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github.com/BioJulia/BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures
https://github.com/BioJulia/BioStructures.jl

fix 1alw test after PDB changes

0e06b25e8e96d73343acabf121e9f0191eb88b86 authored 11 months ago by Joe Greener <[email protected]>
update news, bump version

69b48127811f0ec235bd17e25838af7ceffd4087 authored about 1 year ago by Joe Greener <[email protected]>
mention package extensions in API docs

7b6da74252b01c9b9e72b915d1fe3a1b1e210be0 authored about 1 year ago by Joe Greener <[email protected]>
update related software

ec59703158c5b4329ded5a5005bbcf35b61d493a authored about 1 year ago by Joe Greener <[email protected]>
selector inversion

47c53d327a9515925dd3e26cc5792edc663fd009 authored about 1 year ago by Joe Greener <[email protected]>
remove BioCore dependency

75aa29063519cc24236de3e761caa950d74df1a1 authored about 1 year ago by Joe Greener <[email protected]>
fix extension docs links

299d87533b64ec3bae80633cba0e8cf23b478455 authored about 1 year ago by Joe Greener <[email protected]>
deps in docs/Project.toml

3cb35cf8a0ff34f64a088deb41c76bfd2860b1a6 authored about 1 year ago by Joe Greener <[email protected]>
access extensions during docs build

09930ac5a3713e33c858580e97629875534be5d3 authored about 1 year ago by Joe Greener <[email protected]>
move DataFrame to extension

9024cbb7c87655322365fedc6966b32a6890de9b authored about 1 year ago by Joe Greener <[email protected]>
move MetaGraph to extension

192fe5438f98071fd5146bc71357710e5144ca3a authored about 1 year ago by Joe Greener <[email protected]>
update Aqua compat

24550de8e0f98abc01825fd868d9bb9b8f326c27 authored about 1 year ago by Joe Greener <[email protected]>
stdlib compat entries

728cc78fd7da5cd019efe524c521579d96600c9c authored about 1 year ago by Joe Greener <[email protected]>
remove assertion

69912b5b188dfa00b323455bf99b018cde5eca95 authored about 1 year ago by Joe Greener <[email protected]>
update news

0f99f859faec9df1bd2fd7df0cf7707b13239abf authored about 1 year ago by Joe Greener <[email protected]>
changes to secondary structure

953d28b340290552543c1a238e66fa641dc170e7 authored about 1 year ago by Joe Greener <[email protected]>
mention BioMakie.jl in docs

32a0e88ee2b5fa4ec68c39f1b3bb3744db1aff52 authored about 1 year ago by Joe Greener <[email protected]>
docs fix page size error

5e388d7ce592aceada6634dfce531332b9329675 authored over 1 year ago by Joe Greener <[email protected]>
update Documenter compat

ac2af0f783037e311da005c0b152fdd14b1d4227 authored over 1 year ago by Joe Greener <[email protected]>
add test/Project.toml

269755ffd12e9f533bed1adaa6421509d75f67fa authored over 1 year ago by Joe Greener <[email protected]>
add secondary structure Information (#43)

* add secondary structure Information

* Bump to 2.1.0

* Add tests.

* Modification befor...

00c432d2a33b48e1fb65fc06cdbcb8bb499e6d19 authored over 1 year ago by Shu Li <[email protected]>
update news, bump version

bc70e73e596c63e72dc809ce3c3930ef2bd554f3 authored almost 2 years ago by Joe Greener <[email protected]>
point to Slack not Gitter

e1190bdd24f3ef194f24af7ff03e5061027e0675 authored almost 2 years ago by Joe Greener <[email protected]>
docs example output

09c9f3f3346ea7d8136e418f174c9d8b2c60a343 authored almost 2 years ago by Joe Greener <[email protected]>
more robust reading of PDB entry list

1342688f8a1794961b4af126c54b0a66586c8221 authored almost 2 years ago by Joe Greener <[email protected]>
use LongAA alias

a34c22a9e15c3b2f16c1aaa1c6e760e451b57e04 authored almost 2 years ago by Joe Greener <[email protected]>
remove contributing and CoC

1502aee146e7962ce6476566b077e960ccc5da79 authored almost 2 years ago by Joe Greener <[email protected]>
remove issue/PR templates

51bd4d33370f7268176e2a29081710054668d725 authored almost 2 years ago by Joe Greener <[email protected]>
update compat

58d0afae01526e4ec4131f6435b303500d779698 authored almost 2 years ago by Joe Greener <[email protected]>
Update BioAlignments and BioSequences compat. Change LongAminoAcidSeq to LongSequence{AminoAcidAlphabet} (#39)

* Update compat, LongAminoAcidSeq type change.

* Update Project.toml

* export LongSequence...

81bf89bc376d3fa12b252ca027931e25aa53c903 authored almost 2 years ago by Dan Kool <[email protected]>
reuse transpose, bump version

453c233a445cd271f9e111c18e360708471fca02 authored almost 3 years ago by Joe Greener <[email protected]>
Fix Kabsch Algorithm to Prevent Reflections (#37)

* fix kabsch algorithm

* suggestions

19e7106856acbb3e7a89f5222899b3b2747de01f authored almost 3 years ago by nhz2 <[email protected]>
require Julia v1.6

876de6bf928546bf9710c0b14965866eec64a383 authored about 3 years ago by Joe Greener <[email protected]>
enable CI on Mac

31bb7f6376389bbf3621f0da5dee08750b605e01 authored about 3 years ago by Joe Greener <[email protected]>
firstindex and lastindex

9ec5632180707b5a4c053ca8efe19f29318150f2 authored about 3 years ago by Joe Greener <[email protected]>
disable CI on Mac

e78dcbf583f43c5c5019ab24fba49a9f4404ec16 authored about 3 years ago by Joe Greener <[email protected]>
update news

37b72bcf5dd10ab72aa6c2dc7980ef9b12a5a9a8 authored about 3 years ago by Joe Greener <[email protected]>
consistent error printing

bc747e77f4133c658805ae9517f9e39ee9abb681 authored about 3 years ago by Joe Greener <[email protected]>
mention chainid! in docs

3cfd6d9fb185c90c6de07881f1d37c081117847a authored about 3 years ago by Joe Greener <[email protected]>
docs for writing contact and distance maps

cfb60e685b9f86b1473baaa33abae2b734c5d67b authored about 3 years ago by Joe Greener <[email protected]>
switch from LightGraphs to Graphs

a538f9165b6e6a08e85f558c28ae2b65e5decf73 authored about 3 years ago by Joe Greener <[email protected]>
add WAT to water residue names

3d54777ca04651b9a896d2a1decd78be57fbf64c authored about 3 years ago by Joe Greener <[email protected]>
Allow chain id to be assigned with chainid!() (#35)

* Allow chain id to be assigned with chainid!()

Adds two function for assigning the chainid, ...

74a643a9014d55e8a878ebc9844efd1998185bf5 authored about 3 years ago by Nate Guerin <[email protected]>
Aqua test not recursive

d1fc832a605b07438ae2edd3a18d5a7a1a35c5b4 authored over 3 years ago by Joe Greener <[email protected]>
CompatHelper: bump compat for "BioSymbols" to "5" (#31)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

609dc738845ccea059feed88b035127a6b2f7197 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
no alias in plot recipe

9983f9066d8dcdba8ab5c00cc6664b95cb366706 authored over 3 years ago by Joe Greener <[email protected]>
bump version

fe63347dac5927743a0a0469141ff2bf14b9ca9c authored over 3 years ago by Joe Greener <[email protected]>
docstring for read

693bda7c18a7a3b23e19ef64aeed0382425a0716 authored over 3 years ago by Joe Greener <[email protected]>
MMTF compat bounds

db027b06970061b0afe6197ce45b5bdfc6d33516 authored over 3 years ago by Joe Greener <[email protected]>
export Base functions for API docstrings

ae2cea405f1e3e33f219d3b687b2e1a9c5ce0ce8 authored over 3 years ago by Joe Greener <[email protected]>
docstring for read

a98cda824b5c914de88730c9a27cba3293a68abd authored over 3 years ago by Joe Greener <[email protected]>
use Downloads package

777b90297feba80ea456fbb616d30bcd12481ed1 authored over 3 years ago by Joe Greener <[email protected]>
residue sorting sorts hetero last

fb6f87cf3054cd1ebb7f8b9a51caf92a9607cb3c authored over 3 years ago by Joe Greener <[email protected]>
add Aqua to tests

d71b0edf2a84e6ffda0dcca367e631edb188561d authored over 3 years ago by Joe Greener <[email protected]>
bump version

cf24e65799ce4f4fdc1854ee34adbd4382425937 authored over 3 years ago by Joe Greener <[email protected]>
CompatHelper: bump compat for "DataFrames" to "1.0" (#30)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

a6ce70fbeb284ae9ed454306052c989268b5084a authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
residue selectors before expanding disorder

1a1274c49ae7ed0460c9970989ad2cfc2079d4c3 authored almost 4 years ago by Joe Greener <[email protected]>
bump version

21de6534495b0b5da37fd9ca3deaf361df36d16f authored almost 4 years ago by Joe Greener <[email protected]>
atom selectors before expanding disorder

39d30a15be842f0a132c7c1e0112271ca47fc447 authored almost 4 years ago by Joe Greener <[email protected]>
not kwarg

e1d539d749689253a3368c10f0f5d60805ef509c authored almost 4 years ago by Joe Greener <[email protected]>
don't skip Linux tests

83fecf82742b69bddf1ee7c122fa68433400e82f authored almost 4 years ago by Joe Greener <[email protected]>
file format specimens checkout

032fdc5ffba3034d1cb8bed374b487631baa3ff1 authored almost 4 years ago by Joe Greener <[email protected]>
sidechain centroid docs example

3f62456290d33a35caf4f5a048766949e8aced21 authored about 4 years ago by Joe Greener <[email protected]>
bump version

2b9ac8d921ff34fe7887ce0f7de6e093a7f6bb86 authored about 4 years ago by Joe Greener <[email protected]>
run CI every week with cron job

a475a1e8412104a8fbb18f8530d5c9fe7593b81b authored about 4 years ago by Joe Greener <[email protected]>
update CompatHelper

17ee6342fd3d828110f33d32a0b804856f738101 authored about 4 years ago by Joe Greener <[email protected]>
CI status badge

11b9ee8ad66bafaadc7c4c35733605921e8fd6af authored about 4 years ago by Joe Greener <[email protected]>
move CI from Travis/AppVeyor to GitHub Actions

befc591ea2b54644507309a6697950509e91c6e3 authored about 4 years ago by Joe Greener <[email protected]>
paper PDF

21f76c843dc962333d0b69e449bf41b5cef98517 authored about 4 years ago by Joe Greener <[email protected]>
citation file

c8bb017071f710e5f89d439de9dd4b2b611cf9c9 authored about 4 years ago by Joe Greener <[email protected]>
CompatHelper: bump compat for "DataFrames" to "0.22" (#29)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

58f59fb0c0c338348b65b8ac4617c3ce92ec5af3 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
relax Format.jl compat

b69e5dd5a441dfe62f1b03d6d3c8f16457a1907a authored about 4 years ago by Joe Greener <[email protected]>
bump version

144135fbabf976aa671ed9b12e46f89d83a6ed23 authored about 4 years ago by Joe Greener <[email protected]>
disallow Format.jl v1.2

e4099430444d2de806ec8ac8caebc613e7b54b0c authored about 4 years ago by Joe Greener <[email protected]>
fix benchmark import clash

7625c94683259314346e5d8f0388a95191987b33 authored about 4 years ago by Joe Greener <[email protected]>
bump version

60cf74d60d3ad1fba7de48941efad47b4b1b81ea authored about 4 years ago by Joe Greener <[email protected]>
minor formatting

a02fad64f6b95f714dce5bf1353b784f7904e35a authored about 4 years ago by Joe Greener <[email protected]>
Add readmultimmcif, writemultimmcif functions (#28)

An mmCIF file can have multiple data_ blocks, thereby
containing multiple `MMCIFDict`s. An exam...

bfe2c91652d5a0bdef696e024e3ecf55c3603c82 authored about 4 years ago by Marco Matthies <[email protected]>
minor formatting

467eb8110f14189f3df686333bf83bdd815ecbd7 authored about 4 years ago by Joe Greener <[email protected]>
Tab completion in the REPL for MMCIFDict and MMTFDict (#27)

* Add support for tab-completion of MMCIFDict keys

This is achieved by subtyping from `Abstra...

e44e4873e2900b9cfa63cbb9aff0d081aaec2c3c authored about 4 years ago by Marco Matthies <[email protected]>
bump version

cbdb7df2fd33eb6d24a1aba75b5d71defe3ef1e3 authored over 4 years ago by Joe Greener <[email protected]>
get method for MMTFDict

f16e6891d11ea05345951b8cfe67008d19202955 authored over 4 years ago by Joe Greener <[email protected]>
Add ProteinStructure constructors from MMCIFDict and MMTFDict (#26)

* Add ProteinStructure constructors from MMCIFDict and MMTFDict

* Add docs for constructing P...

643f1e4139391f64ff19d8372cb76fb4507a5864 authored over 4 years ago by Marco <[email protected]>
bump version

996de9a4348115e5770dfc65ce61dc5226caa2b4 authored over 4 years ago by Joe Greener <[email protected]>
Add MMCIF reading and writing with gzip compression (#25)

* Add gzip keyword argument to function signature in docstring for mmtf functions.

* Add MMCI...

c93edfb51f7d05c67572935be1443e3d8bb7a257 authored over 4 years ago by Marco <[email protected]>
bump version

68c891a6237160f5ea49b705d2d9deaa2465c5ea authored over 4 years ago by Joe Greener <[email protected]>
Add get(mmcif, key, default) method for MMCIFDict. (#24)

e25b96993000a5db816323bbf997a6d2c651505b authored over 4 years ago by Marco <[email protected]>
script to compare mmCIF dicts to Biopython

e58f6c1fc86ab1e233dc0c0fef207c0161ee343e authored over 4 years ago by Joe Greener <[email protected]>
bump version

cfa6bc45ad125b865cdde3b58c53a982dbe9e002 authored over 4 years ago by Joe Greener <[email protected]>
allow comment character in mmCIF data value

32809c225f79dba59e22741f8cc4c77cc01ef9df authored over 4 years ago by Joe Greener <[email protected]>
update docs build setup

058a5d1021f2ca05fa17dfcf28aeb046e5f3a354 authored over 4 years ago by Joe Greener <[email protected]>
test on Julia v1.5

ff90bb2b77ea704506272c05cc060f7ec5f162aa authored over 4 years ago by Joe Greener <[email protected]>
paper citation info

538b9f5cd917cf6359eb6884961c3c0e6cbe4019 authored over 4 years ago by Joe Greener <[email protected]>
test on Julia v1.0

1d934fb989c70bb720bab26dd09e5baa5456ab40 authored over 4 years ago by Joe Greener <[email protected]>
switch testing to Julia 1.1 until dependencies resolved

59ea559fc354ab13dc3bb4b74524bd6f27f04e0a authored over 4 years ago by Joe Greener <[email protected]>
support newer BioSequences/BioAlignments, add threeletter_to_aa

19813c7f3860ec1292fab0ad65f3abb9217eaad4 authored over 4 years ago by Joe Greener <[email protected]>
tag release

deee9eefd7e20323acef763e4a51bfab6ce84504 authored over 4 years ago by Joe Greener <[email protected]>
CompatHelper: bump compat for "DataFrames" to "0.21" (#19)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

6472208b5909f8ea53dd1b442f91e959ae14f087 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
PdbTool ref to docs

6e4ecac4f231cdfea8c02a1cd184b6b0f430e459 authored over 4 years ago by Joe Greener <[email protected]>
line endings in mmtf.jl

b8cc531ac5758b9a63abc00eea856ea3d175509e authored over 4 years ago by Joe Greener <[email protected]>