Index

A

AIAssistantDialog (class in BFEE2.gui) AISkillExecutor (class in BFEE2.skills) alchemicalAdvancedSettings (class in BFEE2.gui) alchemicalBindingFreeEnergy() (BFEE2.postTreatment.postTreatment method)

alchemicalFreeEnergy() (BFEE2.postTreatment.postTreatment method) alchemicalFreeEnergyPMF() (BFEE2.postTreatment.postTreatment method) amberToGromacs() (in module BFEE2.commonTools.fileParser) applyTheme() (BFEE2.gui.AIAssistantDialog method)

B

BAR_free_energy() (BFEE2.third_party.py_bar.FEPAnalyzer method) 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.skills module BFEE2.templates_gromacs.BFEEGromacs module BFEE2.templates_namd.configTemplate module BFEE2.templates_namd.scriptTemplate module BFEE2.templates_namd.updateCenters module BFEE2.third_party.py_bar module BFEEGromacs (class in BFEE2.templates_gromacs.BFEEGromacs)

C

calcRMSD() (in module BFEE2.commonTools.ploter) centerSystem() (BFEE2.commonTools.fileParser.fileParser method) changeABFRange() (in module BFEE2.templates_namd.updateCenters) changeCenters() (in module BFEE2.templates_namd.updateCenters) charmmToGromacs() (in module BFEE2.commonTools.fileParser) charmmToGromacsTemplate() (in module BFEE2.templates_namd.scriptTemplate) ColvarsParser (class in BFEE2.third_party.py_bar) configTemplate (class in BFEE2.templates_namd.configTemplate) correctGaWTM() (in module BFEE2.commonTools.ploter) correctGaWTMHist() (in module BFEE2.commonTools.ploter) cvABFTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method)

cvAngleTemplate() (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) cvHistogramTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvLambdaTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvPolarAngleTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvProteinTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvReweightAMDTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvRMSDTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) cvRTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method)

D

DirectoryExistError

E

execute() (BFEE2.skills.AISkillExecutor method)

F

FEP_free_energy() (BFEE2.third_party.py_bar.FEPAnalyzer method) FEPAnalyzer (class in BFEE2.third_party.py_bar)

fileParser (class in BFEE2.commonTools.fileParser) FileTypeUnknownError findOptimalCVs() (in module BFEE2.templates_namd.updateCenters)

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) geometricBindingFreeEnergyHistPMF() (BFEE2.postTreatment.postTreatment method) get_cell() (in module BFEE2.templates_gromacs.BFEEGromacs) get_data() (BFEE2.third_party.py_bar.ColvarsParser method) (BFEE2.third_party.py_bar.NAMDParser method) get_restraint_contribution() (BFEE2.third_party.py_bar.ColvarsParser method) getGaWTMBaseName() (in module BFEE2.commonTools.ploter) getGaWTMBaseNames() (in module BFEE2.commonTools.ploter) getGaWTMHistBaseName() (in module BFEE2.commonTools.ploter) getGaWTMHistBaseNames() (in module BFEE2.commonTools.ploter) getResid() (BFEE2.commonTools.fileParser.fileParser method) gromacsConfigTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) gromacsMinimizeConfigTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) gromacsToAmber() (in module BFEE2.commonTools.fileParser)

H

handler (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

I

inputGenerator (class in BFEE2.inputGenerator) interpolateHistPMFFrames() (in module BFEE2.commonTools.ploter)

isGaWTM() (in module BFEE2.commonTools.ploter) isGaWTMHist() (in module BFEE2.commonTools.ploter) isGeometric() (in module BFEE2.templates_namd.updateCenters)

L

LDDMBindingFreeEnergy() (BFEE2.postTreatment.postTreatment method) 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) MergeData() (BFEE2.third_party.py_bar.FEPAnalyzer method) mergeHistPMF() (in module BFEE2.commonTools.ploter) mergePMF() (in module BFEE2.commonTools.ploter)

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

N

namdConfigTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) NAMDParser (class in BFEE2.third_party.py_bar)

newCvEulerAngleTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) newCvPolarAngleTemplate() (BFEE2.templates_namd.configTemplate.configTemplate method) NoCorrectionFileError

O

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

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

P

pairGaWTMFiles() (in module BFEE2.commonTools.ploter) pairGaWTMHistFiles() (in module BFEE2.commonTools.ploter) parent (BFEE2.skills.AISkillExecutor property) parseDat() (in module BFEE2.templates_namd.updateCenters) parseHistFile() (in module BFEE2.commonTools.ploter)

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

R

readCenters() (in module BFEE2.templates_namd.updateCenters) readFrame() (in module BFEE2.commonTools.ploter) readHistPMF() (in module BFEE2.commonTools.ploter)

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

S

saveConvergence() (in module BFEE2.commonTools.ploter) saveFile() (BFEE2.commonTools.fileParser.fileParser method) saveHysteresis() (in module BFEE2.commonTools.ploter) saveNDX() (BFEE2.commonTools.fileParser.fileParser method) saveStructure() (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs method) scanGromacsTopologyInclude() (in module BFEE2.templates_gromacs.BFEEGromacs) SCHEMA_NAME (BFEE2.skills.AISkillExecutor attribute) 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) showEvent() (BFEE2.gui.AIAssistantDialog method) solvent (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute) staticMetaObject (BFEE2.gui.AIAssistantDialog attribute) (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)

THEME_COLORS (BFEE2.gui.AIAssistantDialog attribute) topologyFile (BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs attribute)

U

updateAlchemicalFiles() (in module BFEE2.templates_namd.updateCenters)

updateGeometricFiles() (in module BFEE2.templates_namd.updateCenters)

W

Window_boundaries() (BFEE2.third_party.py_bar.FEPAnalyzer method)

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