qmmd
QMMD Usage Demonstration
CHANGELOG
Contributing
Code of Conduct
API Reference
qmmd
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
W
_
_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)