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