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
- get_moveable_names(pivot)[source]
Return all atom names that are further away than the pivot atom.
- Parameters
residue (Residue) – the residue to use
pivot (str) – the pivot atomname
- Returns
names of atoms further away than pivot atom
- Return type
[str]
- has_atom(name)[source]
Return True if atom in residue.
- Parameters
name (str) – atom name in question
- Returns
True if atom in residue
- Return type
bool
- static letter_code()[source]
Default letter code for residue.
- Returns
letter code for residue
- Return type
str
- 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.
- Parameters
residue (Residue) – residue that is being debumped
conflict_names ([str]) – list of atom names that are currently conflicts
oldnum (int) – old dihedral angle number
- Returns
new dihedral angle number
- Return type
int
- remove_atom(atomname)[source]
Remove an atom from the residue object.
- Parameters
atomname (str) – the name of the atom to be removed
- rename_atom(oldname, newname)[source]
Rename an atom to a new name.
- Parameters
oldname (str) – old atom name
newname (str) – new atom name
- 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