Package gromacs :: Package analysis :: Package plugins :: Module dist :: Class GdistData

Class GdistData

object --+
         |
        GdistData

Object that represents the standard output of g_dist -dist CUTOFF.

Initialize from a stream (e.g. a pipe) and the iterate over the instance to get the data line by line. Each line consists of a tuple

(frame, distance)

Instance Methods

[hide private]

__init__(self, stream)
Initialize with an open stream to the data (eg stdin or file).

source code

__iter__(self)
Iterator that filters the input stream and returns (frame, distance) tuples.

source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Variables

[hide private]

data_pattern = re.compile("""t:\s* # marker fo...

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, stream)
(Constructor)

source code

Initialize with an open stream to the data (eg stdin or file).

Overrides: object.__init__

Arguments:

stream: open stream (file or pipe or really any iterator providing the data from g_dist); the stream is not closed automatically when the iterator completes.

Class Variable Details

[hide private]

data_pattern

Value:

re.compile("""t:\s*                 # marker for beginning of line
                (?P<FRAME>\d+)\s+                      # frame number 
(?)
                (?P<RESID>\d+)\s+(?P<RESNAME>\w+)\s+   # resid and res
idue name
                (?P<ATOMID>\d+)\s+(?P<ATOMNAME>\w+)\s+ # atomid and at
om name
                (?P<DISTANCE>[0-9]+\.?[0-9]+)          # distance
...

Class GdistData

__init__(self, stream) (Constructor)

data_pattern

init(self, stream)
(Constructor)