na

Nucleic Acid Structures for PDB2PQR

This module contains the base nucleic acid structures for pdb2pqr.

Code author: Todd Dolinsky

Code author: Nathan Baker

class pdb2pqr.na.ADE(atoms, ref)

Adenosine class.

__init__(atoms, ref)

Initialize residue.

Parameters:atoms ([Atom]) – add atoms to residue

letter_code()

Return letter code for nucleic acid.

Returns:letter code for nucleic acid Return type:str

set_state()

Set ribo- vs. deoxyribo- state of this residue.

class pdb2pqr.na.CYT(atoms, ref)

Cytidine class

__init__(atoms, ref)

Initialize residue.

Parameters:atoms ([Atom]) – add atoms to residue

letter_code()

Return letter code for nucleic acid.

Returns:letter code for nucleic acid Return type:str

set_state()

Set ribo- vs. deoxyribo- state of this residue.

pdb2pqr.na.DA

alias of pdb2pqr.na.ADE

pdb2pqr.na.DC

alias of pdb2pqr.na.CYT

pdb2pqr.na.DG

alias of pdb2pqr.na.GUA

pdb2pqr.na.DT

alias of pdb2pqr.na.THY

class pdb2pqr.na.GUA(atoms, ref)

Guanosine class

__init__(atoms, ref)

Initialize residue.

Parameters:atoms ([Atom]) – add atoms to residue

letter_code()

Return letter code for nucleic acid.

Returns:letter code for nucleic acid Return type:str

set_state()

Set ribo- vs. deoxyribo- state of this residue.

class pdb2pqr.na.Nucleic(atoms, ref)

This class provides standard features of the nucleic acids listed below.

__init__(atoms, ref)

Initialize the class

Parameters:atoms (list) – list of atom-like (HETATM or ATOM) objects to be stored

add_atom(atom)

Add existing atom to system.

Override the existing add_atom - include the link to the reference object.

Parameters:atom (Atom) – atom to add to system.

add_dihedral_angle(value)

Add the value to the list of chi angles.

Parameters:value (float) – dihedral angle to add to list (in degrees)

create_atom(atomname, newcoords)

Create an atom.

Overrides the generic residue’s create_atom().

Todo

This code is duplicated in several places.

Parameters:

• atomname (str) – the name of the atom to add
• newcoords ([(float, float, float)]) – the coordinates of the atom

set_state()

Adds the termini for all inherited objects.

pdb2pqr.na.RA

alias of pdb2pqr.na.ADE

pdb2pqr.na.RC

alias of pdb2pqr.na.CYT

pdb2pqr.na.RG

alias of pdb2pqr.na.GUA

pdb2pqr.na.RU

alias of pdb2pqr.na.URA

class pdb2pqr.na.THY(atoms, ref)

Thymine class

__init__(atoms, ref)

Initialize residue.

Parameters:atoms ([Atom]) – add atoms to residue

letter_code()

Return letter code for nucleic acid.

Returns:letter code for nucleic acid Return type:str

set_state()

Set ribo- vs. deoxyribo- state of this residue.

class pdb2pqr.na.URA(atoms, ref)

Uridine class

__init__(atoms, ref)

Initialize residue.

Parameters:atoms ([Atom]) – add atoms to residue

letter_code()

Return letter code for nucleic acid.

Returns:letter code for nucleic acid Return type:str

set_state()

Set ribo- vs. deoxyribo- state of this residue.