mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-11-14 22:33:58 +00:00
41 lines
1.3 KiB
Python
41 lines
1.3 KiB
Python
import torch
|
|
|
|
from rf2aa.data.data_loader import RawInputData
|
|
from rf2aa.data.data_loader_utils import blank_template
|
|
from rf2aa.data.parsers import parse_mol
|
|
from rf2aa.kinematics import get_chirals
|
|
from rf2aa.util import get_bond_feats, get_nxgraph, get_atom_frames
|
|
|
|
|
|
def load_small_molecule(input_file, input_type, model_runner):
|
|
if input_type == "smiles":
|
|
is_string = True
|
|
else:
|
|
is_string = False
|
|
|
|
obmol, msa, ins, xyz, mask = parse_mol(
|
|
input_file, filetype=input_type, string=is_string, generate_conformer=True
|
|
)
|
|
return compute_features_from_obmol(obmol, msa, xyz, model_runner)
|
|
|
|
def compute_features_from_obmol(obmol, msa, xyz, model_runner):
|
|
L = msa.shape[0]
|
|
ins = torch.zeros_like(msa)
|
|
bond_feats = get_bond_feats(obmol)
|
|
|
|
xyz_t, t1d, mask_t, _ = blank_template(
|
|
model_runner.config.loader_params.n_templ,
|
|
L,
|
|
deterministic=model_runner.deterministic,
|
|
)
|
|
chirals = get_chirals(obmol, xyz[0])
|
|
G = get_nxgraph(obmol)
|
|
atom_frames = get_atom_frames(msa, G)
|
|
msa, ins = msa[None], ins[None]
|
|
return RawInputData(
|
|
msa, ins, bond_feats, xyz_t, mask_t, t1d, chirals, atom_frames, taxids=None
|
|
)
|
|
|
|
def remove_leaving_atoms(input, is_leaving):
|
|
keep = ~is_leaving
|
|
return input.keep_features(keep)
|