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Biskit
Package Biskit :: Module AmberCrdEntropist :: Class AmberCrdEntropist
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Class AmberCrdEntropist

source code

Run ptraj entropy analysis on existing amber trajectory (.crd) and topology (.parm7) file.

Instance Methods [hide private]
  __init__(self, f_parm, f_crd, f_template=None, s=0, e=None, step=1, **kw)
Create Executor.
str version(self)
Version of class.
str command(self)
Build the command string.
  __tryMatch(self, regex, str, integer=0)
  finish(self)
Overrides Executor method
  isFailed(self)
Detect whether external program failed, override!
dict parsePtrajResult(self, f_out)
Extract results from ptraj.

Inherited from Executor.Executor: cleanup, communicate, convertInput, environment, execute, fail, fillTemplate, generateInp, postProcess, prepare, run


Class Variables [hide private]
  ptraj_script = """ trajin %(f_crd)s %(start)i %(stop)i %(step)i mat...

Instance Variables [hide private]

Inherited from Executor.Executor: error, f_in, log, output, pid, result, returncode, runTime


Method Details [hide private]

__init__(self, f_parm, f_crd, f_template=None, s=0, e=None, step=1, **kw)
(Constructor)

source code 

Create Executor. *name* must point to an existing program configuration unless *strict*=0. Executor will create a program input from the template and its own fields and put it into f_in. If f_in but no template is given, the unchanged f_in is used as input. If neither is given, the program is called without input. If a node is given, the process is wrapped in a ssh call. If *nice* != 0, the process is preceeded by nice. *cwd* specifies the working directory. By default, this setting is taken from the configuration file which defaults to the current working directory.
Parameters:
  • f_parm (str) - path to amber topology file
  • f_crd (str) - path to amber trajectory file
  • f_template (str) - alternative ptraj input template (default: None)
  • s (int) - start frame (default: 0, first)
  • e (int) - end frame (default: None, last)
  • step (int) - frame offset (default: 1, no offset )
  • 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:
Overrides: Executor.Executor.__init__

version(self)

source code 

Version of class.
Returns: str
version
Overrides: Executor.Executor.version

command(self)

source code 

Build the command string.
Returns: str
command
Overrides: Executor.Executor.command

__tryMatch(self, regex, str, integer=0)

source code 

finish(self)

source code 

Overrides Executor method
Overrides: Executor.Executor.finish

isFailed(self)

source code 

Detect whether external program failed, override!
Overrides: Executor.Executor.isFailed

parsePtrajResult(self, f_out)

source code 

Extract results from ptraj.
Parameters:
  • f_out (str) - result of ptraj run
Returns: dict
extracted prtaj result
Raises:

Class Variable Details [hide private]

ptraj_script

Value:
"""
    trajin %(f_crd)s %(start)i %(stop)i %(step)i
    matrix mwcovar name mwc
    analyze matrix mwc vecs 0 thermo
    """

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