Package schrodinger :: Package application :: Module prepwizard :: Class _CommonProblemsFixer

Class _CommonProblemsFixer

Class for fixing common structure problems.

Instance Methods

_hasZobs(self, atom)
Return True if any of the bonds of this atom are zero-order.

_setFormalCharge(self, atom, new_charge)
Set the formal charge for the given atom.

_deprotCarbAcid(self, carbon)
De-protonate the specified carboxylic acid.

_fixElement(self, atom)
If an atom's element (Whether it's an oxygen, nitrogen, or carbon) does not correspond to its PDB name, it gets reset.

_processSulfur(self, atom)
Ev:105338 Fix formal charges on sulfurs

_processBackboneOxygen(self, atom)
PPREP-875 Remove extra bonds when residue oxygens are bound to covalent ligands

list of strings

run(self, st)
Fix common structure problems in the given Structure.

Method Details

Set the formal charge for the given atom. Logs the change in the self._corrections_list.

De-protonate the specified carboxylic acid.

Parameters:

carbon (structure._StructureAtom object) - The carbon of the carboxylic acid.

If an atom's element (Whether it's an oxygen, nitrogen, or carbon) does not correspond to its PDB name, it gets reset. (Ev:69207)

Fix common structure problems in the given Structure.

Returns: list of strings: A list of texts describing what changes were made.