From 65bfab9765f9816ff84fd905c766d36dbc421128 Mon Sep 17 00:00:00 2001 From: Gabriel Studer <gabriel.studer@unibas.ch> Date: Mon, 23 Jan 2017 13:53:23 +0100 Subject: [PATCH] remove experimental feature We decided to only implement a very basic pipeline as default. --- modelling/pymod/_pipeline.py | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py index c56a3d07..92e8dacd 100644 --- a/modelling/pymod/_pipeline.py +++ b/modelling/pymod/_pipeline.py @@ -403,8 +403,7 @@ def CheckFinalModel(mhandle): ost.LogInfo("Stereo-chemical problem in sidechain " + \ "of residue " + str(res)) -def BuildFromRawModel(mhandle, alternative_mhandles=None, - use_amber_ff=False, extra_force_fields=list()): +def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()): '''Build a model starting with a raw model (see :func:`BuildRawModel`). This function implements a recommended pipeline to generate complete models @@ -459,19 +458,6 @@ def BuildFromRawModel(mhandle, alternative_mhandles=None, torsion_sampler = loop.LoadTorsionSamplerCoil() merge_distance = 4 - # try to extend terminal coverage using alternative rawmodels - if alternative_mhandles != None: - # iterate extensions until nothing happens anymore - 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() - # remove terminal gaps RemoveTerminalGaps(mhandle) -- GitLab