Trait StructureFeatures

pub trait StructureFeatures {
    // Required methods
    fn decode_amino_acids(&self, device: &Device) -> Result<Tensor>;
    fn encode_amino_acids(&self, device: &Device) -> Result<Tensor>;
    fn create_cb(&self, device: &Device) -> Result<Tensor>;
    fn featurize_lmpnn(&self, device: &Device) -> Result<ProteinFeatures>;
    fn get_res_index(&self) -> Vec<u32>;
    fn to_numeric_backbone_atoms(&self, device: &Device) -> Result<Tensor>;
    fn to_numeric_atom37(&self, device: &Device) -> Result<Tensor>;
    fn to_numeric_ligand_atoms(
        &self,
        device: &Device,
    ) -> Result<(Tensor, Tensor, Tensor)>;
}

. Trait defining Protein->Tensor utilities useful for Machine Learning

Required Methods

fn decode_amino_acids(&self, device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn encode_amino_acids(&self, device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn create_cb(&self, device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn featurize_lmpnn(&self, device: &Device) -> Result<ProteinFeatures>

Prepare for ProteinMPNN

fn get_res_index(&self) -> Vec<u32>

Get residue indices

fn to_numeric_backbone_atoms(&self, device: &Device) -> Result<Tensor>

Extract backbone atom coordinates (N, CA, C, O)

fn to_numeric_atom37(&self, device: &Device) -> Result<Tensor>

Extract all atom coordinates in standard ordering

fn to_numeric_ligand_atoms( &self, device: &Device, ) -> Result<(Tensor, Tensor, Tensor)>

Extract ligand atom coordinates and properties

Implementations on Foreign Types

impl StructureFeatures for AtomCollection

fn decode_amino_acids(&self, _device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn encode_amino_acids(&self, device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn create_cb(&self, device: &Device) -> Result<Tensor>

Calculate CB for each residue

fn get_res_index(&self) -> Vec<u32>

Get residue indices

fn to_numeric_backbone_atoms(&self, device: &Device) -> Result<Tensor>

create numeric Tensor of shape [1, , 4, 3] where the 4 is N/CA/C/O

fn to_numeric_atom37(&self, device: &Device) -> Result<Tensor>

create numeric Tensor of shape [1, , 37, 3]

fn featurize_lmpnn(&self, device: &Device) -> Result<ProteinFeatures>

fn to_numeric_ligand_atoms( &self, device: &Device, ) -> Result<(Tensor, Tensor, Tensor)>

Implementors