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: | |||||||
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Returns: | |||||||
Raises: |
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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>
See also