Also support mmCIF with getchain (#27)

HolyLab · Aug 28, 2024 · 4efd19d · 4efd19d
1 parent 3ec1b69
commit 4efd19d
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "GPCRAnalysis"
 uuid = "c1d73f9e-d42a-418a-8d5b-c7b00ec0358f"
 authors = ["Tim Holy <[email protected]> and contributors"]
-version = "0.5.0"
+version = "0.5.1"
 
 [deps]
 BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"

diff --git a/src/utils.jl b/src/utils.jl
@@ -40,9 +40,12 @@ end
 """
     getchain(filename::AbstractString; model=1, chain="A")
 
-Read a PDB file `filename` and extract the specified chain.
+Read a PDB or mmCIF file `filename` and extract the specified chain.
 """
-getchain(filename::AbstractString; model=1, chain="A") = read(filename, PDBFormat)[model][chain]
+getchain(filename::AbstractString; model=1, chain="A") =
+    endswith(filename, ".pdb") ? read(filename, PDBFormat)[model][chain] :
+    endswith(filename, ".cif") ? read(filename, MMCIFFormat)[model][chain] :
+    throw(ArgumentError("Unknown file format"))
 
 function validate_seq_residues(seq::AnnotatedAlignedSequence, chain)
     for (i, r) in zip(getsequencemapping(seq), seq)