packman.molecule.hetmol module

The ‘HetMol’ object host file.

This is file information, not the class information. This information is only for the API developers. Please read the ‘HetMol’ object documentation for details.

Citation:
Pranav M Khade, Robert L Jernigan, PACKMAN-Molecule: Python Toolbox for Structural Bioinformatics, Bioinformatics Advances, 2022;, vbac007, https://doi.org/10.1093/bioadv/vbac007

Example:

from packman.molecule import HetMol
help( HetMol )
Authors:
class packman.molecule.hetmol.HetMol(id, name, parent)

Bases: object

This class contains the information about the ‘HetMol’ object (packman.molecule.Residue).

This class contains all the information available about the HetMol and stores the corresponding ‘Atom’ objects in itself. The Residue class is the second lowest in the hierarchy of the ‘molecule’ API classes. the order of hierarchy being: Protein> Model> Chain> HetMol> Atom. This class is also the component of the ‘molecule’ module API. Please read the Tutorials and Documentation for more details.

Note

Parameters:
  • id (int) – Residue ID from the PDB file as it is. Each Residue in a PDB file Model/Frame has unique ID. (essential)
  • name (str) – Residue Name from the PDB file as it is.
  • parent (packman.molecule.Chain) – The Chain Object (parent) this Residue belongs to.
get_atom(key)

Get the specific Atom by id/name. Please note that this is different than get_atoms()

Parameters:key (int/str) – Get atom by the id/name
Returns:Atom of the given ID if successful; None otherwise.
Return type:atom (packman.molecule.Atom)
get_atoms()

Get the generator of corresponding ‘Atom’ objects of the ‘HetMol’

Returns:generator of ‘Atom’ objects if successful, None otherwise.
get_centerofgravity()

Get the center of gravity of the given ‘HetMol’

Note

Yet to add the atomic masses.

Returns:Cartesian Coordinates as numpy.array of the centre of the gravity.
get_domain_id()

Get the Domain Identifier of the given ‘HetMol’. Hinge Prediction is Necessary for this option.

Note

Domain Identifiers (Obtained after running PACKMAN): ‘FL’: Flexible Linkers (Hinges); Followed by the domain number ‘DM’: Domain; Followed by the domain number

Returns:str if successful, None otherwise.
get_id()

Get the ID of the ‘HetMol’

Returns:int if successful, None otherwise.
get_name()

Get the Name of the ‘HetMol’

Returns:str if successful, None otherwise.
get_parent()

Get the Parent of the ‘HetMol’

Returns:packman.molecule.Chain if successful, None otherwise.
get_property(property_name)

Get the Property of the given ‘HetMol’.

Property is any key and value combination that can be assigned to this object. This (along with the set_property) feature is mainly useful for the user customization. Properties are like pinboards. You can pin anything to the object with a key as a pin.

Parameters:property_name (object) – The ‘Key’ or a name the user wants to assign to to the property

Note

  • Users can add custom annotations; for example: If particular chain becomes disordered, it can be annotated with this feature.
set_domain_id(new_domain_id)

Set the Domain Identifier of the given ‘HetMol’.

Note

Domain Identifiers Format: ‘FL’: Flexible Linkers (Hinges); Followed by the domain number ‘DM’: Domain; Followed by the domain number

Parameters:new_domain_id (str) – The Domain Identifies User wishes to assign to the given ‘HetMol’
set_id(new_id)

Set the ID of the given ‘HetMol’

Parameters:new_id (int) – The ID User wishes to assign to the given ‘HetMol’
set_name(new_name)

Set the Name of the given ‘HetMol’

Parameters:new_name (str) – The Name User wishes to assign to the given ‘HetMol’
set_parent(new_parent)

Set the Parent of the given ‘HetMol’

Parameters:new_parent (packman.molecule.Chain) – The parent ‘Chain’ User wishes to assign to the given ‘HetMol’
set_property(property_name, value)

Set the Property of the given ‘HetMol’.

Property is any key and value combination that can be assigned to this object. This (along with the get_property) feature is mainly useful for the user customization. Properties are like pinboards. You can pin anything to the object with a key as a pin.

Parameters:
  • property_name (object) – The ‘Key’ or a name the user wants to assign to to the property
  • value (object) – The value the user wants to assign to the property

Note

  • Users can add custom annotations; for example: If particular amino acid becomes disordered, it can be annotated with this feature.