pierrepo grodecoder issues

pierrepo / grodecoder

GroDecoder extracts and identifies the molecular components of a structure file (PDB or GRO) issued from a molecular dynamics simulation.

https://grodecoder.streamlit.app/

BSD 3-Clause "New" or "Revised" License

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Add new crd file as example file and add it in the test

#95 KarinDuong opened 3 months ago
0
Update the vdwradii dictionnary (where there is Van der Waals radius value for each atom type)

#94 KarinDuong opened 3 months ago
0
Add new data file (.crd) and update the test file

#93 KarinDuong opened 3 months ago
0
Create a function to load the system instead of doing it in remove_hydrogen

#92 KarinDuong opened 3 months ago
0
Update the streamlit app with the new structural file extension (.coor, .crd, .psf)

#91 KarinDuong opened 3 months ago
0
Add new file, that containt nucleic acids

#90 KarinDuong opened 3 months ago
0
Add new file, that containt nucleic acids and update the README with their composition

#89 KarinDuong opened 3 months ago
0
Add new structure file extention to analyze, the .crd

#88 KarinDuong closed 3 months ago
0
Manage a bug, because one variable name didn't follow after I rename it in is_nucleic_acid

#87 KarinDuong closed 3 months ago
0
Build the structure of the project into a package

#86 KarinDuong opened 3 months ago
0
Bug with current version

#85 pierrepo closed 3 months ago
0
Build the structure of the project into a package

#84 KarinDuong closed 3 months ago
1
Change script to include .coor and .psf file

#83 KarinDuong closed 3 months ago
1
Change the option in the argument for the parse_arg

#82 KarinDuong closed 3 months ago
0
Adapt the format of some file, so it can be readable by MDAnalysis

#81 KarinDuong opened 3 months ago
1
Manage periodic condition, if there are still there

#80 KarinDuong opened 3 months ago
1
Manage other structures files, other than GRO and PDB

#79 KarinDuong closed 3 months ago
0
Change some typing of function that create error with mypy

#78 KarinDuong closed 3 months ago
2
Add new files to the 'data/examples' directory

#77 KarinDuong closed 3 months ago
5
Add new files to `data/examples`

#76 KarinDuong closed 3 months ago
0
Streamlit sidebar

#75 KarinDuong closed 3 months ago
7
Nucleic acid docstring

#74 KarinDuong closed 3 months ago
2
Sandbox transfert

#73 KarinDuong closed 3 months ago
2
Name moldef lowercase

#72 KarinDuong closed 3 months ago
2
Do the packaging of the project

#71 KarinDuong opened 3 months ago
2
Add docstring to the function `is_nucleic_acids` and `extract_nucleic_acids_sequence`

#70 KarinDuong closed 3 months ago
0
Add the last commit date and the last commit hash to the streamlit app's sidebar

#69 KarinDuong closed 3 months ago
0
Add the script to scrap lipid database (CSML and MAD) in a repertory `script` and update the README

#68 KarinDuong closed 3 months ago
0
Name of ions and solvant in lower case (in `mol_def.py`)

#67 KarinDuong closed 3 months ago
0
New method selection lipid, in `is_lipid` for AA model

#66 KarinDuong closed 4 months ago
5
New method of lipid selection (for AA model) in the database for `is_lipid`

#65 KarinDuong closed 4 months ago
2
Add a system with methionine rich protein and solvant (methanol, urea, ethanol).

#64 KarinDuong closed 4 months ago
3
Add new function to identify nucleic acids and extract their sequence. And add the correspondance between nucleic acids resname and the 1-letter code

#63 KarinDuong closed 4 months ago
2
Add `is_nucleic_acids` function in grodecoder.py and `NUCLEIC_ACIDS` dictionary in mol_def.py

#62 KarinDuong closed 4 months ago
6
Create unit test for most of all the function of grodecoder

#61 KarinDuong closed 4 months ago
2
Update the field to test in the inventory (and the JSON file corresponding)

#60 KarinDuong closed 4 months ago
1
Create a new `molecular_type` field in the molecular inventory

#59 pierrepo closed 3 months ago
2
GroDecoder is crashing with example files

#58 pierrepo closed 4 months ago
1
Export to JSON last commit date and hash

#57 pierrepo closed 4 months ago
0
For the CG model, we identify and remive lipid at the same time we did for the ion and solvant

#56 KarinDuong closed 3 months ago
6
Pytest of grodecoder.py on all the file in data/exemples/

#55 KarinDuong closed 4 months ago
5
Improve README formating

#54 pierrepo closed 4 months ago
0
Save the current commit date and hash into the JSON file

#53 pierrepo closed 4 months ago
1
Shorten guess_resolution()

#52 pierrepo closed 5 months ago
0
Reorganize app

#51 pierrepo closed 5 months ago
0
Add CSML database in repo

#50 pierrepo closed 5 months ago
1
Create Streamlit app prototype

#49 pierrepo closed 5 months ago
0
Save execution time in the JSON file

#48 pierrepo closed 5 months ago
0
Add new molecules for test

#47 pierrepo closed 5 months ago
1
Improve JSON export

#46 pierrepo closed 5 months ago
3