Python API

BFEE2 Python API provides information for the end-user to use BFEE in a console program / streamline.

One may always use BFEE2.inputGenerator and BFEE2.postTreatment when using BFEE2 Python API in automated/streamlined binding free-energy calculation. If one wants to use BFEE as an NAMD, GROMACS, Colvars, or FEP parser, BFEE2.templates_namd, BFEE2.templates_gromacs, and BFEE2.third_party also deserve a look. The GUI and AI-assistant support modules are documented for completeness.

See BFEE2 user guide if one wants to know how to use BFEE2.

• BFEE2.commonTools
  • BFEE2.commonTools.commonSlots
    • openFileDialog()
    • openFilesDialog()
  • BFEE2.commonTools.fileParser
    • SelectionError
    • amberToGromacs()
    • charmmToGromacs()
    • fileParser
      • fileParser.centerSystem()
      • fileParser.getResid()
      • fileParser.measureCenter()
      • fileParser.measureDistance()
      • fileParser.measureMinmax()
      • fileParser.measurePBC()
      • fileParser.measurePolarAngles()
      • fileParser.moveSystem()
      • fileParser.rotateSystem()
      • fileParser.saveFile()
      • fileParser.saveNDX()
      • fileParser.setBeta()
    • gromacsToAmber()
  • BFEE2.commonTools.ploter
    • NoCorrectionFileError
    • calcRMSD()
    • correctGaWTM()
    • correctGaWTMHist()
    • getGaWTMBaseName()
    • getGaWTMBaseNames()
    • getGaWTMHistBaseName()
    • getGaWTMHistBaseNames()
    • interpolateHistPMFFrames()
    • isGaWTM()
    • isGaWTMHist()
    • mergeHistPMF()
    • mergePMF()
    • pairGaWTMFiles()
    • pairGaWTMHistFiles()
    • parseHistFile()
    • plotConvergence()
    • plotHysteresis()
    • plotPMF()
    • readFrame()
    • readHistPMF()
    • readPMF()
    • saveConvergence()
    • saveHysteresis()
    • writeHistPMF()
    • writePMF()
• BFEE2.gui
  • AIAssistantDialog
    • AIAssistantDialog.THEME_COLORS
    • AIAssistantDialog.applyTheme()
    • AIAssistantDialog.showEvent()
    • AIAssistantDialog.staticMetaObject
  • alchemicalAdvancedSettings
    • alchemicalAdvancedSettings.staticMetaObject
  • geometricAdvancedSettings
    • geometricAdvancedSettings.staticMetaObject
  • mainSettings
    • mainSettings.staticMetaObject
  • mainUI
    • mainUI.staticMetaObject
• BFEE2.inputGenerator
  • DirectoryExistError
  • FileTypeUnknownError
  • inputGenerator
    • inputGenerator.generateGromacsGeometricFiles()
    • inputGenerator.generateNAMDAlchemicalFiles()
    • inputGenerator.generateNAMDGeometricFiles()
• BFEE2.templates_namd
  • BFEE2.templates_namd.configTemplate
    • configTemplate
      • configTemplate.cvABFTemplate()
      • configTemplate.cvAngleTemplate()
      • configTemplate.cvEulerAngleTemplate()
      • configTemplate.cvHarmonicTemplate()
      • configTemplate.cvHarmonicWallsTemplate()
      • configTemplate.cvHeadTemplate()
      • configTemplate.cvHistogramTemplate()
      • configTemplate.cvLambdaTemplate()
      • configTemplate.cvPolarAngleTemplate()
      • configTemplate.cvProteinTemplate()
      • configTemplate.cvRMSDTemplate()
      • configTemplate.cvRTemplate()
      • configTemplate.cvReweightAMDTemplate()
      • configTemplate.gromacsConfigTemplate()
      • configTemplate.gromacsMinimizeConfigTemplate()
      • configTemplate.namdConfigTemplate()
      • configTemplate.newCvEulerAngleTemplate()
      • configTemplate.newCvPolarAngleTemplate()
  • BFEE2.templates_namd.scriptTemplate
    • charmmToGromacsTemplate()
  • BFEE2.templates_namd.updateCenters
    • changeABFRange()
    • changeCenters()
    • findOptimalCVs()
    • isGeometric()
    • parseDat()
    • readCenters()
    • updateAlchemicalFiles()
    • updateGeometricFiles()
• BFEE2.templates_gromacs
  • BFEEGromacs
    • BFEEGromacs.logger
    • BFEEGromacs.handler
    • BFEEGromacs.baseDirectory
    • BFEEGromacs.structureFile
    • BFEEGromacs.topologyFile
    • BFEEGromacs.ligandOnlyStructureFile
    • BFEEGromacs.system
    • BFEEGromacs.ligandOnlySystem
    • BFEEGromacs.basenames
    • BFEEGromacs.ligand
    • BFEEGromacs.ligandOnly
    • BFEEGromacs.protein
    • BFEEGromacs.solvent
    • BFEEGromacs.temperature
    • BFEEGromacs.generate000()
    • BFEEGromacs.generate001()
    • BFEEGromacs.generate002()
    • BFEEGromacs.generate003()
    • BFEEGromacs.generate004()
    • BFEEGromacs.generate005()
    • BFEEGromacs.generate006()
    • BFEEGromacs.generate007()
    • BFEEGromacs.generate008()
    • BFEEGromacs.generateGromacsIndex()
    • BFEEGromacs.saveStructure()
    • BFEEGromacs.setLigandHeavyAtomsGroup()
    • BFEEGromacs.setProteinHeavyAtomsGroup()
    • BFEEGromacs.setSolventAtomsGroup()
    • BFEEGromacs.setTemperature()
  • SelectionError
  • generateColvars()
  • generateMDP()
  • generateShellScript()
  • get_cell()
  • mearsurePolarAngles()
  • measure_center()
  • measure_minmax()
  • scanGromacsTopologyInclude()
• BFEE2.postTreatment
  • RStarTooLargeError
  • postTreatment
    • postTreatment.LDDMBindingFreeEnergy()
    • postTreatment.alchemicalBindingFreeEnergy()
    • postTreatment.alchemicalFreeEnergy()
    • postTreatment.alchemicalFreeEnergyPMF()
    • postTreatment.geometricBindingFreeEnergy()
    • postTreatment.geometricBindingFreeEnergyHistPMF()
• BFEE2.third_party
  • BFEE2.third_party.py_bar
    • ColvarsParser
      • ColvarsParser.get_data()
      • ColvarsParser.get_restraint_contribution()
    • FEPAnalyzer
      • FEPAnalyzer.BAR_free_energy()
      • FEPAnalyzer.FEP_free_energy()
      • FEPAnalyzer.MergeData()
      • FEPAnalyzer.Window_boundaries()
    • NAMDParser
      • NAMDParser.get_data()
• BFEE2.skills
  • AISkillExecutor
    • AISkillExecutor.SCHEMA_NAME
    • AISkillExecutor.execute()
    • AISkillExecutor.parent