import rpxdock as rp, concurrent
[docs]def test_cage_hier_onecomp_notrim(hscore, bodyC3):
arg = rp.app.defaults()
arg.wts = rp.Bunch(ncontact=0.01, rpx=1.0)
arg.beam_size = 2e4
arg.max_bb_redundancy = 2.0
arg.max_delta_h = 9999
arg.nout_debug = 0
arg.nout_top = 0
arg.nout_each = 0
arg.score_only_ss = 'H'
arg.max_trim = 0
# arg.debug = True
arg.executor = concurrent.futures.ThreadPoolExecutor(min(4, arg.ncpu / 2))
spec = rp.search.DockSpec1CompCage('T3')
sampler = rp.sampling.hier_axis_sampler(spec.nfold, lb=0, ub=100, axis=spec.axis,
flipax=spec.flip_axis)
result = rp.search.make_onecomp(bodyC3, spec, hscore, rp.hier_search, sampler, **arg)
# print(result)
# result.dump_pdbs_top_score(
# hscore=hscore, **arg.sub(nout_top=10, output_prefix='test_cage_hier_onecomp_notrim'))
# rp.dump(result, 'rpxdock/data/testdata/test_cage_hier_onecomp_notrim.pickle')
ref = rp.data.get_test_data('test_cage_hier_onecomp_notrim')
rp.search.assert_results_close(result, ref)
# result.dump_pdbs_top_score(10)
[docs]def test_cage_hier_D3_onecomp_notrim(hscore, bodyC3):
arg = rp.app.defaults()
arg.wts = rp.Bunch(ncontact=0.01, rpx=1.0)
arg.beam_size = 2e4
arg.max_bb_redundancy = 2.0
arg.max_delta_h = 9999
arg.nout_debug = 0
arg.nout_top = 0
arg.nout_each = 0
arg.score_only_ss = 'H'
arg.max_trim = 0
# arg.debug = True
arg.executor = concurrent.futures.ThreadPoolExecutor(min(4, arg.ncpu / 2))
spec = rp.search.DockSpec1CompCage('D3_3')
sampler = rp.sampling.hier_axis_sampler(spec.nfold, lb=0, ub=100, axis=spec.axis,
flipax=spec.flip_axis)
result = rp.search.make_onecomp(bodyC3, spec, hscore, rp.hier_search, sampler, **arg)
# print(result)
# result.dump_pdbs_top_score(
# hscore=hscore, **arg.sub(nout_top=10, output_prefix='test_cage_hier_D3_onecomp_notrim'))
# rp.dump(result, 'rpxdock/data/testdata/test_cage_hier_D3_onecomp_notrim.pickle')
ref = rp.data.get_test_data('test_cage_hier_D3_onecomp_notrim')
rp.search.assert_results_close(result, ref)
# result.dump_pdbs_top_score(10)
[docs]def test_cage_hier_D3_2_onecomp_notrim(hscore, bodyC2):
arg = rp.app.defaults()
arg.wts = rp.Bunch(ncontact=0.01, rpx=1.0)
arg.beam_size = 2e4
arg.max_bb_redundancy = 2.0
arg.max_delta_h = 9999
arg.nout_debug = 0
arg.nout_top = 0
arg.nout_each = 0
arg.score_only_ss = 'H'
arg.max_trim = 0
# arg.debug = True
arg.executor = concurrent.futures.ThreadPoolExecutor(min(4, arg.ncpu / 2))
spec = rp.search.DockSpec1CompCage('D3_2')
sampler = rp.sampling.hier_axis_sampler(spec.nfold, lb=0, ub=100, axis=spec.axis,
flipax=spec.flip_axis)
result = rp.search.make_onecomp(bodyC2, spec, hscore, rp.hier_search, sampler, **arg)
# print(result)
# result.dump_pdbs_top_score(
# hscore=hscore, **arg.sub(nout_top=10, output_prefix='test_cage_hier_D3_2_onecomp_notrim'))
# rp.dump(result, 'rpxdock/data/testdata/test_cage_hier_D3_2_onecomp_notrim.pickle')
ref = rp.data.get_test_data('test_cage_hier_D3_2_onecomp_notrim')
rp.search.assert_results_close(result, ref)
# result.dump_pdbs_top_score(10)
def _test_cage_hier_onecomp_trim(hscore, bodyC3):
arg = rp.app.defaults()
arg.wts = rp.Bunch(ncontact=0.01, rpx=1.0)
arg.beam_size = 2e4
arg.max_bb_redundancy = 2.0
arg.max_delta_h = 9999
arg.nout_debug = 0
arg.nout_top = 0
arg.nout_each = 0
arg.score_only_ss = 'H'
arg.max_trim = 200
arg.trim_direction = 'C'
# arg.debug = True
# arg.executor = concurrent.futures.ThreadPoolExecutor(min(4, arg.ncpu / 2))
spec = rp.search.DockSpec1CompCage('T3')
sampler = rp.sampling.hier_axis_sampler(spec.nfold, lb=0, ub=200, resl=5, angresl=5,
axis=spec.axis, flipax=spec.flip_axis)
result = rp.search.make_onecomp(bodyC3, spec, hscore, rp.hier_search, sampler, **arg)
print(result)
result.dump_pdbs_top_score(10)
# rp.dump(result, 'rpxdock/data/testdata/test_cage_hier_onecomp_trim.pickle')
# ref = rp.data.get_test_data('test_cage_hier_onecomp_trim')
# rp.search.assert_results_close(result, ref)
[docs]def main():
hscore = rp.data.small_hscore()
# hscore = rp.RpxHier('ilv_h/1000', hscore_data_dir='/home/sheffler/data/rpx/hscore')
# C2 = rp.data.get_body('C2_REFS10_1')
C3 = rp.data.get_body('C3_1na0-1_1')
# test_cage_hier_onecomp_notrim(hscore, C3)
test_cage_hier_D3_onecomp_notrim(hscore, C3)
# test_cage_hier_D3_2_onecomp_notrim(hscore, C2)
# _test_cage_hier_onecomp_trim(hscore, C3)
if __name__ == '__main__':
main()