Parser

class Parser(filename, mode='r', **kwargs)

Bases: ABC

Base class for structure file parsers.

Classes inheriting from Parser need to define a function Parser.parse_input() that creates a dictionary representation of the given file. The input is a deque of all lines in the file.

Parameters:

filenamestr

File name to parse data from.

modestr, optional

Mode to open the file. Default is ‘r’ for read.

kwargsDict, optional

Optional keyword arguments passed to the child’s parse_input method.

Attributes

Parser.get(key[, default])	Retrieve a value from the internal data using a given key.
Parser.keys()	List keys available in internal dictionary.
Parser.values()	List values available in internal dictionary.
Parser.items()	List items available in internal dictionary.
Parser.parse_input(lines)	Parse a list of lines from a file and convert the data into a dictionary.

Supported formats

PDBParser(filename[, mode])	Convert PDB file data into a dictionary representation [Ra4c9f6a816d0-1].
MMCIFParser(filename[, mode])	Convert MMCIF file data into a dictionary representation.
GROParser(filename[, mode])	Convert GRO file in Gromos87 format into a dictionary representation [R9139f7711c9e-1].
StarParser(filename[, mode])	Convert STAR file data into a dictionary representation [Rd1c0acc01191-1].
XMLParser(filename[, mode])	Parser for XML files.
MDOCParser(filename[, mode])	Convert MDOC file (SerialEM metadata) into a dictionary representation.