Index

_

_plot_charge_correlations() (in module qmmd.qmcalc.visAnalysis.plotFigs)

_plot_single_regression() (in module qmmd.qmcalc.visAnalysis.plotFigs)

A

AddState() (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram method)

analyse_base_interaction() (in module qmmd.mdsim.baseID) ax (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute)

B

barrier_data (in module qmmd.qmcalc.visAnalysis.plotConfig)

benchmarking_data (in module qmmd.qmcalc.visAnalysis.plotConfig)

C

cal2J (in module qmmd.qmcalc.unitConv) charge_list (in module qmmd.qmcalc.visAnalysis.plotConfig) charge_list_A (in module qmmd.qmcalc.visAnalysis.plotConfig) charge_list_B (in module qmmd.qmcalc.visAnalysis.plotConfig) color (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute)

COLORS (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) column (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) columns (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) combination_dict (in module qmmd.qmcalc.visAnalysis.plotConfig) covbond_dict (in module qmmd.mdsim.prepMTB)

D

dashes (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) DetermineEnergyRange() (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram method) DI_list (in module qmmd.qmcalc.visAnalysis.plotConfig)

Diagram (class in qmmd.qmcalc.visAnalysis.energyLeveller) do_legend (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) Draw() (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram method)

E

energy (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) energyUnits (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute)

energyUnitsConversion() (in module qmmd.qmcalc.unitConv) eyringEquation() (in module qmmd.qmcalc.unitConv)

F

fig (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) find_line_index() (in module qmmd.mdsim.prepMTB)

findVal() (in module qmmd.qmcalc.tabulate) FOUR_PLOTS_HEIGHT (in module qmmd.mdsim.config) FOUR_PLOTS_WIDTH (in module qmmd.mdsim.config)

G

genAllScripts() (in module qmmd.qmcalc.genScripts) genExampleXYZs() (in module qmmd.datasets)

getExampleChargePath() (in module qmmd.datasets) getExampleEnergyLevellerInputPath() (in module qmmd.datasets) groupFilesIntoDir() (in module qmmd.qmcalc.admin)

H

h (in module qmmd.qmcalc.unitConv)

height (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute)

I

index_dict (in module qmmd.mdsim.prepMTB) index_dict_template (in module qmmd.mdsim.prepMTB) inhibitor_list (in module qmmd.mdsim.config)

inpDirPath (in module qmmd.qmcalc.admin) (in module qmmd.qmcalc.genScripts) inputDirPath (in module qmmd.qmcalc.tabulate)

K

kappa (in module qmmd.qmcalc.unitConv)

kB (in module qmmd.qmcalc.unitConv) keywordDict (in module qmmd.qmcalc.constants)

L

label (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) labelColor (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) labelOffset (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) leftPointx (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute)

leftPointy (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) legend (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) ligand_dict (in module qmmd.mdsim.prepMTB) lin_reg() (in module qmmd.qmcalc.visAnalysis.plotFigs) linksTo (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute)

M

main() (in module qmmd.main) (in module qmmd.qmcalc.visAnalysis.energyLeveller) makeDirForXYZs() (in module qmmd.qmcalc.admin) MakeExampleFile() (in module qmmd.qmcalc.visAnalysis.energyLeveller) MakeLeftRightPoints() (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram method) map_index() (in module qmmd.mdsim.prepMTB) module qmmd qmmd.data qmmd.datasets qmmd.main qmmd.mdsim qmmd.mdsim.baseID qmmd.mdsim.bbRMSD qmmd.mdsim.config qmmd.mdsim.hbondAnalysis qmmd.mdsim.ligDihedral qmmd.mdsim.mdAnalyse qmmd.mdsim.prepMTB qmmd.mdsim.SCbondDist qmmd.qmcalc qmmd.qmcalc.admin qmmd.qmcalc.constants qmmd.qmcalc.genScripts qmmd.qmcalc.jobSubmit qmmd.qmcalc.tabulate qmmd.qmcalc.unitConv qmmd.qmcalc.visAnalysis qmmd.qmcalc.visAnalysis.energyLeveller qmmd.qmcalc.visAnalysis.plotConfig qmmd.qmcalc.visAnalysis.plotFigs

N

name (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute)

normalisedPosition (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute)

O

outputName (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute)

P

parser (in module qmmd.mdsim.baseID) (in module qmmd.mdsim.bbRMSD) (in module qmmd.mdsim.hbondAnalysis) (in module qmmd.mdsim.ligDihedral) (in module qmmd.mdsim.SCbondDist) (in module qmmd.qmcalc.jobSubmit) (in module qmmd.qmcalc.visAnalysis.plotFigs)

plot_barriers_bar() (in module qmmd.qmcalc.visAnalysis.plotFigs) plot_bb_rmsd() (in module qmmd.mdsim.bbRMSD) plot_benchmarking_bar() (in module qmmd.qmcalc.visAnalysis.plotFigs) plot_hbond_analysis() (in module qmmd.mdsim.hbondAnalysis) plot_lig_dihedral() (in module qmmd.mdsim.ligDihedral) plot_regression_analysis() (in module qmmd.qmcalc.visAnalysis.plotFigs) plot_sc_bond_dist() (in module qmmd.mdsim.SCbondDist) pop_dict() (in module qmmd.mdsim.prepMTB)

Q

qmmd module qmmd.data module qmmd.datasets module qmmd.main module qmmd.mdsim module qmmd.mdsim.baseID module qmmd.mdsim.bbRMSD module qmmd.mdsim.config module qmmd.mdsim.hbondAnalysis module qmmd.mdsim.ligDihedral module qmmd.mdsim.mdAnalyse module qmmd.mdsim.prepMTB module

qmmd.mdsim.SCbondDist module qmmd.qmcalc module qmmd.qmcalc.admin module qmmd.qmcalc.constants module qmmd.qmcalc.genScripts module qmmd.qmcalc.jobSubmit module qmmd.qmcalc.tabulate module qmmd.qmcalc.unitConv module qmmd.qmcalc.visAnalysis module qmmd.qmcalc.visAnalysis.energyLeveller module qmmd.qmcalc.visAnalysis.plotConfig module qmmd.qmcalc.visAnalysis.plotFigs module

R

R (in module qmmd.qmcalc.unitConv) ReadInput() (in module qmmd.qmcalc.visAnalysis.energyLeveller) replaceMultiple() (in module qmmd.qmcalc.tabulate)

rightPointx (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) rightPointy (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) rmExtension() (in module qmmd.qmcalc.admin)

S

SEPARATOR (in module qmmd.mdsim.prepMTB) SINGLE_PLOT_HEIGHT (in module qmmd.mdsim.config) SINGLE_PLOT_LEG_HEIGHT (in module qmmd.mdsim.config) SINGLE_PLOT_LEG_WIDTH (in module qmmd.mdsim.config) SINGLE_PLOT_WIDTH (in module qmmd.mdsim.config) SIX_PLOTS_HEIGHT (in module qmmd.mdsim.config) SIX_PLOTS_HORIZONTAL_HEIGHT (in module qmmd.mdsim.config)

SIX_PLOTS_HORIZONTAL_WIDTH (in module qmmd.mdsim.config) SIX_PLOTS_WIDTH (in module qmmd.mdsim.config) sortNatural() (in module qmmd.qmcalc.tabulate) State (class in qmmd.qmcalc.visAnalysis.energyLeveller) statesList (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) submit_jobs() (in module qmmd.qmcalc.jobSubmit) sumCharge() (in module qmmd.mdsim.mdAnalyse)

T

T (in module qmmd.qmcalc.unitConv) test() (in module qmmd)

textOffset (qmmd.qmcalc.visAnalysis.energyLeveller.State attribute) timeUnitsConversion() (in module qmmd.qmcalc.unitConv)

W

width (qmmd.qmcalc.visAnalysis.energyLeveller.Diagram attribute) write_map_file() (in module qmmd.mdsim.prepMTB)

writeGaussInpFile() (in module qmmd.qmcalc.genScripts) writeHPCJobScript() (in module qmmd.qmcalc.genScripts) writeToExcel() (in module qmmd.qmcalc.tabulate)