Split ferritin-featurizes into amplify and ligandmpnn (#65)

* refactored Amplify and Ligandmpnn

* fix imports and tests

Cargo.toml

@@ -3,7 +3,8 @@ members = [
     "ferritin-bevy",
     "ferritin-cellscape",
     "ferritin-core",
-    "ferritin-featurizers",
+    "ferritin-amplify",
+    "ferritin-ligandmpnn",
     "ferritin-molviewspec",
     "ferritin-pymol",
     "ferritin-test-data",

docs/index.qmd

@@ -39,6 +39,10 @@ Native Rust access to pymol `pse` binary files.  [rust-docs](https://zachcp.gith
 
 Utilities for consuming and creating [molviewspec files](https://molstar.org/mol-view-spec/).  [rust-docs](https://zachcp.github.io/ferritin/doc/ferritin_molviewspec/index.html). [source](https://github.com/zachcp/ferritin/tree/main/ferritin-molviewspec).
 
-### Ferritin-Featurizer
+### Ferritin-Amplify
 
-Utilities for converting proteins into tensors. [rust-docs](https://zachcp.github.io/ferritin/doc/ferritin_featurizers/index.html). [source](https://github.com/zachcp/ferritin/tree/main/ferritin-featurizers).
+Inference using amplify. [rust-docs](https://zachcp.github.io/ferritin/doc/ferritin_amplify/index.html). [source](https://github.com/zachcp/ferritin/tree/main/ferritin-amplify).
+
+### Ferritin-LigandMPNN
+
+Inference using proteinmpnn/ligandmpnn. [rust-docs](https://zachcp.github.io/ferritin/doc/ferritin_ligandmpnn/index.html). [source](https://github.com/zachcp/ferritin/tree/main/ferritin-ligandmpnn).

ferritin-amplify/Cargo.toml

@@ -0,0 +1,33 @@
+[package]
+name = "ferritin-amplify"
+version.workspace = true
+edition.workspace = true
+authors.workspace = true
+license.workspace = true
+description.workspace = true
+
+[features]
+metal = ["candle-core/metal", "candle-nn/metal", "candle-metal-kernels"]
+
+[dependencies]
+anyhow.workspace = true
+candle-core = { git = "https://github.com/huggingface/candle.git", package = "candle-core", features = [
+] }
+candle-hf-hub = "0.3.3"
+candle-nn = { git = "https://github.com/huggingface/candle.git", package = "candle-nn" }
+ferritin-test-data = { path = "../ferritin-test-data" }
+rand = "0.8.5"
+safetensors = "0.4.5"
+tokenizers = "0.21.0"
+
+[target.'cfg(target_os = "macos")'.features]
+metal = []
+
+[target.'cfg(target_os = "macos")'.dependencies]
+candle-metal-kernels = { git = "https://github.com/huggingface/candle.git", package = "candle-metal-kernels", optional = true }
+
+[dev-dependencies]
+candle-examples = { git = "https://github.com/huggingface/candle.git", package = "candle-examples" }
+ferritin-test-data = { path = "../ferritin-test-data" }
+assert_cmd = "2.0.16"
+tempfile = "3.14.0"

ferritin-amplify/Readme.md

@@ -0,0 +1,8 @@
+# ferritin-amplify
+
+- use the AMPLIFY_120M model from Candle
+
+
+```shell
+just amplify
+```

ferritin-featurizers/examples/amplify/Readme.md → ferritin-amplify/examples/amplify/Readme.md

@@ -6,7 +6,7 @@
 
 ```sh
 RUST_BACKTRACE=1 cargo run --example amplify
-cargo test -p ferritin-featurizers test_amplify_round_trip -- --nocapture
+cargo test -p ferritin-amplify test_amplify_round_trip -- --nocapture
 ```
 
 ## Model Tensors

ferritin-featurizers/examples/amplify/main.rs → ferritin-amplify/examples/amplify/main.rs

@@ -2,7 +2,7 @@ use anyhow::Result;
 use candle_core::{DType, Device, D};
 use candle_hf_hub::{api::sync::Api, Repo, RepoType};
 use candle_nn::VarBuilder;
-use ferritin_featurizers::{AMPLIFYConfig, ProteinTokenizer, AMPLIFY};
+use ferritin_amplify::{AMPLIFYConfig, ProteinTokenizer, AMPLIFY};
 use safetensors::SafeTensors;
 
 fn main() -> Result<()> {

ferritin-amplify/src/lib.rs

@@ -0,0 +1,8 @@
+//! ferritin-amplify
+//! - [amplify model](https://github.com/chandar-lab/AMPLIFY)
+//! - [amplify hf - 120M](https://huggingface.co/chandar-lab/AMPLIFY_120M)
+//!
+
+mod amplify;
+pub use amplify::amplify::{AMPLIFYConfig, ModelOutput, AMPLIFY};
+pub use amplify::tokenizer::ProteinTokenizer;

ferritin-featurizers/tests/test_amplify_model.rs → ferritin-amplify/tests/test_amplify_model.rs

@@ -1,7 +1,7 @@
 use anyhow::Result;
 use candle_core::utils::{cuda_is_available, metal_is_available};
 use candle_core::{Device, D};
-use ferritin_featurizers::AMPLIFY;
+use ferritin_amplify::AMPLIFY;
 
 pub fn device(cpu: bool) -> Result<Device> {
     if cpu {

ferritin-featurizers/tests/test_amplify_vocab.rs → ferritin-amplify/tests/test_amplify_vocab.rs

@@ -1,5 +1,5 @@
 use candle_hf_hub::{api::sync::Api, Repo, RepoType};
-use ferritin_featurizers::ProteinTokenizer;
+use ferritin_amplify::ProteinTokenizer;
 
 #[test]
 #[ignore]

ferritin-cellscape/Cargo.toml

@@ -9,5 +9,5 @@ description.workspace = true
 [dependencies]
 ferritin-core = { path = "../ferritin-core" }
 pdbtbx = { workspace = true }
-geo = "0.29.2"
+geo = "0.29.3"
 svg = "0.18.0"