Class CovalentMsjGenerator

        object --+    
                 |    
MapperMsjGenerator --+
                     |
                    CovalentMsjGenerator

Known Subclasses:

No support for GraphDB yet

Instance Methods

[hide private]

__init__(self, mutation_site, *args, **kw)
Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

modify_graph_stage(self, raw)
Not support custom .pkl file for now

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

Inherited from MapperMsjGenerator: generate_complex_msj, generate_master_msj, generate_solvent_msj, get_fep_analysis_stage_number, modify_fep_launcher_stage, set_box_buffer_width, set_coul_correction, set_cubic_box, set_ff, set_lambda_hopping, set_lambda_windows, set_subjob_msj, write_complex_msj, write_master_msj, write_solvent_msj

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, mutation_site, *args, **kw)
(Constructor)

Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

Overrides: object.__init__

modify_graph_stage(self, raw)

Not support custom .pkl file for now

Overrides: MapperMsjGenerator.modify_graph_stage

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

Overrides: MapperMsjGenerator.generate_subjob_msj

Class CovalentMsjGenerator

__init__(self, mutation_site, *args, **kw) (Constructor)

modify_graph_stage(self, raw)

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

init(self, mutation_site, *args, **kw)
(Constructor)