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Issues list

[restraints] define restraints by componentA/B instead of host/guest
#1065 opened Dec 20, 2024 by IAlibay
gather should support a list of paths
#1064 opened Dec 18, 2024 by atravitz
add documentation for gather's supported directory structure
#1063 opened Dec 18, 2024 by atravitz
@jthorton @atravitz
Default solvent padding is often nsufficient for solute-only dodecahedron boxes.
#1062 opened Dec 18, 2024 by IAlibay
1
Make MD output_settings fully optional
#1061 opened Dec 18, 2024 by jthorton
refactor the CLI
#1056 opened Dec 13, 2024 by atravitz
2 tasks
add tests for cofactor support cli command-line interface priority:low
#1049 opened Dec 12, 2024 by jthorton
1
@jthorton
Stable sort edges in network generation
#1039 opened Dec 6, 2024 by IAlibay
@jthorton
add python 3.13 to ci matrix
#1028 opened Nov 23, 2024 by atravitz
@atravitz
make manual trigger for long tests
#1027 opened Nov 22, 2024 by atravitz
@mikemhenry
1
RFE Protocol - disallow mappings instead on the fly fixing constrained bond mappings
#1021 opened Nov 19, 2024 by IAlibay v2.0.0
2
resolve disconnected network handling
#1020 opened Nov 18, 2024 by atravitz
resolve konnektor behavior for maximal network generation
#1019 opened Nov 18, 2024 by atravitz
ligand network user guide rewrite documentation Improvements or additions to documentation
#1017 opened Nov 15, 2024 by atravitz
CI fails with OpenMM 8.2 in HTF.hyrid_system to mdtraj.topology transformation
#1016 opened Nov 13, 2024 by IAlibay
2
Protein mutation -- Allow optional small molecules in system generation Modeller
#1014 opened Nov 12, 2024 by ijpulidos
docs review: cli cli command-line interface documentation Improvements or additions to documentation
#1013 opened Nov 12, 2024 by atravitz
1
@atravitz
1
Switch to bootstrapping for MBAR errors. priority:medium
#1012 opened Nov 12, 2024 by IAlibay
@IAlibay
gather should be accessible through the API
#1010 opened Nov 8, 2024 by atravitz
@atravitz
1
How to add a restraint to a system
#1008 opened Nov 8, 2024 by ErikZhang-9762
improve gather error message when output JSON is missing "data" entry cli command-line interface
#1002 opened Nov 5, 2024 by atravitz
add plotting cookbook to docs
#999 opened Nov 1, 2024 by atravitz v1.x.0 CLI updates
1
cinnabar error handling from cli needs improvements cli command-line interface
#998 opened Nov 1, 2024 by atravitz v1.x.0 CLI updates
improve cli gather's handling of failed edges cli command-line interface priority:high
#997 opened Nov 1, 2024 by atravitz v1.x.0 CLI updates
support net charges from CLI quickrun cli command-line interface enhancement New feature or request
#996 opened Nov 1, 2024 by atravitz v1.x.0 CLI updates
1
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