Pymol Refactor (#75)

* refactoring pymol conversion to its own crate

* optimize imports

ferritin-amplify/src/amplify/amplify.rs

@@ -11,8 +11,8 @@
 //!
 use super::config::AMPLIFYConfig;
 use super::encoder::EncoderBlock;
-use super::rotary::precompute_freqs_cis;
 use super::outputs::ModelOutput;
+use super::rotary::precompute_freqs_cis;
 use candle_core::{Device, Module, Result, Tensor, D};
 use candle_nn::{embedding, linear, rms_norm, Embedding, Linear, RmsNorm, VarBuilder};
 use tokenizers::Tokenizer;

ferritin-amplify/src/amplify/encoder.rs

@@ -2,7 +2,7 @@ use super::config::AMPLIFYConfig;
 use super::rotary::apply_rotary_emb;
 use candle_core::{Module, Result, Tensor, D};
 use candle_nn::{
-    linear, linear_no_bias, ops::softmax_last_dim, rms_norm, Dropout, Linear, RmsNorm, VarBuilder,
+    linear_no_bias, ops::softmax_last_dim, rms_norm, Dropout, Linear, RmsNorm, VarBuilder,
 };
 
 /// An encoder block in the AMPLIFY transformer architecture.

ferritin-core/Cargo.toml

@@ -7,7 +7,6 @@ license.workspace = true
 description.workspace = true
 
 [dependencies]
-ferritin-pymol = { path = "../ferritin-pymol", optional = true }
 pdbtbx.workspace = true
 itertools.workspace = true
 lazy_static = "1.5.0"

ferritin-core/src/conversions/mod.rs

@@ -1,2 +1 @@
 mod pdb;
-mod pse;

ferritin-pymol/Cargo.toml

@@ -7,6 +7,7 @@ license.workspace = true
 description.workspace = true
 
 [dependencies]
+ferritin-core = { path = "../ferritin-core" }
 ferritin-molviewspec = { path = "../ferritin-molviewspec" }
 clap = { version = "4.5.23", features = ["derive"] }
 serde-pickle = "1.2"

ferritin-core/src/conversions/pse.rs → ferritin-pymol/src/conversions/atomcollection.rs

@@ -1,5 +1,5 @@
-use crate::{AtomCollection, Bond, BondOrder};
-use ferritin_pymol::PSEData;
+use ferritin_core::{AtomCollection, Bond, BondOrder};
+use crate::{PSEData,pymolparsing};
 use itertools::Itertools;
 use pdbtbx::Element;
 
@@ -8,11 +8,11 @@ impl From<&PSEData> for AtomCollection {
         let mols = pse_data.get_molecule_data();
 
         // Pymol: most of the descriptive data is there
-        let atoms: Vec<&ferritin_pymol::pymolparsing::parsing::AtomInfo> =
+        let atoms: Vec<&pymolparsing::parsing::AtomInfo> =
             mols.iter().flat_map(|mol| mol.atom.iter()).collect();
 
         // Pymol: coord sets are maintained seperately.
-        let coord_sets: Vec<&ferritin_pymol::pymolparsing::parsing::CoordSet> =
+        let coord_sets: Vec<&pymolparsing::parsing::CoordSet> =
             mols.iter().flat_map(|mol| mol.coord_set.iter()).collect();
 
         let coords: Vec<[f32; 3]> = coord_sets
@@ -21,7 +21,7 @@ impl From<&PSEData> for AtomCollection {
             .collect();
 
         // Pymol: most of the descriptive data is there
-        let pymol_bonds: Vec<&ferritin_pymol::pymolparsing::parsing::Bond> =
+        let pymol_bonds: Vec<&pymolparsing::parsing::Bond> =
             mols.iter().flat_map(|mol| mol.bond.iter()).collect();
 
         let bonds = pymol_bonds
@@ -67,8 +67,8 @@ impl From<&PSEData> for AtomCollection {
 
 #[cfg(test)]
 mod tests {
-    use crate::AtomCollection;
-    use ferritin_pymol::PSEData;
+    use ferritin_core::AtomCollection;
+    use crate::PSEData;
     use ferritin_test_data::TestFile;
 
     #[test]

ferritin-pymol/src/conversions/mod.rs

@@ -0,0 +1 @@
+pub mod atomcollection;

ferritin-pymol/src/lib.rs

@@ -18,5 +18,6 @@
 //! ```
 //!
 pub mod pymolparsing;
+pub mod conversions;
 pub use self::pymolparsing::parsing::PyObjectMolecule;
 pub use self::pymolparsing::psedata::PSEData;