Loop modeling

SOAP loop model.

class loop.MyLoop(env, sequence, alnfile=None, knowns=[], inimodel=None, deviation=None, library_schedule=None, csrfile=None, inifile=None, assess_methods=None, loop_assess_methods=None, refinepot=['$(LIB)/atmcls-mf.lib', '$(LIB)/dist-mf.lib'], loops=[], calcrmsds='111', nonbond_spine=0.1, contact_shell=12.0, deviations=50, energytrace=False, assess_trace=True)

SOAP loop modeling class

get_loop_actions()

Get actions to carry out during loop optimization

loop_model_analysis(atmsel, ini_model, filename, out, id1, num)

Energy evaluation and assessment, and write out the loop model

multiple_loop_models(atmsel, ini_model, num, sched)

Build all loop models for a given initial model

single_loop_model(atmsel, ini_model, num, id1, sched, parallel=False)

Build a single loop model

class loop.ORLoop(env, sequence, alnfile=None, knowns=[], inimodel=None, deviation=None, library_schedule=None, csrfile=None, inifile=None, assess_methods=None, loop_assess_methods=None, refinepot=['$(LIB)/atmcls-mf.lib', '$(LIB)/dist-mf.lib'], assess_trace=False, loops=[], calcrmsds='111', nonbond_spine=0.1, contact_shell=12.0, deviations=50, energytrace=False)

Original loop modeling class

get_loop_actions()

Get actions to carry out during loop optimization

loop_model_analysis(atmsel, ini_model, filename, out, id1, num)

Energy evaluation and assessment, and write out the loop model

single_loop_model(atmsel, ini_model, num, id1, sched, parallel=False)

Build a single loop model

class loop.checkRMSD(skip, loopObj, first=False, last=False, start=0)

Calculate the RMSDs of intermediate loops

loop.sgmd(atmsel, actions)

Very slow MD annealing

class loop.sprefine(dslist='101', bm='loop.100.8', criteria='bestrmsd', nonbond_spline=0.1, contact_shell=12.0, deviations=50, assess='', mcrmsdonly=False, spmodel=None, refineProtocal=None, trace=True, saveStructure=False)

SOAP loop refinement benchmark class