schrodinger.application.desmond.packages.msys.molfile package

Structure and coordinate file manipulation library.

Reading a structure file:

reader = molfile.mae.read('/path/to/foo.mae')

Iterating through the frames in a file:

for frame in molfile.dtr.read('/path/to/foo.dtr').frames():
    function( frame.pos, frame.vel, frame.time, frame.box )

Random access to frames (only dtr files support this currently):

f27 = molfile.dtr.read('/path/to/foo.dtr').frame(27) # 0-based index

Convert an mae file to a pdb file:

input=molfile.mae.read('foo.mae')
output=molfile.pdb.write('foo.pdb', atoms=input.atoms)
output.frame(input.frames().next())
output.close()

Write every 10th frame in a dtr to a trr:

input=molfile.dtr.read('big.dtr')
output=molfile.trr.write('out.trr, natoms=input.natoms)
for i in range(0,input.nframes, 10):
    output.frame( input.frame(i) )
output.close()

Write a frame with a specified set of gids:

f = molfile.Frame(natoms, with_gids=True
f.gid[:] = my_gids
f.pos[:] = my_positions
w.frame(f)

Read the raw fields from a frameset (dtr):

dtr = molfile.DtrReader('input.dtr')    # also works for stk
for i in range(dtr.nframes):
    f = dtr.frame(i)
    keyvals = dict()
    frame = dtr.frame(i, keyvals=keyvals)
    ## use data in keyvals

Write raw fields to a frameset (dtr):

dtr = molfile.DtrWriter('output.dtr', natoms=natoms)
keyvals = dict( s = "a string",
                f = positions.flatten(),    # must be 1d arrays
                i = numpy.array([1,2,3]),
                )
dtr.append( time = my_time, keyvals = keyvals )

schrodinger.application.desmond.packages.msys.molfile.register_plugin(plugin)

put plugin in the global namespace, and add to extensiondict

schrodinger.application.desmond.packages.msys.molfile.load_shared_library(path)

schrodinger.application.desmond.packages.msys.molfile.guess_filetype(filename, default=None)

return plugin name based on filename, or default if none found.

class schrodinger.application.desmond.packages.msys.molfile.FrameIter(reader)

Bases: object

__init__(reader)

Initialize self. See help(type(self)) for accurate signature.

skip(count=1)

class schrodinger.application.desmond.packages.msys.molfile.Grid(data, name='', axis=None, origin=None)

Bases: object

__init__(data, name='', axis=None, origin=None)

construct a new Grid object. data - 3d array of data; a copy is made. name - name for the grid. default empty string. axis - 3x3 array with grid axes in the rows. Default diag(1,1,1) origin - 0,0,0 corner of grid. Defaults to [0,0,0]

name

data

axis

origin

class schrodinger.application.desmond.packages.msys.molfile.StkFile

Bases: object

Generalized stk file: handles any molfile format that provides times

name = 'ls'

filename_extensions = 'ls'

classmethod read(path, filetype=None)

class Reader(path, filetype)

Bases: object

__init__(path, filetype)

Initialize self. See help(type(self)) for accurate signature.

natoms

nframes

frames()

frame(n)

get_prop(prop)

Use the same technique as used for times to generate a properly ordered set of properties across all readers

at_time_near(time)

__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.packages.msys.molfile.SeqFile

Bases: object

Read csv-like files with column names in the first row

filename_extensions = 'seq'

name = 'seq'

classmethod read(path)

Open an eneseq file for reading

class Reader(path)

Bases: object

__init__(path)

Only use a direct read to determine the header for the file Otherwise, use numpy.loadtxt

natoms

nframes

get_prop(prop)

frame(n)

frames()

at_time_near(time)

__init__

Initialize self. See help(type(self)) for accurate signature.

schrodinger.application.desmond.packages.msys.molfile.ls

alias of schrodinger.application.desmond.packages.msys.molfile.StkFile

schrodinger.application.desmond.packages.msys.molfile.seq

alias of schrodinger.application.desmond.packages.msys.molfile.SeqFile