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import gradio as gr
from utils.foldseek_util import get_struc_seq
####################################################
# gradio blocks #
####################################################
def upload_pdb_button(visible: bool = True, chain_visible: bool = True):
"""
Provide an upload button to upload a pdb file
Args:
visible: Whether the block is visible or not
"""
with gr.Column(scale=0):
# Which chain to be extracted
chain_box = gr.Textbox(label="Chain (to be extracted from the pdb file)", value="A",
visible=chain_visible, interactive=True)
upload_btn = gr.UploadButton(label="Upload .pdb/.cif file", visible=visible)
return upload_btn, chain_box
####################################################
# Trigger functions #
####################################################
def parse_pdb_file(input_type: str, file: str, chain: str) -> str:
"""
Parse the uploaded structure file
Args:
input_type: Type of input. Must be one of ["protein sequence", "protein structure"]
file: Path to the uploaded file
chain: Chain to be extracted from the pdb file
Returns:
Protein sequence or Foldseek sequence
"""
try:
parsed_seqs = get_struc_seq("/tmp/foldseek", file, [chain])[chain]
if input_type == "sequence":
return parsed_seqs[0]
else:
return parsed_seqs[1].lower()
except Exception:
raise gr.Error(f"Chain '{chain}' not found in the pdb file. Please check the chain id and try again.")
def set_upload_visible(visible: bool) -> gr.Interface:
"""
Set the visibility of the upload button
Args:
visible: Whether the block is visible or not
Returns:
gr.Interface: Updated interface
"""
return gr.update(visible=visible)
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