Commits · ddc80a51a1bc438c82e62af81d2ce625f99c9e0a · Mustafa Tekpinar / PRESCOTT

20 Jul, 2022 3 commits
- A small bug in gemme.py about user provided pdb files was corrected. · ddc80a51
```
If the user does not provide a pdbfile and asks the program to calculate
structural-dynamical parameters like Bfactor, CV or DFI, the program will
give an error and quit. Before, there was not such a thing.
```
  Mustafa Tekpinar authored Jul 20, 2022
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- Clean tree files in Newick format produced by JET · c04a6b44
  Mustafa Tekpinar authored Jul 20, 2022
  
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- Added bfactor and max-bfactor-trace options to normweightmode · 282a71e7
  Mustafa Tekpinar authored Jul 20, 2022
  
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15 Jul, 2022 3 commits
- Readded the mt.20.txt file. · 7bd7fcd5
  Mustafa Tekpinar authored Jul 15, 2022
  
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- Reverted NA values from 2.0 to 0.0 bbc it was causing too much difference in the… · e9dcd04c
```
Reverted NA values from 2.0 to 0.0 bbc it was causing too much difference in the epistatic model maps.
```
  Mustafa Tekpinar authored Jul 15, 2022
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- Changed the default value for the wild type (namely, NA values) from 0.0 to 2.0. · 606b4597
  Mustafa Tekpinar authored Jul 15, 2022
  
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07 Jul, 2022 1 commit
- Added mt.20.txt, namely full alphabet! · bd075e8c
  Mustafa Tekpinar authored Jul 07, 2022
  
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14 Jun, 2022 2 commits
- alphabet selection was added as an input argument! · 2eef3ef9
  Mustafa Tekpinar authored Jun 14, 2022
  
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- Corrected a bug in createPDB() · 49d39490
```
If the query sequence contains a gap, createPDB() was blowing up.
This bug was corrected!
```
  Mustafa Tekpinar authored Jun 14, 2022
  49d39490 Browse Files
03 Jun, 2022 1 commit

Added an amino acid based alpha index called alpha[i]. · 4eaa0f37

For now, alpha[i] is still 0.6 for the all residues to produce
similar outputs for all residues. In addition to this change,
corrected a bug related to the chain naming.

authored Jun 03, 2022

4eaa0f37 Browse Files

30 May, 2022 1 commit
- Some minor code annotations! · 33693642
  Mustafa Tekpinar authored May 30, 2022
  
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25 May, 2022 1 commit
- Added DFI calculation and weighting option. · 1383201b
  Mustafa Tekpinar authored May 25, 2022
  
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20 May, 2022 1 commit
- Added more options to the normweightmode! · e82bf1a9
  Mustafa Tekpinar authored May 20, 2022
  
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19 May, 2022 2 commits
- Minor change in .gitignore · 00a298ae
  Mustafa Tekpinar authored May 19, 2022
  
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- Added half-pc+cv option to normweightmode! · 06ff7a4c
  Mustafa Tekpinar authored May 19, 2022
  
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18 May, 2022 1 commit
- Added --pdbfile option to parse PDB files provided by the user. · ba2786df
  Mustafa Tekpinar authored May 18, 2022
  
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09 May, 2022 4 commits
- Changed the argument --isjet2off to --jetfile. · d7774e36
  Mustafa Tekpinar authored May 09, 2022
  
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- Added normweightmode as an argument to Python part of the code · 49dff695
  Mustafa Tekpinar authored May 09, 2022
  
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- Added more user error flexibility to normWeightMode variable in computePred.R · e197ed88
  Mustafa Tekpinar authored May 09, 2022
  
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- Now, checking if normalized data files are created or not for figs. · 4c796a06
  Mustafa Tekpinar authored May 09, 2022
  
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06 May, 2022 1 commit
- Added normWeightMode to computePred.R! · 4cee9b3b
  Mustafa Tekpinar authored May 06, 2022
  
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29 Apr, 2022 2 commits
- Tried to automatize difference checks with check-diffs.sh. · 64d8076d
  Mustafa Tekpinar authored Apr 29, 2022
  
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- Implemented --isjet2on option for reproducibility checks. · 2af63caf
  Mustafa Tekpinar authored Apr 29, 2022
  
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28 Apr, 2022 4 commits
- Changed the location of normalization procedures for independent and epistatic models! · 05fb8c57
  Mustafa Tekpinar authored Apr 28, 2022
  
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- Plotting part was moved from R to Python. · 11b750b2
  Mustafa Tekpinar authored Apr 28, 2022
  
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- Some changes to make the program run on python3 (tested with 3.9.7 ). · a12e8938
  Mustafa Tekpinar authored Apr 28, 2022
  
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- Corrected a bug of overwriting on the fasta file · f61b87d1
  Mustafa Tekpinar authored Apr 28, 2022
  
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25 Apr, 2022 1 commit
- Initial Commit · 2d1df3ad
  Mustafa Tekpinar authored Apr 25, 2022
  
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