Merge branch 'release-2.0.0'

CHANGELOG

@@ -5,6 +5,24 @@
 Changelog
 ================================================================================
 
+Release 2.0.0
+--------------------------------------------------------------------------------
+
+* Generalize particle scoring and rotamer construction in sidechain module.
+  This simplifies the addition of other scoring functions in the future.
+  Be aware of breaking changes introduced in the process!
+  (SCWRLRotamerConstructor -> SCWRL4RotamerConstructor, changed interface of
+  Particle and RotamerConstructor classes).
+* Enable possibility to use structural fragments in default modelling pipeline
+  and build-model action
+* Enable possibility to enforce full coverage models including termini without
+  template coverage in default modelling pipeline and build-model action
+* Modelling pipeline can track issues in the ModellingHandle object
+* External example scripts can now be found in extras/external_scripts
+* Improved support for recent compilers and libraries.
+* Several minor bug fixes, improvements, and speed-ups  
+
+
 Release 1.3.0
 --------------------------------------------------------------------------------
 

CMakeLists.txt

@@ -15,8 +15,8 @@ project(ProMod3 CXX C)
 include(PROMOD3)
 
 # versioning info
-set(PROMOD3_VERSION_MAJOR 1)
-set(PROMOD3_VERSION_MINOR 3)
+set(PROMOD3_VERSION_MAJOR 2)
+set(PROMOD3_VERSION_MINOR 0)
 set(PROMOD3_VERSION_PATCH 0)
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -77,16 +77,23 @@ file(MAKE_DIRECTORY ${STAGE_DIR}
      ${LIBEXEC_STAGE_PATH})
 
 setup_compiler_flags()
-setup_boost()
 
+# Python needed before Boost
 find_package(Python 2.7 REQUIRED)
+# Split version string
+string(REPLACE "." ";" _python_version_list ${PYTHON_VERSION})
+list(GET _python_version_list 0 PYTHON_VERSION_MAJOR)
+list(GET _python_version_list 1 PYTHON_VERSION_MINOR)
+
+setup_boost()
+
 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 "https://www.openstructure.org/docs/dev")
+  # this URL should always point to the latest version of OST
+  set(OST_DOC_URL "https://www.openstructure.org/docs")
 endif()
-find_package(OPENSTRUCTURE 1.8 REQUIRED
+find_package(OPENSTRUCTURE 1.10.0 REQUIRED
              COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
 
 if(CMAKE_COMPILER_IS_GNUCXX)

actions/doc/index.rst

@@ -21,6 +21,7 @@ with
 
   $ pm build-model [-h] (-f <FILE> | -c <FILE> | -j <OBJECT>|<FILE>)
                    (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]
+                   [-r] [-t]
 
 Example usage:
 
@@ -129,6 +130,23 @@ Example usage:
 
   $ pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
 
+A fast torsion angle based sampling is performed in case of Monte Carlo 
+sampling. You can enforce the usage of structural fragments with ``-r``
+but this increases runtime due to searching the required fragments.
+Setup of the according :class:`promod3.modelling.FraggerHandle`
+objects is performed in the 
+:class:`~promod3.core.pm3argparse.PM3ArgumentParser` class as described in
+detail :meth:`here <promod3.core.pm3argparse.PM3ArgumentParser.AddFragments>`.
+
+The default modelling pipeline in ProMod3 is optimized to generate a gap-free 
+model of the region in the target sequence(s) that is covered with template 
+information. Terminal extensions without template coverage are negelected. 
+You can enforce a model of the full target sequence(s) by adding ``-t``. 
+The terminal parts will be modelled with a crude Monte Carlo approach. Be aware
+that the accuracy of those termini is likely to be limited. Termini of length 1 
+won't be modelled.
+
+
 Possible exit codes of the action:
 
 - 0: all went well
@@ -190,3 +208,8 @@ Several flags control the modelling behaviour:
 
   Dont do subrotamer optimization if flexible rotamer model is used
 
+.. option:: -f, --energy_function
+
+  The energy function to be used. Default is SCWRL4, can be any function
+  supported by :meth:`promod3.modelling.ReconstructSidechains`.
+

actions/pm-build-model

@@ -40,10 +40,17 @@ parser = pm3argparse.PM3ArgumentParser(__doc__, action=True)
 parser.AddAlignment()
 parser.AddStructure(attach_views=True)
 parser.AddProfile()
+parser.AddFragments()
 parser.AssembleParser()
 parser.add_argument('-o', '--model-file', metavar='<FILENAME>', type=str,
                     default='model.pdb', help='File to store model coordinates'+
                                               ' (default: %(default)s).')
+parser.add_argument('-t', '--model-termini', help="Enforce modelling of " +
+                    "terminal stretches without template coverage with a " +
+                    "crude Monte Carlo approach. The accuracy of those " +
+                    "termini is likely to be limited.", action="store_true")
+
+
 # lots of checking being done here -> see PM3ArgumentParser
 opts = parser.Parse()
 
@@ -70,14 +77,24 @@ try:
     # pssm files would not be sufficient and we would be restricted to hhm.
     if len(opts.profiles) > 0:
         modelling.SetSequenceProfiles(mhandle, opts.profiles)
+    # add fragment support for Monte Carlo sampling. The fragment search
+    # is setup in the argument parser. If activated you get fragment support
+    # in any case but for optimal performance you should provide profiles
+    # in hhm format (for profile AND secondary structure information).
+    if len(opts.fragger_handles) > 0:
+        modelling.SetFraggerHandles(mhandle, opts.fragger_handles)
     # build final model
-    final_model = modelling.BuildFromRawModel(mhandle)
+    final_model = modelling.BuildFromRawModel(mhandle, 
+                                              model_termini=opts.model_termini)
 except Exception as ex:
     helper.MsgErrorAndExit("Failed to perform modelling! An exception of type "+
                            type(ex).__name__ + " occured: " + str(ex), 3)
 
 # output
 ost.PopVerbosityLevel()
-io.SavePDB(final_model, opts.model_file)
-if not os.path.isfile(opts.model_file):
+try:
+    io.SavePDB(final_model, opts.model_file)
+    if not os.path.isfile(opts.model_file):
+        raise IOError("Failed to write model file.")
+except Exception as ex:
     helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 4)

actions/pm-build-rawmodel

@@ -58,6 +58,9 @@ except Exception as ex:
 
 # output
 ost.PopVerbosityLevel()
-io.SavePDB(mhandle.model, opts.model_file)
-if not os.path.isfile(opts.model_file):
+try:
+    io.SavePDB(mhandle.model, opts.model_file)
+    if not os.path.isfile(opts.model_file):
+        raise IOError("Failed to write model file.")
+except Exception as ex:
     helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 4)

actions/pm-build-sidechains

@@ -54,6 +54,8 @@ parser.add_argument('-i', '--backbone-independent', action='store_true',
 parser.add_argument('-s', '--no-subrotamer-optimization', action='store_true',
                     help='Dont do subrotamer optimization if flexible ' +
                          'rotamer model is used.')
+parser.add_argument('-f', '--energy_function', action = 'store', 
+                    dest = "energy_function", default = "SCWRL4")
 
 opts = parser.Parse()
 
@@ -80,7 +82,8 @@ modelling.ReconstructSidechains(prot, keep_sidechains=opts.keep_sidechains,
                                 build_disulfids=opts.no_disulfids==False, 
                                 rotamer_model=rotamer_model, 
                                 rotamer_library=lib, 
-                                optimize_subrotamers=opt_subrot)
+                                optimize_subrotamers=opt_subrot,
+                                energy_function = opts.energy_function)
 
 # output
 ost.PopVerbosityLevel()

cmake_support/PROMOD3.cmake

@@ -1009,8 +1009,28 @@ endmacro(setup_compiler_flags)
 set(_BOOST_MIN_VERSION 1.53)
 
 macro(setup_boost)
-  find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS python REQUIRED)
-  set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
+  # starting with CMake 3.11 we could use the following instead of the foreach
+  # find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS
+  #              python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR} REQUIRED)
+  # set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
+  # see https://cmake.org/cmake/help/v3.11/module/FindBoost.html
+  foreach(_python_lib_name python
+                           python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}
+                           python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
+                           python${PYTHON_VERSION_MAJOR})
+    find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS ${_python_lib_name} QUIET)
+    if(Boost_FOUND)
+      message(STATUS "Found Boost package: " ${_python_lib_name})
+      set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
+      break()
+    else()
+      message(STATUS "Boost package not found: " ${_python_lib_name}
+                     ". Trying alternative names!")
+    endif()
+  endforeach(_python_lib_name)
+  if(NOT BOOST_PYTHON_LIBRARIES)
+    message(FATAL_ERROR "Failed to find any Boost Python library!")
+  endif()
   set(Boost_LIBRARIES)
   find_package(Boost ${_BOOST_MIN_VERSION}
                COMPONENTS unit_test_framework REQUIRED)

cmake_support/substitute.cmake

+# force configure_file to update ${OUT_FILE}
+# -> otherwise it can cause continuous rebuilds if file was just touched
+file(REMOVE ${OUT_FILE})
 configure_file(${INPUT_FILE} ${OUT_FILE} @ONLY)
\ No newline at end of file

container/Dockerfile

@@ -2,10 +2,10 @@ FROM ubuntu:18.04
 
 # ARGUMENTS
 ###########
-ARG OPENSTRUCTURE_VERSION="1.9.0"
-ARG PROMOD_VERSION="1.3.0"
+ARG OPENSTRUCTURE_VERSION="1.10.0"
+ARG PROMOD_VERSION="2.0.0"
 ARG SRC_FOLDER="/usr/local/src"
-ARG CPUS_FOR_MAKE=2
+ARG CPUS_FOR_MAKE=4
 ARG COMPLIB_DIR="/usr/local/share/ost_complib"
 ARG OPENMM_VERSION="7.1.1"
 ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
@@ -16,32 +16,34 @@ ENV DEBIAN_FRONTEND=noninteractive
 # INSTALL SYSTEM DEPS
 #####################
 RUN apt-get update -y && apt-get install -y cmake \
-										                        sip-dev \
-										                        libtiff-dev \
-										                        libfftw3-dev \
-										                        libeigen3-dev \
-										                        libboost-all-dev \
-										                        libpng-dev \
-										                        python2.7 \
-										                        python-qt4 \
+                                            g++ \
+                                            sip-dev \
+                                            libtiff-dev \
+                                            libfftw3-dev \
+                                            libeigen3-dev \
+                                            libboost-all-dev \
+                                            libpng-dev \
+                                            python2.7 \
+                                            python-pyqt5 \
+                                            qt5-qmake \
+                                            qtbase5-dev \
+                                            python-qt4 \
                                             python-numpy \
                                             python-scipy \
                                             python-pandas \
                                             python-matplotlib \
-										                        qt4-qtconfig \
-										                        qt4-qmake \
-										                        libqt4-dev \
-										                        libpng-dev \
-										                        wget \
-										                        gfortran \
-										                        python-pip \
+                                            wget \
+                                            gfortran \
+                                            python-pip \
                                             python-sphinx \
-										                        tar \
-										                        libbz2-dev \
-										                        doxygen \
-										                        swig \
-										                        clustalw \
+                                            tar \
+                                            libbz2-dev \
+                                            doxygen \
+                                            swig \
+                                            clustalw \
+                                            libsqlite3-dev \
                                             dssp \
+                                            python-enum34 \
                                             locales && \
                       # CLEANUP
                       rm -rf /var/lib/apt/lists/*
@@ -102,7 +104,7 @@ RUN cd ${SRC_FOLDER} && \
     wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz &&\
     stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update modules/conop/data/charmm.cif compounds.chemlib charmm &&\
     mkdir -p $COMPLIB_DIR && chmod a+rw -R $COMPLIB_DIR && mv compounds.chemlib $COMPLIB_DIR && \
-    # rerun cmake and specify compount lib location
+    # rerun cmake and specify compound lib location
     cmake .. -DCOMPOUND_LIB=$COMPLIB_DIR/compounds.chemlib && \
     # Build OST with compound library
     make -j ${CPUS_FOR_MAKE} && make check && make install && \
@@ -133,7 +135,8 @@ RUN cd ${SRC_FOLDER} && \
              -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
              -DOPTIMIZE=ON \
              -DENABLE_SSE=1 && \
-             make && make codetest && make install && \
+    make -j ${CPUS_FOR_MAKE} && make codetest && make doctest && \
+    make install && \
     # cleanup
     cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/promod-${PROMOD_VERSION}.tar.gz && \
     rm -rf ${SRC_FOLDER}/promod-${PROMOD_VERSION}

core/CMakeLists.txt

 add_subdirectory(init)
+add_subdirectory(src)
 add_subdirectory(pymod)
 add_subdirectory(doc)
 add_subdirectory(tests)
-add_subdirectory(src)

core/pymod/pm3argparse.py

@@ -32,6 +32,7 @@ import ost
 from ost import io, seq
 
 from promod3.core import helper
+from promod3 import loop, modelling
 
 def _TmpForGZip(filename, suffix, msg_prefix):
     """Unpack a file to a tmp file if gzipped.
@@ -259,6 +260,18 @@ def _FetchProfileFromFile(filename):
                                str(exc), 52)        
     return prof
 
+def _FetchPsipredFromFile(filename):
+    """Load psipred prediction from filename and return it."""
+    argstr = filename + ": "
+    helper.FileExists("Profile", 51, filename)
+    try:
+        pred = loop.PsipredPrediction.FromHHM(filename)
+    except Exception, exc:
+        helper.MsgErrorAndExit(argstr + ": failure to parse psipred " +
+                               "prediction: " + str(exc), 56)        
+    return pred
+
+
 def _GetChains(structures, structure_sources):
     """Get chain id to entity view (single chain) mapping (dict)."""
     # IDs: (file_base = base file name with no extensions)
@@ -427,6 +440,8 @@ class PM3ArgumentParser(argparse.ArgumentParser):
             self._AssembleStructure()
         if 'PROFILE' in self.activate:
             self._AssembleProfile()
+        if 'FRAGMENTS' in self.activate:
+            self._AssembleFragments()
 
     def AddAlignment(self, allow_multitemplate=False):
         """Commandline options for alignments.
@@ -603,6 +618,51 @@ class PM3ArgumentParser(argparse.ArgumentParser):
         """
         self.activate.add('PROFILE')
 
+
+    def AddFragments(self):
+        """Commandline option for usage of Fragments
+
+        Activate everything needed to setup 
+        :class:`promod3.modelling.FraggerHandle` objects in the argument parser.
+        Command line arguments are then added in :meth:`AssembleParser` and the
+        input is post processed and checked in :meth:`Parse`.
+
+        Options/arguments added:
+
+        * ``-r/--use-fragments`` - Boolean flag whether to setup fragger handles.
+
+        Notes:
+
+        * Fragger handles are setup to identify fragments in a 
+          :class:`promod3.loop.StructureDB`.
+
+        * If no profiles are provided as additional argument 
+          (``-s/--seqprof <FILE>``), fragments are identified based on BLOSUM62 
+          sequence similarity.
+
+        * If you provide profiles that are not in hhm format, fragments are 
+          identified based on BLOSUM62 sequence similarity, sequence profile 
+          scoring and structural profile scoring.
+
+        * If you provide profiles in hhm format (optimal case), psipred 
+          predictions are fetched from there and fragments are identified based
+          on secondary structure agreement, secondary structure dependent
+          torsion probabilities, sequence profile scoring and structure 
+          profile scoring.
+
+        Attributes added to the namespace returned by :meth:`Parse`:
+
+        * :attr:`fragger_handles` - :class:`list` of 
+          :class:`promod3.modelling.FraggerHandle`, ordered to match the target 
+          sequences.
+
+        Exit codes related to fragments input:
+
+        * 56 - cannot read psipred prediction from hhm file
+        """
+        self.activate.add('FRAGMENTS')
+
+
     def _AssembleAlignment(self):
         """Actually add alignment arguments/options."""
         aln_grp = self.add_mutually_exclusive_group(required=True)
@@ -650,6 +710,15 @@ class PM3ArgumentParser(argparse.ArgumentParser):
                           ".hhm, .hhm.gz, .pssm, .pssm.gz", action='append',
                           default=list())
 
+    def _AssembleFragments(self):
+        self.add_argument('-r', '--use-fragments',
+                          help="Use fragments instead of torsion angle "+
+                          "based sampling for Monte Carlo approaches. "+
+                          "For optimal performance you should provide "+
+                          "sequence profiles in hhm format. (File "+
+                          "extensions: .hhm or .hhm.gz). BUT: be aware of "+
+                          "increased runtime.", action="store_true")
+
 class PM3OptionsNamespace(object):
     # class will grow, so for the moment pylint is ignored
     #pylint: disable=too-few-public-methods
@@ -672,6 +741,8 @@ class PM3OptionsNamespace(object):
             self._AttachViews()
         if 'PROFILE' in activated:
             self._PostProcessProfile()
+        if 'FRAGMENTS' in activated:
+            self._PostProcessFragments()
 
     def _PostProcessAlignment(self):
         #pylint: disable=no-member
@@ -730,11 +801,11 @@ class PM3OptionsNamespace(object):
             # so not having any profile is fine
             return
 
-        loaded_profiles = list()
+        self.loaded_profiles = list()
         for src in self.seqprof:
-            loaded_profiles.append(_FetchProfileFromFile(src))
+            self.loaded_profiles.append(_FetchProfileFromFile(src))
 
-        prof_sequences = [p.sequence for p in loaded_profiles]
+        prof_sequences = [p.sequence for p in self.loaded_profiles]
 
         # check uniqueness of loaded profiles
         if len(set(prof_sequences)) != len(prof_sequences):
@@ -746,7 +817,7 @@ class PM3OptionsNamespace(object):
                          for aln in self.alignments]
         for s in trg_sequences:
             try:
-                self.profiles.append(loaded_profiles[prof_sequences.index(s)])
+                self.profiles.append(self.loaded_profiles[prof_sequences.index(s)])
             except Exception, exc:
                 helper.MsgErrorAndExit("Could not find profile with sequence " +
                                        "that exactly matches trg seq: " + s, 55)
@@ -758,6 +829,80 @@ class PM3OptionsNamespace(object):
             helper.MsgErrorAndExit("Could not map every profile to a target " +
                                    "sequence", 53)
 
+    def _PostProcessFragments(self):
+
+        self.fragger_handles = list()
+
+        if not self.use_fragments:
+            # no fragments requested, so lets just return
+            return
+
+        trg_sequences = [aln.GetSequence(0).GetGaplessString() \
+                         for aln in self.alignments]
+
+        # we only want to setup a Fragger for every unique target sequence
+        unique_trg_sequences = list(set(trg_sequences))
+
+        # already setup variables, fill later if required data is present
+        profiles = [None] * len(unique_trg_sequences)
+        psipred_predictions = [None] * len(unique_trg_sequences)
+        ts_coil = None
+        ts_helix = None
+        ts_extended = None
+
+        # a structure db we need anyway. Load once and assign the same to all 
+        # fraggers to avoid memory explosion
+        structure_db = loop.LoadStructureDB()
+
+        # load the profiles
+        if hasattr(self, "profiles") and len(self.profiles) > 0:
+            profile_dict = dict()
+            for p in self.loaded_profiles:
+                profile_dict[p.sequence] = p
+            # as we already mapped the profiles in _PostProcessProfiles,
+            # the following is guaranteed to find the right profile
+            # for every unique target sequence
+            for s_idx, s in enumerate(unique_trg_sequences):
+                profiles[s_idx] = profile_dict[s]
+
+            # For the psipred predictions we have to go back to the
+            # input files. If they all end with .hhm or hhm.gz we're ready to go
+            file_endings_ok = True
+            for src in self.seqprof:
+                if not (src.endswith(".hhm") or src.endswith(".hhm.gz")):
+                    file_endings_ok = False
+                    break
+
+            if file_endings_ok:
+                # lets load the torsion samplers now as they are only required
+                # if we also add psipred handlers
+                ts_coil = loop.LoadTorsionSamplerCoil()
+                ts_extended = loop.LoadTorsionSamplerExtended()
+                ts_helix = loop.LoadTorsionSamplerHelical()
+
+                # to get the right filenames we use the sequences of the 
+                # loaded profiles that are in the same order as self.seqprof
+                profile_sequences = [p.sequence for p in self.loaded_profiles]
+                for s_idx, s in enumerate(unique_trg_sequences):
+                    fn = self.seqprof[profile_sequences.index(s)]
+                    psipred_predictions[s_idx] = _FetchPsipredFromFile(fn)
+        
+        # setup one fragger handle for each unique sequence
+        fraggers = list()
+        for i in range(len(unique_trg_sequences)):
+            fraggers.append(modelling.FraggerHandle(unique_trg_sequences[i],
+                                                    profile = profiles[i],
+                                                    psipred_pred = psipred_predictions[i],
+                                                    rmsd_thresh = 0.02,
+                                                    structure_db = structure_db,
+                                                    torsion_sampler_coil = ts_coil,
+                                                    torsion_sampler_helix = ts_helix,
+                                                    torsion_sampler_extended = ts_extended))
+        # map them to the chains
+        for s in trg_sequences:
+            self.fragger_handles.append(fraggers[unique_trg_sequences.index(s)])
+
+
 #  LocalWords:  param attr prog argparse ArgumentParser bool sys os init str
 #  LocalWords:  progattr descattr argpinit argv formatter meth args namespace
 #  LocalWords:  ArgumentDefaultsHelpFormatter sysargv AssembleParser fasta io

core/tests/test_pm3argparse.py

@@ -1225,6 +1225,71 @@ class PM3ArgParseTests(unittest.TestCase):
                          opts.profiles[1].sequence)
 
 
+    def testFraggerNotRequested(self):
+        parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+        parser.AddAlignment()
+        parser.AddFragments()
+        parser.AssembleParser()
+        opts =  parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+                              '-f', 'data/aln_tpl/5ua4_B.fasta'])
+        self.assertEqual(len(opts.alignments), 2)
+        self.assertEqual(len(opts.fragger_handles), 0)
+
+    def testFraggerAttachedWithoutProfile(self):
+        parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+        parser.AddAlignment()
+        parser.AddFragments()
+        parser.AssembleParser()
+        opts =  parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+                              '-f', 'data/aln_tpl/5ua4_B.fasta',
+                              '--use-fragments'])
+        self.assertEqual(len(opts.alignments), 2)
+        self.assertEqual(len(opts.fragger_handles), 2)
+        self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+                         opts.fragger_handles[0].sequence)
+        self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
+                         opts.fragger_handles[1].sequence)
+        # most of the stuff in the fragger handles should be None
+        self.assertIsNone(opts.fragger_handles[0].profile)
+        self.assertIsNone(opts.fragger_handles[0].psipred_pred)
+        self.assertIsNone(opts.fragger_handles[0].torsion_sampler_coil)
+        self.assertIsNone(opts.fragger_handles[0].torsion_sampler_helix)
+        self.assertIsNone(opts.fragger_handles[0].torsion_sampler_extended)
+        self.assertIsNone(opts.fragger_handles[1].profile)
+        self.assertIsNone(opts.fragger_handles[1].psipred_pred)
+        self.assertIsNone(opts.fragger_handles[1].torsion_sampler_coil)
+        self.assertIsNone(opts.fragger_handles[1].torsion_sampler_helix)
+        self.assertIsNone(opts.fragger_handles[1].torsion_sampler_extended)
+
+    def testFraggerAttachedWithProfile(self):
+        parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
+        parser.AddAlignment()
+        parser.AddProfile()
+        parser.AddFragments()
+        parser.AssembleParser()
+        opts =  parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
+                              '-f', 'data/aln_tpl/5ua4_B.fasta',
+                              '-s', 'data/aln_tpl/1crn.hhm',
+                              '-s', 'data/aln_tpl/5ua4_B.hhm',
+                              '--use-fragments'])
+        self.assertEqual(len(opts.alignments), 2)
+        self.assertEqual(len(opts.fragger_handles), 2)
+        self.assertEqual(opts.alignments[0].GetSequence(0).GetGaplessString(),
+                         opts.fragger_handles[0].sequence)
+        self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
+                         opts.fragger_handles[1].sequence)
+        # most of the stuff in the fragger handles should be set
+        self.assertIsNotNone(opts.fragger_handles[0].profile)
+        self.assertIsNotNone(opts.fragger_handles[0].psipred_pred)
+        self.assertIsNotNone(opts.fragger_handles[0].torsion_sampler_coil)
+        self.assertIsNotNone(opts.fragger_handles[0].torsion_sampler_helix)
+        self.assertIsNotNone(opts.fragger_handles[0].torsion_sampler_extended)
+        self.assertIsNotNone(opts.fragger_handles[1].profile)
+        self.assertIsNotNone(opts.fragger_handles[1].psipred_pred)
+        self.assertIsNotNone(opts.fragger_handles[1].torsion_sampler_coil)
+        self.assertIsNotNone(opts.fragger_handles[1].torsion_sampler_helix)
+        self.assertIsNotNone(opts.fragger_handles[1].torsion_sampler_extended)
+
 # test options: --disable-aln check (for amino acids)
 # test options: --disable-input-checks (for all)
 # test option: --disable-mm-check (macromolecule)

doc/CMakeLists.txt

@@ -12,6 +12,7 @@ dev_setup.rst
 users.rst
 buildsystem.rst
 contributing.rst
+user_contributions.rst
 gettingstarted.rst
 portableIO.rst
 references.rst
@@ -127,6 +128,13 @@ endforeach()
 
 # add dependencies from doctests
 list(APPEND _DOC_MODULE_DEPS "${PM3_DOC_DEPS_doctests}")
+# ensure that we wait for all modules to be done (solves parallel compile issue)
+# -> since this is a custom target, it will not trigger a rebuild
+# -> this is intended as rebuild is only needed for files in _DOC_MODULE_DEPS
+add_custom_target(doc_wait_for_modules DEPENDS ${PM3_PYMODULES})
+# add custom target also for all custom commands (solves parallel compile issue)
+# -> https://samthursfield.wordpress.com/2015/11/21/cmake-dependencies-between-targets-and-files-and-custom-commands/
+add_custom_target(doc_wait_for_rst DEPENDS "${_SPHINX_CONF_PY}" ${_RST_DEPS})
 
 # create targets for sphinx