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src/b/i/biskit-2.4/Biskit/SettingsManager.py   biskit(Download)
                if self.verbose: B.EHandler.warning(\
                    'User setting %s is reset to default (%r),\n\treason: %s'\
                    % (name, default.value, next.error)\
                    + '\n\tPlease check %s!' % self.fuser )
            except IOError, e:
                if self.verbose: B.EHandler.warning(
                    'Could not find file with user-defined settings in %s' \
                    % self.fuser, trace=0, error=0)
            if not os.path.exists( fpath ):
                if self.verbose:
                    B.EHandler.warning('Creating folder %s for Biskit settings.'\
                                       %fpath )
                os.mkdir( fpath )
        if self.fusermissing and self.createmissing:
            if self.verbose:
                B.EHandler.warning('Creating new user configuration file %s.' \
                                   % self.fuser, trace=0, error=0)
            self.writeUserSettings( errorsonly=True )

src/b/i/biskit-2.4/Biskit/SettingsParser.py   biskit(Download)
            if verbose and s.error:
                B.EHandler.warning( s.error, trace=0, error=0 )
        return r

src/b/i/biskit-2.4/Biskit/PDBModel.py   biskit(Download)
            ## fall-back solution: assign 0 to all entries that raise
            ## exception
            EHandler.warning("mask(): Error while mapping funtion "+
                             "to all atoms.")
            result = []
                ## put 0 if something goes wrong
                except :
                    EHandler.warning("mask(): Error while save-mapping ")
        if len(i)==self.lenAtoms() and max(i)<2:
            EHandler.warning('dont use PDBModel.keep() with mask.', trace=0) 
        r = self.take( i )
                if verbose:
                    EHandler.warning("addChainId(): Problem with atom "+str(a))

src/b/i/biskit-2.4/Biskit/Mod/SequenceSearcher.py   biskit(Download)
        err, o = commands.getstatusoutput( cmd )
        if err:
            EHandler.warning('%s returned error: %r' % (cmd, err) )
            raise BlastError( 'fastacmd failed. Error code: ' + str(err) )
                result[i] = r
            except BlastError, why:
                EHandler.warning("couldn't fetch %s"%str(i),trace=0 )
        if self.verbose:
        except IOError, why:
            EHandler.warning( "Can't write cluster report." + str(why) )
        except Exception, why:
            EHandler.warning("Error while writing blast result to %s" %outFile)
            EHandler.warning("function namespace published to globals")

src/b/i/biskit-2.4/Biskit/Mod/__init__.py   biskit(Download)
except ImportError, why:
    B.EHandler.warning( 'Error importing Biskit/Mod modules', trace=1 )

src/b/i/biskit-2.4/Biskit/Trajectory.py   biskit(Download)
            if type( self.frames ) == list or self.frames.dtype.char == 'd':
                EHandler.warning("Converting coordinates to float array.")
                self.frames = N.array( self.frames ).astype(N.Float32)
            EHandler.warning('Could not convert frames to float array.', 1)

src/b/i/biskit-2.4/Biskit/Dock/__init__.py   biskit(Download)
except IOError, why:
    EHandler.warning("Couldn't import all Biskit.Dock modules.\n" + str(why))
## PVM-dependent modules
    from ContactMaster import ContactMaster
    from ContactSlave import ContactSlave
except Exception, why:
    EHandler.warning("Couldn't import PVM-dependent modules of Biskit.Dock.\n"+\

src/b/i/biskit-2.4/Biskit/Dock/Complex.py   biskit(Download)
        if self.contacts != None and type( self.contacts ) == str:
            self.contacts = t.load( self.contacts )
            EHandler.warning("loading old-style pickled contacts.") 
            return self.contacts
                lenRec, lenLig = self.contacts['shape']
                EHandler.warning("uncompressing contacts without shape")
                lenRec = self.rec().lenResidues()
                lenLig = self.lig().lenResidues()

src/b/i/biskit-2.4/Biskit/SurfaceRacer.py   biskit(Download)
                EHandler.warning("No relative accessabilities calculated "+\
                                 "when using a prob radius other than 1.4 A"+\
                                 " or not using the Richards vdw radii set.")
        except KeyError, what:
            EHandler.warning("Missing standard accessibilities for some "+\

src/b/i/biskit-2.4/Biskit/Mod/TemplateSearcher.py   biskit(Download)
        err, o = commands.getstatusoutput( cmd )
        if err:
            EHandler.warning('%s returned error: %r' % (cmd, err) )
            raise BlastError( err )
                result[ i['pdb'] ] = r
            except BlastError, why:
                EHandler.warning("ERROR (ignored): couldn't fetch "+ str(i) )
        return result

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