navicatGA.chemistry_xyz

Attributes

logger

Classes

Hashable_Geometry

This is a modified version of the Geometry class in AaronTools.py, which is identical but hashable.

Functions

check_xyz(chromosome)	Check if a list of Geometries can lead to a valid structure.
draw_xyz(geom, outname)
get_alphabet_from_path([path])
get_default_alphabet()
get_starting_xyz_from_file(file_list)
get_starting_xyz_from_path([path])
get_starting_xyz_from_smi(smiles_list)
pad_xyz_list(xyz, maxchars)	Pads chromosome with empty elements.
random_merge_xyz()	Default chromosome manipulator: randomly generates an XYZ structure from fragments.

Module Contents

class navicatGA.chemistry_xyz.Hashable_Geometry(*args, **kw)

Bases: AaronTools.geometry.Geometry

This is a modified version of the Geometry class in AaronTools.py, which is identical but hashable.

navicatGA.chemistry_xyz.check_xyz(chromosome)

Check if a list of Geometries can lead to a valid structure.

navicatGA.chemistry_xyz.draw_xyz(geom, outname)

navicatGA.chemistry_xyz.get_alphabet_from_path(path='alphabet/')

navicatGA.chemistry_xyz.get_default_alphabet()

navicatGA.chemistry_xyz.get_starting_xyz_from_file(file_list)

navicatGA.chemistry_xyz.get_starting_xyz_from_path(path='scaffolds')

navicatGA.chemistry_xyz.get_starting_xyz_from_smi(smiles_list)

navicatGA.chemistry_xyz.pad_xyz_list(xyz, maxchars)

Pads chromosome with empty elements.

navicatGA.chemistry_xyz.random_merge_xyz()

Default chromosome manipulator: randomly generates an XYZ structure from fragments.

navicatGA.chemistry_xyz.logger