paramagpy.protein.CustomStructure

class paramagpy.protein.CustomStructure(*arg, **kwargs)

This is an overload hack of the BioPython Structure object

__init__(*arg, **kwargs)

Initialize the class.

Methods

add(entity)	Add a child to the Entity.
atom_to_internal_coordinates([verbose])	Create/update internal coordinates from Atom X,Y,Z coordinates.
center_of_mass([geometric])	Return the center of mass of the Entity as a numpy array.
copy()	Copy entity recursively.
detach_child(id)	Remove a child.
detach_parent()	Detach the parent.
get_atoms()	Return atoms from residue.
get_chains()	Return chains from models.
get_full_id()	Return the full id.
get_id()	Return the id.
get_iterator()	Return iterator over children.
get_level()	Return level in hierarchy.
get_list()	Return a copy of the list of children.
get_models()	Return models.
get_parent()	Return the parent Entity object.
get_residues()	Return residues from chains.
has_id(id)	Check if a child with given id exists.
insert(pos, entity)	Add a child to the Entity at a specified position.
internal_to_atom_coordinates([verbose])	Create/update atom coordinates from internal coordinates.
parse(dataValues[, models])	Associate experimental data with atoms of the PDB file This method takes a DataContainer instance from the dataparse module
set_parent(entity)	Set the parent Entity object.
transform(rot, tran)	Apply rotation and translation to the atomic coordinates.

Attributes

id	Return identifier.