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#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import biotite.structure.io.pdbx as pdbx
import numpy as np
from Bio.PDB import PDBParser
from biotite.structure import annotate_sse
from biotite.structure.io.pdb import PDBFile
def cacl_secondary_structure(path, binder_chain=None):
"""
Calculate the ratio of secondary structures in a PDB or CIF file.
Args:
path (str): Path to the PDB (.pdb) or CIF (.cif) file.
binder_chain (str, optional): The chain ID to filter the structure.
If provided, only atoms from this chain will be considered. Defaults to None.
Returns:
tuple: The ratio of secondary structures (alpha, beta, loop)
"""
# Check the file extension and read the file accordingly
if path.endswith(".cif"):
pdb_name = pdbx.PDBxFile.read(path)
atom_array = pdbx.get_structure(pdb_name, model=1)
elif path.endswith(".pdb"):
pdb_name = PDBFile.read(path)
atom_array = pdb_name.get_structure()[0]
else:
raise ValueError("File must be either a .pdb or .cif file")
if binder_chain is not None:
chain_mask = atom_array.chain_id == binder_chain
atom_array = atom_array[chain_mask]
sse_array = annotate_sse(atom_array)
count_a = np.sum(sse_array == "a")
count_b = np.sum(sse_array == "b")
count_c = np.sum(sse_array == "c")
total = len(sse_array)
return (
round(count_a / total, 3),
round(count_b / total, 3),
round(count_c / total, 3),
)
def cacl_ref_rg(num_res):
"""
reference radius of gyration value.
Ref: Bindcraft repo (https://github.com/martinpacesa/BindCraft/blob/05702c435e2172a99c2b3faf87487badb6e54727/functions/colabdesign_utils.py#L369)
"""
return 2.38 * num_res**0.365
def get_chain_rg(pdb_file, chain_id, atom_name="CA"):
"""
Calculate the radius of gyration of a specific chain in a PDB file.
Args:
pdb_file (str): Path to the PDB file.
chain_id (str): The chain ID to calculate the radius of gyration for.
atom_name (str, optional): The name of the atom to use for calculation. Defaults to "CA".
Returns:
tuple: The radius of gyration and the normalized radius of gyration.
"""
parser = PDBParser(QUIET=True)
structure = parser.get_structure("struct", pdb_file)
coords = []
for model in structure:
for chain in model:
if chain.id == chain_id:
for res in chain:
if atom_name in res:
atom = res[atom_name]
coords.append(atom.coord)
coords = np.array(coords)
if coords.size == 0:
raise ValueError("No atoms found!")
center = coords.mean(axis=0)
num_res = len(coords)
rg = np.sqrt(((coords - center) ** 2).sum(axis=1).mean())
return round(rg, 2), round(rg / cacl_ref_rg(num_res), 4)
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