Public API

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sire.io.get_coords_array(mol, units=None, map=None)[source]

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

sire.io.resolve_path(path, directory='.', auto_unzip=True, silent=False)[source]

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.

Parameters:

  • 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