residue
Biomolecular residue class.
Code author: Todd Dolinsky
Code author: Nathan Baker
- class pdb2pqr.residue.Residue(atoms)[source]
Residue class
Todo
Should this class have a member variable for dihedrals? Pylint complains!
The residue class contains a list of Atom objects associated with that residue and other helper functions.
- __init__(atoms)[source]
Initialize the class
- Parameters
atoms (list) – list of atom-like (
HETATM
orATOM
) objects to be stored
- add_atom(atom)[source]
Add the atom object to the residue.
- Parameters
atom – atom-like object, e.g.,
HETATM
orATOM
- property charge
Get the total charge of the residue.
In order to get rid of floating point rounding error, do a string transformation.
- Returns
The charge of the residue (float)
- Return type
charge
- get_atom(name)[source]
Retrieve a residue atom based on its name.
- Parameters
resname (str) – name of the residue to retrieve
- Returns
residue
- Return type
- static letter_code()[source]
Default letter code for residue.
- Returns
letter code for residue
- Return type
- pick_dihedral_angle(conflict_names, oldnum=None)[source]
Choose an angle number to use in debumping.
Instead of simply picking a random chiangle, this function uses a more intelligent method to improve efficiency. The algorithm uses the names of the conflicting atoms within the residue to determine which angle number has the best chance of fixing the problem(s). The method also insures that the same chiangle will not be run twice in a row.
- remove_atom(atomname)[source]
Remove an atom from the residue object.
- Parameters
atomname (str) – the name of the atom to be removed
- rename_residue(name)[source]
Rename the residue.
- Parameters
name (str) – the new name of the residue
- classmethod rotate_tetrahedral(atom1, atom2, angle)[source]
Rotate about the atom1-atom2 bond by a given angle.
All atoms connected to atom2 will rotate.
- Parameters
atom1 (structures.Atom) – first atom of the bond to rotate about
atom2 (structures.Atom) – second atom of the bond to rotate about
angle (float) – degrees to rotate