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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Streamlit sidebar

#75 KarinDuong opened 1 day ago
6
Nucleic acid docstring

#74 KarinDuong closed 1 day ago
2
Sandbox transfert

#73 KarinDuong opened 1 day ago
0
Name moldef lowercase

#72 KarinDuong opened 1 day ago
0
Do the packaging of the project

#71 KarinDuong opened 1 day ago
1
Add docstring to the function `is_nucleic_acids` and `extract_nucleic_acids_sequence`

#70 KarinDuong closed 1 day ago
0
Add the last commit date and the last commit hash to the streamlit app's sidebar

#69 KarinDuong opened 1 day ago
0
Add the script to scrap lipid database (CSML and MAD) in a repertory `script` and update the README

#68 KarinDuong opened 1 day ago
0
Name of ions and solvant in lower case (in `mol_def.py`)

#67 KarinDuong opened 1 day ago
0
New method selection lipid, in `is_lipid` for AA model

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

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

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

#62 KarinDuong closed 2 days ago
6
Create unit test for most of all the function of grodecoder

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

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

#59 pierrepo closed 1 day ago
2
GroDecoder is crashing with example files

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

#57 pierrepo closed 1 week ago
0
For the CG model, we identify and remive lipid at the same time we did for the ion and solvant

#56 KarinDuong opened 1 week ago
4
Pytest of grodecoder.py on all the file in data/exemples/

#55 KarinDuong closed 1 week ago
5
Improve README formating

#54 pierrepo closed 3 weeks ago
0
Save the current commit date and hash into the JSON file

#53 pierrepo closed 1 week ago
1
Shorten guess_resolution()

#52 pierrepo closed 1 month ago
0
Reorganize app

#51 pierrepo closed 1 month ago
0
Add CSML database in repo

#50 pierrepo closed 1 month ago
1
Create Streamlit app prototype

#49 pierrepo closed 1 month ago
0
Save execution time in the JSON file

#48 pierrepo closed 1 month ago
0
Add new molecules for test

#47 pierrepo closed 1 month ago
1
Improve JSON export

#46 pierrepo closed 1 month ago
3
Improve molecular inventory export

#45 pierrepo closed 1 month ago
1
List residues id instead of atom id start / end in `count_molecules()`

#44 pierrepo closed 1 month ago
2
Update documentation in README

#43 pierrepo closed 1 month ago
0
Error with `is_lipid()` function

#42 pierrepo closed 1 month ago
0
Update `is_protein` to use `get_graph_fingerprint2()`

#41 pierrepo closed 2 months ago
0
Update `get_graph_fingerprint2()`

#40 pierrepo closed 2 months ago
0
Create a system with methionine rich protein and methanol

#39 pierrepo closed 4 days ago
2
Create a protein complex in water

#38 pierrepo closed 3 weeks ago
2
Create a complex molecular system

#37 pierrepo closed 1 week ago
2
Remove the remove_ion_solvant() function

#36 pierrepo closed 2 months ago
0
Add structure description

#35 pierrepo closed 2 months ago
4
Avoid rcsbsearchapi

#34 pierrepo closed 2 months ago
1
Use biopython

#33 pierrepo closed 2 months ago
5
Add organic solvants

#32 pierrepo closed 2 months ago
4
Verify graph is really an instance of a graph

#31 pierrepo closed 2 months ago
0
Preserve same order in function inputs and outputs

#30 pierrepo closed 2 months ago
0
Refactor function

#29 pierrepo closed 2 months ago
0
Add water model tip5pe, tip4pew and spce

#28 pierrepo closed 2 months ago
2
Add "ion big positive"

#27 pierrepo closed 2 months ago
0
Add "ion Aluminum"

#26 pierrepo closed 2 months ago
0