Package Biskit :: Module msms :: Class MSMS

Class MSMS

MSMS

Calculate SAS (Solvent Accessible surface) and SES (Solvent Excluded Surface) using the msms applicaton.

Run msms analytical surface calculation i.e.:

  msms -if xyzr.coord -af atoms.area -surface ases

Result

out     - dictionary - probe radii used, total SAS and SES
sesList - array of lenght atoms with SES (Solvent Excluded Surface)
sasList - array of lenght atoms with SAS (Solvent Accessible surface)

Note: The current default class for calculating MS and AS is Biskit.SurfaceRacer.

Instance Methods

[hide private]

__init__(self, model, verbose=1, debug=1, **kw)

prepare(self)
Write a xyzrn coordinate file to disc.

cleanup(self)
Remove temp files.

dict, array, array, [str] parse_msms(self)
Parse the result file from a msms calculation.

isFailed(self)
Overrides Executor method

finish(self)
Overrides Executor method

Method Details

[hide private]

init(self, model, verbose=1, debug=1, **kw)
(Constructor)

source code

Parameters:

model () - PDBModel

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:

prepare(self)

source code

Write a xyzrn coordinate file to disc. Overrides Executor method.

cleanup(self)

source code

Remove temp files.

parse_msms(self)

source code

Parse the result file from a msms calculation.

Returns: dict, array, array, [str]: probe radii used, total SAS and SES, array of lenght atoms with SES (Solvent Excluded Surface), array of lenght atoms with SAS (Solvent Accessible surface), and a list of atom names

isFailed(self)

source code

Overrides Executor method

finish(self)

source code

Overrides Executor method

Class MSMS

MSMS

Result

__init__(self, model, verbose=1, debug=1, **kw) (Constructor)

prepare(self)

cleanup(self)

parse_msms(self)

isFailed(self)

finish(self)

init(self, model, verbose=1, debug=1, **kw)
(Constructor)