diff --git a/extras/scoring_weight_training/analyze_bft_candidates.py b/extras/scoring_weight_training/analyze_bft_candidates.py index e4cdd20f8d4878487a599c3077e7765f657570bc..e612725449d3dfac914565cad6bad630aa0a8c9e 100644 --- a/extras/scoring_weight_training/analyze_bft_candidates.py +++ b/extras/scoring_weight_training/analyze_bft_candidates.py @@ -86,7 +86,7 @@ if not os.path.exists(out_path): print "Creating output folder", out_path os.mkdir(out_path) -# how quick to load, how much mem wasted? +# load input data bft = np.load(in_loop_bft) json_obj = json.load(open(in_loop_infos, "r")) loop_data_keys = json_obj["loop_data_keys"] diff --git a/extras/scoring_weight_training/analyze_bft_scores.py b/extras/scoring_weight_training/analyze_bft_scores.py index 94c8eb40eb4e49b209410a7bb08295dd3c884f50..76118ce98d3f6a7ae983a36a211645ca05036ce6 100644 --- a/extras/scoring_weight_training/analyze_bft_scores.py +++ b/extras/scoring_weight_training/analyze_bft_scores.py @@ -133,7 +133,7 @@ if not os.path.exists(out_path): print "Creating output folder", out_path os.mkdir(out_path) -# how quick to load, how much mem wasted? +# load input data bft = np.load(in_loop_bft) json_obj = json.load(open(in_loop_infos, "r")) loop_data_keys = json_obj["loop_data_keys"] diff --git a/sidechain/doc/reconstruct.rst b/sidechain/doc/reconstruct.rst index ff0e9c2fbdcb2474f4bed561a642c3e718d9c723..e778ffc06460e9b4c1a153b88be95ad8a8002790 100644 --- a/sidechain/doc/reconstruct.rst +++ b/sidechain/doc/reconstruct.rst @@ -87,10 +87,8 @@ SidechainReconstructor Class to an environment or if parameters lead to invalid / unset positions in environment. - .. method:: AttachEnvironment(env, use_frm=True, use_bbdep_lib=True, \ - consider_hbonds=True) - AttachEnvironment(env, use_frm, rotamer_library, \ - consider_hbonds=True) + .. method:: AttachEnvironment(env, use_frm=True, use_bbdep_lib=True) + AttachEnvironment(env, use_frm, rotamer_library) Link reconstructor to given *env*. A helper class is used in the background to provide sidechain-objects for the environment. As this class is reused by @@ -108,10 +106,6 @@ SidechainReconstructor Class :type use_bbdep_lib: :class:`bool` :param rotamer_library: Custom rotamer library to be used. :type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib` - :param consider_hbonds: Flag, whether hbonds should be evaluated in the - energy function. If set to False, no hydrogens will - be built when building rotamers and frames. - :type consider_hbonds: :class:`bool` :raises: :exc:`~exceptions.RuntimeError` if *env* was already linked to another reconstructor with inconsistent parameters. Acceptable diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py index 8a2ced98b9dc1ffe58177726e788b39358cdf7f6..ce043c8affd8af53f0b0518ee2292356d84412d7 100644 --- a/sidechain/pymod/_reconstruct_sidechains.py +++ b/sidechain/pymod/_reconstruct_sidechains.py @@ -398,11 +398,6 @@ def Reconstruct(ent, keep_sidechains=False, build_disulfids=True, :param rotamer_model: Rotamer model to be used, can either be "frm" or "rrm" :type rotamer_model: :class:`str` - :param consider_hbonds: Flag, whether hbonds should be evaluated in the - energy function. If set to False, no hydrogens will - be built when building rotamers and frame. - :type consider_hbonds: :class:`bool` - :param consider_ligands: Flag, whether to add ligands (anything in chain '_') as static objects. :type consider_ligands: :class:`bool`