Class AmberCrdParser

source code

Convert an Amber-generated crd file into a Trajectory object.

Instance Methods

__init__(self, fcrd, fref, box=0, rnAmber=0, pdbCode=None, log=StdLog(), verbose=0)

[float] line2numbers(self, l)
convert a line from crd/vel file to list of float numbers

[float] nextLine(self)
extract next 10 coordinates from crd file

array nextFrame(self)
Collect next complete coordinate frame

Trajectory crd2traj(self)
Convert coordinates into a Trajectory object.

Method Details

fcrd (str) - path to input coordinate file
fref (str) - PDB or pickled PDBModel with same atom content and order
box (1|0) - expect line with box info at the end of each frame (default: 0)
rnAmber (1|0) - rename amber style residues into standard (default: 0)
pdbCode (str) - pdb code to be put into the model (default: None)
log (Biskit.LogFile) - LogFile instance [Biskit.StdLog]
verbose (int) - print progress to log [0]