biobb_amber
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biobb_amber
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Index
A
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C
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F
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L
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M
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N
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P
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S
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)
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