debump
¶
Routines for biomolecule optimization.
Code author: Jens Erik Nielsen
Code author: Todd Dolinsky
Code author: Yong Huang
Code author: Nathan Baker
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class
pdb2pqr.debump.
Debump
(biomolecule, definition=None)[source]¶ Grab bag of random stuff that apparently didn’t fit elsewhere.
Todo
This class needs to be susbtantially refactored in to multiple classes with clear responsibilities.
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__init__
(biomolecule, definition=None)[source]¶ Initialize the Debump object.
Parameters: - biomolecule (Biomolecule) – the biomolecule to debump
- definition (Definition) – topology definition file
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debump_biomolecule
()[source]¶ Minimize bump score for molecule.
Make sure that none of the added atoms were rebuilt on top of existing atoms. See each called function for more information.
Raises: ValueError – if missing (backbone) atoms are encountered
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debump_residue
(residue, conflict_names)[source]¶ Debump a specific residue.
Only should be called if the residue has been detected to have a conflict. If called, try to rotate about dihedral angles to resolve the conflict.
Parameters: Returns: True if successful, False otherwise
Return type:
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find_nearby_atoms
(atom)[source]¶ Find nearby atoms for conflict-checking.
Uses neighboring cells to compare atoms rather than an all versus all O(n^2) algorithm, which saves a great deal of time. There are several instances where we ignore potential conflicts; these include donor/acceptor pairs, atoms in the same residue, and bonded CYS bridges.
Parameters: atom (Atom) – find nearby atoms to this atom Returns: a dictionary of Atom too close
toamount of overlap for that atom
Return type: dict
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find_residue_conflicts
(residue, write_conflict_info=False)[source]¶ Find conflicts between residues.
Parameters: Returns: list of conflicts
Return type: [str]
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get_bump_score
(residue)[source]¶ Get a bump score for a residue.
Parameters: residue (Residue) – residue with bumping to evaluate Returns: bump score Return type: float
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get_bump_score_atom
(atom)[source]¶ Find nearby atoms for conflict-checking.
Uses neighboring cells to compare atoms rather than an all versus all O(n^2) algorithm, which saves a great deal of time. There are several instances where we ignore potential conflicts; these include donor/acceptor pairs, atoms in the same residue, and bonded CYS bridges.
Parameters: atom (Atom) – find nearby atoms to this atom Returns: a bump score sum((dist-cutoff)**20 for all nearby atoms Return type: float
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get_closest_atom
(atom)[source]¶ Get the closest atom that does not form a donor/acceptor pair.
Used to detect potential conflicts.
Note
Cells must be set before using this function.
Parameters: atom (Atom) – the atom to test Returns: the closest atom to the input atom that does not satisfy a donor/acceptor pair. Return type: Atom
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