From cb15daea7437a5470d071b4806fff38f2f88e7f9 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 1 Dec 2016 13:05:44 +0100
Subject: [PATCH] Code cleanup: remove consider_hbonds traces and fix comments.
---
.../scoring_weight_training/analyze_bft_candidates.py | 2 +-
extras/scoring_weight_training/analyze_bft_scores.py | 2 +-
sidechain/doc/reconstruct.rst | 10 ++--------
sidechain/pymod/_reconstruct_sidechains.py | 5 -----
4 files changed, 4 insertions(+), 15 deletions(-)
diff --git a/extras/scoring_weight_training/analyze_bft_candidates.py b/extras/scoring_weight_training/analyze_bft_candidates.py
index e4cdd20f..e6127254 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 94c8eb40..76118ce9 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 ff0e9c2f..e778ffc0 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 8a2ced98..ce043c8a 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`
--
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