BiochemicalAlgorithms - v0.5.5

BiochemicalAlgorithms v0.5.5

Diff since v0.5.4

Merged pull requests: - CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat) (#199) (@github-actions[bot]) - Bump actions/checkout from 4 to 5 (#201) (@dependabot[bot])

- Julia
Published by github-actions[bot] 10 months ago

BiochemicalAlgorithms - v0.5.4

BiochemicalAlgorithms v0.5.4

Diff since v0.5.3

Merged pull requests: - CompatHelper: bump compat for MolecularGraph to 0.19, (keep existing compat) (#191) (@github-actions[bot]) - FF: fix parameter assignment on Julia nightly (#193) (@tkemmer) - Backports v0.5.4 (#194) (@tkemmer)

Closed issues: - Incorrect bond stretches and angle bends in Julia 1.13 (#192)

- Julia
Published by github-actions[bot] 12 months ago

BiochemicalAlgorithms - v0.5.3

BiochemicalAlgorithms v0.5.3

Diff since v0.5.2

Merged pull requests: - CompatHelper: bump compat for MolecularGraph to 0.18, (keep existing compat) (#189) (@github-actions[bot]) - Backports v0.5.3 (#190) (@tkemmer)

- Julia
Published by github-actions[bot] about 1 year ago

BiochemicalAlgorithms - v0.5.2

BiochemicalAlgorithms v0.5.2

Diff since v0.5.1

Merged pull requests: - Backports v0.5.2 (#180) (@tkemmer) - Core: relax type restrictions on squared_norm and distance (#186) (@tkemmer)

Closed issues: - match_points fails for certain inputs (#185)

- Julia
Published by github-actions[bot] about 1 year ago

BiochemicalAlgorithms - v0.5.1

BiochemicalAlgorithms v0.5.1

Diff since v0.5.0

Merged pull requests: - Fix add_hydrogens (#178) (@jeleclaire) - Backports v0.5.1 (#179) (@tkemmer)

Closed issues: - add_hydrogens fails due to constructor calls with keywords to Atom() and Bond() (#177)

- Julia
Published by github-actions[bot] about 1 year ago

BiochemicalAlgorithms - v0.5.0

BiochemicalAlgorithms v0.5.0

Diff since v0.4.0 Diff since v0.4.9

Breaking changes: - Clean up deprecated functions (#137) (@tkemmer) - Bump minimum supported Julia version to 1.10 LTS (#161) (@tkemmer) - Fix compat lower bounds (#162) (@tkemmer) - FF: remove unused data files (#171) (@tkemmer)

Merged pull requests: - Extended benchmarking (#129) (@jeleclaire) - Clean up deprecated functions (#137) (@tkemmer) - Reintroduce structure optimization (#141) (@tkemmer) - Implement reading and writing of HIN files (#145) (@tkemmer) - FileFormats: unify and document I/O interface (#146) (@tkemmer) - Allow strings to be passed as AbstractStrings where possible (#152) (@tkemmer) - FileFormats: fix missing bond orders read from HIN files (#155) (@tkemmer) - Bump minimum supported Julia version to 1.10 LTS (#161) (@tkemmer) - Fix compat lower bounds (#162) (@tkemmer) - FF: allow AMBER options to be modified (#168) (@tkemmer) - FF: remove unused data files (#171) (@tkemmer) - FF: include all warnings in message shown after force field setup (#172) (@tkemmer)

Closed issues: - FileFormats: HIN parser does not recognize bond orders (#154) - FF: allow modification of AmberFF options (#148) - FF: warnings from nonbonded components are not included in warning count after setup (#169)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.9

BiochemicalAlgorithms v0.4.9

Diff since v0.4.8

Merged pull requests: - Backports v0.4.9 (#173) (@tkemmer)

Closed issues: - FF: unassigned LJ interactions are not being reset on update!(ff) (#170)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.8

BiochemicalAlgorithms v0.4.8

Diff since v0.4.7

Merged pull requests: - FF: use the ForceField float type for parameter file reading (#165) (@tkemmer) - FF: read 1-4 ES scaling factor from parameter file (#167) (@tkemmer) - Backports v0.4.8 (#166) (@tkemmer)

Closed issues: - FF: Amber ignores force field-specific 1-4 scaling from params file (#163) - FF: AmberFF() always reads parameter file assuming Float32 as float type (#164)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.7

BiochemicalAlgorithms v0.4.7

Diff since v0.4.6

Merged pull requests: - Atom: fix no parent found (#157) (@anmabu) - Backports 0.4.7 (#158) (@tkemmer) - FileFormats: fix missing import for write_mmcif (#160) (@tkemmer)

Closed issues: - Atom: getfullname throws error if no parent molecule is found (#156) - write_mmcif fails due to missing import (#159)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.6

BiochemicalAlgorithms v0.4.6

Diff since v0.4.5

Merged pull requests: - Substructure fixes (#151) (@tkemmer) - Backports v0.4 (#153) (@tkemmer)

Closed issues: - FF: type name and charge assignments fail if atom name is given as SubString (#147) - Substructures: SMARTS matching is broken (#149) - Substructures: constructor fails for non-Float32 atom containers (#150)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.5

BiochemicalAlgorithms v0.4.5

Diff since v0.4.4

Merged pull requests: - Fix indexing of atoms in MolecularGraph wrapper w/ non-unique atom numbering (#143) (@tkemmer) - Backports v0.4 (#144) (@tkemmer)

Closed issues: - Non-unique atom indexing in molgraph wrapper (#142)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.4

BiochemicalAlgorithms v0.4.4

Diff since v0.4.3

Merged pull requests: - FF: fix compute_force! for constrained systems (#139) (@tkemmer) - Backports v0.4 (#140) (@tkemmer)

Closed issues: - compute_forces! with constrained atoms fails (#138)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.3

BiochemicalAlgorithms v0.4.3

Diff since v0.4.2

Merged pull requests: - FF: don't cache atom positions (#135) (@tkemmer) - Backports v0.4 (#136) (@tkemmer)

Closed issues: - FF: update! does not actually update cached atom positions (#134)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.2

BiochemicalAlgorithms v0.4.2

Diff since v0.4.1

Merged pull requests: - FF: fix no-op push! for untracked LJ interactions (#132) (@tkemmer)

Closed issues: - FF: unassigned Lennard-Jones interactions are not tracked (#131)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.1

BiochemicalAlgorithms v0.4.1

Diff since v0.4.0

Merged pull requests: - Remove GraphDataFrameBridge, fix compatibility w/ Julia 1.12-DEV (#130) (@tkemmer)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.4.0

BiochemicalAlgorithms v0.4.0

Diff since v0.3.2

Merged pull requests: - System: introduce ColumnTableRow type (#107) (@tkemmer) - System: simplify SystemComponent (#108) (@tkemmer) - System: open system component interface to tables (#109) (@tkemmer) - System: allow deletion of components (#110) (@tkemmer) - System: introduce SystemComponentTableCol to replace _RowProjectionVector (#113) (@tkemmer) - Added SecondaryStructure (#116) (@anhi) - System: support BitVector-based indexing for component tables (#118) (@tkemmer) - System: add Base.propertynames for system components and tables (#119) (@tkemmer) - System: support column selection for component tables (#121) (@tkemmer) - System: support sorting (#122) (@tkemmer) - System: add full_table for component tables (incl. hidden columns) (#123) (@tkemmer)

- Julia
Published by github-actions[bot] over 1 year ago

BiochemicalAlgorithms - v0.3.2

BiochemicalAlgorithms v0.3.2

Diff since v0.3.1

Merged pull requests: - System: fix inconsistent return values w/ table generators (#115) (@tkemmer) - PubChem: simplify load_pubchem_json (#117) (@tkemmer) - System: relax value type for setindex! of SystemComponentTableCols (#127) (@tkemmer) - Backports v0.3 (#128) (@tkemmer)

Closed issues: - Excessive load_pubchem_json compilation time (Julia 1.11+) (#88) - Inconsistent return values with table generators (atoms(), bonds(), ...) (#114) - setindex! value type for SystemComponentTableCol is too specific (#126)

- Julia
Published by github-actions[bot] almost 2 years ago

BiochemicalAlgorithms - v0.3.1

BiochemicalAlgorithms v0.3.1

Diff since v0.3.0

Closed issues: - PDB: fragment variant guessing fails when names contain trailing spaces (#111)

- Julia
Published by github-actions[bot] almost 2 years ago

BiochemicalAlgorithms - v0.3.0

BiochemicalAlgorithms v0.3.0

Diff since v0.2.1

Merged pull requests: - Introduce Molecule/Fragment variants, replacing previous protein/residue/nucleotide handling (#89) (@tkemmer) - System: allow more methods to implicitly use the default system (#99) (@tkemmer) - Refactor mappings (atom bijections, RMSD-minimizing rigid transforms, ...) (#103) (@tkemmer) - Mappings: include center of rotation in RigidTransform (#104) (@tkemmer) - Force fields: fixes and refactoring (#106) (@tkemmer)

Closed issues: - Residue creation upon loading pdb data (#81) - compute_energy!() and compute_forces!() (#98) - compute_rmsd_minimizer returns rotation w.r.t. B -> A but translation w.r.t. A -> B (#100) - map_rigid! does not transform hydrogens w/ heavy_atoms_only=true (#101) - map_rigid! does not re-translate to original location (#102) - ForceField: hydrogen bond handling fails due to broken constructor call (#105)

- Julia
Published by github-actions[bot] almost 2 years ago

BiochemicalAlgorithms - v0.2.1

BiochemicalAlgorithms v0.2.1

Diff since v0.2.0

Merged pull requests: - Reintroduce and update tutorial files (#97) (@tkemmer)

Closed issues: - TagBot trigger issue (#95)

- Julia
Published by github-actions[bot] almost 2 years ago

BiochemicalAlgorithms - v0.2.0

First official release of the BiochemicalAlgorithms.jl package. Read more about it in the documentation.

- Julia
Published by tkemmer almost 2 years ago