Class ProteinMapperMsjGenerator

        object --+        
                 |        
MapperMsjGenerator --+    
                     |    
  CovalentMsjGenerator --+
                         |
                        ProteinMapperMsjGenerator

Instance Methods

[hide private]

__init__(self, solvent_asl=None, mutation_filename='mutations.txt', *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, MSJ_TEMPLATE=None, net_charge=False, modify_dihe=False, h_mass=False, ch=False)
For protein residue mutation, the subjob msj file will be the same as small molecule workflow; For protein stability, the subjob msj file will be the same as covalent bond workflow.

Inherited from MapperMsjGenerator: generate_complex_msj, generate_master_msj, generate_solvent_msj, 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, solvent_asl=None, mutation_filename=`'mutations.txt'`, *args, **kw)
(Constructor)

Valid FF : OPLS_2005 OPLS3 CHARMM AMBER

Overrides: object.__init__: (inherited documentation)

modify_graph_stage(self, raw)

Not support custom .pkl file for now

Overrides: MapperMsjGenerator.modify_graph_stage

generate_subjob_msj(self, buffer_width, MSJ_TEMPLATE=None, net_charge=False, modify_dihe=False, h_mass=False, ch=False)

For protein residue mutation, the subjob msj file will be the same as small molecule workflow; For protein stability, the subjob msj file will be the same as covalent bond workflow.

Overrides: MapperMsjGenerator.generate_subjob_msj

Class ProteinMapperMsjGenerator

__init__(self, solvent_asl=None, mutation_filename='mutations.txt', *args, **kw) (Constructor)

modify_graph_stage(self, raw)

generate_subjob_msj(self, buffer_width, MSJ_TEMPLATE=None, net_charge=False, modify_dihe=False, h_mass=False, ch=False)

init(self, solvent_asl=None, mutation_filename=`'mutations.txt'`, *args, **kw)
(Constructor)