AmberToPDB
AmberToPDB.check_data_params()
AmberToPDB.launch()
amber_to_pdb()
main()
CpptrajRandomizeIons
CpptrajRandomizeIons.check_data_params()
CpptrajRandomizeIons.launch()
cpptraj_randomize_ions()
LeapAddIons
LeapAddIons.find_leaprc_paths()
LeapAddIons.find_out_number_of_ions()
LeapAddIons.launch()
leap_add_ions()
LeapBuildLinearStructure
LeapBuildLinearStructure.check_data_params()
LeapBuildLinearStructure.find_leaprc_paths()
LeapBuildLinearStructure.launch()
leap_build_linear_structure()
LeapGenTop
LeapGenTop.find_leaprc_paths()
LeapGenTop.launch()
leap_gen_top()
LeapSolvate
LeapSolvate.find_leaprc_paths()
LeapSolvate.launch()
leap_solvate()
NabBuildDNAStructure
NabBuildDNAStructure.check_data_params()
NabBuildDNAStructure.launch()
nab_build_dna_structure()
ParmedCpinUtil
ParmedCpinUtil.check_data_params()
ParmedCpinUtil.launch()
parmed_cpinutil()
ParmedHMassRepartition
ParmedHMassRepartition.check_data_params()
ParmedHMassRepartition.launch()
parmed_hmassrepartition()
Pdb4amberRun
Pdb4amberRun.check_data_params()
Pdb4amberRun.launch()
pdb4amber_run()
ProcessMinOut
ProcessMinOut.check_data_params()
ProcessMinOut.launch()
process_minout()
ProcessMDOut
ProcessMDOut.check_data_params()
ProcessMDOut.launch()
process_mdout()
SanderMDRun
SanderMDRun.check_data_params()
SanderMDRun.create_mdin()
SanderMDRun.launch()
sander_mdrun()
PmemdMDRun
PmemdMDRun.check_data_params()
PmemdMDRun.create_mdin()
PmemdMDRun.launch()
pmemd_mdrun()
CphstatsRun
CphstatsRun.check_data_params()
CphstatsRun.launch()
cphstats_run()
CestatsRun
CestatsRun.check_data_params()
CestatsRun.launch()
cestats_run()