Changelog for cobot-io
[Unreleased]
[0.1.3.12] - 2020-11-11
Fixed
- PDB parser error: it didn't account for segment identifier field.
- Bond restoring in PDB for non-standard residue names.
[0.1.3.11] - 2020-11-08
Changed
[0.1.3.10] - 2020-11-06
Fixed
SOURCE
and ORIGIN
in GB parser.
[0.1.3.9] - 2020-10-27
Fixed
- FASTA parser can now parse empty lines with spaces.
[0.1.3.8] - 2020-10-22
Fixed
- A couple of issues, that caused parametrization failures, fixed in bond restoring for PDB format.
[0.1.3.7] - 2020-10-14
Added
[0.1.3.6] - 2020-07-14
Added
- Convertation from
Model
s to PDB
.
- Writer for
PDB
.
renameChains
function that renames chains in a model.
[0.1.3.5] - 2020-05-26
Fixed
- Correctly clean
BasecalledSequenceWithRawData
, including inner quality.
[0.1.3.4] - 2020-05-14
Added
instance Cleanable BasecalledSequenceWithRawData
.
[0.1.3.3] - 2020-05-07
Added
- Type and decoder for
ab1
with raw channel data and peak locations.
Fixed
- Use supplied thresholds instead of default ones in the implementation of
cleanWith
;
- Do not run
IO
in hspec
Spec
monad, use beforeAll
.
[0.1.3.2] - 2020-04-15
Changed
- Resolver version up.
- Moving from
less-wrong
to biocad
.
[0.1.3.1] - 2020-04-02
Fixed
- Reading of insertion code for residues in MAE.
[0.1.3.0] - 2020-03-27
Added
- Residue index in
Structure
.
- Atom input index in
Structure
.
- Bond restoring for PDB.
- Tests for PDB -> Model conversion.
Changed
- GlobalID now 0-based in mae, PDB, and MMTF.
Fixed
[0.1.2.10] - 2020-03-27
Added
[0.1.2.9] - 2020-03-12
Added
- Function
filterAtomsOfModel
to filter atoms of model by the given predicate.
Fixed
- Grouping by residues when converting
Mae
to Model
.
[0.1.2.8] - 2020-03-12
Added
instance Traversable (Sequence mk w)
.
[0.1.2.7] - 2020-02-11
Changed
[0.1.2.6] - 2019-12-12
Fixed
- Fixes for instance of
StructureModels
for Mae
when working with structures without explicit chain names.
[0.1.2.5] - 2019-12-24
Fixed
- Possibility to have spaces in Fasta sequences.
[0.1.2.4] - 2019-12-23
Added
- Preprocessing for pdb-files.
- Pdb parser.
[0.1.2.3] - 2019-12-12
Fixed
- Fixes for .mae pasrser.
- Fixes for instance of
StructureModels
for Mae
.
[0.1.2.2] - 2019-11-27
Added
- Instance of
StructureModels
for Mae
.
Fixed
[0.1.2.1] - 2019-11-25
Added
[0.1.2.0] - 2019-09-03
Added
- Parser for
FASTA
.
- Writer for
FASTA
.
[0.1.1.1] - 2019-06-05
Changed
length
on Sequence
now works in O(1).
[0.1.1.0] - 2019-05-13
Added
- New version of module Bio.Sequence hat introduces
IsSequence
type class and Sequence
datatype.
- Type
GenBankSequence
describing structure of .gb file.
- Parser for
GenBankSequence
.
- Writer for
GenBankSequence
.
Changed
- ABI cleaner and decoder now work with type
ABIRaw
.
[0.1.0.1] - 2019-02-28
Added
- Field
chemCompType
in Residue
.
Fixed