Package Biskit :: Module msms :: Class Pdb2xyzrn

Class Pdb2xyzrn

MSMS - pdb2xyzrn

Run the awk script pdb_to_xyzrn to extract names and radii. This is nessesary to run msms. The radii and atoms depend on where in the sequence an atom resides. The radii used is determined by the information in the atomtypenumbers file provided with the MSMS application.

Result

 r   - atom radii array
 n   - atom name list

Instance Methods

[hide private]

__init__(self, model, **kw)

prepare(self)
Overrides Executor method.

cleanup(self)

array, array parse_xyzrn(self, output)
Extract xyz and r from output.

isFailed(self)
Overrides Executor method

finish(self)
Overrides Executor method

Method Details

[hide private]

init(self, model, **kw)
(Constructor)

source code

Parameters:

model (PDBModel) - reference

kw (

key=value pairs :
 debug    - 0|1, keep all temporary files (default: 0)
 verbose  - 0|1, print progress messages to log (log != STDOUT)
 node     - str, host for calculation (None->local) NOT TESTED
                 (default: None)
 nice     - int, nice level (default: 0)
 log      - Biskit.LogFile, program log (None->STOUT) (default: None)

) - additional key=value parameters for Executor: