diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index b49b82fd25ca14e1b25d6ef7b0a30b8495945aa8..bf0038767689cd2a15be79e3c7cf472d55fcd0dd 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -206,7 +206,7 @@ can influence it.
files directly)
* `PNG_LIBRARY` defines the location of the libpng library (file name starting
with `libpng`)
- * `PNG_INCLUDE_DIR` defines the include folder of libpng (contains include
+ * `PNG_PNG_INCLUDE_DIR` defines the include folder of libpng (contains include
files directly)
* `ZLIB_LIBRARY` defines the location of the zlib library (file name starting
with `libz`)
diff --git a/modules/gfx/src/CMakeLists.txt b/modules/gfx/src/CMakeLists.txt
index acd3f9eb4bf94f4fe29b2e4dccd863a0659f8ecc..d7790789e5c38d1bac5fcd90a29cba681aac1297 100644
--- a/modules/gfx/src/CMakeLists.txt
+++ b/modules/gfx/src/CMakeLists.txt
@@ -210,7 +210,7 @@ module(NAME gfx SOURCES ${OST_GFX_SOURCES} ${OST_GFX_MAP_SOURCES}
${OST_GFX_HEADERS} ${OST_GFX_MAP_HEADERS}
DEPENDS_ON ${OST_GFX_DEPENDENCIES})
-include_directories(${PNG_INCLUDE_DIR} ${OPENGL_INCLUDE_DIR})
+include_directories(${PNG_INCLUDE_DIRS} ${OPENGL_INCLUDE_DIR})
# link against OpenGL and PNG libraries
target_link_libraries(ost_gfx ${OPENGL_LIBRARIES} ${PNG_LIBRARIES})
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 85e1a325e72d2fab09c2c62216b1b4a300ba8286..9dea7dbc552b94b198cb8c80c9746dff8712e240 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -290,13 +290,20 @@ def LoadMMCIF(filename, fault_tolerant=None, calpha_only=None, profile='DEFAULT'
remote pdb repository www.pdb.org. The filename is then interpreted as the
pdb id.
- :rtype: :class:`~ost.mol.EntityHandle`.
-
- :param seqres: Whether to read SEQRES records. If set to True, the loaded
- entity and seqres entry will be returned as second item.
+ :rtype: :class:`~ost.mol.EntityHandle` (or tuple if *seqres* or *info* are
+ True).
+
+ :param seqres: Whether to read SEQRES records. If True, a
+ :class:`~ost.seq.SequenceList` object is returned as the second
+ item. The sequences in the list are named according to the
+ mmCIF chain name.
+ This feature requires a default
+ :class:`compound library <ost.conop.CompoundLib>`
+ to be defined and accessible via
+ :func:`~ost.conop.GetDefaultLib` or an empty list is returned.
:param info: Whether to return an info container with the other output.
- Returns a :class:`MMCifInfo` object as last item.
+ If True, a :class:`MMCifInfo` object is returned as last item.
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous
or non-existent file.
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 8f9286b49bc1f36624c6f4786da289edca765ee5..adab36d6c7931a3e2a6955e509f60111c18e9f85 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -553,6 +553,8 @@ class QSscorer:
def GetOligoLDDTScorer(self, settings, penalize_extra_chains=True):
"""
:return: :class:`OligoLDDTScorer` object, setup for this QS scoring problem.
+ The scorer is set up with :attr:`qs_ent_1` as the reference and
+ :attr:`qs_ent_2` as the model.
:param settings: Passed to :class:`OligoLDDTScorer` constructor.
:param penalize_extra_chains: Passed to :class:`OligoLDDTScorer` constructor.
"""
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 9ce2fff112b942dd6e2a6fa1d207bae78ee6bb10..2e9c5fcffca4375afb80a13cea941658f62c508a 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -3,13 +3,15 @@ from ost.seq.alg.mat import *
def ValidateSEQRESAlignment(aln, chain=None):
"""
- Checks a sequence aligned to a SEQRES sequence to be free of strand breaks.
- Residues divided by gaps are not considered as breakage but may also not be
- connected.
+ Checks if sequence in alignment has same connectivity as residues in chain.
+ This looks for connected stretches in both the sequence and the chain and
+ returns False if they don't match. This uses the connectivity of the protein
+ backbone.
- :param aln: Alignment
+ :param aln: Alignment of two sequences with second one expected to map to
+ residues in *chain*.
:type aln: :class:`~ost.seq.AlignmentHandle`
- :param chain: Source of the sequence
+ :param chain: Source of the sequence.
:type chain: :class:`~ost.mol.ChainHandle`
:returns: True if all residues (beside gapped ones) are connected, False
@@ -66,20 +68,20 @@ def AlignToSEQRES(chain, seqres, try_resnum_first=False, validate=True):
SEQRES. If there are any additional residues in the chain, the function
raises a ValueError.
- If 'try_resnum_first' is set, building the alignment following residue numbers
- is tried first.
-
- If 'validate' is set (default), the alignment is checked using
- :func:`~ost.seq.alg.ValidateSEQRESAlignment`.
-
:param chain: Source of the sequence
:type chain: :class:`~ost.mol.ChainHandle`
:param seqres: SEQRES sequence
:type seqres: :class:`str`
- :param try_resnum_first: Try to align by residue number
+ :param try_resnum_first: If set to True, this first builds an alignment using
+ residue numbers and checks if the one-letter-codes
+ match. If they all match, this alignment is used
+ (and possibly validated). Otherwise, it displays a
+ warning and falls back to the connectivity-based
+ alignment.
:type try_resnum_first: :class:`bool`
- :param validate: Validate alignment by
- :func:`~ost.seq.alg.ValidateSEQRESAlignment`
+ :param validate: If set to True, the alignment is additionally checked by
+ :func:`~ost.seq.alg.ValidateSEQRESAlignment` and raises
+ a ValueError if the validation failed.
:type validate: :class:`bool`
:returns: The alignment of the residues in the chain and the SEQRES entries.