forlilab Meeko issues - Githubissues

forlilab / Meeko

Interfacing RDKit and AutoDock

GNU Lesser General Public License v2.1

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#186 diogomart opened 1 day ago
2
Fixing NME in #180 by fallback logics instead of additional information from chem template

#185 rwxayheee opened 1 day ago
0
Fixing NME in #180

#184 rwxayheee closed 1 day ago
1
Fix delete_residues in chorizo (polymer) and mk_prepare_receptor

#183 diogomart closed 3 days ago
0
update_H_positions duplicated in linked_rdkit_chorizo.py

#182 diogomart opened 4 days ago
0
RDKit's Chem.MolFromPDBBlock ignores atoms if AltLoc is not ' ' or 'A' or '1'

#181 rwxayheee opened 4 days ago
0
adjacent_res_smarts requires more atoms in adjacent_mol than capping residues (NME, ACE, phosphate) can provide

#180 rwxayheee opened 6 days ago
0
minimal fix for delete_residues in mk_prepare_receptor.py

#179 rwxayheee closed 4 days ago
2
Raise RuntimeError when MolFromPDBBlock failed to return a mol

#178 rwxayheee closed 1 week ago
4
Bump actions/upload-artifact@v2 to v4

#177 rwxayheee closed 1 week ago
0
Add nucleic acid residues to residue_chem_templates.json

#176 rwxayheee closed 1 day ago
4
remove unneeded code for prody to rdkit conversion

#175 diogomart closed 1 week ago
1
make prody optional

#174 diogomart closed 1 week ago
1
Small fix in prodyutils.py

#173 rwxayheee closed 1 week ago
1
Minor edit to atom_name_to_molsetup_index; Support input in both ways: --macromol (ProDy) and --pdb (RDKit)

#172 rwxayheee closed 1 week ago
3
Fix for PDBQT names with multimode_outdir

#171 althea-hansel closed 1 week ago
0
Not reading molecule names from SDF

#170 althea-hansel closed 1 week ago
8
Use of mk_prepare_receptor.py instead of prepare_receptor in Vina basic docking

#169 xavgit opened 2 weeks ago
1
mk_prepare_receptor for reactive docking isn't working with --macromol (Prody parser)

#168 rwxayheee closed 1 week ago
5
remove dropped attribute from molsetup.show()

#167 diogomart closed 1 week ago
1
Problem using mk_prepare_ligand.py with -v in version 0.5.1

#166 xavgit closed 3 weeks ago
2
mk_prepare_receptor output flags improvement

#165 diogomart opened 3 weeks ago
0
Blunt sidechains for mk_prepare_receptor?

#164 rwxayheee opened 3 weeks ago
1
update UniqAtomParams to refactored Molsetup

#163 diogomart closed 3 weeks ago
0
rename mk_prepare_receptor.py arg --ligand to --box_enveloping

#162 diogomart closed 3 weeks ago
1
Raise helpful error message when reactive smarts doesn't match

#161 diogomart closed 3 weeks ago
1
`molsetup.atoms[atom_index].atom_type` doesn't sync with `molsetup.atom_type`

#160 rwxayheee closed 3 weeks ago
1
flexible side chain recognition

#159 Alan-Abdallah closed 4 days ago
1
The ligand prepared by Meeko for docking using AutoDock-GPU has unusual atoms

#158 aprijal99 closed 3 weeks ago
2
Draft reactive sidechain

#157 diogomart closed 3 weeks ago
3
Segmentation faults using .prepare

#156 alrichardbollans closed 1 month ago
1
Minimal Fixes for --reactive_flexres and --box_center_off_reactive_res

#155 rwxayheee closed 1 month ago
1
update function to write PDB from chorizo, and fix a bug that ignored input H positions

#154 diogomart closed 1 month ago
1
Quick Fixes for Inconsistent Selection Formats in reactive_flexres and all_flexres

#153 rwxayheee closed 1 month ago
2
RuntimeError when converting dlg to sdf using mk_export.py

#152 SejeongPark8354 closed 1 month ago
3
Can't serialize MoleculeSetup dihedrals to JSON

#151 diogomart opened 1 month ago
0
optionally allow breaking macrocycle bonds with A atom types (re-implements #106)

#150 diogomart closed 1 month ago
0
Combined PR #133 and PR #109 (superseeds #147)

#149 diogomart closed 1 month ago
0
Covalent docking - ModuleNotFoundError: No module named 'rdkit'

#148 Brett628 closed 1 month ago
8
Combined PR #133 and PR #109

#147 diogomart closed 1 month ago
2
Covalent Docking

#146 kunal19977835 opened 1 month ago
23
remove openbabel for v0.6

#145 diogomart closed 3 weeks ago
1
Redo Flexibility Model Structure in Meeko

#144 psharma-sr opened 2 months ago
0
Remove coords from MoleculeSetups in Meeko

#143 psharma-sr closed 2 months ago
2
NameError Encountered as Using `mk_prepare_ligand.py` with Argument `--multimol_prefix`

#142 proline8314 opened 2 months ago
3
ERROR : import meeko rdkit.six module mot found

#141 layal-khayal closed 1 month ago
1
Converting PQBQT to multiple RDKIT molecules

#140 QY0831 closed 2 months ago
2
Python Packaging Issues

#139 xavierholt closed 4 days ago
6
mk_export embeds information in string

#138 mattholc opened 2 months ago
1
calc_box function fails to handle some PDBQT formatting

#137 rkosai closed 3 months ago
7