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>`
--
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