Index

A

addConnetivityForce() (wechrom.WechromSystem method) addDefaultForces() (wechrom.SingleNucleoSystem method) (wechrom.WechromSystem method) addExcludVolumeForce() (wechrom.SingleNucleoSystem method) (wechrom.WechromSystem method)

addForce() (wechrom.WechromSystem method) addInterStrandMemoryForce() (wechrom.WechromSystem method) addIntraStrandMemoryForce() (wechrom.WechromSystem method) addNucleoCenterMemoryForce() (wechrom.SingleNucleoSystem method) addNucleoNeighborMemoryForce() (wechrom.SingleNucleoSystem method) atoms (wechrom.WechromSystem attribute)

C

coarse_grain_atompdb_2_wechromcif() (in module wechrom.utils)

constructDNAIndex() (wechrom.WechromSystem method)

D

dnaRes (wechrom.WechromSystem attribute)

dnaStrands (wechrom.WechromSystem attribute) dnaTypes (wechrom.WechromSystem attribute)

F

forcefield (wechrom.WechromSystem attribute)

G

generate_naked_memory_files() (in module wechrom.prepare_memory) generate_nucleo_memory_files() (in module wechrom.prepare_memory)

get_naked_memory_template_bonds() (in module wechrom.prepare_memory) get_nucleo_memory_template_bonds() (in module wechrom.prepare_memory)

I

initializeSimulation() (wechrom.WechromSystem method)

integrator (wechrom.WechromSystem attribute)

M

module wechrom.prepare_memory wechrom.utils

N

nBp (wechrom.WechromSystem attribute) nucZero (wechrom.SingleNucleoSystem attribute)

num_inter_memory_bonds() (in module wechrom.utils) num_intra_memory_bonds() (in module wechrom.utils)

P

pdbx (wechrom.WechromSystem attribute) platform (wechrom.WechromSystem attribute) positions (wechrom.WechromSystem attribute) pro_Atom2Res (wechrom.SingleNucleoSystem attribute)

pro_Res2Atom (wechrom.SingleNucleoSystem attribute) proRes (wechrom.SingleNucleoSystem attribute) protein (wechrom.SingleNucleoSystem attribute) proTypes (wechrom.SingleNucleoSystem attribute)

R

read_memory_template() (in module wechrom.prepare_memory)

residues (wechrom.WechromSystem attribute) runSteps() (wechrom.WechromSystem method)

S

simulation (wechrom.WechromSystem attribute)

SingleNucleoSystem (class in wechrom) system (wechrom.WechromSystem attribute)

W

wechrom.prepare_memory module

wechrom.utils module WechromSystem (class in wechrom)