residue
¶
Biomolecular residue class.
Code author: Todd Dolinsky
Code author: Nathan Baker
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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.
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__init__
(atoms)[source]¶ Initialize the class
Parameters: atoms (list) – list of atom-like ( HETATM
orATOM
) objects to be stored
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add_atom
(atom)[source]¶ Add the atom object to the residue.
Parameters: atom – atom-like object, e.g., HETATM
orATOM
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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
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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: structures.Atom
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get_moveable_names
(pivot)[source]¶ Return all atom names that are further away than the pivot atom.
Parameters: Returns: names of atoms further away than pivot atom
Return type: [str]
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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
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static
letter_code
()[source]¶ Default letter code for residue.
Returns: letter code for residue Return type: str
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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: Returns: new dihedral angle number
Return type:
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remove_atom
(atomname)[source]¶ Remove an atom from the residue object.
Parameters: atomname (str) – the name of the atom to be removed
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rename_residue
(name)[source]¶ Rename the residue.
Parameters: name (str) – the new name of the residue
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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
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