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WIP: Add .bcif support #71

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WIP: Add .bcif support #71

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cf71a8f
initial working BCIF decoding
BradyAJohnston May 7, 2025
8bdb53f
turn into `read()` function
BradyAJohnston May 7, 2025
a7defb2
cleanup
BradyAJohnston May 7, 2025
7367a76
cleanup
BradyAJohnston May 7, 2025
c0911d7
run JuliaFormatter
BradyAJohnston May 7, 2025
0886b58
cleanup and multithread column decoding
BradyAJohnston May 7, 2025
c427d66
Return as MolecularStructure
BradyAJohnston May 8, 2025
070fd36
entire datablock to dict
BradyAJohnston May 8, 2025
c1ee984
cleanup
BradyAJohnston May 9, 2025
9fb8b7b
cleanup
BradyAJohnston May 9, 2025
88d6940
add download and cleanup
BradyAJohnston May 9, 2025
6ffcbfc
Merge branch 'master' into bcif
BradyAJohnston May 13, 2025
4f191cc
Revert "add download and cleanup"
BradyAJohnston May 13, 2025
137186b
BCIF support for downloading
BradyAJohnston May 13, 2025
1bdf0fc
format
BradyAJohnston May 13, 2025
b168125
fix downloading
BradyAJohnston May 13, 2025
f91a94a
parsing working again
BradyAJohnston May 13, 2025
cd08209
fix parsing of multi-model files
BradyAJohnston May 14, 2025
df0a03d
initial test comparison
BradyAJohnston May 14, 2025
5421031
remove extra type lookups and conversions
BradyAJohnston May 14, 2025
8270f08
incorporate most feedback
BradyAJohnston May 15, 2025
244a6a0
Update src/bcif.jl
BradyAJohnston May 15, 2025
622f4b7
remove 1BNA
BradyAJohnston May 15, 2025
512bb8b
Merge branch 'bcif' of github.com:BradyAJohnston/BioStructures.jl int…
BradyAJohnston May 15, 2025
080ad27
make structs immutable
BradyAJohnston May 15, 2025
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2 changes: 2 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
Format = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
MsgPack = "99f44e22-a591-53d1-9472-aa23ef4bd671"
PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Expand Down Expand Up @@ -47,6 +48,7 @@ Graphs = "1"
LinearAlgebra = "1.9"
MMTF = "1"
MetaGraphs = "0.7, 0.8"
MsgPack = "1.2.1"
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Would be good to know how much time this adds to using BioStructures. I expect not a lot, but it can be put in an extension if it is significant.

PrecompileTools = "1"
RecipesBase = "1"
STRIDE_jll = "1"
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1 change: 1 addition & 0 deletions src/BioStructures.jl
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Expand Up @@ -24,6 +24,7 @@ include("model.jl")
include("select.jl")
include("pdb.jl")
include("mmcif.jl")
include("bcif.jl")
include("download.jl")
include("spatial.jl")
include("bonding.jl")
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