Index

_

_results (pmda.density.DensityAnalysis attribute) (pmda.leaflet.LeafletFinder attribute) (pmda.parallel.ParallelAnalysisBase attribute) (pmda.rdf.InterRDF attribute) (pmda.rms.rmsd.RMSD attribute) (pmda.rms.rmsf.RMSF attribute)

A

analysis_class() (in module pmda.custom)

AnalysisFromFunction (class in pmda.custom)

B

bins (pmda.rdf.InterRDF attribute)

C

cdf() (pmda.rdf.InterRDF property) compute() (pmda.parallel.Timing property) compute_block() (pmda.parallel.Timing property) conclude() (pmda.parallel.Timing property) Contacts (class in pmda.contacts)

count_by_ids() (pmda.hbond_analysis.HydrogenBondAnalysis method) count_by_time() (pmda.hbond_analysis.HydrogenBondAnalysis method) count_by_type() (pmda.hbond_analysis.HydrogenBondAnalysis method) cumulate_time() (pmda.parallel.Timing property) current_coordinates() (pmda.density.DensityAnalysis static method)

D

DensityAnalysis (class in pmda.density)

E

elapsed (pmda.util.timeit attribute)

F

fold_second_order_moments() (in module pmda.util)

G

guess_acceptors() (pmda.hbond_analysis.HydrogenBondAnalysis method)

guess_donors() (pmda.hbond_analysis.HydrogenBondAnalysis method) guess_hydrogens() (pmda.hbond_analysis.HydrogenBondAnalysis method)

H

HydrogenBondAnalysis (class in pmda.hbond_analysis)

I

InterRDF (class in pmda.rdf)

io() (pmda.parallel.Timing property) io_block() (pmda.parallel.Timing property)

L

LeafletFinder (class in pmda.leaflet)

M

make_balanced_slices() (in module pmda.util) module pmda.contacts pmda.custom pmda.density pmda.hbond_analysis pmda.leaflet pmda.parallel pmda.rdf pmda.rms.rmsd pmda.rms.rmsf pmda.util

P

ParallelAnalysisBase (class in pmda.parallel) ParallelAnalysisClass (built-in class) pmda.contacts module pmda.custom module pmda.density module pmda.hbond_analysis module pmda.leaflet module

pmda.parallel module pmda.rdf module pmda.rms.rmsd module pmda.rms.rmsf module pmda.util module prepare() (pmda.parallel.Timing property)

Q

q1q2() (in module pmda.contacts)

R

rdf (pmda.rdf.InterRDF attribute) readonly_attributes() (pmda.contacts.Contacts method) (pmda.density.DensityAnalysis method) (pmda.leaflet.LeafletFinder method) (pmda.parallel.ParallelAnalysisBase method) (pmda.rdf.InterRDF method) (pmda.rms.rmsd.RMSD method) (pmda.rms.rmsf.RMSF method) results (ParallelAnalysisClass attribute) (pmda.custom.AnalysisFromFunction attribute) RMSD (class in pmda.rms.rmsd)

rmsd (pmda.rms.rmsd.RMSD attribute) RMSF (class in pmda.rms.rmsf) rmsf (pmda.rms.rmsf.RMSF attribute) run() (ParallelAnalysisClass method) (pmda.contacts.Contacts method) (pmda.density.DensityAnalysis method) (pmda.leaflet.LeafletFinder method) (pmda.parallel.ParallelAnalysisBase method) (pmda.rdf.InterRDF method) (pmda.rms.rmsd.RMSD method) (pmda.rms.rmsf.RMSF method)

S

second_order_moments() (in module pmda.util)

T

timeit (class in pmda.util) timeseries (pmda.contacts.Contacts attribute)

Timing (class in pmda.parallel) total() (pmda.parallel.Timing property)

U

universe() (pmda.parallel.Timing property)

W

wait() (pmda.parallel.Timing property)