Skip to content

Issues: forlilab/Meeko

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

37 Open 156 Closed
37 Open 156 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Format Docstrings to a Consistent Style for Auto-generation of API Documentation documentation Improvements or additions to documentation
#314 opened Jan 27, 2025 by rwxayheee
@rwxayheee
Parameterization issue for protein receptor + Zn ion with espaloma charges
#310 opened Jan 15, 2025 by itaneja2
4
bug in cmdline parsing of --add_atom_types after v0.6.1
#309 opened Jan 14, 2025 by diogomart
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
1
(Install problem, with a quick solution) TypeError: canonicalize_version() got an unexpected keyword argument 'strip_trailing_zero' installation
#303 opened Jan 6, 2025 by rwxayheee
@rwxayheee
Triply protonated N-terminal amines should not be modeled blunt
#300 opened Dec 27, 2024 by diogomart
5
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
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
Excess (padding) hydrogens in the exported PDB from mk_export.py bug Something isn't working
#280 opened Dec 12, 2024 by rwxayheee
1
@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 refactor Improvements to the code without necessarily adding features
#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
Receptor charge from PQR enhancement New feature or request
#264 opened Dec 4, 2024 by rwxayheee
@rwxayheee
Support for metal atoms
#252 opened Nov 19, 2024 by frgoe003
1
@rwxayheee
6
restrict rdkit version to those that support mol.HasQuery() documentation Improvements or additions to documentation installation
#246 opened Nov 15, 2024 by diogomart
How to cite Meeko?
#236 opened Nov 12, 2024 by and-tos
1
Remove python < 3.12 from setup.py, clarify prody installation from docs
#232 opened Nov 12, 2024 by diogomart
Report (raise warning or error for) lone hydrogens from bad input PDB
#231 opened Nov 11, 2024 by rwxayheee
1
@rwxayheee
1
Update polymer/chorizo padded molecule with positions from adjacent residue when there are multiple bonds between a pair of residues
#215 opened Oct 26, 2024 by diogomart
Cache templates downloaded from CCD
#209 opened Oct 23, 2024 by diogomart
1
@rwxayheee
add insertion code (icode) to BEGIN_RES keyword in flexres pdbqt
#201 opened Oct 15, 2024 by diogomart
write receptor json by default if flexres
#196 opened Oct 14, 2024 by diogomart
Include screening examples in doc documentation Improvements or additions to documentation enhancement New feature or request
#192 opened Oct 12, 2024 by rwxayheee
1 of 2 tasks
@rwxayheee
1
ProTip! Add no:assignee to see everything that’s not assigned.