haddocking / pdb-tools

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

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

Apache License 2.0

383 stars 113 forks source link

added pdb_deinsert #14

Closed joaomcteixeira closed 5 years ago

joaomcteixeira commented 5 years ago

addressed #13

input:

ATOM   2537  H   ASN B  52      -3.256 -36.866 -23.312  1.00 15.00           H  
ATOM   2538 HD21 ASN B  52      -3.216 -39.968 -27.105  1.00 15.00           H  
ATOM   2539 HD22 ASN B  52      -3.148 -41.154 -25.865  1.00 15.00           H  
ATOM   2540  N   PRO B  52A     -0.811 -39.882 -23.882  1.00  2.00           N  
ATOM   2541  CA  PRO B  52A      0.530 -39.717 -24.436  1.00  2.00           C  
ATOM   2542  C   PRO B  52A      0.551 -38.668 -25.518  1.00  2.00           C

tested output:

ATOM   2537  H   ASN B  52      -3.256 -36.866 -23.312  1.00 15.00           H  
ATOM   2538 HD21 ASN B  52      -3.216 -39.968 -27.105  1.00 15.00           H  
ATOM   2539 HD22 ASN B  52      -3.148 -41.154 -25.865  1.00 15.00           H  
ATOM   2540  N   PRO B  53      -0.811 -39.882 -23.882  1.00  2.00           N  
ATOM   2541  CA  PRO B  53       0.530 -39.717 -24.436  1.00  2.00           C  
ATOM   2542  C   PRO B  53       0.551 -38.668 -25.518  1.00  2.00           C

Added also tests and test files.

codecov[bot] commented 5 years ago

Codecov Report

Merging #14 into master will increase coverage by <.01%. The diff coverage is 82.02%.

@@            Coverage Diff             @@
##           master      #14      +/-   ##
==========================================
+ Coverage   81.63%   81.64%   +<.01%     
==========================================
  Files          42       43       +1     
  Lines        3366     3455      +89     
  Branches      704      720      +16     
==========================================
+ Hits         2748     2821      +73     
- Misses        438      448      +10     
- Partials      180      186       +6

Impacted Files	Coverage Δ
pdbtools/pdb_deinsert.py	`82.02% <82.02%> (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...cab344b. Read the comment docs.

codecov[bot] commented 5 years ago

Codecov Report

Merging #14 into master will increase coverage by <.01%. The diff coverage is 82.02%.

@@            Coverage Diff             @@
##           master      #14      +/-   ##
==========================================
+ Coverage   81.63%   81.64%   +<.01%     
==========================================
  Files          42       43       +1     
  Lines        3366     3455      +89     
  Branches      704      720      +16     
==========================================
+ Hits         2748     2821      +73     
- Misses        438      448      +10     
- Partials      180      186       +6

Impacted Files	Coverage Δ
pdbtools/pdb_deinsert.py	`82.02% <82.02%> (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...cab344b. Read the comment docs.

amjjbonvin commented 5 years ago

Will it keep the gaps if present? E.g. somewhere else in the structure?

JoaoRodrigues commented 5 years ago

Superseeded by #16 ! Thanks!