hildebrandtlab BiochemicalAlgorithms.jl issues

hildebrandtlab / BiochemicalAlgorithms.jl

The Biochemical Algorithms Library in Julia

MIT License

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issues

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Extended benchmarking

#129 jeleclaire opened 1 month ago
0
Backports v0.3

#128 tkemmer closed 1 month ago
0
System: relax value type for `setindex!` of `SystemComponentTableCol`s

#127 tkemmer closed 1 month ago
0
`setindex!` value type for `SystemComponentTableCol` is too specific

#126 tkemmer closed 1 month ago
0
FDB: Allow for the addition of fragments to the fragment database

#125 jeleclaire opened 1 month ago
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FDB: build_bonds for ions fails due to not finding reference ligand

#124 jeleclaire opened 1 month ago
0
System: add `full_table` for component tables (incl. hidden columns)

#123 tkemmer closed 1 month ago
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System: support sorting

#122 tkemmer closed 1 month ago
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System: support column selection for component tables

#121 tkemmer closed 1 month ago
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Implement reading and writing of HIN files

#120 anhi opened 1 month ago
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System: add `Base.propertynames` for system components and tables

#119 tkemmer closed 1 month ago
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System: support BitVector-based indexing for component tables

#118 tkemmer closed 1 month ago
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PubChem: simplify `load_pubchem_json`

#117 tkemmer closed 1 month ago
0
Added SecondaryStructure

#116 anhi closed 1 month ago
0
System: fix inconsistent return values w/ table generators

#115 tkemmer closed 1 month ago
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Inconsistent return values with table generators (`atoms()`, `bonds()`, ...)

#114 tkemmer closed 1 month ago
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System: introduce `SystemComponentTableCol` to replace `_RowProjectionVector`

#113 tkemmer closed 1 month ago
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Backports v0.3

#112 tkemmer closed 1 month ago
0
PDB: fragment variant guessing fails when names contain trailing spaces

#111 tkemmer closed 2 months ago
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System: allow deletion of components

#110 tkemmer closed 1 month ago
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System: open system component interface to tables

#109 tkemmer closed 2 months ago
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System: simplify `SystemComponent`

#108 tkemmer closed 2 months ago
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System: introduce `ColumnTableRow` type

#107 tkemmer closed 2 months ago
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Force fields: fixes and refactoring

#106 tkemmer closed 2 months ago
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ForceField: hydrogen bond handling fails due to broken constructor call

#105 tkemmer closed 2 months ago
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Mappings: include center of rotation in RigidTransform

#104 tkemmer closed 2 months ago
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Refactor mappings (atom bijections, RMSD-minimizing rigid transforms, ...)

#103 tkemmer closed 2 months ago
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`map_rigid!` does not re-translate to original location

#102 tkemmer closed 2 months ago
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`map_rigid!` does not transform hydrogens w/ `heavy_atoms_only=true`

#101 tkemmer closed 2 months ago
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`compute_rmsd_minimizer` returns rotation w.r.t. `B -> A` but translation w.r.t. `A -> B`

#100 tkemmer closed 2 months ago
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System: allow more methods to implicitly use the default system

#99 tkemmer closed 2 months ago
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`compute_energy!()` and `compute_forces!()`

#98 tkemmer closed 2 months ago
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Reintroduce and update tutorial files

#97 tkemmer closed 2 months ago
0
CompatHelper: bump compat for MolecularGraph to 0.17, (keep existing compat)

#96 github-actions[bot] closed 3 months ago
0
TagBot trigger issue

#95 JuliaTagBot closed 3 months ago
6
Jl/tutorials doc

#94 jeleclaire closed 2 months ago
0
BioStructures.jl compat

#93 jgreener64 closed 3 months ago
3
CompatHelper: bump compat for BioStructures to 4, (keep existing compat)

#92 github-actions[bot] closed 3 months ago
2
Jl/tutorials

#91 jeleclaire closed 3 months ago
0
Bump `actions/setup-python` to v5

#90 tkemmer closed 4 months ago
0
Introduce Molecule/Fragment variants, replacing previous protein/residue/nucleotide handling

#89 tkemmer closed 2 months ago
0
Excessive `load_pubchem_json` compilation time (Julia 1.11+)

#88 tkemmer closed 1 month ago
0
[mappings] version of mapping with heavy atoms only fixed

#87 jeleclaire closed 5 months ago
0
CompatHelper: bump compat for CellListMap to 0.9, (keep existing compat)

#86 github-actions[bot] closed 5 months ago
0
Jl/rmsd minimizer

#85 jeleclaire closed 5 months ago
0
[DONOTMERGE] Avoid running jobs multiple times for fork-based PRs

#84 tkemmer closed 6 months ago
0
CI: Avoid running jobs multiple times for PRs of local branches

#83 tkemmer closed 6 months ago
0
Symbol e0 could not be found while parsing ball_ini_file under Windows

#82 jeleclaire closed 6 months ago
0
Residue creation upon loading pdb data

#81 jeleclaire closed 2 months ago
1
Molecule name is still the file name

#80 jeleclaire opened 7 months ago
0