na

Nucleic Acid Structures for PDB2PQR

This module contains the base nucleic acid structures for pdb2pqr.

Code author: Todd Dolinsky

Code author: Nathan Baker

pdb2pqr.na.A

alias of ADE

class pdb2pqr.na.ADE(atoms, ref: DefinitionResidue)

Adenosine class.

__init__(atoms, ref: DefinitionResidue)

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.C

alias of CYT

class pdb2pqr.na.CYT(atoms, ref: DefinitionResidue)

Cytidine class

__init__(atoms, ref: DefinitionResidue)

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 ADE

pdb2pqr.na.DC

alias of CYT

pdb2pqr.na.DG

alias of GUA

pdb2pqr.na.DT

alias of THY

pdb2pqr.na.G

alias of GUA

class pdb2pqr.na.GUA(atoms, ref: DefinitionResidue)

Guanosine class

__init__(atoms, ref: DefinitionResidue)

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: list[ATOM | HETATM], ref: DefinitionResidue)

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

__init__(atoms: list[ATOM | HETATM], ref: DefinitionResidue)

Initialize the class

Parameters:

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

add_atom(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: str, newcoords: list[float] | tuple[float, float, float])

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 ADE

pdb2pqr.na.RC

alias of CYT

pdb2pqr.na.RG

alias of GUA

pdb2pqr.na.RU

alias of URA

class pdb2pqr.na.THY(atoms, ref: DefinitionResidue)

Thymine class

__init__(atoms, ref: DefinitionResidue)

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.U

alias of URA

class pdb2pqr.na.URA(atoms, ref: DefinitionResidue)

Uridine class

__init__(atoms, ref: DefinitionResidue)

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.