Class EnergyGroupAnalysis

Known Subclasses:

General Energy Group analysis class.

Instance Methods

__init__(self, cst, trjfile, orig_cfgfile, groups)
Initialize

getGroups(self)
Return energy groups.

getEnergyTimeSeries(self)
return energy values

_prepareCfg(self, orig_cfgfile, new_cfgfile, cmsfile, trjfile, outputfile)
Prepare a config file for vrun using backend config file.

_prepareCmsfile(self, cst, cmsfile, groups)
Create a cms file for vrun based on group definition.

_launchVrun(self, cfgfile, cmsfile)
Launch vrun to evaluate energy.

_processLine(self, energy_match, line, ngroups)

_parseOutput(self, filename)
Parse output from vrun to retrieve energy.

_sort_dict(self, d)
sort dictionary values by keys; return two lists

_calcEnergy(self)

_cleanup(self, file_list)
Cleanup temporary created files

Class Variables

MAX_NGROUPS_SUPPORTED = 255

energy_term_pattern = '(angle|dihedral|far_exclusion|far_terms...

floating_number_pattern = '([-+]?\\b(?:[0-9]*\\.)?[0-9]+(?:[eE...

Method Details

Cleanup temporary created files

Parameters:

Class Variable Details

Value:

'(angle|dihedral|far_exclusion|far_terms|nonbonded_elec|nonbonded_vdw|
pair_elec|pair_vdw|stretch|Total)'

Value:

'([-+]?\\b(?:[0-9]*\\.)?[0-9]+(?:[eE][-+]?[0-9]+)?\\b)'