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Collection of structures & TMAlign #143

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Collection of structures & TMAlign #143

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ba7f46d
added possiblity of collection of structures and function to work on …
gezmi Apr 30, 2024
5642c20
added testing for cases when error is raised
gezmi Apr 30, 2024
cd9b14e
fixing import of stack
gezmi May 1, 2024
b74265b
initial implementation of tmalign
gezmi May 1, 2024
1650bba
installation of package with TMalign (USalign)
gezmi May 2, 2024
a2c0476
added accidentally deleted test data
gezmi May 2, 2024
93f8600
tmalign working and tested
gezmi May 2, 2024
b3c0c7f
stack writing test updated with absolute paths, so they do not faile …
gezmi May 2, 2024
407ef44
deleted stack import to prevent circular import
gezmi May 2, 2024
164701f
modify, so that it does not need stack import for checking type of va…
gezmi May 2, 2024
82fc69f
tmalign inside alignment works
gezmi May 2, 2024
d569cab
changed type of equality check
gezmi May 2, 2024
541bea7
removed unnecessary print
gezmi May 2, 2024
7c5cd8d
added new line
gezmi May 2, 2024
55c4205
corrected typos in functions' names
gezmi May 2, 2024
35bb8f7
added clean up after temporary matrix file
gezmi May 2, 2024
2b29780
added possibility to specify target when aligning stack
gezmi May 2, 2024
f5e4ddc
added tutorials and necessary files for TMalign and stack
gezmi May 6, 2024
2d1c0c0
installation requires TMalign
gezmi May 6, 2024
29fa124
added TMalign and stacks to changelog
gezmi May 6, 2024
6ad051e
rearranged tmalign of stacks, updated tests
gezmi May 6, 2024
ccf56ba
changed version
gezmi May 6, 2024
664111f
updated installation with usalign
gezmi May 6, 2024
9a20af5
added api docs and tutorial md
gezmi May 6, 2024
7b52570
updated gitignore
gezmi May 6, 2024
a6cd5ed
Merge branch 'main' into stack_tmalign
a-r-j Jul 8, 2024
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added TMalign and stacks to changelog
@gezmi
gezmi committed May 6, 2024
commit 29fa124901bcdd55cc1f2815d24cdba8bf08caa8
4 changes: 4 additions & 0 deletions docs/CHANGELOG.md
View file
Original file line number Diff line number Diff line change
@@ -4,6 +4,10 @@
The CHANGELOG for the current development version is available at
[https://github.com/rasbt/biopandas/blob/main/docs/sources/CHANGELOG.md](https://github.com/rasbt/biopandas/blob/main/docs/sources/CHANGELOG.md).

### 0.5.0dev2 (2/5/2024)
- Adds support for constructing a collection of PDB files and perform actions on them (Via [Julia K. Varga](https://github.com/gezmi)
- Adds the possibility of performing alignments, translation and rotation on the structure, via an extendable Align class (Via [Julia K. Varga](https://github.com/gezmi)
- TMAlign is installed alongside the package to perform the alignments (Via [Julia K. Varga](https://github.com/gezmi)

### 0.5.0dev1 (31/7/2023)
- Implement add_remark for PandasPdb, (Via [Anton Bushuiev](https://github.com/anton-bushuiev) PR #[129](https://github.com/BioPandas/biopandas/pull/129))