Residue Type¶

class rnamake.residue_type.ResidueType(name, atom_map)[source]¶

Bases: object

Simple class to hold the topology of the residue, currrently only holds which atoms are included in the atomtype but might be later expanded to include bonds and charges. This class should not be initiated by itself, initiation occurs in ResidueTypeSet

Parameters:	name (str) – residue name atom_map (dict) – the position of where each atom should in a residue by name
Attributes:

name : str: Residue name
atom_map : dict: The position of where each atom should in a residue by name
alt_name : list: Other names the residue can go by, ex. G is also GUA

class rnamake.residue_type.ResidueTypeSet[source]¶

Bases: object

Holds all the ResidueType objects, for initiation of new residues. Do not initiate a instantance of ResidueTypeSet, if you want a new ResidueType do

>>>import rnamake.residue_type
>>>rnamake.residue_type.get_rtype("GUA")
<ResidueType(name='GUA')>

Attributes:

residue_types : list of ResidueTypes: Contains all residue types that are acceptable in rnamake

get_rtype_by_resname(resname)[source]¶: get the ResidueType object for a given residue by name, this method should not be called directly! Should call rnamake.residue_type.get_rtype for simplicity :param resname: name of residue that you want the ResidueType for :type resname: str

rnamake.residue_type.get_rtype(resname)[source]¶

Get a reference to a ResidueType by name. This is the only way you should get a ResidueType reference

Parameters:	resname (str) – the name of the residue you want the ResidueType

>>>rnamake.residue_type.get_rtype("GUA")
<ResidueType(name='GUA')>