B โ๊๕bท ใ@sdZddlZGdd„deƒZGdd„deƒZGdd„deƒZGd d „d eƒZGd d „d eƒZGd d„deƒZGdd„deƒZ Gdd„deƒZ Gdd„deƒZ Gdd„deƒZ Gdd„deƒZ Gdd„deƒZGdd„deƒZGdd„deƒZGdd „d eƒZGd!d"„d"eƒZGd#d$„d$eƒZGd%d&„d&eƒZGd'd(„d(eƒZGd)d*„d*eƒZGd+d,„d,eƒZejd-ed.Gd/d0„d0eƒZGd1d2„d2eƒZGd3d4„d4eƒZGd5d6„d6eƒZGd7d8„d8eƒZGd9d:„d:eƒZGd;d<„d„d>eƒZ!Gd?d@„d@eƒZ"GdAdB„dBeƒZ#dS)CzS This module contains all of the exceptions that are used in the chemistry package ้Nc@seZdZdZdS)ฺ ParmedErrorz< Base class for all non-trivial exceptions raised by ParmEd N)ฺ__name__ฺ __module__ฺ __qualname__ฺ__doc__ฉrr๚0lib/python3.7/site-packages/parmed/exceptions.pyr src@seZdZdZdS)ฺ ParsingErrorz1 If there was a problem parsing any kind of file N)rrrrrrrrr sr c@seZdZdZdS)ฺPDBErrorz+ If there was a problem parsing a PDB file N)rrrrrrrrr sr c@seZdZdZdS)ฺ Mol2Errorz, If there was a problem parsing a Mol2 file N)rrrrrrrrr sr c@seZdZdZdS)ฺ MaskErrorz$ Error when a Mask is poorly formed N)rrrrrrrrr sr c@seZdZdZdS)ฺ OpenMMErrorz. If there's a problem making an OpenMM system N)rrrrrrrrr sr c@seZdZdZdS)ฺ AmberErrorz" This is a generic AmberParmError N)rrrrrrrrrsrc@seZdZdZdS)ฺ TinkerErrorz@ Raised when one of the TINKER parsing routines hits a bad file N)rrrrrrrrrsrc@seZdZdZdS)ฺ CharmmErrorz0 If there is a problem parsing CHARMM PSF files N)rrrrrrrrr!src@seZdZdZdS)ฺ ResidueErrorz0 For when there are problems defining a residue N)rrrrrrrrr$src@seZdZdZdS)ฺIncompatiblePatchErrorz> For when applying a PatchTemplate to a ResidueTemplate fails N)rrrrrrrrr'src@seZdZdZdS)ฺParameterErrorz+ If a parameter is missing from a database N)rrrrrrrrr*src@seZdZdZdS)ฺ GromacsErrorz6 If there is a problem parsing GROMACS topology files N)rrrrrrrrr-src@seZdZdZdS)ฺFormatNotFoundz> If the file format does not have a registered parser with it N)rrrrrrrrr0src@seZdZdZdS)ฺ RosettaErrorz5 If there is a problem loading a Rosetta pose object N)rrrrrrrrr3src@seZdZdZdS)ฺPreProcessorErrorz7 If there is a problem running the C-like preprocessor N)rrrrrrrrr6src@seZdZdZdS)ฺ MoleculeErrorz> If there is a problem defining a molecule via the bond graph N)rrrrrrrrr9src@seZdZdZdS)ฺ PdbxErrorz; Class for catching general errors with PDBx/mmCIF parsing N)rrrrrrrrr<src@s"eZdZdZd dd„Zdd„ZdS) ฺPdbxSyntaxErrorz0 Class for catching errors in mmCIF/PDBx syntax ๚-1ฺcCst |ก||_||_dS)N)ฺ Exceptionฺ__init__ฺ lineNumberฺtext)ฺselfrr rrrrAs zPdbxSyntaxError.__init__cCsd|j|jfS)Nz%%ERROR - [at line: %d] %s)rr )r!rrrฺ__str__FszPdbxSyntaxError.__str__N)rr)rrrrrr"rrrrr?s rc@seZdZdZdS)ฺ InputErrorz# When there is an error with input N)rrrrrrrrr#Isr#c@seZdZdZdS)ฺ ParmedWarningz. Base class for all warnings raised by ParmEd N)rrrrrrrrr$Nsr$ฺalways)ฺcategoryc@seZdZdZdS)ฺ PDBWarningz6 A non-fatal error to indicate a problematic PDB file N)rrrrrrrrr'Tsr'c@seZdZdZdS)ฺ AmberWarningz) If there is something that is non-fatal N)rrrrrrrrr(Wsr(c@seZdZdZdS)ฺSplitResidueWarningzD For if a residue with the same number but different names is split N)rrrrrrrrr)Zsr)c@seZdZdZdS)ฺ CharmmWarningz" For non-fatal PSF parsing issues N)rrrrrrrrr*]sr*c@seZdZdZdS)ฺGromacsWarningzI If we are uncertain about something regarding the GROMACS topology file N)rrrrrrrrr+`sr+c@seZdZdZdS)ฺParameterWarningzF If a type of parameter is missing, but you don't want it to be fatal N)rrrrrrrrr,csr,c@s eZdZdS)ฺ TinkerWarningN)rrrrrrrr-fsr-c@seZdZdZdS)ฺPreProcessorWarningz= If there is something we should warn about in preprocessing N)rrrrrrrrr.isr.c@seZdZdZdS)ฺ OpenMMWarningzE If there is something we should warn when processing OpenMM objects N)rrrrrrrrr/lsr/c@seZdZdZdS)ฺ CharmmPsfEOFz2 If we hit an end-of-file in parsing CHARMM files N)rrrrrrrrr0qsr0)$rฺwarningsrrr r r r r rrrrrrrrrrrrrr#ฺWarningr$ฺfilterwarningsr'r(r)r*r+r,r-r.r/r0rrrrฺsB