | |
| molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from | |
| - -h, --help; Show this help message and exit | |
| - -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on | |
| molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from |
| @@ -3,21 +3,28 @@ | |||
| This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. | |||
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| This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. | |
| This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. |
| Script can be run with any multimolecule file e.g. sdf. | ||
| positional arguments: | ||
| * input file; Input file (multi-molecule file). |
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| * input file; Input file (multi-molecule file). | |
| * input file; Input file (multi-molecule file). |
| C. Kingsbury 2024 | ||
| For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](mailto:support@ccdc.cam.ac.uk) No newline at end of file |
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| For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](mailto:support@ccdc.cam.ac.uk) | |
| For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](mailto:support@ccdc.cam.ac.uk) |
| ## Instructions on Running | ||
| Using the [activated CSD Python API environment](../../README.md#running-scripts-through-the-csd-python-api-miniconda-installed) | ||
| Using the [activated CSD Python API environment](../../../README.md#running-scripts-through-the-csd-python-api-miniconda-installed) |
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| Using the [activated CSD Python API environment](../../../README.md#running-scripts-through-the-csd-python-api-miniconda-installed) | |
| Using the [activated CSD Python API environment](../../../README.md#running-scripts-through-the-csd-python-api-miniconda-installed) |
| python find_binding_conformation.py pdb_example.txt | ||
| ``` | ||
| ## Author | ||
| ## Authors |
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| ## Authors | |
| ## Authors |
| ``` | ||
| ## Author | ||
| ## Authors | ||
| _'Brandl, Giangreco, Higueruelo, Schaerfer and Sykes'_ |
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| _'Brandl, Giangreco, Higueruelo, Schaerfer and Sykes'_ |
| ## Authors | ||
| _'Brandl, Giangreco, Higueruelo, Schaerfer and Sykes'_ | ||
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| _'Brandl, Giangreco, Higueruelo, Schaerfer and Sykes'_ | |
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Pull request overview
This PR performs an “open source clean up” across the repository, primarily reorganising the scripts/ tree into clearer categories, adding/refreshing per-script documentation, and standardising embedded URLs from http to https across scripts, notebooks, and examples.
Changes:
- Reorganise scripts into a clearer folder structure (e.g.
scripts/core,scripts/discovery,scripts/materials, etc.) and add/update many script-levelReadMe.mdfiles. - Update numerous URLs from
httptohttpsacross scripts, notebooks, config/docs, and example assets. - Refactor/PEP8 cleanups in several scripts and introduce some new utilities/examples (e.g. GOLD multiprocessing example, conformer filtering tools).
Reviewed changes
Copilot reviewed 78 out of 121 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| scripts/show_semiconductor_properties/ReadMe.md | Removed old README (content moved under scripts/core/show_semiconductor_properties/). |
| scripts/ReadMe.md | Reorganises top-level scripts index into categories. |
| scripts/particle/surface_charge/surface_charge.py | Updates licence URL to https. |
| scripts/particle/surface_charge/surface_charge_calculator.py | Updates licence URL to https. |
| scripts/particle/surface_charge/ReadMe.md | Adjusts CLI usage snippet formatting. |
| scripts/particle/surface_charge/assets/adding_location.png | Adds/updates image asset. |
| scripts/particle/particle_rugosity/ReadMe.md | New README for particle rugosity script. |
| scripts/particle/particle_rugosity/particle_rugosity.py | New/relocated particle rugosity script. |
| scripts/particle/november_2023_morphology_webinar/ReadMe.md | Minor formatting cleanup. |
| scripts/particle/november_2023_morphology_webinar/morphology_plot.py | Updates licence URL to https. |
| scripts/particle/november_2023_morphology_webinar/exploring_surface_properties.py | Updates licence URL to https and whitespace cleanup. |
| scripts/particle/november_2023_morphology_webinar/calculate_morphologies_tabulate_output.py | Consolidates imports + licence URL https. |
| scripts/particle_rugosity/particle_rugosity.py | Removes old location of particle rugosity script. |
| scripts/new_script_readme_template/script_example.py | Updates licence URL to https. |
| scripts/multi_component_hydrogen_bond_propensity/mol2smiles.py | Removes script from this location (cleanup/restructure). |
| scripts/materials/packing_similarity_dendrogram/ReadMe.md | Adds a new detailed README for packing dendrogram tool. |
| scripts/materials/packing_similarity_dendrogram/packing_similarity_dendogram.py | Updates licence URL to https. |
| scripts/materials/multi_component_hydrogen_bond_propensity/ReadMe.md | Adds README for multi-component HBP script. |
| scripts/materials/multi_component_hydrogen_bond_propensity/multi_component_hydrogen_bond_propensity_report.py | Docstring/comment cleanups + licence URL https. |
| scripts/discovery/gold_multi/target/ligand.mol2 | Adds example ligand input for GOLD multiprocessing demo. |
| scripts/discovery/gold_multi/ReadMe.md | Adds documentation for GOLD multiprocessing example. |
| scripts/discovery/gold_multi/gold.conf | Adds example GOLD configuration. |
| scripts/discovery/gold_multi/gold_multi.py | Refactors and reformats GOLD multiprocessing script. |
| scripts/discovery/gold_multi/.gitignore | Adds ignore rules for generated output while keeping target/. |
| scripts/discovery/find_binding_conformation/ReadMe.md | Fixes relative README link and author heading. |
| scripts/discovery/find_binding_conformation/pdb_example.txt | Adds example PDB IDs input file. |
| scripts/discovery/find_binding_conformation/find_binding_conformation.py | Refactors formatting + updates ligand-expo URL to https. |
| scripts/create_gaussian_input/create_gaussian_input.py | Removes old script path (moved under scripts/core/create_gaussian_input/). |
| scripts/core/voids_search/voids_search.py | Updates licence URL to https. |
| scripts/core/voids_search/Readme.md | Adds README for voids search tool. |
| scripts/core/show_semiconductor_properties/show_semiconductor_properties.py | Licence URL https + whitespace cleanup. |
| scripts/core/show_semiconductor_properties/semiconductor_template.html | Updates embedded namespace URLs (and other links). |
| scripts/core/show_semiconductor_properties/ReadMe.md | Adds README under new location. |
| scripts/core/show_semiconductor_properties/hist_data.json | Adds histogram data file for semiconductor report. |
| scripts/core/refcodes_with_properties/test_entry_property_calculator.py | Licence URL https. |
| scripts/core/refcodes_with_properties/refcodes_with_properties.py | Docstring cleanup + is None usage. |
| scripts/core/refcodes_with_properties/ReadMe.md | Adds README for refcodes-with-properties tool. |
| scripts/core/refcodes_with_properties/more_elaborate_control.txt | Adds example control file. |
| scripts/core/refcodes_with_properties/example_control_file.txt | Adds example control file. |
| scripts/core/refcodes_with_properties/entry_property_calculator.py | Refactor filter registration and improve readability. |
| scripts/core/mof_solvent_removal_2017_chem_mater_publication/ReadMe.md | Adds README for MOF solvent removal scripts. |
| scripts/core/mof_solvent_removal_2017_chem_mater_publication/Mercury_MOF_solvent_removal.py | Licence URL https. |
| scripts/core/mof_solvent_removal_2017_chem_mater_publication/Command_prompt_MOF_solvent_removal.py | Licence URL https. |
| scripts/core/hydrogen_bond_propensity/ReadMe.md | Adds README for HBP report script. |
| scripts/core/hydrogen_bond_propensity/hydrogen_bond_propensity_report.py | Docstring cleanup + rename normalise function usage. |
| scripts/core/filter_poses/ReadMe.md | Updates README sections/formatting. |
| scripts/core/filter_poses/filter_poses.py | Adds new pose-filtering tool. |
| scripts/core/create_gaussian_input/ReadMe.md | Adds README for Gaussian input generator. |
| scripts/core/create_gaussian_input/create_gaussian_input.py | Adds new location for Gaussian input generator script. |
| scripts/core/create_castep_input/ReadMe.md | Adds README for CASTEP input generator. |
| scripts/core/create_castep_input/create_castep_input.py | Licence URL https. |
| scripts/core/create_castep_input/assets/select_script.png | Adds/updates image asset. |
| scripts/core/create_castep_input/assets/file_output.png | Adds/updates image asset. |
| scripts/core/create_castep_input/assets/add_script_location.png | Adds/updates image asset. |
| scripts/core/conformer_filter_density/ReadMe.md | Adds licensing section + formatting fixes. |
| scripts/core/conformer_filter_density/conformer_filter_density.py | Adds new conformer torsion-density filtering tool. |
| scripts/core/conformer_demo/ReadMe.md | Rewrites README into structured sections. |
| scripts/core/conformer_demo/conformer_demo.py | Licence URL https + formatting cleanup. |
| scripts/assorted_utilities/concat_mol2/ReadMe.md | Adds README for concat mol2 utility. |
| scripts/assorted_utilities/concat_mol2/concat_mol2.py | Licence URL https + minor typing/boolean simplification. |
| notebooks/Discovery/12_Ensemble_docking/ensemble_docking.ipynb | Updates licence URL to https. |
| notebooks/Discovery/11_Working_With_Proteins/3kk6.cif | Updates embedded URLs to https. |
| notebooks/Discovery/11_Working_With_Proteins/11_Working_With_Proteins.ipynb | Updates licence URL to https. |
| notebooks/Discovery/10_Editing_molecules/Editing_molecules.ipynb | Updates licence URL to https. |
| notebooks/Discovery/09_Covalent_Docking/10_Prochiral_Michael_Acceptors.ipynb | Updates licence URL to https. |
| notebooks/Discovery/09_Covalent_Docking/02b_Covalent_Complexes-substructure.ipynb | Updates licence URL to https. |
| notebooks/Discovery/09_Covalent_Docking/02a_Covalent_Complexes-atom.ipynb | Updates licence URL to https. |
| notebooks/Discovery/09_Covalent_Docking/01_Ligand_Preparation_for_Covalent_Docking.ipynb | Updates licence URL to https. |
| notebooks/Discovery/08_Docking/05_Parameter_tests.ipynb | Updates licence URL to https. |
| notebooks/Discovery/08_Docking/04_Docking_interactive_conf.ipynb | Updates licence URL to https. |
| notebooks/Discovery/08_Docking/03_Docking_interactive.ipynb | Updates licence URL to https. |
| notebooks/Discovery/08_Docking/02_Docking_background_conf.ipynb | Updates licence URL to https. |
| notebooks/Discovery/08_Docking/01_Docking_foreground.ipynb | Updates licence URL to https. |
| notebooks/Discovery/08_Docking/00b_Input_for_GOLD-RDKit.ipynb | Updates licence URL + RDKit links to https. |
| notebooks/Discovery/08_Docking/00a_Input_for_GOLD.ipynb | Updates licence URL + RDKit link to https. |
| notebooks/Discovery/07_Cavities/pdbe_get.ps1 | Updates PDBe download URL to https. |
| notebooks/Discovery/07_Cavities/Cavities.ipynb | Updates licence URL to https. |
| notebooks/Discovery/06_Interaction_maps/Interaction_maps.ipynb | Updates licence URL to https. |
| notebooks/Discovery/05_Molecular_interactions/Molecular_interactions.ipynb | Updates licence URL to https. |
| notebooks/Discovery/04_Conformer_generation/Conformer_generation.ipynb | Updates licence URL to https. |
| notebooks/Discovery/03_Molecular_geometries/Molecular_geometries.ipynb | Updates licence URL to https (+ empty code cell). |
| notebooks/Discovery/02_Protein_Ligand/02_API_Protein-Ligand_search_for_FAD.ipynb | Updates licence URL to https. |
| notebooks/Discovery/02_Protein_Ligand/01_Protein_Ligand_Searching.ipynb | Updates licence URL to https. |
| notebooks/Discovery/01_CSD_Search/03_MCS_searching_the_CSD.ipynb | Updates licence URL to https. |
| notebooks/Discovery/01_CSD_Search/02_Similarity_searching_the_CSD.ipynb | Updates licence URL to https. |
| notebooks/Discovery/01_CSD_Search/01_Substructure_searching_the_CSD.ipynb | Updates licence URL to https. |
| notebooks/Discovery/00_Background/00_Background.ipynb | Updates licence URL + RDKit link to https. |
| notebooks/ccdc_notebook_utilities/run_hermes.py | Updates licence URL to https. |
| notebooks/ccdc_notebook_utilities/create_logger.py | Updates licence URL to https. |
| notebooks/ccdc_notebook_utilities/init.py | Updates licence URL to https. |
| notebooks/API_Training_Exercises/01_Simple_Report.ipynb | Updates licence URL to https. |
| api_paper_2024/example_5/visualiser.py | Updates licence URL to https. |
| api_paper_2024/example_5/shape_classification.py | Updates licence URL to https. |
| api_paper_2024/example_5/particle_shape.py | Updates licence URL to https. |
| api_paper_2024/example_4/voronoi.py | Updates licence URL to https. |
| api_paper_2024/example_4/mercury_molecular_voronoi.py | Updates licence URL to https. |
| api_paper_2024/example_4/mercury_metal_voronoi.py | Updates licence URL to https. |
| api_paper_2024/example_2/url_requesting.py | Updates licence URL to https. |
| api_paper_2024/example_2/references.py | Updates licence URL to https. |
| api_paper_2024/example_2/language_processing.py | Updates DOI URL to https. |
| api_paper_2024/example_2/about_entry.py | Updates licence URL to https. |
| .yamllint.yml | Updates documentation links to https. |
Comments suppressed due to low confidence (4)
scripts/discovery/gold_multi/gold_multi.py:141
logger.error(..., file=sys.stderr)will raiseTypeErrorbecause the logging API does not accept afileargument (that’s forprint). If you want stderr output, configure the logger's StreamHandler to usesys.stderr, or drop thefile=argument here.
scripts/discovery/gold_multi/gold_multi.py:211- The combined
bestranking.lstis being written using f-strings of Python lists (preamble_and_headerandbestranking), which will output their repr (brackets/quotes) instead of the original file format. This will break downstream consumption in Hermes. Join the lines with newlines (as before) and ensure exactly one trailing newline.
scripts/core/show_semiconductor_properties/semiconductor_template.html:65 - The SVG/XML namespace attributes were changed from
http://tohttps://. For SVG these values are namespaces, not fetchable URLs, and the correct values arehttp://www.w3.org/2000/svgandhttp://www.w3.org/1999/xlink. Usinghttps://can cause the SVG to be treated as invalid in some renderers.
scripts/discovery/gold_multi/gold_multi.py:102 do_batchcallschdir(batch.dir)but never restores the original working directory. Pool workers can execute multiple batches sequentially, so later batches may create/chdir into paths relative to the previous chunk dir (sincebatch.diris based on a potentially relativesettings.output_directory). Use absolute paths and/or restore cwd in atry/finally.
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| def file_writer(molecule, name): | ||
| """Writes a standard Gaussian input file for all molecules contained in the structure files.""" | ||
| if not mol.all_atoms_have_sites: | ||
| raise RuntimeError(f'{entry_id} has some atoms without coordinates') | ||
| mol.normalise_hydrogens() |
| # check rugosity of crystal plane at 0, 0.25, 0.5, and 0.75 offset from origin | ||
| for split in range(1, 5): | ||
| os = all_d_hkl[i] / split | ||
| surface = Surface(crystal, hkl, offset=os) | ||
| rug_list.append(surface.descriptors.rugosity) |
| except: | ||
| raise RuntimeError("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file") |
| except: | ||
| raise RuntimeError("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file") |
Alex-AMC
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Nice. Thank you for sorting all that. I've had an initial view will come back to it again ... but I thought some early feedback would be important here.
I like the different sections I think it focuses the mind and gives the context. I don't think we need to worry about saying it's based on licesing as people don't typically know what licence they have, they just know what tools they can use.
For the script/ReadMe.md I wonder if it would be nicer to have tables of scripts as opposed to a long list 🤔
mccabe-ccdc
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Obviously, a big thanks for taking on this task.
I've had a quickish scan. It's large, so if possible I would break down the changes into more atomic PRs. This makes it much easier to get a feel for what was done and makes each PR smaller and simpler. It's also good as a clearer overall record of what was done and easier to unravel any problems that might arise as a result of the changes.
What I mean is for example:
1 PR for http -> https
1 PR for reordering imports (and btw I'm not sure about the motivation for those re-orderings)
1 PR for changing ''' to """ and note if this is due to a PEP recommendation to justify it
1 PR for whitespace adjustments
etc. etc.
Only scripts directory has been altered, except for link changes (http to https)