schrodinger.application.desmond.mapper_msj_generator module

class schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator(jobname, cd_params, force_field='OPLS3e', 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, gcmc=False, disable_custom_charge=False)

Bases: object

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

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

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

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

write_master_msj()

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, gcmc=False)

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, gcmc=False)

generate_master_msj()

modify_fep_launcher_stage(raw)

modify_graph_stage(raw)

set_box_buffer_width(raw, width)

set_ff(raw)

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

set_net_charge_box(raw)

set_coul_correction(raw)

static find_production_stage()

set_lambda_hopping(raw, h_mass=False, rest_property='i_rest_hot_region')

set_solvate(raw: schrodinger.utils.sea.Map)

In cpu mode, enables the solvate pocket stage. In GPU mode, the solvate pocket stage and following full temp Langevin stage(s) before the lambda hopping stage (for NPT, one unrestrained and one restrained, for NVT just one unrestrained) are replaced with one restrained and one unrestrained water equalizing GCMC solvate pocket stage. For both, a brownie stage is added after to deal with the effects of removing water from the corners of the simulation box.

Parameters:raw (sea.Map) – The msj to modify

class schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator(jobname, cd_params, force_field='OPLS3e', sim_time='5000', rand_seed='2014', buffer_width=0.0, lambda_windows=None, charged_lambda_windows=None, fep_convergence=0.0, disable_custom_charge=False)

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

write_vacuum_msj(concatenate=False)

generate_vacuum_msj(net_charge=False, core_hopping=False, concatenate=False)

set_subjob_msj(subjobmsj_contents, net_charge, core_hopping, concatenate=False)

modify_fep_launcher_stage(raw)

modify_graph_stage(raw)

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

Bases: schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator

modify_graph_stage(raw)

Not support custom .pkl file for now

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, gcmc=False)

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

Bases: schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator

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

modify_graph_stage(raw)

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, gcmc=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.