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Code2MCP-esm / esm /source /examples /protein-programming-language /language /utilities.py

kabudadada

Add esm folder and minimal app

e76b79a about 1 year ago

631 Bytes

# Copyright (c) Meta Platforms, Inc. and affiliates.

# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.

from io import StringIO
from typing import Union

import numpy as np
from biotite.structure import AtomArray
from biotite.structure.io.pdb import PDBFile


def pdb_file_to_atomarray(pdb_path: Union[str, StringIO]) -> AtomArray:
    return PDBFile.read(pdb_path).get_structure(model=1)


def get_atomarray_in_residue_range(atoms: AtomArray, start: int, end: int) -> AtomArray:
    return atoms[np.logical_and(atoms.res_id >= start, atoms.res_id < end)]

	# Copyright (c) Meta Platforms, Inc. and affiliates.

	# This source code is licensed under the MIT license found in the
	# LICENSE file in the root directory of this source tree.

	from io import StringIO
	from typing import Union

	import numpy as np
	from biotite.structure import AtomArray
	from biotite.structure.io.pdb import PDBFile


	def pdb_file_to_atomarray(pdb_path: Union[str, StringIO]) -> AtomArray:
	return PDBFile.read(pdb_path).get_structure(model=1)


	def get_atomarray_in_residue_range(atoms: AtomArray, start: int, end: int) -> AtomArray:
	return atoms[np.logical_and(atoms.res_id >= start, atoms.res_id < end)]