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Commit cb15daea authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Code cleanup: remove consider_hbonds traces and fix comments.

parent 1f2d3fa8
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...@@ -86,7 +86,7 @@ if not os.path.exists(out_path): ...@@ -86,7 +86,7 @@ if not os.path.exists(out_path):
print "Creating output folder", out_path print "Creating output folder", out_path
os.mkdir(out_path) os.mkdir(out_path)
# how quick to load, how much mem wasted? # load input data
bft = np.load(in_loop_bft) bft = np.load(in_loop_bft)
json_obj = json.load(open(in_loop_infos, "r")) json_obj = json.load(open(in_loop_infos, "r"))
loop_data_keys = json_obj["loop_data_keys"] loop_data_keys = json_obj["loop_data_keys"]
......
...@@ -133,7 +133,7 @@ if not os.path.exists(out_path): ...@@ -133,7 +133,7 @@ if not os.path.exists(out_path):
print "Creating output folder", out_path print "Creating output folder", out_path
os.mkdir(out_path) os.mkdir(out_path)
# how quick to load, how much mem wasted? # load input data
bft = np.load(in_loop_bft) bft = np.load(in_loop_bft)
json_obj = json.load(open(in_loop_infos, "r")) json_obj = json.load(open(in_loop_infos, "r"))
loop_data_keys = json_obj["loop_data_keys"] loop_data_keys = json_obj["loop_data_keys"]
......
...@@ -87,10 +87,8 @@ SidechainReconstructor Class ...@@ -87,10 +87,8 @@ SidechainReconstructor Class
to an environment or if parameters lead to invalid / unset to an environment or if parameters lead to invalid / unset
positions in environment. positions in environment.
.. method:: AttachEnvironment(env, use_frm=True, use_bbdep_lib=True, \ .. method:: AttachEnvironment(env, use_frm=True, use_bbdep_lib=True)
consider_hbonds=True) AttachEnvironment(env, use_frm, rotamer_library)
AttachEnvironment(env, use_frm, rotamer_library, \
consider_hbonds=True)
Link reconstructor to given *env*. A helper class is used in the background 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 to provide sidechain-objects for the environment. As this class is reused by
...@@ -108,10 +106,6 @@ SidechainReconstructor Class ...@@ -108,10 +106,6 @@ SidechainReconstructor Class
:type use_bbdep_lib: :class:`bool` :type use_bbdep_lib: :class:`bool`
:param rotamer_library: Custom rotamer library to be used. :param rotamer_library: Custom rotamer library to be used.
:type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib` :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 :raises: :exc:`~exceptions.RuntimeError` if *env* was already linked to
another reconstructor with inconsistent parameters. Acceptable another reconstructor with inconsistent parameters. Acceptable
......
...@@ -398,11 +398,6 @@ def Reconstruct(ent, keep_sidechains=False, build_disulfids=True, ...@@ -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" :param rotamer_model: Rotamer model to be used, can either be "frm" or "rrm"
:type rotamer_model: :class:`str` :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 :param consider_ligands: Flag, whether to add ligands (anything in chain
'_') as static objects. '_') as static objects.
:type consider_ligands: :class:`bool` :type consider_ligands: :class:`bool`
......
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