flatten the ligandmpnn flder (#85)

ferritin-plms/src/amplify/amplify.rs

@@ -133,4 +133,4 @@ impl AMPLIFY {
         Tokenizer::from_bytes(tokenizer_bytes)
             .map_err(|e| candle_core::Error::Msg(format!("Failed to load tokenizer: {}", e)))
     }
-}
+}

ferritin-plms/src/amplify/mod.rs

@@ -12,4 +12,4 @@ pub mod encoder;
 pub mod outputs;
 pub mod rotary;
 // pub mod loss;
-//
+//

ferritin-plms/src/lib.rs

@@ -18,11 +18,12 @@ pub use amplify::config::AMPLIFYConfig;
 pub use amplify::outputs::ModelOutput;
 pub use esm::models::esmc::{ESMCConfig, ESMC};
 pub use esm2::models::esm2::{ESM2Config, ESM2};
-pub use ligandmpnn::ligandmpnn::configs::ProteinMPNNConfig;
-pub use ligandmpnn::ligandmpnn::model::ProteinMPNN;
-pub use ligandmpnn::ligandmpnn::proteinfeatures::LMPNNFeatures;
+pub use ligandmpnn::configs::ProteinMPNNConfig;
+pub use ligandmpnn::model::ProteinMPNN;
+pub use ligandmpnn::proteinfeatures::LMPNNFeatures;
 
-pub mod amplify;
+//pub mod amplify;
 pub mod esm;
 pub mod esm2;
 pub mod ligandmpnn;
+mod amplify;

ferritin-plms/src/ligandmpnn/Readme.md

@@ -2,3 +2,25 @@
 
 The initial development sought to create a CLI-equivalent for LigandmMPNN. As of Dec 16 2024, I am no longer pursuing that effort. I'm leavin ghte code here
 as an artifact in case it becomes interesting again.
+
+
+# LigandMPNN-Rust
+
+Rust port of Ligand MPNN.
+
+
+```sh
+bash get_model_params.sh "./model_params"
+python scripts/convert_to_safetensor.py
+python scripts/convert_to_json.py
+#cargo install json_to_rust
+#json_to_rust data/pdb_data.json > src/proteintypes.rs
+#cat data/pdb_data.json| json_to_rust -j json_object -n MyStruct > out.rs
+npm install -g quicktype
+quicktype data/pdb_data.json -o output.rs -l rust
+```
+
+## Resources
+
+- [Candle](https://github.com/huggingface/candle)
+- [Candle Tutorial](https://github.com/ToluClassics/candle-tutorial)

ferritin-plms/src/ligandmpnn/cli.rs → ferritin-plms/src/ligandmpnn/commands/cli.rs

@@ -2,8 +2,8 @@
 //!
 //! ** work in progress **
 //!
-use super::commands;
-use super::ligandmpnn::configs::{
+use crate::ligandmpnn::commands;
+use crate::ligandmpnn::configs::{
     AABiasConfig, LigandMPNNConfig, MembraneMPNNConfig, ModelTypes, MultiPDBConfig, ResidueControl,
     RunConfig,
 };

ferritin-plms/src/ligandmpnn/commands/featurize.rs

@@ -1,4 +1,4 @@
-use crate::ligandmpnn::ligandmpnn::proteinfeatures::LMPNNFeatures;
+use crate::ligandmpnn::proteinfeatures::LMPNNFeatures;
 use candle_core;
 use ferritin_core::AtomCollection;
 use pdbtbx;

ferritin-plms/src/ligandmpnn/commands/mod.rs

@@ -1,2 +1,3 @@
 pub mod featurize;
 pub mod run;
+mod cli;

ferritin-plms/src/ligandmpnn/commands/run.rs

@@ -1,4 +1,5 @@
-use crate::ligandmpnn::ligandmpnn::configs::{
+
+use crate::ligandmpnn::configs::{
     AABiasConfig, LigandMPNNConfig, MPNNExecConfig, MembraneMPNNConfig, ModelTypes, MultiPDBConfig,
     ResidueControl, RunConfig,
 };

ferritin-plms/src/ligandmpnn/mod.rs

@@ -3,10 +3,14 @@
 //! - utilities to convert sequence formats (PDB; mmcif) to ML-ready tensors.
 //! - CLI to handle the above.
 //!
-mod cli;
 mod commands;
-pub mod ligandmpnn;
 
-pub use ligandmpnn::proteinfeatures::LMPNNFeatures;
-pub use ligandmpnn::model::ProteinMPNN;
-pub use ligandmpnn::configs::ProteinMPNNConfig;
+pub mod configs;
+pub mod proteinfeatures;
+pub mod model;
+mod proteinfeaturesmodel;
+mod utilities;
+
+pub use proteinfeatures::LMPNNFeatures;
+pub use model::ProteinMPNN;
+pub use configs::ProteinMPNNConfig;

ferritin-plms/src/ligandmpnn/ligandmpnn/utilities.rs → ferritin-plms/src/ligandmpnn/utilities.rs

@@ -546,7 +546,7 @@ define_residues! {
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::ligandmpnn::ligandmpnn::proteinfeatures::LMPNNFeatures;
+    use crate::ligandmpnn::proteinfeatures::LMPNNFeatures;
     use ferritin_core::AtomCollection;
     use ferritin_test_data::TestFile;
     use pdbtbx;