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| import biotite.structure.io.pdbx as pdbx
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| import numpy as np
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| from Bio.PDB import PDBParser
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| from biotite.structure import annotate_sse
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| from biotite.structure.io.pdb import PDBFile
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| def cacl_secondary_structure(path, binder_chain=None):
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| """
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| Calculate the ratio of secondary structures in a PDB or CIF file.
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| Args:
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| path (str): Path to the PDB (.pdb) or CIF (.cif) file.
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| binder_chain (str, optional): The chain ID to filter the structure.
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| If provided, only atoms from this chain will be considered. Defaults to None.
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| Returns:
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| tuple: The ratio of secondary structures (alpha, beta, loop)
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| """
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| if path.endswith(".cif"):
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| pdb_name = pdbx.PDBxFile.read(path)
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| atom_array = pdbx.get_structure(pdb_name, model=1)
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| elif path.endswith(".pdb"):
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| pdb_name = PDBFile.read(path)
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| atom_array = pdb_name.get_structure()[0]
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| else:
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| raise ValueError("File must be either a .pdb or .cif file")
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| if binder_chain is not None:
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| chain_mask = atom_array.chain_id == binder_chain
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| atom_array = atom_array[chain_mask]
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| sse_array = annotate_sse(atom_array)
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| count_a = np.sum(sse_array == "a")
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| count_b = np.sum(sse_array == "b")
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| count_c = np.sum(sse_array == "c")
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| total = len(sse_array)
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| return (
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| round(count_a / total, 3),
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| round(count_b / total, 3),
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| round(count_c / total, 3),
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| )
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| def cacl_ref_rg(num_res):
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| """
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| reference radius of gyration value.
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| Ref: Bindcraft repo (https://github.com/martinpacesa/BindCraft/blob/05702c435e2172a99c2b3faf87487badb6e54727/functions/colabdesign_utils.py#L369)
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| """
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| return 2.38 * num_res**0.365
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| def get_chain_rg(pdb_file, chain_id, atom_name="CA"):
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| """
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| Calculate the radius of gyration of a specific chain in a PDB file.
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| Args:
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| pdb_file (str): Path to the PDB file.
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| chain_id (str): The chain ID to calculate the radius of gyration for.
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| atom_name (str, optional): The name of the atom to use for calculation. Defaults to "CA".
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| Returns:
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| tuple: The radius of gyration and the normalized radius of gyration.
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| """
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| parser = PDBParser(QUIET=True)
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| structure = parser.get_structure("struct", pdb_file)
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| coords = []
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| for model in structure:
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| for chain in model:
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| if chain.id == chain_id:
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| for res in chain:
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| if atom_name in res:
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| atom = res[atom_name]
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| coords.append(atom.coord)
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| coords = np.array(coords)
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| if coords.size == 0:
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| raise ValueError("No atoms found!")
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| center = coords.mean(axis=0)
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| num_res = len(coords)
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| rg = np.sqrt(((coords - center) ** 2).sum(axis=1).mean())
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| return round(rg, 2), round(rg / cacl_ref_rg(num_res), 4)
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|
