haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

https://haddocking.github.io/pdb-tools/

Apache License 2.0

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Added pdb_delinsertions to (selectively) delete insertion codes. #16

Closed JoaoRodrigues closed 5 years ago

JoaoRodrigues commented 5 years ago

Following issue #13, here is a pull request to try and address that need. pdb_delinsertion removes, by default, all insertions and pads the numbering accordingly. It also allows the user to specify insertions that should be removed, ignoring all others (e.g. pdb_delinsertion -A99,B24 removes only insertions at residues 99 of chain A and 24 of chain B).

Comments? @mtrellet @joaomcteixeira @amjjbonvin

codecov[bot] commented 5 years ago

Codecov Report

Merging #16 into master will increase coverage by 0.15%. The diff coverage is 86.66%.

@@            Coverage Diff             @@
##           master      #16      +/-   ##
==========================================
+ Coverage   81.63%   81.79%   +0.15%     
==========================================
  Files          42       43       +1     
  Lines        3366     3471     +105     
  Branches      704      730      +26     
==========================================
+ Hits         2748     2839      +91     
- Misses        438      447       +9     
- Partials      180      185       +5

Impacted Files	Coverage Δ
pdbtools/pdb_delinsertion.py	`86.66% <86.66%> (ø)`

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update db933d9...811f7b4. Read the comment docs.

codecov[bot] commented 5 years ago

Codecov Report

Merging #16 into master will increase coverage by 0.15%. The diff coverage is 86.66%.

@@            Coverage Diff             @@
##           master      #16      +/-   ##
==========================================
+ Coverage   81.63%   81.79%   +0.15%     
==========================================
  Files          42       43       +1     
  Lines        3366     3471     +105     
  Branches      704      730      +26     
==========================================
+ Hits         2748     2839      +91     
- Misses        438      447       +9     
- Partials      180      185       +5

Impacted Files	Coverage Δ
pdbtools/pdb_delinsertion.py	`86.66% <86.66%> (ø)`

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update db933d9...811f7b4. Read the comment docs.

joaomcteixeira commented 5 years ago

I have visually inspected the output generated from testing the script on data/dummy_delinsertion.pdb with several options and everything looks okay, all outputs seem to agree with what discussed in #13 . setup.py test also passed. :+1: