parmed.amber.AmberFormat

class parmed.amber.AmberFormat(fname=None)

A class that can parse and print files stored in the Amber topology or MDL format. In particular, these files have the general form:

` %VERSION VERSION_STAMP = V00001.000  DATE = XX/XX/XX  XX:XX:XX %FLAG <FLAG_NAME> %COMMENT <comments> %FORMAT(<Fortran_Format>) ... data corresponding to that Fortran Format %FLAG <FLAG_NAME2> %COMMENT <comments> %FORMAT(<Fortran_Format>) ... data corresponding to that Fortran Format `

where the %COMMENT sections are entirely optional

Parameters

fnamestr=None

If provided, this file is parsed and the data structures will be loaded from the data in this file

Attributes

parm_datadict {str

A dictionary that maps FLAG names to all of the data contained in that section of the Amber file.

formatsdict {str

A dictionary that maps FLAG names to the FortranFormat instance in which the data is stored in that section

parm_commentsdict {str

A dictionary that maps FLAG names to the list of COMMENT lines that were stored in the original file

flag_listlist

An ordered list of all FLAG names. This must be kept synchronized with parm_data, formats, and parm_comments such that every item in flag_list is a key to those 3 dicts and no other keys exist

charge_flagstr=’CHARGE’

The name of the name of the FLAG that describes partial atomic charge data. If this flag is found, then its data are multiplied by the ELECTROSTATIC_CONSTANT to convert back to fractions of electrons

versionstr

The VERSION string from the Amber file

namestr

The file name of the originally parsed file (set to the fname parameter)

Methods

add_flag(flag_name, flag_format[, data, …])	Adds a new flag with the given flag name and Fortran format string and initializes the array with the values given, or as an array of 0s of length num_items
delete_flag(flag_name)	Removes a flag from the topology file
id_format(filename)	Identifies the file type as either Amber-format file (like prmtop) or an old-style topology file.
parse(filename, *args, **kwargs)	Meant for use with the automatic file loader, this will automatically return a subclass of AmberFormat corresponding to what the information in the prmtop file contains (i.e., either an AmberParm, ChamberParm, AmoebaParm, or AmberFormat)
rdparm(fname[, slow])	Parses the Amber format file
rdparm_old(prmtop_lines[, check])	This reads an old-style topology file and stores the results in the same data structures as a new-style topology file
rdparm_slow(fname)	Parses the Amber format file.
set_version()	Sets the version string
view_as(cls)	Returns a view of the current object as another object.
write_parm(name)	Writes the current data in parm_data into a new topology file with the given name

__init__(fname=None)

Constructor. Read a file if given

Methods

__init__([fname])	Constructor.
add_flag(flag_name, flag_format[, data, …])	Adds a new flag with the given flag name and Fortran format string and initializes the array with the values given, or as an array of 0s of length num_items
delete_flag(flag_name)	Removes a flag from the topology file
id_format(filename)	Identifies the file type as either Amber-format file (like prmtop) or an old-style topology file.
parse(filename, *args, **kwargs)	Meant for use with the automatic file loader, this will automatically return a subclass of AmberFormat corresponding to what the information in the prmtop file contains (i.e., either an AmberParm, ChamberParm, AmoebaParm, or AmberFormat)
rdparm(fname[, slow])	Parses the Amber format file
rdparm_old(prmtop_lines[, check])	This reads an old-style topology file and stores the results in the same data structures as a new-style topology file
rdparm_slow(fname)	Parses the Amber format file.
set_version()	Sets the version string
view_as(cls)	Returns a view of the current object as another object.
write_parm(name)	Writes the current data in parm_data into a new topology file with the given name