parmed.exceptions module

This module contains all of the exceptions that are used in the chemistry package

exception parmed.exceptions.AmberError

Bases: parmed.exceptions.ParsingError

This is a generic AmberParmError

exception parmed.exceptions.AmberWarning

Bases: parmed.exceptions.ParmedWarning

If there is something that is non-fatal

exception parmed.exceptions.CharmmError

Bases: parmed.exceptions.ParsingError

If there is a problem parsing CHARMM PSF files

exception parmed.exceptions.CharmmPsfEOF

Bases: parmed.exceptions.ParmedError

If we hit an end-of-file in parsing CHARMM files

exception parmed.exceptions.CharmmWarning

Bases: parmed.exceptions.ParmedWarning

For non-fatal PSF parsing issues

exception parmed.exceptions.FormatNotFound

Bases: parmed.exceptions.ParmedError

If the file format does not have a registered parser with it

exception parmed.exceptions.GromacsError

Bases: parmed.exceptions.ParmedError

If there is a problem parsing GROMACS topology files

exception parmed.exceptions.GromacsWarning

Bases: parmed.exceptions.ParmedWarning

If we are uncertain about something regarding the GROMACS topology file

exception parmed.exceptions.IncompatiblePatchError

Bases: parmed.exceptions.ParmedError

For when applying a PatchTemplate to a ResidueTemplate fails

exception parmed.exceptions.InputError

Bases: parmed.exceptions.ParmedError

When there is an error with input

exception parmed.exceptions.MaskError

Bases: parmed.exceptions.ParmedError

Error when a Mask is poorly formed

exception parmed.exceptions.Mol2Error

Bases: parmed.exceptions.ParsingError

If there was a problem parsing a Mol2 file

exception parmed.exceptions.MoleculeError

Bases: parmed.exceptions.ParmedError

If there is a problem defining a molecule via the bond graph

exception parmed.exceptions.OpenMMError

Bases: parmed.exceptions.ParmedError

If there’s a problem making an OpenMM system

exception parmed.exceptions.OpenMMWarning

Bases: parmed.exceptions.ParmedWarning

If there is something we should warn when processing OpenMM objects

exception parmed.exceptions.PDBError

Bases: parmed.exceptions.ParsingError

If there was a problem parsing a PDB file

exception parmed.exceptions.PDBWarning

Bases: parmed.exceptions.ParmedWarning

A non-fatal error to indicate a problematic PDB file

exception parmed.exceptions.ParameterError

Bases: parmed.exceptions.ParmedError

If a parameter is missing from a database

exception parmed.exceptions.ParameterWarning

Bases: parmed.exceptions.ParmedWarning

If a type of parameter is missing, but you don’t want it to be fatal

exception parmed.exceptions.ParmedError

Bases: Exception

Base class for all non-trivial exceptions raised by ParmEd

exception parmed.exceptions.ParmedWarning

Bases: Warning

Base class for all warnings raised by ParmEd

exception parmed.exceptions.ParsingError

Bases: parmed.exceptions.ParmedError

If there was a problem parsing any kind of file

exception parmed.exceptions.PdbxError

Bases: parmed.exceptions.ParmedError

Class for catching general errors with PDBx/mmCIF parsing

exception parmed.exceptions.PdbxSyntaxError(lineNumber='-1', text='')

Bases: parmed.exceptions.PdbxError

Class for catching errors in mmCIF/PDBx syntax

exception parmed.exceptions.PreProcessorError

Bases: parmed.exceptions.ParmedError

If there is a problem running the C-like preprocessor

exception parmed.exceptions.PreProcessorWarning

Bases: parmed.exceptions.ParmedWarning

If there is something we should warn about in preprocessing

exception parmed.exceptions.ResidueError

Bases: parmed.exceptions.ParmedError

For when there are problems defining a residue

exception parmed.exceptions.RosettaError

Bases: parmed.exceptions.ParmedError

If there is a problem loading a Rosetta pose object

exception parmed.exceptions.SplitResidueWarning

Bases: parmed.exceptions.ParmedWarning

For if a residue with the same number but different names is split

exception parmed.exceptions.TinkerError

Bases: parmed.exceptions.ParsingError

Raised when one of the TINKER parsing routines hits a bad file

exception parmed.exceptions.TinkerWarning

Bases: parmed.exceptions.ParmedWarning