diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst index 2db3864dc6da48ea948fa071c816989e3f3dd36b..7ae07b4858f1f77c96592261aee018e11de06b58 100644 --- a/modelling/doc/pipeline.rst +++ b/modelling/doc/pipeline.rst @@ -69,7 +69,7 @@ Build Raw Modelling Handle better by the convenient function :func:`SetSequenceProfiles`, to ensure consistency with the seqres. - .. attribute:: psipred_prediction + .. attribute:: psipred_predictions List of predictions with one :class:`promod3.loop.PsipredPrediction` for each chain of target protein. diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py index bb8bdc0ab85533a4428f222d265f3ac49d01b1c3..dde6c8d7adb5f9dd35e948a93373662a50d022a0 100644 --- a/modelling/pymod/_closegaps.py +++ b/modelling/pymod/_closegaps.py @@ -1162,7 +1162,7 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6, def CloseGaps(mhandle, merge_distance=4, fragment_db=None, structure_db=None, - torsion_sampler=None, chain_idx = None, resnum_range = None): + torsion_sampler=None, chain_idx=None, resnum_range=None): ''' Tries to close all gaps in a model, except termini. It will go through following steps: diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py index efc8c81c73291d7422869b2e30f8696ffc0cc264..006ab4abd682c2d607598418570266c932f56db5 100644 --- a/modelling/pymod/_pipeline.py +++ b/modelling/pymod/_pipeline.py @@ -406,7 +406,7 @@ def CheckFinalModel(mhandle): ost.LogInfo("Stereo-chemical problem in sidechain " + \ "of residue " + str(res)) -def BuildFromRawModel(mhandle, alternative_mhandles = None, +def BuildFromRawModel(mhandle, alternative_mhandles=None, use_amber_ff=False, extra_force_fields=list()): '''Build a model starting with a raw model (see :func:`BuildRawModel`). @@ -475,20 +475,20 @@ def BuildFromRawModel(mhandle, alternative_mhandles = None, current_num_residues = mhandle.model.GetResidueCount() new_num_residues = None while current_num_residues != new_num_residues: - current_num_residues = mhandle.model.GetResidueCount() - ModelExtensions(mhandle, alternative_mhandles, - extension_strategy = "overlapping") - ModelExtensions(mhandle, alternative_mhandles, - extension_strategy = "non-overlapping") - new_num_residues = mhandle.model.GetResidueCount() + current_num_residues = mhandle.model.GetResidueCount() + ModelExtensions(mhandle, alternative_mhandles, + extension_strategy="overlapping") + ModelExtensions(mhandle, alternative_mhandles, + extension_strategy="non-overlapping") + new_num_residues = mhandle.model.GetResidueCount() # remove terminal gaps RemoveTerminalGaps(mhandle) # close gaps - CloseGaps(mhandle, merge_distance = merge_distance, - fragment_db = fragment_db, structure_db = structure_db, - torsion_sampler = torsion_sampler) + CloseGaps(mhandle, merge_distance=merge_distance, + fragment_db=fragment_db, structure_db=structure_db, + torsion_sampler=torsion_sampler) # build sidechains BuildSidechains(mhandle, merge_distance, fragment_db,