pwtools.parse.PDBFile¶

class pwtools.parse.PDBFile(filename=None, *args, **kwds)[source]¶

Very very simple pdb file parser.

Extract only ATOM/HETATM and CRYST1 (if present) records. If you want smth serious, check biopython or openbabel.

Notes

self.cryst_const :: If no CRYST1 record is found, this is None.
parsing:: We use regexes which may not work for more complicated ATOM records. We don’t use the strict column numbers for each field as stated in the PDB spec.

Methods

`apply_units`()	Like _apply_units_raw(), make sure that units are only applied once.
`assert_attr`(attr)	Raise AssertionError if self.<attr> is not set (is_set_attr() returns False.
`assert_attr_lst`(attr_lst)
`assert_set_attr`(attr)	Same as assert_attr(), but run try_set_attr() first.
`assert_set_attr_lst`(attr_lst)
`check_set_attr`(attr)	Run try_set_attr() and return the result of is_set_attr(), i.e. True or False.
`check_set_attr_lst`(attr_lst)
`dump`(dump_filename[, mkdir])	Write object to binary file using pickle.
`get_cont`([auto_calc])	Populate and return a Container object.
`get_coords`()
`get_cryst_const`()
`get_return_attr`(attr_name)	Call try_set_attr() are return self.<attr_name> if set.
`get_struct`(**kwds)
`get_symbols`()
`init_attr_lst`([attr_lst])	Set each self.<attr> in attr_lst to None.
`is_set_attr`(attr)	Check if self has the attribute self.<attr> and if it is _not_ None.
`is_set_attr_lst`(attr_lst)
`load`(dump_filename)	Load pickled object.
`parse`()
`raw_return`(attr_name)	Call `try_set_attr(_<attr_name>_raw)` and return it if set, else None.
`raw_slice_get`(attr_name, sl, axis)	Shortcut method:
`set_all`([attr_lst])	Call getter for each attr name in attr_lst.
`set_attr_lst`(attr_lst)	Set self.attr_lst and init each attr to None.
`try_set_attr`(attr)	If self.<attr> does not exist or is None, then invoke an appropirately named getter as if this command would be executed.
`try_set_attr_lst`(attr_lst)
`update_units`(units)	Update self.units dict from units.

Attributes

pwtools