Protein Methods (#86)

* begin consolidating the structural features for a protein * update the core to use ndarray * src and Cargo * slim utilities * move to NDarray * update tests
ferritin-bio · Dec 27, 2024 · a07b0b0 · a07b0b0
1 parent 00059e9
commit a07b0b0
Show file tree

Hide file tree

Showing 8 changed files with 730 additions and 269 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/ferritin-core/Cargo.toml b/ferritin-core/Cargo.toml
@@ -9,7 +9,9 @@ description.workspace = true
 [dependencies]
 pdbtbx.workspace = true
 itertools.workspace = true
+ndarray = { version = "0.16" }
 lazy_static = "1.5.0"
+strum = { version = "0.25", features = ["derive"] }
 
 [dev-dependencies]
 ferritin-test-data = { path = "../ferritin-test-data" }
diff --git a/ferritin-core/examples/ccd.rs b/ferritin-core/examples/ccd.rs
diff --git a/ferritin-core/src/featurize/mod.rs b/ferritin-core/src/featurize/mod.rs
@@ -0,0 +1,12 @@
+//! Protein Featurizer for ProteinMPNN/LignadMPNN
+//!
+//! Extract protein features for ligandmpnn
+//!
+//! Returns a set of features calculated from protein structure
+//! including:
+//! - Residue-level features like amino acid type, secondary structure
+//! - Geometric features like distances, angles
+//! - Chemical features like hydrophobicity, charge
+//! - Evolutionary features from MSA profiles
+mod ndarray_impl;
+mod utilities;