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| # CHANGELOG | ||
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| ## v0.0.1 (2023-10-26) | ||
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| ### Fix | ||
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| * fix: change branch master -> main ([`a4791dc`](https://github.com/benjiemc/PythonPDB/commit/a4791dc59b64ad587f127bfb350d07fa2d478380)) | ||
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| ### Unknown | ||
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| * Merge pull request #19 from benjiemc/versioning | ||
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| fix: change branch master -> main ([`3c40e70`](https://github.com/benjiemc/PythonPDB/commit/3c40e707676fbe09674dde997ca3e3a9abe6738b)) | ||
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| * Merge pull request #18 from benjiemc/versioning | ||
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| Closes #12 ([`6361d46`](https://github.com/benjiemc/PythonPDB/commit/6361d46db116cd7d7c049f3fa3851bfd76e9633b)) | ||
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| * Add semantic versioning to project ([`f644088`](https://github.com/benjiemc/PythonPDB/commit/f6440888759b86a04bc6e8f611babcc1a2e090b0)) | ||
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| * Merge pull request #17 from benjiemc/update-alignment-code | ||
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| Update alignment code ([`cfe30df`](https://github.com/benjiemc/PythonPDB/commit/cfe30dfb5ee985cef2e8a7b97f8923f3ba03f2f4)) | ||
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| * Refactor aligners | ||
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| - rename `align` to `align_structures` | ||
| - separate code into functions | ||
| - standardize API used in tests ([`b220134`](https://github.com/benjiemc/PythonPDB/commit/b22013410829bb3498e6d27736a2880b4b7453ce)) | ||
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| * Add align function for dataframes ([`b3fd3ce`](https://github.com/benjiemc/PythonPDB/commit/b3fd3ceda9c0c9b8be209d7ac240bdf919c75808)) | ||
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| * Merge pull request #16 from benjiemc/pandas-function | ||
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| Add function to convert PDB file into a dataframe ([`ce2dae4`](https://github.com/benjiemc/PythonPDB/commit/ce2dae4116302c7bbeea285424d86a8289448ec5)) | ||
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| * Add function to convert PDB file into a dataframe | ||
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| This adds functionality so that a pdb file doesn't need to be converted | ||
| to structure object and then a dataframe. | ||
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| Closes #15 ([`748ee88`](https://github.com/benjiemc/PythonPDB/commit/748ee889620560014baa675b3bc2f118b5c1f4db)) | ||
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| * Single source package version ([`b79658e`](https://github.com/benjiemc/PythonPDB/commit/b79658ed6fedc581742c29c79653cbbbd3559523)) | ||
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| * Merge pull request #11 from benjiemc/minor-clean-up | ||
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| Minor clean up ([`ab4b72a`](https://github.com/benjiemc/PythonPDB/commit/ab4b72af20f71000b0f04e3e1dca4478f8a70872)) | ||
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| * Use standard amino acid list ([`b87b81b`](https://github.com/benjiemc/PythonPDB/commit/b87b81bec7ddab1fd1320ccc07aea137bbeb1dfb)) | ||
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| * Add workflow for pull requests | ||
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| Closes #10 ([`caf2db2`](https://github.com/benjiemc/PythonPDB/commit/caf2db2116e2e572165a252e6929eed9771679aa)) | ||
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| * Fix flake8 issues ([`d2f4510`](https://github.com/benjiemc/PythonPDB/commit/d2f451041e8af09d336b5391db3b5fcc5f250a93)) | ||
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| * Merge pull request #9 from fspoendlin/main | ||
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| Handling of exceptions ([`3e57580`](https://github.com/benjiemc/PythonPDB/commit/3e5758091b2b84f325f802029a5ae1d3a9820d4d)) | ||
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| * merge with remote ([`76afd64`](https://github.com/benjiemc/PythonPDB/commit/76afd640cc811eb6ca967e9c749c1fe071806edf)) | ||
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| * fixed bugs in structure.splitstate method ([`0cb4302`](https://github.com/benjiemc/PythonPDB/commit/0cb4302d5ddc297ce116e2523b5355bdfe35a0a8)) | ||
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| * Merge branch 'benjiemc:main' into main ([`cdf1da5`](https://github.com/benjiemc/PythonPDB/commit/cdf1da54b9068cad00d605fba00bfa8b6cdede69)) | ||
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| * Remove 'None' states | ||
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| The split states algorithm added atoms without alt codes in a residue | ||
| that already had other atoms with alt codes to a new state since called | ||
| 'None'. Now, these are copied to all states. ([`6a5c59d`](https://github.com/benjiemc/PythonPDB/commit/6a5c59d3961fe938b2d56dcc038a757e55df5bf2)) | ||
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| * Merge branch 'benjiemc:main' into main ([`69a666b`](https://github.com/benjiemc/PythonPDB/commit/69a666b26476ecf53ecd43e1883b97ab79472958)) | ||
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| * bug fixed ([`d40bbd6`](https://github.com/benjiemc/PythonPDB/commit/d40bbd6a9b32fe3664f47d391c2d59645c389450)) | ||
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| * Update documentation ([`99ab368`](https://github.com/benjiemc/PythonPDB/commit/99ab368b913fdda9985d6327e6743d8d38f9891c)) | ||
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| * Fix failing test and fix flake8 issues ([`96844d9`](https://github.com/benjiemc/PythonPDB/commit/96844d98a4b2ac388ba5e1fdf872850138ce2ef9)) | ||
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| * Merge pull request #8 from fspoendlin/main | ||
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| modified Structure.split_states() function to group alternate residues ([`61b3f03`](https://github.com/benjiemc/PythonPDB/commit/61b3f0340d0be9b03041ba8bc287cde7cb9b8166)) | ||
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| * modified Structure.split_states() function to group alternate residues ([`0b308bc`](https://github.com/benjiemc/PythonPDB/commit/0b308bcf3501bb77d2f28dafcc821ca67bb12645)) | ||
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| * Merge pull request #6 from benjiemc/aligner | ||
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| Aligner ([`6fc2a77`](https://github.com/benjiemc/PythonPDB/commit/6fc2a77a2fae6d38aa81ec79dbf9eaa46c86fa09)) | ||
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| * Update align function to take coordinates ([`434a47b`](https://github.com/benjiemc/PythonPDB/commit/434a47ba57ba864a29fe8aa655dd5c2160d8c23e)) | ||
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| * Added sequence alignment function ([`90ca7ff`](https://github.com/benjiemc/PythonPDB/commit/90ca7ffe79f973f7d97223d8bb7c87e45d161723)) | ||
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| * Aligner for structures ([`873c5b6`](https://github.com/benjiemc/PythonPDB/commit/873c5b63ae0b095fe28fdcbabb119ae879c30cb2)) | ||
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| * Add rmsd function ([`478a2f2`](https://github.com/benjiemc/PythonPDB/commit/478a2f2a20042f81f9b2781445c437cbf9438212)) | ||
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| * Add get_coordinates method to entities ([`217ba7e`](https://github.com/benjiemc/PythonPDB/commit/217ba7e9dc7bf3288b6af0ffddbc4a44cbef8c84)) | ||
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| * Clean up types and docs ([`6aca9c4`](https://github.com/benjiemc/PythonPDB/commit/6aca9c4a0a53b409166b48db37505972adedefa8)) | ||
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| * Create parent class that entities can inherent from | ||
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| Adds a parent class `Entity` that pulls out the logic from shared | ||
| properties of Atoms, Residues, Chains, Models, and Structures. | ||
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| Closes #2 ([`3312451`](https://github.com/benjiemc/PythonPDB/commit/331245131754c4b5c666af00194a520fbe3595ac)) | ||
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| * Add parsing layer | ||
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| The purpose of this layer is to remove the logic of structure building | ||
| from the different formats. Now there is code that converts the | ||
| different possible formats into a standard format, and code that builds | ||
| the structure from this standard format. The API remains unchanged after | ||
| this. | ||
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| Closes #1 ([`d9fcf8f`](https://github.com/benjiemc/PythonPDB/commit/d9fcf8f04a8d97b3d46ec36454f6fd8def415511)) | ||
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| * Fix typo in type in documentation | ||
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| Closes #4 ([`def5510`](https://github.com/benjiemc/PythonPDB/commit/def551079f3e00ef744598f14db0daac3c000303)) | ||
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| * Add functionality to entities | ||
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| Closes #3 ([`7bd9658`](https://github.com/benjiemc/PythonPDB/commit/7bd9658a895379d92665244f1d99a7beb89d6475)) | ||
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| * Add dehydrate functionality | ||
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| Also implements remove_atom/remove_residue functionality to entity | ||
| clases. ([`434fca1`](https://github.com/benjiemc/PythonPDB/commit/434fca135d03df581f559880644ca30586ecb41d)) | ||
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| * Clarify docstring ([`92ae5a9`](https://github.com/benjiemc/PythonPDB/commit/92ae5a9fe287ee6ce8dbf7167a579df8229ecbb5)) | ||
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| * Add `silent` option to parser to suppress warnings ([`320c5ed`](https://github.com/benjiemc/PythonPDB/commit/320c5ed42d124ceb787d091d3f357f2d13d00220)) | ||
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| * Add warning to identify multiple conformations when alt codes are present ([`b682fc0`](https://github.com/benjiemc/PythonPDB/commit/b682fc08400e4cef6fb1efd1438a53e4e3fba79a)) | ||
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| * Fix weird comment message ([`4cdd09e`](https://github.com/benjiemc/PythonPDB/commit/4cdd09e220090e2a52463525105f88477069f50a)) | ||
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| * Remove typing import ([`694aab1`](https://github.com/benjiemc/PythonPDB/commit/694aab1546de470b7107d874c0cc4d161c0dc3c0)) | ||
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| * Remove unecessary None check ([`d94af24`](https://github.com/benjiemc/PythonPDB/commit/d94af24280c179b1d181e3a3df41638b1a912caf)) | ||
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| * Make entities equality more holistic | ||
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| - Fix typo for atom positions | ||
| - Remove dependency on parent equality | ||
| - Add children to equality check | ||
| - Add equality to Structure and Models ([`7f288a2`](https://github.com/benjiemc/PythonPDB/commit/7f288a230954abbd4d0e639be1784cc88ee9e755)) | ||
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| * Add split_states functionality to structure ([`eafa9d4`](https://github.com/benjiemc/PythonPDB/commit/eafa9d43ce72ac687df632e4741038d565d8d033)) | ||
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| * Fix issue with matching seq_ids on different chains | ||
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| This commit fixes cases where atoms aren't added to the correct residue | ||
| if the same seq_id is seen back to back from one chain to another. ([`fdbe672`](https://github.com/benjiemc/PythonPDB/commit/fdbe67292e7dff75d36fcc092d6820f74a3ab579)) | ||
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| * Add model/endmdl to str representation of structure ([`483b299`](https://github.com/benjiemc/PythonPDB/commit/483b299336b7255b8d7a21dde219b5b895cc735e)) | ||
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| * Add copy functionality to all entities ([`6662ac9`](https://github.com/benjiemc/PythonPDB/commit/6662ac9281f60f1bfc2d8bb619e13acb5eea5c6d)) | ||
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| * String -> str ([`b8d7417`](https://github.com/benjiemc/PythonPDB/commit/b8d7417d4daf4b1d6098e2fc887fefef8fccac4e)) | ||
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| * Fix mistake in alt_loc documentation ([`1a39a2f`](https://github.com/benjiemc/PythonPDB/commit/1a39a2f607b5d63848eeb78e41a628ab540c508e)) | ||
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| * Add .DS_Store to .gitignore ([`47adc57`](https://github.com/benjiemc/PythonPDB/commit/47adc5739ff5220ec25aa82c924e6d7cfcbfea89)) | ||
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| * Restructure formatting things as a subpackage ([`48275f6`](https://github.com/benjiemc/PythonPDB/commit/48275f658cd44bebcdabbb0ba45ea71d2099fd08)) | ||
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| * Improve formats documentation ([`1296e91`](https://github.com/benjiemc/PythonPDB/commit/1296e91ee38a8974444745aee93c89d246f9d523)) | ||
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| * Add support for HETATM records ([`dd4e5ad`](https://github.com/benjiemc/PythonPDB/commit/dd4e5adeecf7679753c80a12173e2c283b320e17)) | ||
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| * Remove 'alternates' in Residue ([`c51418f`](https://github.com/benjiemc/PythonPDB/commit/c51418fdfc9a38b001bc83a34b90aa50b4bd421e)) | ||
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| * Add link to documentation in README.md ([`667712b`](https://github.com/benjiemc/PythonPDB/commit/667712ba2a97984afc1270cd52ead662355e1440)) | ||
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| * Add documentation workflow ([`36d223e`](https://github.com/benjiemc/PythonPDB/commit/36d223e6370b5a5d51f06611c11e70409ac532aa)) | ||
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| * Add python 3.11 to test suite ([`9f9e95f`](https://github.com/benjiemc/PythonPDB/commit/9f9e95f3fbead94763d502809c5514b83c62f1fb)) | ||
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| * Add test workflow ([`115c811`](https://github.com/benjiemc/PythonPDB/commit/115c811d4bd16a1a0bcac6ca9a1ffedc55152ee6)) | ||
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| * Move files from other project ([`c3e9dac`](https://github.com/benjiemc/PythonPDB/commit/c3e9dac3ca89a0d1b1381010211b6a67876e44b2)) | ||
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| * Initial commit ([`e2204a4`](https://github.com/benjiemc/PythonPDB/commit/e2204a49712995d816d5a842b3c57cece57ed71e)) |