issues
search
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
0
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Improve molecular inventory export
#45
pierrepo
closed
4 months ago
1
List residues id instead of atom id start / end in `count_molecules()`
#44
pierrepo
closed
4 months ago
2
Update documentation in README
#43
pierrepo
closed
4 months ago
0
Error with `is_lipid()` function
#42
pierrepo
closed
4 months ago
0
Update `is_protein` to use `get_graph_fingerprint2()`
#41
pierrepo
closed
5 months ago
0
Update `get_graph_fingerprint2()`
#40
pierrepo
closed
5 months ago
0
Create a system with methionine rich protein and methanol
#39
pierrepo
closed
3 months ago
2
Create a protein complex in water
#38
pierrepo
closed
3 months ago
2
Create a complex molecular system
#37
pierrepo
closed
3 months ago
2
Remove the remove_ion_solvant() function
#36
pierrepo
closed
5 months ago
0
Add structure description
#35
pierrepo
closed
5 months ago
4
Avoid rcsbsearchapi
#34
pierrepo
closed
5 months ago
1
Use biopython
#33
pierrepo
closed
5 months ago
5
Add organic solvants
#32
pierrepo
closed
5 months ago
4
Verify graph is really an instance of a graph
#31
pierrepo
closed
5 months ago
0
Preserve same order in function inputs and outputs
#30
pierrepo
closed
5 months ago
0
Refactor function
#29
pierrepo
closed
5 months ago
0
Add water model tip5pe, tip4pew and spce
#28
pierrepo
closed
5 months ago
2
Add "ion big positive"
#27
pierrepo
closed
5 months ago
0
Add "ion Aluminum"
#26
pierrepo
closed
5 months ago
0
Replace "ion chlorine" by "ion chloride"
#25
pierrepo
closed
5 months ago
0
Create a new script to search a sequence in a FASTA file with the API of PDB
#24
KarinDuong
closed
5 months ago
0
Move all the constant (molecule's definition) into a new file .py
#23
KarinDuong
closed
5 months ago
0
Rename function
#22
pierrepo
closed
5 months ago
1
Update list of solvent and ions
#21
pierrepo
closed
5 months ago
1
Prevent atom reindexing when writing gro without H
#20
pierrepo
closed
5 months ago
0
Update node attributes
#19
pierrepo
closed
5 months ago
2
Look at graph node relabeling
#18
pierrepo
closed
5 months ago
3
Parse graph to extract protein seq
#17
pierrepo
closed
5 months ago
4
Support PDB format
#16
pierrepo
closed
5 months ago
0
Set check overlapping residue as an option
#15
pierrepo
closed
5 months ago
3
Improve args
#14
pierrepo
closed
5 months ago
0
The `print_graph` function should read one graph at a time and output image
#13
pierrepo
closed
5 months ago
3
Rework function to print molecule inventory
#12
pierrepo
closed
5 months ago
3
Fix wrong res_name field
#11
pierrepo
closed
5 months ago
1
Shorten degrees fingerprint
#10
pierrepo
closed
5 months ago
0
Fix missing results directory
#9
pierrepo
closed
5 months ago
0
Add debug info for gro file reading
#8
pierrepo
closed
6 months ago
0
Refactor contact matric and atom pairs functions
#7
pierrepo
closed
6 months ago
0
Improve README file
#6
pierrepo
closed
6 months ago
1
Fix pymol install
#5
pierrepo
closed
6 months ago
0
Rename main module
#4
pierrepo
closed
6 months ago
1
Clean env file
#3
pierrepo
closed
6 months ago
1
Define environment conda file with minimal package list
#2
pierrepo
closed
6 months ago
4
Update project name
#1
pierrepo
closed
6 months ago
2
Previous