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)[source]
Adenosine class.
-
__init__
(atoms, ref)[source]
Initialize residue.
Parameters: | atoms ([Atom]) – add atoms to residue |
-
letter_code
()[source]
Return letter code for nucleic acid.
Returns: | letter code for nucleic acid |
Return type: | str |
-
set_state
()[source]
Set ribo- vs. deoxyribo- state of this residue.
-
class
pdb2pqr.na.
CYT
(atoms, ref)[source]
Cytidine class
-
__init__
(atoms, ref)[source]
Initialize residue.
Parameters: | atoms ([Atom]) – add atoms to residue |
-
letter_code
()[source]
Return letter code for nucleic acid.
Returns: | letter code for nucleic acid |
Return type: | str |
-
set_state
()[source]
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)[source]
Guanosine class
-
__init__
(atoms, ref)[source]
Initialize residue.
Parameters: | atoms ([Atom]) – add atoms to residue |
-
letter_code
()[source]
Return letter code for nucleic acid.
Returns: | letter code for nucleic acid |
Return type: | str |
-
set_state
()[source]
Set ribo- vs. deoxyribo- state of this residue.
-
class
pdb2pqr.na.
Nucleic
(atoms, ref)[source]
This class provides standard features of the nucleic acids listed
below.
-
__init__
(atoms, ref)[source]
Initialize the class
Parameters: | atoms (list) – list of atom-like (HETATM or ATOM )
objects to be stored |
-
add_atom
(atom)[source]
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)[source]
Add the value to the list of chi angles.
Parameters: | value (float) – dihedral angle to add to list (in degrees) |
-
create_atom
(atomname, newcoords)[source]
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
()[source]
Adds the termini for all inherited objects.
-
pdb2pqr.na.
RA
alias of pdb2pqr.na.URA
-
pdb2pqr.na.
RC
alias of pdb2pqr.na.CYT
-
pdb2pqr.na.
RG
alias of pdb2pqr.na.GUA
-
class
pdb2pqr.na.
THY
(atoms, ref)[source]
Thymine class
-
__init__
(atoms, ref)[source]
Initialize residue.
Parameters: | atoms ([Atom]) – add atoms to residue |
-
letter_code
()[source]
Return letter code for nucleic acid.
Returns: | letter code for nucleic acid |
Return type: | str |
-
set_state
()[source]
Set ribo- vs. deoxyribo- state of this residue.
-
class
pdb2pqr.na.
URA
(atoms, ref)[source]
Uridine class
-
__init__
(atoms, ref)[source]
Initialize residue.
Parameters: | atoms ([Atom]) – add atoms to residue |
-
letter_code
()[source]
Return letter code for nucleic acid.
Returns: | letter code for nucleic acid |
Return type: | str |
-
set_state
()[source]
Set ribo- vs. deoxyribo- state of this residue.