File size: 2,206 Bytes
5631464 | 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 66 67 68 69 70 71 72 73 74 75 76 77 | """Molecular data structures."""
from functools import partial
from pathlib import Path
from typing import Any, Iterable, Optional
from haddock.libs.libontology import PDBFile
class Molecule:
"""
Input molecule, usually a PDB file.
Parameters
----------
file_name : :external:py:class:`pathlib.Path`
The path to the molecule file.
segid : int, optional
The ID of the segment. Defaults to ``None``.
no_parent : boolean
Whether to add the parent path ``..`` to the
:py:attr:`haddock.libs.libstructure.Molecule.with_parent`.
When set to true, the ``with_parent`` attribute returns the same
as ``file_name``.
"""
def __init__(
self, file_name: Path, segid: Optional[int] = None, no_parent: bool = False
) -> None:
# the rest of the code is too dependent on the Path API
assert isinstance(file_name, Path), (
f"`file_name` must be pathlib.Path: {type(file_name)} given"
)
self.file_name = file_name
self.segid = segid
if no_parent:
self.with_parent = file_name
else:
self.with_parent = Path("..", file_name)
def make_molecules(paths: Iterable[Path], **kwargs: Any) -> list[Molecule]:
"""Get input molecules from the data stream."""
return list(map(partial(Molecule, **kwargs), paths))
def find_ff(models: list[PDBFile]) -> str:
"""Finds the force-field information (all-atom or martini) from the topology
associated to the first model. Used in caprieval and caprifilter.
The assumption is that the force-fields will be identical between models.
Parameters
-----------
models : list[PDBFile]
List of models where to find the topology
Return
-------
ff : str
The force-field used in those models.
"""
try:
ff = Path(models[0].topology[0].rel_path).stem.split("_")[-1]
except TypeError:
try:
ff = Path(models[0].topology.rel_path).stem.split("_")[-1]
except AttributeError:
ff = "aa"
# In case of issue, fall back to all-atom
if "martini" not in ff:
ff = "aa"
return ff
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