rstoolbox.io.get_sequence_and_structure¶

rstoolbox.io.get_sequence_and_structure(pdbfile, mk_minisilent=True, ignore_unrecognized_res=True, minimize=False)¶

Provided a PDB file, it will run a small RosettaScript to capture its sequence and structure, i.e. dssp and phi-psi dihedrals.

Note

Depends on rosetta.path and rosetta.compilation, if the corresponding silent file does not exist.

Attention

This function REQUIRES a local installation of Rosetta.

It will generate an output file called: <pdbfile>.dssp.minisilent. If this file already exists, it will be directly read. You can choose to compress it; <pdbfile>.dssp.minisilent.gz will also work.

Parameters:

pdbfile (str) – Name of the input structure.
mk_minisilent (bool) – If True, transeform output into minisilent format.
ignore_unrecognized_res (bool) – If True, Rosetta ignores non-recognizable residues.
minimize (bool) – If True, apply minimization before evaluating the structure.

Returns:

DesignFrame.

Raises:

IOError:	if `pdbfile` cannot be found.
IOError:	if Rosetta executable cannot be found.
ValueError:	if Rosetta execution fails

The script that is runned (and that can be runned outside and then brough back to your computer) is:

In [1]: from rstoolbox.utils import baseline
   ...: print(baseline())
   ...: 
<ROSETTASCRIPTS>
    <MOVERS>
        <WriteSSEMover dssp="1" name="w" write_phipsi="true" />
        <MinMover name="m" bb="true" chi="true" tolerance=".1" />
    </MOVERS>
    <FILTERS>
        <CavityVolume name="cavity" confidence="0" />
        <PackStat name="pack" confidence="0" />
        <AverageDegree name="avdegree" confidence="0" />
    </FILTERS>
    <PROTOCOLS>
        <Add mover="w" />
        <Add filter="cavity" />
        <Add filter="pack" />
        <Add filter="avdegree" />
    </PROTOCOLS>
</ROSETTASCRIPTS>