Python-pdb

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0.0.4

Fix

* fix: add check to workflow step ([`9453a62`](https://github.com/benjiemc/PythonPDB/commit/9453a6222025149fa6e075e7c0d9e96c0e6d95bd))

Unknown

* Merge pull request 26 from benjiemc/publishing

fix: add check to workflow step ([`2d03409`](https://github.com/benjiemc/PythonPDB/commit/2d03409f2b08587642c51772c35848adb550af9d))

* Merge pull request 25 from benjiemc/publishing

fix: Move build command ([`a7be9d3`](https://github.com/benjiemc/PythonPDB/commit/a7be9d351f465db5bef0ea819a125894f6e29a24))

* Move build command ([`f4bea70`](https://github.com/benjiemc/PythonPDB/commit/f4bea7046d1fd9508d17d64178493f8d6c1870f0))

0.0.3

Fix

* fix: pypi release script ([`80f1093`](https://github.com/benjiemc/PythonPDB/commit/80f1093029809c1162bdea6f1181d7d62272e869))

Unknown

* Merge pull request 24 from benjiemc/publishing

fix: pypi release script ([`d7ac466`](https://github.com/benjiemc/PythonPDB/commit/d7ac466da1bedd883910da7cfd1cb05792469360))

0.0.2

Fix

* fix: Fix release workflow ([`f6a4227`](https://github.com/benjiemc/PythonPDB/commit/f6a4227fefc250f40fd3027f737edf2c8e64ac29))

* fix: Add build command ([`908bda2`](https://github.com/benjiemc/PythonPDB/commit/908bda2cc1d3969882f52b0b80b54e760f5dd612))

Unknown

* Merge pull request 23 from benjiemc/publishing

fix: Fix release workflow ([`28041d4`](https://github.com/benjiemc/PythonPDB/commit/28041d49437ac83e69784b546cb6a348ef8217c9))

* Merge pull request 22 from benjiemc/publishing

feat: Add build command ([`d32b743`](https://github.com/benjiemc/PythonPDB/commit/d32b7432c9495ee484f04c235ed6b14270ffea59))

* Merge pull request 21 from benjiemc/license

Add LICENSE file ([`b535a47`](https://github.com/benjiemc/PythonPDB/commit/b535a4756c7b81c1969ce172354ba0ea18cb5818))

* Add LICENSE file

Closes 14 ([`268f29b`](https://github.com/benjiemc/PythonPDB/commit/268f29bd1edfe944d6d875b93dfb5f044de075c6))

* Merge pull request 20 from benjiemc/versioning

Update variables for semantic versioning ([`f52f7d1`](https://github.com/benjiemc/PythonPDB/commit/f52f7d124d7244567f4d0e7e09e68b448efa10d5))

* Update variables for semantic versioning ([`3f45225`](https://github.com/benjiemc/PythonPDB/commit/3f452253f3cdee33c73c71a510e71117ac27b00d))

0.0.1

Fix

* fix: change branch master -> main ([`a4791dc`](https://github.com/benjiemc/PythonPDB/commit/a4791dc59b64ad587f127bfb350d07fa2d478380))

Unknown

* Merge pull request 19 from benjiemc/versioning

fix: change branch master -> main ([`3c40e70`](https://github.com/benjiemc/PythonPDB/commit/3c40e707676fbe09674dde997ca3e3a9abe6738b))

* Merge pull request 18 from benjiemc/versioning

Closes 12 ([`6361d46`](https://github.com/benjiemc/PythonPDB/commit/6361d46db116cd7d7c049f3fa3851bfd76e9633b))

* Add semantic versioning to project ([`f644088`](https://github.com/benjiemc/PythonPDB/commit/f6440888759b86a04bc6e8f611babcc1a2e090b0))

* Merge pull request 17 from benjiemc/update-alignment-code

Update alignment code ([`cfe30df`](https://github.com/benjiemc/PythonPDB/commit/cfe30dfb5ee985cef2e8a7b97f8923f3ba03f2f4))

* Refactor aligners

- rename `align` to `align_structures`
- separate code into functions
- standardize API used in tests ([`b220134`](https://github.com/benjiemc/PythonPDB/commit/b22013410829bb3498e6d27736a2880b4b7453ce))

* Add align function for dataframes ([`b3fd3ce`](https://github.com/benjiemc/PythonPDB/commit/b3fd3ceda9c0c9b8be209d7ac240bdf919c75808))

* Merge pull request 16 from benjiemc/pandas-function

Add function to convert PDB file into a dataframe ([`ce2dae4`](https://github.com/benjiemc/PythonPDB/commit/ce2dae4116302c7bbeea285424d86a8289448ec5))

* Add function to convert PDB file into a dataframe

This adds functionality so that a pdb file doesn&39;t need to be converted
to structure object and then a dataframe.

Closes 15 ([`748ee88`](https://github.com/benjiemc/PythonPDB/commit/748ee889620560014baa675b3bc2f118b5c1f4db))

* Single source package version ([`b79658e`](https://github.com/benjiemc/PythonPDB/commit/b79658ed6fedc581742c29c79653cbbbd3559523))

* Merge pull request 11 from benjiemc/minor-clean-up

Minor clean up ([`ab4b72a`](https://github.com/benjiemc/PythonPDB/commit/ab4b72af20f71000b0f04e3e1dca4478f8a70872))

* Use standard amino acid list ([`b87b81b`](https://github.com/benjiemc/PythonPDB/commit/b87b81bec7ddab1fd1320ccc07aea137bbeb1dfb))

* Add workflow for pull requests

Closes 10 ([`caf2db2`](https://github.com/benjiemc/PythonPDB/commit/caf2db2116e2e572165a252e6929eed9771679aa))

* Fix flake8 issues ([`d2f4510`](https://github.com/benjiemc/PythonPDB/commit/d2f451041e8af09d336b5391db3b5fcc5f250a93))

* Merge pull request 9 from fspoendlin/main

Handling of exceptions ([`3e57580`](https://github.com/benjiemc/PythonPDB/commit/3e5758091b2b84f325f802029a5ae1d3a9820d4d))

* merge with remote ([`76afd64`](https://github.com/benjiemc/PythonPDB/commit/76afd640cc811eb6ca967e9c749c1fe071806edf))

* fixed bugs in structure.splitstate method ([`0cb4302`](https://github.com/benjiemc/PythonPDB/commit/0cb4302d5ddc297ce116e2523b5355bdfe35a0a8))

* Merge branch &39;benjiemc:main&39; into main ([`cdf1da5`](https://github.com/benjiemc/PythonPDB/commit/cdf1da54b9068cad00d605fba00bfa8b6cdede69))

* Remove &39;None&39; states

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
&39;None&39;. Now, these are copied to all states. ([`6a5c59d`](https://github.com/benjiemc/PythonPDB/commit/6a5c59d3961fe938b2d56dcc038a757e55df5bf2))

* Merge branch &39;benjiemc:main&39; into main ([`69a666b`](https://github.com/benjiemc/PythonPDB/commit/69a666b26476ecf53ecd43e1883b97ab79472958))

* bug fixed ([`d40bbd6`](https://github.com/benjiemc/PythonPDB/commit/d40bbd6a9b32fe3664f47d391c2d59645c389450))

* Update documentation ([`99ab368`](https://github.com/benjiemc/PythonPDB/commit/99ab368b913fdda9985d6327e6743d8d38f9891c))

* Fix failing test and fix flake8 issues ([`96844d9`](https://github.com/benjiemc/PythonPDB/commit/96844d98a4b2ac388ba5e1fdf872850138ce2ef9))

* Merge pull request 8 from fspoendlin/main

modified Structure.split_states() function to group alternate residues ([`61b3f03`](https://github.com/benjiemc/PythonPDB/commit/61b3f0340d0be9b03041ba8bc287cde7cb9b8166))

* modified Structure.split_states() function to group alternate residues ([`0b308bc`](https://github.com/benjiemc/PythonPDB/commit/0b308bcf3501bb77d2f28dafcc821ca67bb12645))

* Merge pull request 6 from benjiemc/aligner

Aligner ([`6fc2a77`](https://github.com/benjiemc/PythonPDB/commit/6fc2a77a2fae6d38aa81ec79dbf9eaa46c86fa09))

* Update align function to take coordinates ([`434a47b`](https://github.com/benjiemc/PythonPDB/commit/434a47ba57ba864a29fe8aa655dd5c2160d8c23e))

* Added sequence alignment function ([`90ca7ff`](https://github.com/benjiemc/PythonPDB/commit/90ca7ffe79f973f7d97223d8bb7c87e45d161723))

* Aligner for structures ([`873c5b6`](https://github.com/benjiemc/PythonPDB/commit/873c5b63ae0b095fe28fdcbabb119ae879c30cb2))

* Add rmsd function ([`478a2f2`](https://github.com/benjiemc/PythonPDB/commit/478a2f2a20042f81f9b2781445c437cbf9438212))

* Add get_coordinates method to entities ([`217ba7e`](https://github.com/benjiemc/PythonPDB/commit/217ba7e9dc7bf3288b6af0ffddbc4a44cbef8c84))

* Clean up types and docs ([`6aca9c4`](https://github.com/benjiemc/PythonPDB/commit/6aca9c4a0a53b409166b48db37505972adedefa8))

* Create parent class that entities can inherent from

Adds a parent class `Entity` that pulls out the logic from shared
properties of Atoms, Residues, Chains, Models, and Structures.

Closes 2 ([`3312451`](https://github.com/benjiemc/PythonPDB/commit/331245131754c4b5c666af00194a520fbe3595ac))

* Add parsing layer

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.

Closes 1 ([`d9fcf8f`](https://github.com/benjiemc/PythonPDB/commit/d9fcf8f04a8d97b3d46ec36454f6fd8def415511))

* Fix typo in type in documentation

Closes 4 ([`def5510`](https://github.com/benjiemc/PythonPDB/commit/def551079f3e00ef744598f14db0daac3c000303))

* Add functionality to entities

Closes 3 ([`7bd9658`](https://github.com/benjiemc/PythonPDB/commit/7bd9658a895379d92665244f1d99a7beb89d6475))

* Add dehydrate functionality

Also implements remove_atom/remove_residue functionality to entity
clases. ([`434fca1`](https://github.com/benjiemc/PythonPDB/commit/434fca135d03df581f559880644ca30586ecb41d))

* Clarify docstring ([`92ae5a9`](https://github.com/benjiemc/PythonPDB/commit/92ae5a9fe287ee6ce8dbf7167a579df8229ecbb5))

* Add `silent` option to parser to suppress warnings ([`320c5ed`](https://github.com/benjiemc/PythonPDB/commit/320c5ed42d124ceb787d091d3f357f2d13d00220))

* Add warning to identify multiple conformations when alt codes are present ([`b682fc0`](https://github.com/benjiemc/PythonPDB/commit/b682fc08400e4cef6fb1efd1438a53e4e3fba79a))

* Fix weird comment message ([`4cdd09e`](https://github.com/benjiemc/PythonPDB/commit/4cdd09e220090e2a52463525105f88477069f50a))

* Remove typing import ([`694aab1`](https://github.com/benjiemc/PythonPDB/commit/694aab1546de470b7107d874c0cc4d161c0dc3c0))

* Remove unecessary None check ([`d94af24`](https://github.com/benjiemc/PythonPDB/commit/d94af24280c179b1d181e3a3df41638b1a912caf))

* Make entities equality more holistic

- 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))

* Add split_states functionality to structure ([`eafa9d4`](https://github.com/benjiemc/PythonPDB/commit/eafa9d43ce72ac687df632e4741038d565d8d033))

* Fix issue with matching seq_ids on different chains

This commit fixes cases where atoms aren&39;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))

* Add model/endmdl to str representation of structure ([`483b299`](https://github.com/benjiemc/PythonPDB/commit/483b299336b7255b8d7a21dde219b5b895cc735e))

* Add copy functionality to all entities ([`6662ac9`](https://github.com/benjiemc/PythonPDB/commit/6662ac9281f60f1bfc2d8bb619e13acb5eea5c6d))

* String -> str ([`b8d7417`](https://github.com/benjiemc/PythonPDB/commit/b8d7417d4daf4b1d6098e2fc887fefef8fccac4e))

* Fix mistake in alt_loc documentation ([`1a39a2f`](https://github.com/benjiemc/PythonPDB/commit/1a39a2f607b5d63848eeb78e41a628ab540c508e))

* Add .DS_Store to .gitignore ([`47adc57`](https://github.com/benjiemc/PythonPDB/commit/47adc5739ff5220ec25aa82c924e6d7cfcbfea89))

* Restructure formatting things as a subpackage ([`48275f6`](https://github.com/benjiemc/PythonPDB/commit/48275f658cd44bebcdabbb0ba45ea71d2099fd08))

* Improve formats documentation ([`1296e91`](https://github.com/benjiemc/PythonPDB/commit/1296e91ee38a8974444745aee93c89d246f9d523))

* Add support for HETATM records ([`dd4e5ad`](https://github.com/benjiemc/PythonPDB/commit/dd4e5adeecf7679753c80a12173e2c283b320e17))

* Remove &39;alternates&39; in Residue ([`c51418f`](https://github.com/benjiemc/PythonPDB/commit/c51418fdfc9a38b001bc83a34b90aa50b4bd421e))

* Add link to documentation in README.md ([`667712b`](https://github.com/benjiemc/PythonPDB/commit/667712ba2a97984afc1270cd52ead662355e1440))

* Add documentation workflow ([`36d223e`](https://github.com/benjiemc/PythonPDB/commit/36d223e6370b5a5d51f06611c11e70409ac532aa))

* Add python 3.11 to test suite ([`9f9e95f`](https://github.com/benjiemc/PythonPDB/commit/9f9e95f3fbead94763d502809c5514b83c62f1fb))

* Add test workflow ([`115c811`](https://github.com/benjiemc/PythonPDB/commit/115c811d4bd16a1a0bcac6ca9a1ffedc55152ee6))

* Move files from other project ([`c3e9dac`](https://github.com/benjiemc/PythonPDB/commit/c3e9dac3ca89a0d1b1381010211b6a67876e44b2))

* Initial commit ([`e2204a4`](https://github.com/benjiemc/PythonPDB/commit/e2204a49712995d816d5a842b3c57cece57ed71e))

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