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)

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)

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)

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: get_full_name throws error if no parent molecule is found (#156)
• write_mmcif fails due to missing import (#159)

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)

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)

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)

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)

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)

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)