Class MapperMsjGenerator

object --+
         |
        MapperMsjGenerator

Known Subclasses:

Instance Methods

[hide private]

__init__(self, jobname, cd_params, force_field='OPLS3', ensemble='NPT', sim_time='5000', rand_seed='2014', buffer_width=0.0, atom_mapping='', ats=False, lambda_windows=None, charged_lambda_windows=None, core_hopping=False, fep_convergence=0.0, membrane=False)
Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

generate_complex_msj(self, net_charge, modify_dihe=False, h_mass=False, solvate=False, ch=False)

write_complex_msj(self, modify_dihe=False, h_mass=False, solvate=False)

generate_solvent_msj(self, net_charge, modify_dihe=False, h_mass=False, ch=False)

write_solvent_msj(self, modify_dihe=False, h_mass=False)

write_master_msj(self)

generate_subjob_msj(self, buffer_width, complex=False, net_charge=False, modify_dihe=False, h_mass=False, solvate=False, ch=False)

set_subjob_msj(self, subjobmsj_contents, buffer_width, net_charge, complex=False, modify_dihe=False, h_mass=False, solvate=False, core_hopping=False)

generate_master_msj(self)

get_fep_analysis_stage_number(self, msj_filename)

modify_fep_launcher_stage(self, raw)

modify_graph_stage(self, raw)

set_box_buffer_width(self, raw, width)

set_ff(self, raw)

set_lambda_windows(self, raw, num_windows, schedule_type='default')

set_cubic_box(self, raw)

set_coul_correction(self, raw)

set_lambda_hopping(self, raw, h_mass=False)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, jobname, cd_params, force_field=`'OPLS3'`, ensemble=`'NPT'`, sim_time=`'5000'`, rand_seed=`'2014'`, buffer_width=0.0, atom_mapping=`''`, ats=False, lambda_windows=None, charged_lambda_windows=None, core_hopping=False, fep_convergence=0.0, membrane=False)
(Constructor)

Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

Overrides: object.__init__

Class MapperMsjGenerator

__init__(self, jobname, cd_params, force_field='OPLS3', ensemble='NPT', sim_time='5000', rand_seed='2014', buffer_width=0.0, atom_mapping='', ats=False, lambda_windows=None, charged_lambda_windows=None, core_hopping=False, fep_convergence=0.0, membrane=False) (Constructor)

init(self, jobname, cd_params, force_field=`'OPLS3'`, ensemble=`'NPT'`, sim_time=`'5000'`, rand_seed=`'2014'`, buffer_width=0.0, atom_mapping=`''`, ats=False, lambda_windows=None, charged_lambda_windows=None, core_hopping=False, fep_convergence=0.0, membrane=False)
(Constructor)