mosdef-hub mbuild issues

mosdef-hub / mbuild

A hierarchical, component based molecule builder

https://mbuild.mosdef.org

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issues

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fix label handling during flatten

#1208 CalCraven opened 2 days ago
2
Add Ruff to pre-commit hooks

#1207 chrisjonesBSU opened 1 week ago
1
Issue with reading mol2 file and flattening the hierarchy

#1206 CalCraven opened 1 week ago
1
mBuild 2.0 Release Discussion

#1205 chrisjonesBSU opened 3 weeks ago
0
numpy 2.0 support

#1204 CalCraven opened 3 weeks ago
2
Remove rigid body data structure from `Compound`

#1203 chrisjonesBSU closed 3 weeks ago
2
I think the mb.pattern.Pattern.apply method is not well tested or documented.

#1202 CalCraven opened 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#1201 pre-commit-ci[bot] closed 3 weeks ago
0
Remove rigid body ID assignment from `Compound`

#1200 chrisjonesBSU closed 3 weeks ago
0
Add a cylinder packing method to `packing.py`

#1199 askforarun opened 1 month ago
1
improve speedup of large lattice

#1198 CalCraven closed 2 months ago
1
PyBel based method get_smiles, results in inconsistent outputs

#1197 CalCraven opened 3 months ago
0
Add cap hydrogens to head and tail compounds in the polymer builder

#1196 chrisjonesBSU closed 3 months ago
2
reset_labels kwarg to force_overlap, new method reset_labels

#1195 jaclark5 closed 3 months ago
12
Force_overlap has moving goal posts

#1194 jaclark5 closed 3 months ago
0
[pre-commit.ci] pre-commit autoupdate

#1193 pre-commit-ci[bot] closed 3 months ago
0
Fix deprecation warnig in `packing.py` and replace `.format()` with f-strings where possible.

#1192 chrisjonesBSU closed 3 months ago
2
Remove deprecated formats, update reader and writer backends

#1191 chrisjonesBSU closed 3 weeks ago
8
`mb.Compound.save()` feature returns a PDB file without bonds

#1190 Pablo-Pomares opened 5 months ago
2
Fix failing tests with latest version of packmol

#1189 CalCraven closed 5 months ago
4
Add warnings for deprecated file formats (protobuf, hoomdxml, Hoomd-Blue and LAMMPS simulation writers)

#1188 chrisjonesBSU closed 5 months ago
3
Add warnings for deprecated file formats (protobuf, hoomdxml, Hoomd-Blue and LAMMPS simulation writers)

#1187 chrisjonesBSU closed 5 months ago
3
Add Ruff to pre-commit

#1186 chrisjonesBSU opened 6 months ago
1
add variable in the box packing functions to allow more packmol iterations

#1185 bc118 closed 5 months ago
3
[pre-commit.ci] pre-commit autoupdate

#1184 pre-commit-ci[bot] closed 6 months ago
0
[pre-commit.ci] pre-commit autoupdate

#1183 pre-commit-ci[bot] closed 7 months ago
0
Floating point error converting .gro to .xyz

#1182 dyukovsm closed 7 months ago
1
[pre-commit.ci] pre-commit autoupdate

#1181 pre-commit-ci[bot] closed 7 months ago
1
Bump to python 3.12

#1180 CalCraven closed 6 months ago
11
CI failing for Windowns build

#1179 daico007 closed 7 months ago
1
Update README graphic

#1178 daico007 closed 7 months ago
1
Fix failing doc build

#1177 daico007 closed 8 months ago
1
[pre-commit.ci] pre-commit autoupdate

#1176 pre-commit-ci[bot] closed 8 months ago
1
Plugins error when creating anaconda environment with python 3.12

#1175 chrisjonesBSU closed 8 months ago
7
Error when Compiling Docs Locally

#1174 jaclark5 closed 7 months ago
2
Add option to reset child labels in Compound.remove()

#1173 jaclark5 closed 7 months ago
2
Loss of meaningful port names and labels

#1172 jaclark5 closed 7 months ago
0
Ability for Polymer Builder to connect ends for a loop

#1171 jaclark5 closed 7 months ago
0
Periodic polymer

#1170 jaclark5 closed 7 months ago
14
Attempt to fix docs build

#1169 daico007 closed 8 months ago
1
Documentation defines build.format.charmm_writer which does not exist

#1168 jaclark5 closed 8 months ago
2
[pre-commit.ci] pre-commit autoupdate

#1167 pre-commit-ci[bot] closed 9 months ago
1
Take into the forming of double bonds in Polymer builder

#1166 daico007 opened 9 months ago
0
[pre-commit.ci] pre-commit autoupdate

#1165 pre-commit-ci[bot] closed 9 months ago
1
[pre-commit.ci] pre-commit autoupdate

#1164 pre-commit-ci[bot] closed 10 months ago
1
Speed up json loader

#1163 daico007 closed 9 months ago
1
Performance loading from `.json` file

#1162 daico007 closed 9 months ago
0
[pre-commit.ci] pre-commit autoupdate

#1161 pre-commit-ci[bot] closed 11 months ago
1
Update deprecated syntax in CI.yml

#1160 daico007 closed 11 months ago
1
Issue with mbuild docs

#1159 daico007 closed 8 months ago
2