File size: 2,171 Bytes
48b5986 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | # 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 copy import deepcopy
from biotite.database.rcsb import fetch
from biotite.structure import AtomArray
from language import (
ConstantSequenceSegment,
FixedLengthSequenceSegment,
MaximizePLDDT,
MaximizePTM,
MaximizeSurfaceExposure,
MinimizeCRmsd,
MinimizeDRmsd,
MinimizeSurfaceHydrophobics,
ProgramNode,
SymmetryRing,
get_atomarray_in_residue_range,
pdb_file_to_atomarray,
sequence_from_atomarray,
)
def symmetric_binding_il10(num_binding_sites: int = 3) -> ProgramNode:
binding_site_atoms: AtomArray = pdb_file_to_atomarray(fetch("1y6k", format="pdb"))
binding_site_atoms = get_atomarray_in_residue_range(
binding_site_atoms, start=31, end=40
)
binding_site_sequence: str = sequence_from_atomarray(binding_site_atoms)
leader_amino_acid_sequence = FixedLengthSequenceSegment(45)
binding_site_sequence = ConstantSequenceSegment(binding_site_sequence)
follower_amino_acid_sequence = FixedLengthSequenceSegment(45)
def _binder_protomer_program() -> ProgramNode:
return ProgramNode(
children=[
ProgramNode(sequence_segment=leader_amino_acid_sequence),
ProgramNode(
sequence_segment=binding_site_sequence,
energy_function_terms=[
MaximizeSurfaceExposure(),
MinimizeCRmsd(template=binding_site_atoms),
MinimizeDRmsd(template=binding_site_atoms),
],
energy_function_weights=[1.0, 10.0, 10.0],
),
ProgramNode(sequence_segment=follower_amino_acid_sequence),
]
)
return ProgramNode(
energy_function_terms=[
MaximizePTM(),
MaximizePLDDT(),
SymmetryRing(),
MinimizeSurfaceHydrophobics(),
],
children=[_binder_protomer_program() for _ in range(num_binding_sites)],
)
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