From 00059e9a048ff05e8edbcd8a3387c30550bc8c19 Mon Sep 17 00:00:00 2001
From: zachcp <zachcp@users.noreply.github.com>
Date: Fri, 20 Dec 2024 13:59:57 -0500
Subject: [PATCH] flatten the ligandmpnn flder (#85)

---
 ferritin-plms/src/amplify/amplify.rs          |  2 +-
 ferritin-plms/src/amplify/mod.rs              |  2 +-
 ferritin-plms/src/lib.rs                      |  9 ++++----
 ferritin-plms/src/ligandmpnn/Readme.md        | 22 +++++++++++++++++++
 .../src/ligandmpnn/{ => commands}/cli.rs      |  4 ++--
 .../src/ligandmpnn/commands/featurize.rs      |  2 +-
 ferritin-plms/src/ligandmpnn/commands/mod.rs  |  1 +
 ferritin-plms/src/ligandmpnn/commands/run.rs  |  3 ++-
 .../ligandmpnn/{ligandmpnn => }/configs.rs    |  0
 .../src/ligandmpnn/ligandmpnn/Readme.md       | 20 -----------------
 .../src/ligandmpnn/ligandmpnn/mod.rs          |  5 -----
 ferritin-plms/src/ligandmpnn/mod.rs           | 14 +++++++-----
 .../src/ligandmpnn/{ligandmpnn => }/model.rs  |  0
 .../{ligandmpnn => }/proteinfeatures.rs       |  0
 .../{ligandmpnn => }/proteinfeaturesmodel.rs  |  0
 .../ligandmpnn/{ligandmpnn => }/utilities.rs  |  2 +-
 16 files changed, 45 insertions(+), 41 deletions(-)
 rename ferritin-plms/src/ligandmpnn/{ => commands}/cli.rs (98%)
 rename ferritin-plms/src/ligandmpnn/{ligandmpnn => }/configs.rs (100%)
 delete mode 100644 ferritin-plms/src/ligandmpnn/ligandmpnn/Readme.md
 delete mode 100644 ferritin-plms/src/ligandmpnn/ligandmpnn/mod.rs
 rename ferritin-plms/src/ligandmpnn/{ligandmpnn => }/model.rs (100%)
 rename ferritin-plms/src/ligandmpnn/{ligandmpnn => }/proteinfeatures.rs (100%)
 rename ferritin-plms/src/ligandmpnn/{ligandmpnn => }/proteinfeaturesmodel.rs (100%)
 rename ferritin-plms/src/ligandmpnn/{ligandmpnn => }/utilities.rs (99%)

diff --git a/ferritin-plms/src/amplify/amplify.rs b/ferritin-plms/src/amplify/amplify.rs
index 28d2b611..1c256833 100644
--- a/ferritin-plms/src/amplify/amplify.rs
+++ b/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)))
     }
-}
+}
\ No newline at end of file
diff --git a/ferritin-plms/src/amplify/mod.rs b/ferritin-plms/src/amplify/mod.rs
index b8f12e2a..0eab3b4d 100644
--- a/ferritin-plms/src/amplify/mod.rs
+++ b/ferritin-plms/src/amplify/mod.rs
@@ -12,4 +12,4 @@ pub mod encoder;
 pub mod outputs;
 pub mod rotary;
 // pub mod loss;
-//
+//
\ No newline at end of file
diff --git a/ferritin-plms/src/lib.rs b/ferritin-plms/src/lib.rs
index 2beb8814..db1543a7 100644
--- a/ferritin-plms/src/lib.rs
+++ b/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;
diff --git a/ferritin-plms/src/ligandmpnn/Readme.md b/ferritin-plms/src/ligandmpnn/Readme.md
index 0596c86f..598e4750 100644
--- a/ferritin-plms/src/ligandmpnn/Readme.md
+++ b/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)
diff --git a/ferritin-plms/src/ligandmpnn/cli.rs b/ferritin-plms/src/ligandmpnn/commands/cli.rs
similarity index 98%
rename from ferritin-plms/src/ligandmpnn/cli.rs
rename to ferritin-plms/src/ligandmpnn/commands/cli.rs
index 1b568be6..3660f910 100644
--- a/ferritin-plms/src/ligandmpnn/cli.rs
+++ b/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,
 };
diff --git a/ferritin-plms/src/ligandmpnn/commands/featurize.rs b/ferritin-plms/src/ligandmpnn/commands/featurize.rs
index d4592f7a..dcf1918c 100644
--- a/ferritin-plms/src/ligandmpnn/commands/featurize.rs
+++ b/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;
diff --git a/ferritin-plms/src/ligandmpnn/commands/mod.rs b/ferritin-plms/src/ligandmpnn/commands/mod.rs
index 141b28a7..42aa9096 100644
--- a/ferritin-plms/src/ligandmpnn/commands/mod.rs
+++ b/ferritin-plms/src/ligandmpnn/commands/mod.rs
@@ -1,2 +1,3 @@
 pub mod featurize;
 pub mod run;
+mod cli;
diff --git a/ferritin-plms/src/ligandmpnn/commands/run.rs b/ferritin-plms/src/ligandmpnn/commands/run.rs
index 1c236151..c32c643e 100644
--- a/ferritin-plms/src/ligandmpnn/commands/run.rs
+++ b/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,
 };
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/configs.rs b/ferritin-plms/src/ligandmpnn/configs.rs
similarity index 100%
rename from ferritin-plms/src/ligandmpnn/ligandmpnn/configs.rs
rename to ferritin-plms/src/ligandmpnn/configs.rs
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/Readme.md b/ferritin-plms/src/ligandmpnn/ligandmpnn/Readme.md
deleted file mode 100644
index 62acfad3..00000000
--- a/ferritin-plms/src/ligandmpnn/ligandmpnn/Readme.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# 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)
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/mod.rs b/ferritin-plms/src/ligandmpnn/ligandmpnn/mod.rs
deleted file mode 100644
index 7a978a85..00000000
--- a/ferritin-plms/src/ligandmpnn/ligandmpnn/mod.rs
+++ /dev/null
@@ -1,5 +0,0 @@
-pub mod configs;
-pub mod proteinfeatures;
-pub mod model;
-mod proteinfeaturesmodel;
-mod utilities;
diff --git a/ferritin-plms/src/ligandmpnn/mod.rs b/ferritin-plms/src/ligandmpnn/mod.rs
index 43b65587..ad7e8911 100644
--- a/ferritin-plms/src/ligandmpnn/mod.rs
+++ b/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;
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/model.rs b/ferritin-plms/src/ligandmpnn/model.rs
similarity index 100%
rename from ferritin-plms/src/ligandmpnn/ligandmpnn/model.rs
rename to ferritin-plms/src/ligandmpnn/model.rs
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/proteinfeatures.rs b/ferritin-plms/src/ligandmpnn/proteinfeatures.rs
similarity index 100%
rename from ferritin-plms/src/ligandmpnn/ligandmpnn/proteinfeatures.rs
rename to ferritin-plms/src/ligandmpnn/proteinfeatures.rs
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/proteinfeaturesmodel.rs b/ferritin-plms/src/ligandmpnn/proteinfeaturesmodel.rs
similarity index 100%
rename from ferritin-plms/src/ligandmpnn/ligandmpnn/proteinfeaturesmodel.rs
rename to ferritin-plms/src/ligandmpnn/proteinfeaturesmodel.rs
diff --git a/ferritin-plms/src/ligandmpnn/ligandmpnn/utilities.rs b/ferritin-plms/src/ligandmpnn/utilities.rs
similarity index 99%
rename from ferritin-plms/src/ligandmpnn/ligandmpnn/utilities.rs
rename to ferritin-plms/src/ligandmpnn/utilities.rs
index 29af5575..0909f1d5 100644
--- a/ferritin-plms/src/ligandmpnn/ligandmpnn/utilities.rs
+++ b/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;