parmed.amber.AmberAsciiRestart¶
-
class
parmed.amber.AmberAsciiRestart(fname, mode='r', natom=0, hasbox=None, title=None, time=0.0)[source]¶ Parser for the Amber ASCII inpcrd/restart file format
- Parameters
- fnamestr
File name to open
- modestr={‘r’, ‘w’}
Whether to open this file for ‘r’eading or ‘w’riting
- natomint, optional
Number of atoms in the system (necessary when mode=’w’)
- hasboxbool, optional
Does the system have PBCs? Necessary when mode=’w’
- titlestr, optional
Title to write to a new trajectory (when mode=’w’)
- timefloat, optional
The time to write to the restart file in ps. Default is 0.
- Attributes
boxCombined cell lengths and cell angles
- cell_angles
- cell_lengths
- coordinates
- positions
- velocities
Methods
close()Close the open file handler
id_format(filename)Identifies the file type as an Amber restart/inpcrd file
parse
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__init__(fname, mode='r', natom=0, hasbox=None, title=None, time=0.0)[source]¶ For restart files, natom and hasbox are determined automatically for mode=’r’, and can be determined at write-time when the coordinates are set.
Methods
__init__(fname[, mode, natom, hasbox, …])For restart files, natom and hasbox are determined automatically for mode=’r’, and can be determined at write-time when the coordinates are set.
close()Close the open file handler
id_format(filename)Identifies the file type as an Amber restart/inpcrd file
parse(filename[, structure])Attributes
Combined cell lengths and cell angles
positions