Source code for

__all__ = ["get_coords_array", "resolve_path"]

from ..legacy import IO as _IO
from .. import use_new_api as _use_new_api

# Imported to ensure that sire.maths.Vector is properly wrapped
from ..maths import Vector as _Vector  # noqa: F401

# Importing the parser sub-module so that it autocompletes when used
from . import parser  # noqa: F401


[docs] def resolve_path(path, directory=".", auto_unzip=True, silent=False): """ Resolve the passed path into a local path. This will automatically download the files associated with a URL path to local files that are placed into the specified `directory`. This returns the full path to the locally resolved file. Args: path: The full path that needs resolving. If this is a URL then it will be downloaded (either the original URL, of a bzip2 version if the original doesn't exist). If this is a PDB or alphafold code, then the corresponding PDB or alphafold structure will be downloaded. directory: The full path to the directory you want any downloaded files to be downloaded into. auto_unzip: Automatically unzip any compressed files after download (or if they are local). Note that the original zipped file is not removed. silent: Silence any output printed to the screen when resolving the path. Returns: The list of filenames of all the files that are downloaded / resolved """ from .._load import _resolve_path return _resolve_path( path=path, directory=directory, auto_unzip=auto_unzip, silent=silent )
[docs] def get_coords_array(mol, units=None, map=None): """ Return the coordinates of the passed molecule view as a numpy array of shape (natoms,3). Specify the length units to use, and optionally pass in a map to find the coordinates property """ import numpy as np if units is None: from ..units import angstrom units = angstrom from ..base import create_map map = create_map(map) if hasattr(mol, "to_molecule_group"): mol = mol.to_molecule_group() coords = _IO.getCoordsArray(mol, units, map) natoms = int(len(coords) / 3) return np.reshape(np.asarray(coords, dtype=float), (natoms, 3))
def load_molecules(*args, map=None, **kwargs): from ..legacy.IO import load_molecules as _load_molecules from ..system import System from ..base import create_map map = create_map(map) mols = System(_load_molecules(*args, map=map, **kwargs)) try: mols.add_shared_property("space","space")) except Exception: from ..vol import Cartesian mols.add_shared_property("space", Cartesian()) try: mols.add_shared_property("time","time")) except Exception: from ..units import picosecond from ..base import wrap mols.add_shared_property("time", wrap(0 * picosecond)) if map.specified("make_whole"): if map["make_whole"]: mols.make_whole() return mols