na
Nucleic Acid Structures for PDB2PQR
This module contains the base nucleic acid structures for pdb2pqr.
Code author: Todd Dolinsky
Code author: Nathan Baker
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pdb2pqr.na.A
alias of ADE
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class pdb2pqr.na.ADE(atoms, ref)[source]
Adenosine class.
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__init__(atoms, ref)[source]
Initialize residue.
- Parameters:
atoms ([Atom]) – add atoms to residue
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letter_code()[source]
Return letter code for nucleic acid.
- Returns:
letter code for nucleic acid
- Return type:
str
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set_state()[source]
Set ribo- vs. deoxyribo- state of this residue.
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pdb2pqr.na.C
alias of CYT
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class pdb2pqr.na.CYT(atoms, ref)[source]
Cytidine class
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__init__(atoms, ref)[source]
Initialize residue.
- Parameters:
atoms ([Atom]) – add atoms to residue
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letter_code()[source]
Return letter code for nucleic acid.
- Returns:
letter code for nucleic acid
- Return type:
str
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set_state()[source]
Set ribo- vs. deoxyribo- state of this residue.
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pdb2pqr.na.DA
alias of ADE
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pdb2pqr.na.DC
alias of CYT
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pdb2pqr.na.DG
alias of GUA
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pdb2pqr.na.DT
alias of THY
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pdb2pqr.na.G
alias of GUA
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class pdb2pqr.na.GUA(atoms, ref)[source]
Guanosine class
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__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.
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class pdb2pqr.na.Nucleic(atoms, ref)[source]
This class provides standard features of the nucleic acids listed
below.
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__init__(atoms, ref)[source]
Initialize the class
- Parameters:
atoms (list) – list of atom-like (HETATM
or ATOM
)
objects to be stored
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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.
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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)
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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
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set_state()[source]
Adds the termini for all inherited objects.
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pdb2pqr.na.RA
alias of ADE
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pdb2pqr.na.RC
alias of CYT
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pdb2pqr.na.RG
alias of GUA
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pdb2pqr.na.RU
alias of URA
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class pdb2pqr.na.THY(atoms, ref)[source]
Thymine class
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__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.
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pdb2pqr.na.U
alias of URA
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class pdb2pqr.na.URA(atoms, ref)[source]
Uridine class
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__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.