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27 Open 186 Closed
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Issues list

Report ligand ID & continue on batch ligand preparation error enhancement New feature or request
#362 opened May 9, 2025 by Billsfriend v0.7.0
@diogomart
1
8000
Add docs on how to add templates for 9MXW
#355 opened Apr 26, 2025 by diogomart
@rwxayheee
2
Do not forgive extra bonds by default (#347) - make it optional instead
#354 opened Apr 26, 2025 by diogomart v0.7.0
@diogomart
15
Receptor preparation fails for unexpected atom order bug Something isn't working
#352 opened Apr 24, 2025 by diogomart v0.7.0
@rwxayheee
9
mk_prepare_receptor.py fails if running multiple processes
#351 opened Apr 24, 2025 by diogomart
calling monomer.parameterize should call mk_prep.calc_flex if monomer.is_movable
#334 opened Mar 28, 2025 by diogomart v0.7.0
@diogomart
Use residue template matching to prepare ligands in PDB format enhancement New feature or request
#317 opened Feb 13, 2025 by diogomart
2
Parameterization issue for protein receptor + Zn ion with espaloma charges
#310 opened Jan 15, 2025 by itaneja2
@diogomart
4
Clean up and move the scripts for hydrated docking into Meeko
#308 opened Jan 11, 2025 by rwxayheee
Mk_prepare_ligand fails for Vanadium-containing ligands
#307 opened Jan 9, 2025 by frgoe003
@rwxayheee
3
raise error if user-specified receptor template does not match even if allow_bad_res=True
#299 opened Dec 27, 2024 by diogomart
Templates stored within Polymer
#293 opened Dec 24, 2024 by rwxayheee
6
Skip writing boron-silicon-atom_par.dat from mk_prepare_receptor.py ; add the dat to JSON files in meeko/data/
#282 opened Dec 13, 2024 by rwxayheee
Name and suffix do not contribute to output filenames when output.output_filename is not None:mk_prepare_ligand.py outputs (overwrites) prepared covalent ligands at different residues to the same file wontfix This will not be worked on
#278 opened Dec 11, 2024 by rwxayheee
1
@rwxayheee
1
Reduce overhead in preperation refactor Improvements to the code without necessarily adding features
#275 opened Dec 10, 2024 by rwxayheee
1
@rwxayheee
3
RuntimeError: expected only 1 added H per heavy atom, maybe deleted element had double bond to this heavy atom
#267 opened Dec 7, 2024 by accibio
1
7
Support for metal atoms
#252 opened Nov 19, 2024 by frgoe003
1
@rwxayheee
6
How to cite Meeko?
#236 opened Nov 12, 2024 by and-tos
1
Update polymer/cho 8000 rizo padded molecule with positions from adjacent residue when there are multiple bonds between a pair of residues
#215 opened Oct 26, 2024 by diogomart v0.7.0
1
Covalent Docking
#146 opened Aug 8, 2024 by kunal19977835
23
Redo Flexibility Model Structure in Meeko refactor Improvements to the code without necessarily adding features
#144 opened Jul 26, 2024 by psharma-sr Meeko Refactoring Project
@psharma-sr
mk_export embeds information in string enhancement New feature or request
#138 opened Jul 11, 2024 by mattholc
1
Meeko Documentation documentation Improvements or additions to documentation
#135 opened Jun 20, 2024 by psharma-sr v0.7.0
@rwxayheee
Covalent docking using autodock gpu with ligand prepared by mk_prepare_ligand.py refactor Improvements to the code without necessarily adding features
#104 opened Apr 24, 2024 by lovenicole
12
centroid offsite atoms enhancement New feature or request
#95 opened Mar 27, 2024 by diogomart
ProTip! What’s not been updated in a month: updated:<2025-04-19.
0