Index

A

amber_to_pdb() (in module ambpdb.amber_to_pdb) AmberToPDB (class in ambpdb.amber_to_pdb)

ambpdb.amber_to_pdb module

C

cestats_run() (in module cphstats.cestats_run) CestatsRun (class in cphstats.cestats_run) check_data_params() (ambpdb.amber_to_pdb.AmberToPDB method) (cphstats.cestats_run.CestatsRun method) (cphstats.cphstats_run.CphstatsRun method) (cpptraj.cpptraj_randomize_ions.CpptrajRandomizeIons method) (leap.leap_add_ions.LeapAddIons method) (leap.leap_build_linear_structure.LeapBuildLinearStructure method) (leap.leap_gen_top.LeapGenTop method) (leap.leap_solvate.LeapSolvate method) (nab.nab_build_dna_structure.NabBuildDNAStructure method) (parmed.parmed_cpinutil.ParmedCpinUtil method) (parmed.parmed_hmassrepartition.ParmedHMassRepartition method) (pdb4amber.pdb4amber_run.Pdb4amberRun method) (pmemd.pmemd_mdrun.PmemdMDRun method) (process.process_mdout.ProcessMDOut method) (process.process_minout.ProcessMinOut method) (sander.sander_mdrun.SanderMDRun method)

cphstats.cestats_run module cphstats.cphstats_run module cphstats_run() (in module cphstats.cphstats_run) CphstatsRun (class in cphstats.cphstats_run) cpptraj.cpptraj_randomize_ions module cpptraj_randomize_ions() (in module cpptraj.cpptraj_randomize_ions) CpptrajRandomizeIons (class in cpptraj.cpptraj_randomize_ions) create_mdin() (pmemd.pmemd_mdrun.PmemdMDRun method) (sander.sander_mdrun.SanderMDRun method)

F

find_out_number_of_ions() (leap.leap_add_ions.LeapAddIons method)

L

launch() (ambpdb.amber_to_pdb.AmberToPDB method) (cphstats.cestats_run.CestatsRun method) (cphstats.cphstats_run.CphstatsRun method) (cpptraj.cpptraj_randomize_ions.CpptrajRandomizeIons method) (leap.leap_add_ions.LeapAddIons method) (leap.leap_build_linear_structure.LeapBuildLinearStructure method) (leap.leap_gen_top.LeapGenTop method) (leap.leap_solvate.LeapSolvate method) (nab.nab_build_dna_structure.NabBuildDNAStructure method) (parmed.parmed_cpinutil.ParmedCpinUtil method) (parmed.parmed_hmassrepartition.ParmedHMassRepartition method) (pdb4amber.pdb4amber_run.Pdb4amberRun method) (pmemd.pmemd_mdrun.PmemdMDRun method) (process.process_mdout.ProcessMDOut method) (process.process_minout.ProcessMinOut method) (sander.sander_mdrun.SanderMDRun method)

leap.leap_add_ions module leap.leap_build_linear_structure module leap.leap_gen_top module leap.leap_solvate module leap_add_ions() (in module leap.leap_add_ions) leap_build_linear_structure() (in module leap.leap_build_linear_structure) leap_gen_top() (in module leap.leap_gen_top) leap_solvate() (in module leap.leap_solvate) LeapAddIons (class in leap.leap_add_ions) LeapBuildLinearStructure (class in leap.leap_build_linear_structure) LeapGenTop (class in leap.leap_gen_top) LeapSolvate (class in leap.leap_solvate)

M

main() (in module ambpdb.amber_to_pdb) (in module cphstats.cestats_run) (in module cphstats.cphstats_run) (in module cpptraj.cpptraj_randomize_ions) (in module leap.leap_add_ions) (in module leap.leap_build_linear_structure) (in module leap.leap_gen_top) (in module leap.leap_solvate) (in module nab.nab_build_dna_structure) (in module parmed.parmed_cpinutil) (in module parmed.parmed_hmassrepartition) (in module pdb4amber.pdb4amber_run) (in module pmemd.pmemd_mdrun) (in module process.process_mdout) (in module process.process_minout) (in module sander.sander_mdrun)

module ambpdb.amber_to_pdb cphstats.cestats_run cphstats.cphstats_run cpptraj.cpptraj_randomize_ions leap.leap_add_ions leap.leap_build_linear_structure leap.leap_gen_top leap.leap_solvate nab.nab_build_dna_structure parmed.parmed_cpinutil parmed.parmed_hmassrepartition pdb4amber.pdb4amber_run pmemd.pmemd_mdrun process.process_mdout process.process_minout sander.sander_mdrun

N

nab.nab_build_dna_structure module

nab_build_dna_structure() (in module nab.nab_build_dna_structure) NabBuildDNAStructure (class in nab.nab_build_dna_structure)

P

parmed.parmed_cpinutil module parmed.parmed_hmassrepartition module parmed_cpinutil() (in module parmed.parmed_cpinutil) parmed_hmassrepartition() (in module parmed.parmed_hmassrepartition) ParmedCpinUtil (class in parmed.parmed_cpinutil) ParmedHMassRepartition (class in parmed.parmed_hmassrepartition) pdb4amber.pdb4amber_run module pdb4amber_run() (in module pdb4amber.pdb4amber_run) Pdb4amberRun (class in pdb4amber.pdb4amber_run)

pmemd.pmemd_mdrun module pmemd_mdrun() (in module pmemd.pmemd_mdrun) PmemdMDRun (class in pmemd.pmemd_mdrun) process.process_mdout module process.process_minout module process_mdout() (in module process.process_mdout) process_minout() (in module process.process_minout) ProcessMDOut (class in process.process_mdout) ProcessMinOut (class in process.process_minout)

S

sander.sander_mdrun module

sander_mdrun() (in module sander.sander_mdrun) SanderMDRun (class in sander.sander_mdrun)