Merge pull request #18 from padix-key/performance

Use new PyO3 API to improve performance
biotite-dev · Aug 26, 2024 · bfd4283 · bfd4283
2 parents 68d6053 + 089a8c2
commit bfd4283
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diff --git a/Cargo.toml b/Cargo.toml
@@ -4,11 +4,11 @@ version = "1.3.1"
 edition = "2018"
 
 [dependencies]
-numpy = "0.20"
-ndarray = "0.15"
+numpy = "0.21"
+ndarray = "0.16"
 
 [dependencies.pyo3]
-version = "0.20"
+version = "0.21"
 features = ["extension-module"]
 
 [lib]

diff --git a/benchmark.py b/benchmark.py
@@ -5,8 +5,8 @@
 import matplotlib.ticker as ticker
 import numpy as np
 import biotite.database.rcsb as rcsb
-import biotite.structure.info as info
 import biotite.structure.io.pdb as pdb
+from biotite.structure.info.ccd import get_ccd
 import fastpdb
 
 
@@ -17,7 +17,7 @@
 
 # Call this function before the benchmark
 # to avoid a bias due to the initial loading time
-info.bond_dataset()
+get_ccd()
 
 
 pdb_file_path = rcsb.fetch(PDB_ID, "pdb", tempfile.gettempdir())