schrodinger.application.desmond.mapper_msj_generator module

class schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator(fmp_fname, *args, **kw)

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

No support for GraphDB yet

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

modify_graph_stage(raw)

Not support custom .pkl file for now

class schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator(jobname, cd_params, force_field='OPLS3', ensemble='NPT', sim_time='5000', rand_seed='2014', buffer_width=0.0, atom_mapping='', align_core_only=False, ats=False, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0, membrane=False, salt_concentration=0.15)

Bases: object

generate_complex_msj(net_charge, modify_dihe=False, h_mass=False, solvate=False, ch=False, minimize_volume=False, concatenate=False)

generate_master_msj()

generate_solvent_msj(net_charge, modify_dihe=False, h_mass=False, ch=False, minimize_volume=False, concatenate=False)

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

get_fep_analysis_stage_number(msj_filename)

modify_fep_launcher_stage(raw)

modify_graph_stage(raw)

set_box_buffer_width(raw, width)

set_coul_correction(raw)

set_ff(raw)

set_lambda_hopping(raw, h_mass=False)

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

set_net_charge_box(raw)

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

write_complex_msj(modify_dihe=False, h_mass=False, solvate=False, minimize_volume=False, concatenate=False)

write_master_msj()

write_solvent_msj(modify_dihe=False, h_mass=False, minimize_volume=False, concatenate=False)

class schrodinger.application.desmond.mapper_msj_generator.MetalMsjGenerator(mp, *args, **kw)

Bases: schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator

No support for GraphDB yet

modify_graph_stage(raw)

class schrodinger.application.desmond.mapper_msj_generator.ProteinMapperMsjGenerator(fep_type, solvent_asl=None, mutation_filename='mutations.txt', residue_structure='', *args, **kw)

Bases: schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator

generate_subjob_msj(buffer_width, complex=False, net_charge=False, modify_dihe=False, h_mass=False, solvate=False, ch=False, minimize_volume=False, concatenate=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.

modify_graph_stage(raw)

class schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator(jobname, cd_params, force_field='OPLS3', sim_time='5000', rand_seed='2014', buffer_width=0.0, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0)

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

generate_vacuum_msj(net_charge=False, core_hopping=False)

modify_fep_launcher_stage(raw)

modify_graph_stage(raw)

set_subjob_msj(subjobmsj_contents, net_charge, core_hopping)

write_vacuum_msj()