From 601aa9fce8d3f25d6a09d27e102a0902d37f4bb9 Mon Sep 17 00:00:00 2001 From: Gerardo Tauriello <gerardo.tauriello@unibas.ch> Date: Tue, 9 Aug 2016 10:58:33 +0200 Subject: [PATCH] Small fixes and updated doc. --- CMakeLists.txt | 2 +- modelling/pymod/_closegaps.py | 5 ++--- modelling/pymod/_molprobity.py | 2 +- modelling/pymod/_pipeline.py | 4 ++-- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 45df55f6..7911e0c5 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -78,7 +78,7 @@ if(NOT DISABLE_DOCUMENTATION) find_package(Sphinx ${PYTHON_VERSION} REQUIRED) set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}") # set this to the URL corresponding to the version of OST you are using - set(OST_DOC_URL "http://www.openstructure.org/docs/1.3") + set(OST_DOC_URL "http://www.openstructure.org/docs/1.5") endif() find_package(OPENSTRUCTURE 1.4 REQUIRED COMPONENTS io mol seq seq_alg mol_alg conop) diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py index 91886522..ab5441b4 100644 --- a/modelling/pymod/_closegaps.py +++ b/modelling/pymod/_closegaps.py @@ -1251,9 +1251,8 @@ def CloseLargeDeletions(mhandle, scorer, structure_db, linker_length=8, # these methods will be exported into module -__all__ = ('SetupBackboneScorer', 'CloseSmallDeletions', 'MergeGapsByDistance', - 'FillLoopsByDatabase', 'FillLoopsByMonteCarlo', 'ModelTermini', - 'CloseLargeDeletions') +__all__ = ('CloseSmallDeletions', 'MergeGapsByDistance', 'FillLoopsByDatabase', + 'FillLoopsByMonteCarlo', 'ModelTermini', 'CloseLargeDeletions') # LocalWords: modeling stereochemically param idx init # LocalWords: py ost pylint modelling promod CloseSmallDeletions diff --git a/modelling/pymod/_molprobity.py b/modelling/pymod/_molprobity.py index 0bae610b..d1fe777a 100644 --- a/modelling/pymod/_molprobity.py +++ b/modelling/pymod/_molprobity.py @@ -33,7 +33,7 @@ def RunMolProbity(target_pdb, molprobity_bin=None): - "Ramachandran outliers" (percentage [0,100] as :class:`float`) - "Ramachandran favored" (percentage [0,100] as :class:`float`) - "Rotamer outliers" (percentage [0,100] as :class:`float`) - - "C-beta deviations" (:class:`integer`) + - "C-beta deviations" (:class:`int`) - "Clashscore" (:class:`float`) - "MolProbity score" (:class:`float`) - "RMS(bonds)" (:class:`float`) diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py index 0e0cd9cb..779ecc7a 100644 --- a/modelling/pymod/_pipeline.py +++ b/modelling/pymod/_pipeline.py @@ -271,7 +271,7 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20, :param extra_force_fields: Additional list of force fields to use (see :meth:`BuildFromRawModel`). - :type extra_force_fields: :class:`list` of :class:`ost.mol.Forcefield` + :type extra_force_fields: :class:`list` of :class:`ost.mol.mm.Forcefield` :return: The model including all oxygens as used in the minimizer. :rtype: :class:`Entity <ost.mol.EntityHandle>` @@ -433,7 +433,7 @@ def BuildFromRawModel(mhandle, scorer = None, use_amber_ff=False, extra_force_fi default force field. The force fields are tried in the order as given and ligands without an existing parametrization are skipped. - :type extra_force_fields: :class:`list` of :class:`ost.mol.Forcefield` + :type extra_force_fields: :class:`list` of :class:`ost.mol.mm.Forcefield` :return: Delivers the model as an |ost_s| entity. :rtype: :class:`Entity <ost.mol.EntityHandle>` -- GitLab