parmed.amber.AmberMdcrd¶
-
class
parmed.amber.AmberMdcrd(fname, natom, hasbox, mode='r', title=None)[source]¶ A class to parse Amber ASCII trajectory files. This is much slower than parsing NetCDF files (or the equivalent parsing done in a compiled language like C or C++). For large trajectories, this may be significant.
- Attributes
- box
- coordinates
- frame
- positions
Methods
add_box(stuff)Prints ‘stuff’ (which must be a 3-element list, array.array, tuple, or np.ndarray) as the box lengths for this frame
add_coordinates(stuff)Prints ‘stuff’ (which must be either an iterable of 3*natom or have an attribute ‘flatten’ that converts it into an iterable of 3*natom) to the open file handler.
close()Close the open file handler
id_format(filename)Identifies the file type as an Amber mdcrd file
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__init__(fname, natom, hasbox, mode='r', title=None)¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__(fname, natom, hasbox[, mode, title])Initialize self.
add_box(stuff)Prints ‘stuff’ (which must be a 3-element list, array.array, tuple, or np.ndarray) as the box lengths for this frame
add_coordinates(stuff)Prints ‘stuff’ (which must be either an iterable of 3*natom or have an attribute ‘flatten’ that converts it into an iterable of 3*natom) to the open file handler.
close()Close the open file handler
id_format(filename)Identifies the file type as an Amber mdcrd file
Attributes
positions