schrodinger.application.desmond.stage.analysis module

class schrodinger.application.desmond.stage.analysis.Reporter(fname, plotter='gchart')

Bases: object

__init__(fname, plotter='gchart')

plot(*arg, **kwarg)

Generates the plot and returns an url to the plot.

plot_2d(*arg, **kwarg)

Generates the plot and returns an url to the plot.

write(msg)

close()

class schrodinger.application.desmond.stage.analysis.AnalysisJob(model_fname, traj_fname, reporter, title, *arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.Job

__init__(model_fname, traj_fname, reporter, title, *arg, **kwarg)

run()

class schrodinger.application.desmond.stage.analysis.TimeSeriesAnalysisJob(time_series, prob_profile, *arg, **kwarg)

Bases: schrodinger.application.desmond.stage.analysis.AnalysisJob

Y_MARKER = {'angle': ('angle (deg)', 'x', 'purple', 'red'), 'dihedral': ('dihe (deg)', 'circle', 'skyblue', 'blue'), 'distance': ('dist (A)', 'diamond', 'grey', 'black')}

TS_NAME = {'angle': 'angle(t)', 'dihedral': 'dihe(t)', 'distance': 'dist(t)'}

PR_NAME = {'angle': 'P(angle)', 'dihedral': 'P(dihe)', 'distance': 'P(dist)'}

__init__(time_series, prob_profile, *arg, **kwarg)

run()

class schrodinger.application.desmond.stage.analysis.MetadynamicsAnalysisJob(meta_setting, reporter, title='', *arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.Job

__init__(meta_setting, reporter, title='', *arg, **kwarg)

run()

class schrodinger.application.desmond.stage.analysis.SeaJob(SEA, *arg, **kwarg)

Bases: schrodinger.application.desmond.stage.analysis.AnalysisJob

__init__(SEA, *arg, **kwarg)

run()

class schrodinger.application.desmond.stage.analysis.PLAnalysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

This class sets up and runs analysis for protein-ligand complex. The input parameters are ligand and protein ASLs, if not specified the class will automatically try to detect appropriate values, if “none” is specified the class will ignore analysis for the parameter and in other cases use the parameter value to run the analysis job.

NAME = 'pl_analysis'

PARAM = <schrodinger.utils.sea.sea.Map object>

__init__(*arg, **kwarg)

initialization of pl-analysis stage

crunch()

do all the setup and submit the calculations

hook_captured_successful_job(job)

class schrodinger.application.desmond.stage.analysis.Analysis(*arg, **kwarg)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'analysis'

PARAM = <schrodinger.utils.sea.sea.Map object>

DEFAULT_PROB_PROFILE_SETTING = {'angle': [2, 0, 180, True], 'dihedral': [2, 0, 360, True]}

__init__(*arg, **kwarg)

crunch()

hook_captured_successful_job(job)

class schrodinger.application.desmond.stage.analysis.FepanaJob(fepid=None, n_win=None, sim_job=None, mutation=None, temperature=300.0, correct_restr=False, correct_coul=False, correct_vdw=False, bennett=None, reporter=None, fep_type=None, include_sid=True, *arg, **kwarg)

Bases: schrodinger.application.desmond.stage.jobs.DesmondJob, schrodinger.application.desmond.picklejar.Picklable

id = 0

__init__(fepid=None, n_win=None, sim_job=None, mutation=None, temperature=300.0, correct_restr=False, correct_coul=False, correct_vdw=False, bennett=None, reporter=None, fep_type=None, include_sid=True, *arg, **kwarg)

describe()

get_endpoint_cmsfiles()

run()

class schrodinger.application.desmond.stage.analysis.FepAnalysis(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

NAME = 'fep_analysis'

PARAM = <schrodinger.utils.sea.sea.Map object>

crunch()

poststage()