rstoolbox.io.make_structures¶

rstoolbox.io.make_structures(df, outdir=None, tagsfilename='tags', prefix=None, keep_tagfile=True)¶

Extract the selected decoys (if any).

Note

Depends on rosetta.path and rosetta.compilation. Depends on system.overwrite and system.output.

Attention

This function REQUIRES a local installation of Rosetta.

It basicall runs the extract_pdbs Rosetta application over the selected decoys.

extract_pdbs.linuxgccrelease -in:file:silent <pdb> -tags <selected>

It requires the DesignFrame to have source_file attached identifying the silent files from which the data can be extracted. minisilent files will not work here. This should happen by default with the library, if one reads from actual silent files, but can be set up with:

# (1) Read from a minisilent file that does not contain structural data: substitute
``df.replace_source_files(["file1", "file2", ])``
# (2) Add files to a recently casted DesignFrame
``df.add_source_files(["file1", "file2", ])``

Parameters:

df (DesignFrame) – Selected set of decoy that have to be extracted. outdir (str) – Directory in which to save the PDB files. If none is provided, it will be loaded from the system.output global option. tagsfilename (str) – Name of the file containing the ids of the decoys of interest. It will be created in the outdir. An previously existing file will not be overwritten if the global option system.overwrite is False. prefix (str) – If provided, a prefix is added to the PDB files. keep_tagfile (bool) – If True, do not delete the tag file after using it.

Raises:

ValueError: if the provided data does not have a description column. ValueError: if the description column has repeated identifiers. AttributeError: if silent files from where to extract structures are not found. IOError: if the attached silent files do not exist. IOError: when trying to overwrite the tagsfilename if system.overwrite is False. IOError: if the rosetta executable is not found. Depends on rosetta.path and rosetta.compilation.