rpxdock.search package

Submodules

rpxdock.search.asym module

class rpxdock.search.asym.AsymEvaluator(bodies, hscore, **kw)

Bases: object

rpxdock.search.asym.asym_get_sample_hierarchy(body, hscore, extent=100)

set up XformHier with appropriate bounds and resolution

rpxdock.search.asym.make_asym(bodies, hscore, sampler, search=<function hier_search>, **kw)

rpxdock.search.basic module

rpxdock.search.basic.evaluate_positions(evaluator, xforms, executor=None, **kw)

rpxdock.search.basic.evaluate_positions_executor(executor, evaluator, xforms, **kw)

rpxdock.search.basic.grid_search(sampler, evaluator, **kw)

rpxdock.search.basic.trim_ok(trim, nres, max_trim, **kw)

rpxdock.search.cyclic module

class rpxdock.search.cyclic.CyclicEvaluator(body, sym, hscore, **kw)

Bases: object

rpxdock.search.cyclic.make_cyclic(monomer, sym, hscore, search=<function hier_search>, sampler=None, **kw)

rpxdock.search.cyclic.make_cyclic_hier_sampler(monomer, hscore)

rpxdock.search.dockspec module

class rpxdock.search.dockspec.DockSpec1CompCage(arch)

Bases: object

place_along_axis(pos, slide_dist)

placements(angles)

placements_second(placements)

slide_dir()

symframes(cellspacing=None, radius=None)

class rpxdock.search.dockspec.DockSpec1CompMirrorLayer(arch)

Bases: object

class rpxdock.search.dockspec.DockSpec2CompCage(arch)

Bases: object

move_to_canonical_unit(pos1, pos2)

place_along_axes(pos1, pos2)

placements1(angles, flip=True)

placements2(angles)

slide_dir(angles)

symframes(cellspacing=None, radius=None)

class rpxdock.search.dockspec.DockSpec3CompCage(arch)

Bases: object

class rpxdock.search.dockspec.DockSpec3CompLayer(arch)

Bases: object

class rpxdock.search.dockspec.DockSpecMonomerToCyclic(arch)

Bases: object

place_along_axis(pos, slide_dist)

placements_second(placements)

slide_dir()

symframes(cellspacing=None, radius=None)

rpxdock.search.gridslide module

rpxdock.search.gridslide.find_connected_1xCyclic_slide(spec, body, samples, min_contacts=30, contact_dis=8.0)

rpxdock.search.gridslide.find_connected_2xCyclic_slide(spec, body1, body2, samples, min_contacts=30, contact_dis=8.0, onebody=True, **kw)

rpxdock.search.gridslide.find_connected_monomer_to_cyclic_slide(spec, body, samples, min_contacts, contact_dis)

rpxdock.search.gridslide.samples_1xCyclic(spec, resl=1)

rpxdock.search.gridslide.samples_1xMonomer_orientations(resl)

rpxdock.search.gridslide.samples_2xCyclic_slide(spec, resl=1, max_out_of_plane_angle=10, **kw)

rpxdock.search.helix module

class rpxdock.search.helix.HelixEvaluator(body, hscore, **kw)

Bases: object

rpxdock.search.helix.helix_get_sample_hierarchy(body, hscore, extent=100)

set up XformHier with appropriate bounds and resolution

rpxdock.search.helix.make_helix(body, hscore, sampler, search=<function hier_search>, **kw)

rpxdock.search.hierarchical module

rpxdock.search.hierarchical.expand_samples(iresl, sampler, indices=None, scores=None, beam_size=None, **kw)

rpxdock.search.hierarchical.hier_search(sampler, evaluator, **kw)

rpxdock.search.multicomp module

class rpxdock.search.multicomp.MultiCompEvaluator(*arg, **kw)

Bases: rpxdock.search.multicomp.MultiCompEvaluatorBase

class rpxdock.search.multicomp.MultiCompEvaluatorBase(bodies, spec, hscore, wts={'ncontact': 0.1, 'rpx': 1.0}, **kw)

Bases: object

class rpxdock.search.multicomp.TwoCompEvaluatorWithTrim(*arg, trimmable_components='AB', **kw)

Bases: rpxdock.search.multicomp.MultiCompEvaluatorBase

eval_trim_one(trim_component, x, iresl=- 1, wts={}, **kw)

rpxdock.search.multicomp.make_multicomp(bodies, spec, hscore, search=<function hier_search>, sampler=None, fixed_components=False, **kw)

rpxdock.search.onecomp module

class rpxdock.search.onecomp.OneCompEvaluator(body, spec, hscore, wts={'ncontact': 0.1, 'rpx': 1.0}, trimmable_components='AB', **kw)

Bases: object

rpxdock.search.onecomp.make_onecomp(body, spec, hscore, search=<function hier_search>, sampler=None, fixed_components=False, **kw)

rpxdock.search.plug module

class rpxdock.search.plug.PlugEvaluator(plug, hole, hscore, **kw)

Bases: object

iface_scores(xforms, iresl=- 1, wts={}, **_)

rpxdock.search.plug.make_plugs(plug, hole, hscore, search=<function hier_search>, sampler=None, **kw)

rpxdock.search.plug.plug_get_sample_hierarchy(plug, hole, hscore)

set up XformHier with appropriate bounds and resolution

rpxdock.search.plug.plug_test_hier_sampler(plug, hole, hscore, n=6)

rpxdock.search.result module

class rpxdock.search.result.Result(data_or_file=None, body_=[], body_label_=None, **kw)

Bases: object

copy()

dump_pdb(imodel, output_prefix='', output_suffix='', fname=None, output_body='ALL', sym='', sep='_', skip=[], hscore=None, output_asym_only=False, **kw)

dump_pdbs(which, ndigwhich=None, ndigmdl=None, lbl='', skip=[], output_prefix='rpx', **kw)

dump_pdbs_top_score(nout_top=10, **kw)

dump_pdbs_top_score_each(nout_each=1, **kw)

getstate()

property ndocks

sel(*args, **kw)

setstate(state)

sortby(*args, **kw)

top_each(neach=1)

rpxdock.search.result.assert_results_close(r, s, n=- 1)

rpxdock.search.result.concat_results(results, **kw)

rpxdock.search.result.dict_coherent_entries(alldicts)

rpxdock.search.result.dummy_result(size=1000)

Module contents