Package gromacs :: Package analysis :: Package plugins :: Module gridmatmd :: Class GridMatMD

Class GridMatMD

object --+
         |
        GridMatMD

Analysis of lipid bilayers with GridMAT-MD.

It requires a configuration file and a list of structure files (gro or pdb) as input. See the documentation (pdf_) for the format of the config file. Note that the *bilayer* keyword will be ignored in the config file.

.. _pdf: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/doc/GridMAT-MD_ug_v1.0.2.pdf

Instance Methods

[hide private]

__init__(self, config, filenames)
Set up GridMAT-MD analysis.

source code

run_frame(self, frame)
Run GridMAT-MD on a single *frame* and return results.

source code

run(self)
Run analysis on all files and average results.

source code

imshow(self, name, **kwargs)
Display array *name* with ``pylab.imshow``.

source code

save(self, name)
Save object as pickle.

source code

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

Class Variables

[hide private]

pNX = re.compile("There are (?P<NX>\d+) grid points in the X d...

pNY = re.compile("There are (?P<NY>\d+) grid points in the Y d...

pTOP = re.compile('The top leaflet "thickness" will be printed...

pAVG = re.compile('The average bilayer "thickness" will be pri...

pBOT = re.compile('The bottom leaflet "thickness" will be prin...

Instance Variables

[hide private]

filenames
list of filenames (gro or pdb files)

nx
Number of bins in the *x* direction.

ny
Numberof bins in the *y* direction.

dx
Bin width in *x*.

dy
Bin width in *y*.

thickness
Thickness results (dict of :class:`GridMatData` instances); used to store the results from the last processed frame.

averages
Final result: averaged thickness profiles, indexed by "top", "bottom", "average"

GridMatMD
Instance of :class:`gromacs.tools.GridMAT_MD` which always uses *config* for input.

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, config, filenames)
(Constructor)

source code

Set up GridMAT-MD analysis.

:Arguments:
  *config* : filename
     input file for GridMAT-MD (see docs)
  *filenames* : list or glob-pattern
     list of gro or pdb files, or a glob pattern that creates
     such a list

Overrides: object.__init__

run_frame(self, frame)

source code

Run GridMAT-MD on a single *frame* and return results.

:Arguments: *frame* is a filename (gro or pdb)
:Returns:   a dict of :class:`GridMapData` objects; the keys
            are "top", "bottom", "average"

Class Variable Details

[hide private]

pNX

Value:

re.compile("There are (?P<NX>\d+) grid points in the X direction, " "s
paced every (?P<DX>[0-9.]+) nanometers")

pNY

Value:

re.compile("There are (?P<NY>\d+) grid points in the Y direction, " "s
paced every (?P<DY>[0-9.]+) nanometers")

pTOP

Value:

re.compile('The top leaflet "thickness" will be printed to (?P<FILENAM
E>.*_top_.*\.dat)')

pAVG

Value:

re.compile('The average bilayer "thickness" will be printed to (?P<FIL
ENAME>.*_average_.*\.dat)')

pBOT

Value:

re.compile('The bottom leaflet "thickness" will be printed to (?P<FILE
NAME>.*_bottom_.*\.dat)')

Class GridMatMD

__init__(self, config, filenames) (Constructor)

run_frame(self, frame)

pNX

pNY

pTOP

pAVG

pBOT

init(self, config, filenames)
(Constructor)