Index

A

alchemicalAdvancedSettings (class in BFEE2.gui)

alchemicalBindingFreeEnergy() (BFEE2.postTreatment.postTreatment method)

B

baseDirectory (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) basenames (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) BFEE2.commonTools.commonSlots module BFEE2.commonTools.fileParser module BFEE2.commonTools.ploter module BFEE2.gui module

BFEE2.inputGenerator module BFEE2.postTreatment module BFEE2.templates_gromacs.BFEEGromacs module BFEE2.templates_namd.configTemplate module BFEE2.templates_namd.scriptTemplate module BFEEGromacs (class in BFEE2.templates_gromacs.BFEEGromacs)

C

calcRMSD() (in module BFEE2.commonTools.ploter) centerSystem() (BFEE2.commonTools.fileParser.fileParser method) configTemplate (class in BFEE2.templates_namd.configTemplate) cvABFTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvEulerAngleTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvHarmonicTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method)

cvHarmonicWallsTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvHeadTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvPolarAngleTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvProteinTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvRMSDTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvRTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method)

D

DirectoryExistError

F

fileParser (class in BFEE2.commonTools.fileParser)

FileTypeUnknownError

G

generate000() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate001() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate002() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate003() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate004() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate005() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate006() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate007() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generate008() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generateColvars() (in module BFEE2.templates_gromacs.BFEEGromacs)

generateGromacsGeometricFiles() (BFEE2.inputGenerator.inputGenerator method) generateGromacsIndex() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) generateMDP() (in module BFEE2.templates_gromacs.BFEEGromacs) generateNAMDAlchemicalFiles() (BFEE2.inputGenerator.inputGenerator method) generateNAMDGeometricFiles() (BFEE2.inputGenerator.inputGenerator method) generateShellScript() (in module BFEE2.templates_gromacs.BFEEGromacs) geometricAdvancedSettings (class in BFEE2.gui) geometricBindingFreeEnergy() (BFEE2.postTreatment.postTreatment method) get_cell() (in module BFEE2.templates_gromacs.BFEEGromacs) getResid() (BFEE2.commonTools.fileParser.fileParser method)

H

handler (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

I

inputGenerator (class in BFEE2.inputGenerator)

L

ligand (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) ligandOnly (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

ligandOnlyStructureFile (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) ligandOnlySystem (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) logger (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

M

mainSettings (class in BFEE2.gui) mainUI (class in BFEE2.gui) mearsurePolarAngles() (in module BFEE2.templates_gromacs.BFEEGromacs) measure_center() (in module BFEE2.templates_gromacs.BFEEGromacs) measure_minmax() (in module BFEE2.templates_gromacs.BFEEGromacs) measureCenter() (BFEE2.commonTools.fileParser.fileParser method) measureDistance() (BFEE2.commonTools.fileParser.fileParser method) measureMinmax() (BFEE2.commonTools.fileParser.fileParser method) measurePBC() (BFEE2.commonTools.fileParser.fileParser method) measurePolarAngles() (BFEE2.commonTools.fileParser.fileParser method) mergePMF() (in module BFEE2.commonTools.ploter)

module BFEE2.commonTools.commonSlots BFEE2.commonTools.fileParser BFEE2.commonTools.ploter BFEE2.gui BFEE2.inputGenerator BFEE2.postTreatment BFEE2.templates_gromacs.BFEEGromacs BFEE2.templates_namd.configTemplate BFEE2.templates_namd.scriptTemplate moveSystem() (BFEE2.commonTools.fileParser.fileParser method)

N

namdConfigTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method)

O

openFileDialog() (in module BFEE2.commonTools.commonSlots)

openFilesDialog() (in module BFEE2.commonTools.commonSlots)

P

parseHistFile() (in module BFEE2.commonTools.ploter) plotConvergence() (in module BFEE2.commonTools.ploter)

plotPMF() (in module BFEE2.commonTools.ploter) postTreatment (class in BFEE2.postTreatment) protein (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

R

readFrame() (in module BFEE2.commonTools.ploter)

readPMF() (in module BFEE2.commonTools.ploter) rotateSystem() (BFEE2.commonTools.fileParser.fileParser method)

S

saveFile() (BFEE2.commonTools.fileParser.fileParser method) saveNDX() (BFEE2.commonTools.fileParser.fileParser method) saveStructure() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) scanGromacsTopologyInclude() (in module BFEE2.templates_gromacs.BFEEGromacs) SelectionError, [1] setBeta() (BFEE2.commonTools.fileParser.fileParser method) setLigandHeavyAtomsGroup() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) setProteinHeavyAtomsGroup() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method)

setSolventAtomsGroup() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) setTemperature() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) solvent (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) staticMetaObject (BFEE2.gui.alchemicalAdvancedSettings attribute) (BFEE2.gui.geometricAdvancedSettings attribute) (BFEE2.gui.mainSettings attribute) (BFEE2.gui.mainUI attribute) structureFile (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) system (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

T

temperature (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

topologyFile (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

W

writePMF() (in module BFEE2.commonTools.ploter)