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A Python platform for Structural Bioinformatics

Home Page: http://biskit.pasteur.fr

License: Other

Python 97.10% Shell 0.60% MATLAB 0.04% Perl 0.14% Prolog 2.11% Dockerfile 0.01%

bioinformatics biophysics python scientific

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ashish07791 neb9 tybiot miaecle rdk suliat16 dprada qwp-ryan minghao2016 tsenapathi greatlse aspirincode ggutierrez-bio gazalk dalvgar asclepiusinformatica soilqualitylab pteritim guzmanfj

biskit's Issues

set version to 3.0.0-pre

change version throughout project.

DSSP.py returning with "IndexError: list index out of range"

Different error from last time here... For an example, try running Dssp() on PDB protein 2W3A.

For me this and some other proteins returns;

File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/Executor.py", line 557, in run
self.finish()
File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/DSSP.py", line 240, in finish
self.result = self.parse_result( )
File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/DSSP.py", line 202, in parse_result
complete = __completeBB( resDic[j] )
IndexError: list index out of range

Use of deprecated mktemp

According to the documentation:
Use of this function may introduce a security hole in your program. By the time you get around to doing anything with the file name it returns, someone else may have beaten you to the punch. mktemp() usage can be replaced easily with NamedTemporaryFile(), passing it the delete=False parameter.
Thus far, I've spotted mktemp() in executor.py.

DSSP.py returns AssertionError

I've now switched over to the latest master. However, on 1AM7, just straight up doing

m = PDBModel(file)
d = Dssp(m)
sec = d.run()

breaks, returning:

File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/Executor.py", line 557, in run
    self.finish()
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/DSSP.py", line 240, in finish
    self.result = self.parse_result( )
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/DSSP.py", line 230, in parse_result
    assert len(secStruc) == self.model.lenResidues()
AssertionError

add BiskitTest cases to Model, Polymer, ProfileMirror

modules in future package are lacking proper test cases.

ERROR: Failed building wheel for biskit

Hello Sir,
I tried installing Biskit as below and am getting the Error:

(base) m992c693@alveo:~$ pip install biskit
Collecting biskit
  Downloading biskit-2.4.3.tar.gz (20.5 MB)
     |████████████████████████████████| 20.5 MB 20.2 MB/s
Requirement already satisfied: numpy in ./anaconda3/lib/python3.9/site-packages (from biskit) (1.21.5)
Requirement already satisfied: scipy in ./anaconda3/lib/python3.9/site-packages (from biskit) (1.7.3)
Collecting biopython
  Downloading biopython-1.79-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.7 MB)
     |████████████████████████████████| 2.7 MB 63.3 MB/s
Building wheels for collected packages: biskit
  Building wheel for biskit (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/m992c693/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-w6oip1d1
       cwd: /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/
  Complete output (190 lines):
  /home/m992c693/anaconda3/lib/python3.9/site-packages/setuptools/dist.py:757: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib
  creating build/lib/Biskit
  copying Biskit/molUtils.py -> build/lib/Biskit
  copying Biskit/ExeConfig.py -> build/lib/Biskit
  copying Biskit/ExeConfigCache.py -> build/lib/Biskit
  copying Biskit/PCRModel.py -> build/lib/Biskit
  copying Biskit/Model.py -> build/lib/Biskit
  copying Biskit/Trajectory.py -> build/lib/Biskit
  copying Biskit/SettingsParser.py -> build/lib/Biskit
  copying Biskit/molTools.py -> build/lib/Biskit
  copying Biskit/DSSP.py -> build/lib/Biskit
  copying Biskit/AmberRstParser.py -> build/lib/Biskit
  copying Biskit/BioUnit.py -> build/lib/Biskit
  copying Biskit/PDBParserFactory.py -> build/lib/Biskit
  copying Biskit/PDBParseNCBI.py -> build/lib/Biskit
  copying Biskit/Executor.py -> build/lib/Biskit
  copying Biskit/wormlikechain.py -> build/lib/Biskit
  copying Biskit/SurfaceRacer.py -> build/lib/Biskit
  copying Biskit/amberResidues.py -> build/lib/Biskit
  copying Biskit/QualSlave.py -> build/lib/Biskit
  copying Biskit/CommandLine.py -> build/lib/Biskit
  copying Biskit/PDBModel.py -> build/lib/Biskit
  copying Biskit/AmberParmBuilder.py -> build/lib/Biskit
  copying Biskit/ModelList.py -> build/lib/Biskit
  copying Biskit/Hmmer.py -> build/lib/Biskit
  copying Biskit/gnuplot.py -> build/lib/Biskit
  copying Biskit/ProfileMirror.py -> build/lib/Biskit
  copying Biskit/LocalPath.py -> build/lib/Biskit
  copying Biskit/reduce.py -> build/lib/Biskit
  copying Biskit/TrajFlexMaster.py -> build/lib/Biskit
  copying Biskit/PDBParseModel.py -> build/lib/Biskit
  copying Biskit/AmberCrdParser.py -> build/lib/Biskit
  copying Biskit/ErrorHandler.py -> build/lib/Biskit
  copying Biskit/decorators.py -> build/lib/Biskit
  copying Biskit/AmberCrdEntropist.py -> build/lib/Biskit
  copying Biskit/PDBParsePickle.py -> build/lib/Biskit
  copying Biskit/amberResidueLibrary.py -> build/lib/Biskit
  copying Biskit/Polymer.py -> build/lib/Biskit
  copying Biskit/StructureMaster.py -> build/lib/Biskit
  copying Biskit/surfaceRacerTools.py -> build/lib/Biskit
  copying Biskit/ReduceCoordinates.py -> build/lib/Biskit
  copying Biskit/ColorSpectrum.py -> build/lib/Biskit
  copying Biskit/FuzzyCluster.py -> build/lib/Biskit
  copying Biskit/PDBCleaner.py -> build/lib/Biskit
  copying Biskit/Xplorer.py -> build/lib/Biskit
  copying Biskit/PDBDope.py -> build/lib/Biskit
  copying Biskit/WhatIf.py -> build/lib/Biskit
  copying Biskit/AmberEntropist.py -> build/lib/Biskit
  copying Biskit/ProfileCollection.py -> build/lib/Biskit
  copying Biskit/AmberEntropySlave.py -> build/lib/Biskit
  copying Biskit/Blast2Seq.py -> build/lib/Biskit
  copying Biskit/match2seq.py -> build/lib/Biskit
  copying Biskit/mathUtils.py -> build/lib/Biskit
  copying Biskit/DictList.py -> build/lib/Biskit
  copying Biskit/wlc.py -> build/lib/Biskit
  copying Biskit/residue.py -> build/lib/Biskit
  copying Biskit/TrajFlexSlave.py -> build/lib/Biskit
  copying Biskit/MatrixPlot.py -> build/lib/Biskit
  copying Biskit/ez_setup.py -> build/lib/Biskit
  copying Biskit/Fold_X.py -> build/lib/Biskit
  copying Biskit/QualMaster.py -> build/lib/Biskit
  copying Biskit/hist.py -> build/lib/Biskit
  copying Biskit/atomCharger.py -> build/lib/Biskit
  copying Biskit/SparseArray.py -> build/lib/Biskit
  copying Biskit/difflib_old.py -> build/lib/Biskit
  copying Biskit/tmalign.py -> build/lib/Biskit
  copying Biskit/EnsembleTraj.py -> build/lib/Biskit
  copying Biskit/test.py -> build/lib/Biskit
  copying Biskit/__init__.py -> build/lib/Biskit
  copying Biskit/EDParser.py -> build/lib/Biskit
  copying Biskit/Prosa2003.py -> build/lib/Biskit
  copying Biskit/PDBParseFile.py -> build/lib/Biskit
  copying Biskit/SettingsManager.py -> build/lib/Biskit
  copying Biskit/Pymoler.py -> build/lib/Biskit
  copying Biskit/tools.py -> build/lib/Biskit
  copying Biskit/msms.py -> build/lib/Biskit
  copying Biskit/Errors.py -> build/lib/Biskit
  copying Biskit/LogFile.py -> build/lib/Biskit
  copying Biskit/settings.py -> build/lib/Biskit
  copying Biskit/BisList.py -> build/lib/Biskit
  copying Biskit/plotUtils.py -> build/lib/Biskit
  copying Biskit/Ramachandran.py -> build/lib/Biskit
  copying Biskit/AmberLeap.py -> build/lib/Biskit
  copying Biskit/TrajCluster.py -> build/lib/Biskit
  copying Biskit/AmberEntropyMaster.py -> build/lib/Biskit
  copying Biskit/IcmCad.py -> build/lib/Biskit
  copying Biskit/rmsFit.py -> build/lib/Biskit
  copying Biskit/XplorInput.py -> build/lib/Biskit
  copying Biskit/PDBParser.py -> build/lib/Biskit
  copying Biskit/delphi.py -> build/lib/Biskit
  copying Biskit/StructureSlave.py -> build/lib/Biskit
  creating build/lib/Biskit/Mod
  copying Biskit/Mod/Analyse.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/ModelSlave.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/Modeller.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/TemplateSearcher.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/TemplateFilter.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/ModelMaster.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/AlignerMaster.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/ValidationSetup.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/TemplateCleaner.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/Benchmark.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/modUtils.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/__init__.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/Aligner.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/AlignerSlave.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/SequenceSearcher.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/settings.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/CheckIdentities.py -> build/lib/Biskit/Mod
  creating build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/PDBExportFilters.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/PDB.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/__init__.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/FortranFormat.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/TextFile.py -> build/lib/Biskit/ScientificIO
  creating build/lib/Biskit/deprecated
  copying Biskit/deprecated/ChainWriter.py -> build/lib/Biskit/deprecated
  copying Biskit/deprecated/__init__.py -> build/lib/Biskit/deprecated
  copying Biskit/deprecated/ChainSeparator.py -> build/lib/Biskit/deprecated
  copying Biskit/deprecated/ChainCleaner.py -> build/lib/Biskit/deprecated
  creating build/lib/Biskit/Statistics
  copying Biskit/Statistics/Density.py -> build/lib/Biskit/Statistics
  copying Biskit/Statistics/ROCalyzer.py -> build/lib/Biskit/Statistics
  copying Biskit/Statistics/__init__.py -> build/lib/Biskit/Statistics
  copying Biskit/Statistics/lognormal.py -> build/lib/Biskit/Statistics
  creating build/lib/Biskit/PVM
  copying Biskit/PVM/Status.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/dispatcher.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/TrackingJobMaster.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/pvm.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/hosts.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/ExampleSlave.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/PVMThread.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/__init__.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/ExampleMaster.py -> build/lib/Biskit/PVM
  creating build/lib/Biskit/Dock
  copying Biskit/Dock/XRefineComplex.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexEvolving.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Analyzer.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexRandomizer.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexList.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ContactSlave.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexModelRegistry.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexEvolvingList.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexTraj.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/PatchGeneratorFromOrbit.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/HexParser.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/PatchGenerator.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Intervor.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/hexTools.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/__init__.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/delphiBindingEnergy.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/settings.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Complex.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/FixedList.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Docker.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ContactMaster.py -> build/lib/Biskit/Dock
  creating build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/ufuncs.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/compat.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/typeconv.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/alter_code.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/__init__.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/functions.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/array_printer.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/misc.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/precision.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/__analyze_oldnumeric.py -> build/lib/Biskit/oldnumeric
  running egg_info
  writing biskit.egg-info/PKG-INFO
  writing dependency_links to biskit.egg-info/dependency_links.txt
  writing requirements to biskit.egg-info/requires.txt
  writing top-level names to biskit.egg-info/top_level.txt
  reading manifest file 'biskit.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE.txt'
  writing manifest file 'biskit.egg-info/SOURCES.txt'
  error: Error: setup script specifies an absolute path:
 
      /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/Biskit/data/[spectrum.pl](http://spectrum.pl/)
 
  setup() arguments must *always* be /-separated paths relative to the
  setup.py directory, *never* absolute paths.
 
  ----------------------------------------
  ERROR: Failed building wheel for biskit
  Running setup.py clean for biskit
Failed to build biskit
Installing collected packages: biopython, biskit
    Running setup.py install for biskit ... error
    ERROR: Command errored out with exit status 1:
     command: /home/m992c693/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-kgonm3c0/install-record.txt --single-version-externally-managed --compile --install-headers /home/m992c693/anaconda3/include/python3.9/biskit
         cwd: /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/
    Complete output (192 lines):
    /home/m992c693/anaconda3/lib/python3.9/site-packages/setuptools/dist.py:757: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
      warnings.warn(
    running install
    /home/m992c693/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    running build
    running build_py
    creating build
    creating build/lib
    creating build/lib/Biskit
    copying Biskit/molUtils.py -> build/lib/Biskit
    copying Biskit/ExeConfig.py -> build/lib/Biskit
    copying Biskit/ExeConfigCache.py -> build/lib/Biskit
    copying Biskit/PCRModel.py -> build/lib/Biskit
    copying Biskit/Model.py -> build/lib/Biskit
    copying Biskit/Trajectory.py -> build/lib/Biskit
    copying Biskit/SettingsParser.py -> build/lib/Biskit
    copying Biskit/molTools.py -> build/lib/Biskit
    copying Biskit/DSSP.py -> build/lib/Biskit
    copying Biskit/AmberRstParser.py -> build/lib/Biskit
    copying Biskit/BioUnit.py -> build/lib/Biskit
    copying Biskit/PDBParserFactory.py -> build/lib/Biskit
    copying Biskit/PDBParseNCBI.py -> build/lib/Biskit
    copying Biskit/Executor.py -> build/lib/Biskit
    copying Biskit/wormlikechain.py -> build/lib/Biskit
    copying Biskit/SurfaceRacer.py -> build/lib/Biskit
    copying Biskit/amberResidues.py -> build/lib/Biskit
    copying Biskit/QualSlave.py -> build/lib/Biskit
    copying Biskit/CommandLine.py -> build/lib/Biskit
    copying Biskit/PDBModel.py -> build/lib/Biskit
    copying Biskit/AmberParmBuilder.py -> build/lib/Biskit
    copying Biskit/ModelList.py -> build/lib/Biskit
    copying Biskit/Hmmer.py -> build/lib/Biskit
    copying Biskit/gnuplot.py -> build/lib/Biskit
    copying Biskit/ProfileMirror.py -> build/lib/Biskit
    copying Biskit/LocalPath.py -> build/lib/Biskit
    copying Biskit/reduce.py -> build/lib/Biskit
    copying Biskit/TrajFlexMaster.py -> build/lib/Biskit
    copying Biskit/PDBParseModel.py -> build/lib/Biskit
    copying Biskit/AmberCrdParser.py -> build/lib/Biskit
    copying Biskit/ErrorHandler.py -> build/lib/Biskit
    copying Biskit/decorators.py -> build/lib/Biskit
    copying Biskit/AmberCrdEntropist.py -> build/lib/Biskit
    copying Biskit/PDBParsePickle.py -> build/lib/Biskit
    copying Biskit/amberResidueLibrary.py -> build/lib/Biskit
    copying Biskit/Polymer.py -> build/lib/Biskit
    copying Biskit/StructureMaster.py -> build/lib/Biskit
    copying Biskit/surfaceRacerTools.py -> build/lib/Biskit
    copying Biskit/ReduceCoordinates.py -> build/lib/Biskit
    copying Biskit/ColorSpectrum.py -> build/lib/Biskit
    copying Biskit/FuzzyCluster.py -> build/lib/Biskit
    copying Biskit/PDBCleaner.py -> build/lib/Biskit
    copying Biskit/Xplorer.py -> build/lib/Biskit
    copying Biskit/PDBDope.py -> build/lib/Biskit
    copying Biskit/WhatIf.py -> build/lib/Biskit
    copying Biskit/AmberEntropist.py -> build/lib/Biskit
    copying Biskit/ProfileCollection.py -> build/lib/Biskit
    copying Biskit/AmberEntropySlave.py -> build/lib/Biskit
    copying Biskit/Blast2Seq.py -> build/lib/Biskit
    copying Biskit/match2seq.py -> build/lib/Biskit
    copying Biskit/mathUtils.py -> build/lib/Biskit
    copying Biskit/DictList.py -> build/lib/Biskit
    copying Biskit/wlc.py -> build/lib/Biskit
    copying Biskit/residue.py -> build/lib/Biskit
    copying Biskit/TrajFlexSlave.py -> build/lib/Biskit
    copying Biskit/MatrixPlot.py -> build/lib/Biskit
    copying Biskit/ez_setup.py -> build/lib/Biskit
    copying Biskit/Fold_X.py -> build/lib/Biskit
    copying Biskit/QualMaster.py -> build/lib/Biskit
    copying Biskit/hist.py -> build/lib/Biskit
    copying Biskit/atomCharger.py -> build/lib/Biskit
    copying Biskit/SparseArray.py -> build/lib/Biskit
    copying Biskit/difflib_old.py -> build/lib/Biskit
    copying Biskit/tmalign.py -> build/lib/Biskit
    copying Biskit/EnsembleTraj.py -> build/lib/Biskit
    copying Biskit/test.py -> build/lib/Biskit
    copying Biskit/__init__.py -> build/lib/Biskit
    copying Biskit/EDParser.py -> build/lib/Biskit
    copying Biskit/Prosa2003.py -> build/lib/Biskit
    copying Biskit/PDBParseFile.py -> build/lib/Biskit
    copying Biskit/SettingsManager.py -> build/lib/Biskit
    copying Biskit/Pymoler.py -> build/lib/Biskit
    copying Biskit/tools.py -> build/lib/Biskit
    copying Biskit/msms.py -> build/lib/Biskit
    copying Biskit/Errors.py -> build/lib/Biskit
    copying Biskit/LogFile.py -> build/lib/Biskit
    copying Biskit/settings.py -> build/lib/Biskit
    copying Biskit/BisList.py -> build/lib/Biskit
    copying Biskit/plotUtils.py -> build/lib/Biskit
    copying Biskit/Ramachandran.py -> build/lib/Biskit
    copying Biskit/AmberLeap.py -> build/lib/Biskit
    copying Biskit/TrajCluster.py -> build/lib/Biskit
    copying Biskit/AmberEntropyMaster.py -> build/lib/Biskit
    copying Biskit/IcmCad.py -> build/lib/Biskit
    copying Biskit/rmsFit.py -> build/lib/Biskit
    copying Biskit/XplorInput.py -> build/lib/Biskit
    copying Biskit/PDBParser.py -> build/lib/Biskit
    copying Biskit/delphi.py -> build/lib/Biskit
    copying Biskit/StructureSlave.py -> build/lib/Biskit
    creating build/lib/Biskit/Mod
    copying Biskit/Mod/Analyse.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/ModelSlave.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/Modeller.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/TemplateSearcher.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/TemplateFilter.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/ModelMaster.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/AlignerMaster.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/ValidationSetup.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/TemplateCleaner.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/Benchmark.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/modUtils.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/__init__.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/Aligner.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/AlignerSlave.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/SequenceSearcher.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/settings.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/CheckIdentities.py -> build/lib/Biskit/Mod
    creating build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/PDBExportFilters.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/PDB.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/__init__.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/FortranFormat.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/TextFile.py -> build/lib/Biskit/ScientificIO
    creating build/lib/Biskit/deprecated
    copying Biskit/deprecated/ChainWriter.py -> build/lib/Biskit/deprecated
    copying Biskit/deprecated/__init__.py -> build/lib/Biskit/deprecated
    copying Biskit/deprecated/ChainSeparator.py -> build/lib/Biskit/deprecated
    copying Biskit/deprecated/ChainCleaner.py -> build/lib/Biskit/deprecated
    creating build/lib/Biskit/Statistics
    copying Biskit/Statistics/Density.py -> build/lib/Biskit/Statistics
    copying Biskit/Statistics/ROCalyzer.py -> build/lib/Biskit/Statistics
    copying Biskit/Statistics/__init__.py -> build/lib/Biskit/Statistics
    copying Biskit/Statistics/lognormal.py -> build/lib/Biskit/Statistics
    creating build/lib/Biskit/PVM
    copying Biskit/PVM/Status.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/dispatcher.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/TrackingJobMaster.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/pvm.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/hosts.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/ExampleSlave.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/PVMThread.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/__init__.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/ExampleMaster.py -> build/lib/Biskit/PVM
    creating build/lib/Biskit/Dock
    copying Biskit/Dock/XRefineComplex.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexEvolving.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Analyzer.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexRandomizer.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexList.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ContactSlave.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexModelRegistry.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexEvolvingList.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexTraj.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/PatchGeneratorFromOrbit.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/HexParser.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/PatchGenerator.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Intervor.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/hexTools.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/__init__.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/delphiBindingEnergy.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/settings.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Complex.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/FixedList.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Docker.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ContactMaster.py -> build/lib/Biskit/Dock
    creating build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/ufuncs.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/compat.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/typeconv.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/alter_code.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/__init__.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/functions.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/array_printer.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/misc.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/precision.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/__analyze_oldnumeric.py -> build/lib/Biskit/oldnumeric
    running egg_info
    writing biskit.egg-info/PKG-INFO
    writing dependency_links to biskit.egg-info/dependency_links.txt
    writing requirements to biskit.egg-info/requires.txt
    writing top-level names to biskit.egg-info/top_level.txt
    reading manifest file 'biskit.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    adding license file 'LICENSE.txt'
    writing manifest file 'biskit.egg-info/SOURCES.txt'
    error: Error: setup script specifies an absolute path:
   
        /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/Biskit/data/[spectrum.pl](http://spectrum.pl/)
   
    setup() arguments must *always* be /-separated paths relative to the
    setup.py directory, *never* absolute paths.
   
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/m992c693/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-kgonm3c0/install-record.txt --single-version-externally-managed --compile --install-headers /home/m992c693/anaconda3/include/python3.9/biskit Check the logs for full command output.

Not sure how to resolve this error and install biskit correctly.
Thank you for the kind help.

some temporary files not removed

running test.py -i exe -p Biskit

leaves behind in /tmp:

1 executor_*** folder
5 tmp****model files
1 tmp***.pml file

DSSP.py mask & compress fail, returing KeyError 4 and 5

With 1AM7:

Traceback (most recent call last):
  File "1.py", line 11, in <module>
    m = m.compress(m.maskProtein())
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2309, in compress
    return self.take( N0.nonzero( mask ), *initArgs, **initKw )
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2249, in take
    r.biounit = self.biounit.take(i)
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/BioUnit.py", line 107, in take
    r.biomol = dict([ (bm , self.biomol[bm]) for bm in remaining_biomols ])
KeyError: 4

With 1CA1:

  File "1.py", line 11, in <module>
    m = m.compress(m.maskProtein())
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2309, in compress
    return self.take( N0.nonzero( mask ), *initArgs, **initKw )
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2249, in take
    r.biounit = self.biounit.take(i)
  File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/BioUnit.py", line 107, in take
    r.biomol = dict([ (bm , self.biomol[bm]) for bm in remaining_biomols ])
KeyError: 5

Loading PDB files remotely from PDB website failed

The RCSB PDB website has changed the direct link to PDB records.

docker.py: use ExeConfig.bin

docker.py currently uses a hard-coded binary path. Convert to ExeConfig usage.

See:

biskit/biskit/dock/docker.py

Lines 64 to 68 in d2d4965

    
           def __init__( self, recDic, ligDic, recPdb=None, ligPdb=None, 
        
                         comPdb=None, out='hex_%s', soln=512, 
        
                         recChainId=None, ligChainId=None, macDock=None, 
        
                         bin='hex', verbose=1 ):  ## use ExeConfig instead of bin=... 
        
               """

delphi 7.0 and lates reduce fail in delphiBindingEnergy.py

Error log:

Reduce version 3.23
Delphi version 7.0

test_bindingE (__main__.Test)
bindingEnergyDelphi test (Barnase:Barstar) ...
Re-building hydrogen atoms...
executing: /home/parashar/software/reduce_3.23.130521.linuxi386/reduce  -BUILD -Nterm2 -DB /home/parashar/software/biskit/Biskit/data/reduce/reduce_wwPDB_het_dict.txt /tmp/reduce_HvDdqn_in.pdb
    in folder: None
    input:     None
    output:    <open file '/tmp/reduce_4T_9c7_out.pdb', mode 'w' at 0x7f8f7187fb70>
    errors:    <open file '/tmp/reduce_zswu1P.err', mode 'w' at 0x7f8f7187fc00>
    wrapped:   0
    shell:     None
    environment: None
.. finished.

Assigning charges from Amber topologies...
parsing all_amino03.in...
Read 33 residue definitions.

parsing all_aminoct03.in...
Read 22 residue definitions.

parsing all_aminont03.in...
Read 22 residue definitions.

parsing all_nuc02.in...
Read 37 residue definitions.


Delphi calculations with 0.150 M salt
=======================================

running Delphi for complex...

creating temporary directory /tmp/delphi_Ing4WF
Creating Delphi charge file /tmp/delphi_Ing4WF/delphi_Y7wKHq.crg

Atoms without charges: 0
executing: /home/parashar/software/Delphi_Linux/executable/delphi /tmp/delphi_Ing4WF/delphi_UQRThO.inp
    in folder: /tmp/delphi_Ing4WF
    input:     <open file '/tmp/delphi_Ing4WF/delphi_UQRThO.inp', mode 'r' at 0x7f8f7187fc00>
    output:    <open file '/tmp/delphi_Ing4WF/delphi_yvotaS.out', mode 'w' at 0x7f8f7187fb70>
    errors:    <open file '/tmp/delphi_Ing4WF/delphi_5AL2Dp.err', mode 'w' at 0x7f8f7187fc90>
    wrapped:   0
    shell:     None
    environment: None
.. finished.
Delphi failed. Please check the program output in the field `output` of this Delphi instance (e.g. `print x.output`)!

The last message from DelPhi reads as follows:
 .........  PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 3473 WARNING(S) ........


Removing non-empty temporary folder /tmp/delphi_Ing4WF
ERROR
test_errorcase1 (__main__.Test)
bindinEnergyDelphi test (error case 01) ...
Re-building hydrogen atoms...
executing: /home/parashar/software/reduce_3.23.130521.linuxi386/reduce  -BUILD -Nterm3 -DB /home/parashar/software/biskit/Biskit/data/reduce/reduce_wwPDB_het_dict.txt /tmp/reduce_goTDxO_in.pdb
    in folder: None
    input:     None
    output:    <open file '/tmp/reduce_qKoQGa_out.pdb', mode 'w' at 0x7f8f7187fdb0>
    errors:    <open file '/tmp/reduce_gq23ed.err', mode 'w' at 0x7f8f7187fc90>
    wrapped:   0
    shell:     None
    environment: None
.. finished.

Assigning charges from Amber topologies...
parsing all_amino03.in...
Read 33 residue definitions.

parsing all_aminoct03.in...
Read 22 residue definitions.

parsing all_aminont03.in...
Read 22 residue definitions.

parsing all_nuc02.in...
Read 37 residue definitions.

Warning: 1 atoms missing from residue #0   (VAL  74 A):
        ['H']
        Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #75  (GLU 179 A):
        ['H']
        Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #100 (THR  71 B):
        ['H']
        Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #178 (GLU 179 B):
        ['H']
        Ignored. Residue will have incomplete charge.
Warning: 1 atoms missing from residue #203 (THR  85 C):
        ['H']
        Ignored. Residue will have incomplete charge.

Delphi calculations with 0.150 M salt
=======================================

running Delphi for complex...

creating temporary directory /tmp/delphi_8h4Cwr
Creating Delphi charge file /tmp/delphi_8h4Cwr/delphi_AZ4ghY.crg

Atoms without charges: 0
executing: /home/parashar/software/Delphi_Linux/executable/delphi /tmp/delphi_8h4Cwr/delphi_Z8qteD.inp
    in folder: /tmp/delphi_8h4Cwr
    input:     <open file '/tmp/delphi_8h4Cwr/delphi_Z8qteD.inp', mode 'r' at 0x7f8f7187fc90>
    output:    <open file '/tmp/delphi_8h4Cwr/delphi_Q1UFAk.out', mode 'w' at 0x7f8f7187fdb0>
    errors:    <open file '/tmp/delphi_8h4Cwr/delphi_2_cvol.err', mode 'w' at 0x7f8f7187fb70>
    wrapped:   0
    shell:     None
    environment: None
.. finished.
Delphi failed. Please check the program output in the field `output` of this Delphi instance (e.g. `print x.output`)!

The last message from DelPhi reads as follows:
 .........  PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 4774 WARNING(S) ........


Removing non-empty temporary folder /tmp/delphi_8h4Cwr
ERROR

======================================================================
ERROR: test_bindingE (__main__.Test)
bindingEnergyDelphi test (Barnase:Barstar)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "delphiBindingEnergy.py", line 431, in test_bindingE
    self.r = self.dG.run()
  File "delphiBindingEnergy.py", line 397, in run
    self.ezero, self.esalt = self.processSixsome()
  File "delphiBindingEnergy.py", line 327, in processSixsome
    ri_com, ri_rec, ri_lig = self.processThreesome( salt=self.salt, **kw )
  File "delphiBindingEnergy.py", line 304, in processThreesome
    r_com = dcom.run()
  File "/home/parashar/software/biskit/Biskit/Executor.py", line 555, in run
    self.fail()
  File "/home/parashar/software/biskit/Biskit/delphi.py", line 600, in fail
    raise DelphiError, s
DelphiError: The last message from DelPhi reads as follows:
 .........  PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 3473 WARNING(S) ........



======================================================================
ERROR: test_errorcase1 (__main__.Test)
bindinEnergyDelphi test (error case 01)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "delphiBindingEnergy.py", line 449, in test_errorcase1
    self.r = self.dG.run()
  File "delphiBindingEnergy.py", line 397, in run
    self.ezero, self.esalt = self.processSixsome()
  File "delphiBindingEnergy.py", line 327, in processSixsome
    ri_com, ri_rec, ri_lig = self.processThreesome( salt=self.salt, **kw )
  File "delphiBindingEnergy.py", line 304, in processThreesome
    r_com = dcom.run()
  File "/home/parashar/software/biskit/Biskit/Executor.py", line 555, in run
    self.fail()
  File "/home/parashar/software/biskit/Biskit/delphi.py", line 600, in fail
    raise DelphiError, s
DelphiError: The last message from DelPhi reads as follows:
 .........  PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 4774 WARNING(S) ........



----------------------------------------------------------------------
Ran 2 tests in 31.733s

FAILED (errors=2)

remove old $revision$ tags from codebase version() methods

These were SVN - specific and don't work any longer.

failed test: Delphi wrapper

Tested on Ubuntu 14.04, with delphi95 (SP)

ERROR: delphi.Test.test_delphi

Traceback (most recent call last):
File "/home/raik/data/py/Biskit/delphi.py", line 694, in test_delphi
self.assertAlmostEqual( expect[k], self.r[k], -1 )
KeyError: 'scharge'

update biskitbase docker image to include Hex 8.0

A new image needs to be created and uploaded to dockerstore.

clone biskitbase locally
download xplor-nih, delphi
download hex for linux to downloads
add hex installation to docker script
rebuild and test dockerbase image
upload new image to dockerstore

merge biskit3 into master

merge biskit3 branch into master branch after biskit 2.x codebase has been relocated into its own branch.

Delphi.py failure prints to STDOUT

The Delphi wrapper writes to STDERR or STDOUT when execution fails. This obstructs testing:

exe.reduce.Test.test_reduce  .................................. ok
exe.delphi.Test.test_delphi  .................................. Delphi failed. Please check the program output in the field `output` of this Delphi instance (e.g. `print x.output`)!

The last message from DelPhi reads as follows:
 .........  PROGRAM EXITS SUCCESSFULLY : WITH TOTAL 221 WARNING(S) ........


ERROR
exe.delphi.Test.test_delphiCharges2  .......................... ok

Remove print() statements or adjust verbosity.

Delphi C++ output has changed

The failed method is triggered in all test cases despite "successful" finishing of the delphi run.

Porting to Python 3?

Hi,

Are there plans that this awesome library will be ported to Python3?

AmberLeap: need to adapt leaprc path for AmberTools 17

tested with AmberTools 17

test_AmberLeap_findLeaprc (__main__.Test)
AmberLeap.findLeaprc test ... 
target leaprc: /opt/amber16/dat/leap/cmd/oldff/leaprc.ff10
ok
test_AmberLeap_run (__main__.Test)
AmberLeap.run test ... ERROR

======================================================================
ERROR: test_AmberLeap_run (__main__.Test)
AmberLeap.run test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "AmberLeap.py", line 227, in test_AmberLeap_run
    debug=self.DEBUG)
  File "AmberLeap.py", line 125, in __init__
    self.leaprc = self.findLeaprc( leaprc or self.exe.leaprc )
  File "AmberLeap.py", line 178, in findLeaprc
    'Check exe_tleap.dat or provide an explicit leaprc parameter!'
LeapError: Could not find Forcefield definition ff03.r1. Check exe_tleap.dat or provide an explicit leaprc parameter!

----------------------------------------------------------------------
Ran 2 tests in 0.004s

FAILED (errors=1)

test failure: Executor.Test.test_tempfiles

FAIL: Executor.Test.test_tempfiles

Traceback (most recent call last):
File "/home/raik/data/py/Biskit/Executor.py", line 802, in test_tempfiles
'tempfolder has not been removed.')
AssertionError: tempfolder has not been removed.

DSSP.py fails with certain PDB files

I'm using Biskit in conjunction with DSSP for my current work, and I've found that it'll work with some PDB files, but not with others. When it finds a PDB file it doesn't like, the program breaks and returns the following error:

File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/Executor.py", line 538, in run
   self.prepare()
 File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/DSSP.py", line 99, in prepare
   self.model = self.model.compress( self.model.maskHeavy() )
 File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2309, in compress
   return self.take( N0.nonzero( mask ), *initArgs, **initKw )
 File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/PDBModel.py", line 2249, in take
   r.biounit = self.biounit.take(i)
 File "/usr/local/lib/python2.7/dist-packages/biskit-2.4.3-py2.7.egg/Biskit/BioUnit.py", line 107, in take
   r.biomol = dict([ (bm , self.biomol[bm]) for bm in remaining_biomols ])
KeyError: 2

I'm not entirely sure why this doesn't work. For me, some examples of PDBs that work (by id on the PDB sites) include: 3AUJ, 4PRK and 2R56; some PDBs that don't work include 3OET, 3CPM and 4XQ4.

remove trajectory.TrajProfiles class

the TrajProfiles class in trajectory.py does not change anything over ProfileCollection. Remove but verify integrity of testdata pickles.

Biskit 2.x tests fail in recent (trusty) build environment

A single test fails (for numeric issues) on travis-ci "trusty" build environment:

======================================================================
FAIL: PDBCleaner.Test.test_capping_extra  
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/virtualenv/python2.7_with_system_site_packages/local/lib/python2.7/site-packages/biskit-2.5.0-py2.7.egg/Biskit/PDBCleaner.py", line 725, in test_capping_extra
    self.assertRaises(CappingError, self.c.capTerminals, auto=True)
AssertionError: CappingError not raised
----------------------------------------------------------------------

Workaround: set dist: precise

delphi (C++ v7.1) does not understand old radius file

C++ Delphi versions do not seem to understand the radii.siz (default.siz) file used together with previous versions. The beauty (and shortcoming) of the old file was that it only assigned a single radius per element. This does not seem to work any longer.

As a temporary workaround, I am adding the new "sample radius file" from the Delphi web site:
https://honiglab.c2b2.columbia.edu/software/DelPhi/doc/parseres.siz

added to biskit/data/delphi/radii_delphi_v7.siz
adapt atom and residue names in this file to Amber topology
make this the default radii file of Delphi wrapper

This file is optimized to be used with a different charge set. Not sure though, whether it makes any sense physically to combine these radii with amber charges. Better would be to re-create this file from the Amber topology. Radii are not given in the leap prep library files. Instead, they may be fetched from AmberTools/src/pbsa/sa_driver.F90, at least this is what is claimed here:
http://archive.ambermd.org/201610/0088.html

AmberParmBuilder test case assertion error

Tested using AmberTools 17 on Ubuntu 16.04

Something wrong with chain break detection:

FAIL: test_AmberParmSolvated (__main__.Test)
AmberParmBuilder.parmSolvated test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "AmberParmBuilder.py", line 669, in test_AmberParmSolvated
    self.assertEqual( self.ref.lenChains(), self.m3.lenChains() )
AssertionError: 3 != 2

----------------------------------------------------------------------

Hex 8 generating output with nan energies

Unmodified test case now yields the following result (example solution):

Orientation: 1
Solution: 1
ReceptorModel: 1
LigandModel: 1
Bumps: -1
ReferenceRMS: -1.00
Vshape: 0.0
Vclash: 0.0
Future: 0.0
Etotal: nan
Eshape: nan
Eforce: 0.00
Eair:   0.00
ReceptorMatrix:
  1.000000e+00   0.000000e+00   0.000000e+00   0.000000e+00 
  0.000000e+00   1.000000e+00   0.000000e+00   0.000000e+00 
  0.000000e+00   0.000000e+00   1.000000e+00   0.000000e+00 
  0.000000e+00   0.000000e+00   0.000000e+00   1.000000e+00 
LigandMatrix:
 -9.944818e-01   1.008306e-01   2.896955e-02   1.422414e+02 
  2.492328e-02   4.953042e-01  -8.683620e-01   1.777419e+01 
 -1.019062e-01  -8.628482e-01  -4.950840e-01   8.817038e+01 
  0.000000e+00   0.000000e+00   0.000000e+00   1.000000e+00

Etotal, Eshape and Eforce are expected to have a value (which is useful for sorting complexes). Potentially, this could mean that the docking solutions don't actually touch.

docker.py hex wrapper not removing temporary (result) files

As evident from the test case. The result folder with all its content persists after the run.

move master to biskit2

Clone current master branch to a biskit 2.x branch.
This branch will continue to hold the old Python 2.x version of Biskit

biskit 2.x branch testing fails with segmentation fault on travis-ci

This was apparently caused by importing and executing biggles code (including show) in the main-body of the wlc.py module.

Fixed on branch 2.x but not in latest release.

replace / retire [email protected] mailing list

biskit.pasteur.fr is still referring to the sourceforge-hosted mailing list.

docker.py failure prints to STDOUT

A failing Hex run in docker.py leads to verbose output in the test suite:

dock.hextools.Test.test_hexTools  ............................. ok
dock.docker.TestLong.test_DockerLong  ......................... ssh: connect to host localhost port 22: Cannot assign requested address
FAILED:  localhost   1A2P_1-1A19_1_hex
	Job details:
	Command:  ssh localhost hex -ncpu 6 -nice 0 -noexec -e /tmp/tmpuh76r3l0_test_docker_0804/1A2P_1-1A19_1_hex.mac > /tmp/tmpuh76r3l0_test_docker_0804/1A2P_1-1A19_1_hex.mac.log
	input:    /tmp/tmpuh76r3l0_test_docker_0804/1A2P_1-1A19_1_hex.mac
	Hex log:  1
	Hex out:  /tmp/tmpuh76r3l0_test_docker_0804/1A2P_1-1A19_1_hex.out

	 <class 'biskit.dock.docker.DockerError'> in /app/biskit/dock/docker.py line 464:
	('Hex returned exit status 255',).
ok
dock.docker.TestShort.test_DockerShort  ....................... ok

ensembleTraj.fitMembers seems to reset n_members to 10

The newly ported script a_ensemble.py reveals some bug in EnsembleTraj when applied to a EnsembleTraj object with 50 members: after running the fitMembers method, the trajectory n_members is reduced from 50 to 10. Frames are still all there.

get working Delphi version into docker image

The currently used Delphi F95 SP tar.gz release is not available any longer on http://compbio.clemson.edu/delphi_credentials/downloadDelphi.php.
The release that is available is now source-only without included binary. It does not compile on the docker image (presumably it requires a very recent fortran compiler version).

Delphi C++ v 8.0 is released with linux binary. However, the delphi.py test case fails. Does not look like a insurmountable problem but it needs serious step-by-step debugging. Preferably, the delphi wrapper should be updated to Delphi 8.0. Simpler would be to get hold of a Delphi F95 binary (authors contacted).

List of some PBDs that work and that don't

For reference, the following work (on the July 21 commit, using compress(maskProtein())):

1a7s.pdb  1lt6.pdb  2crt.pdb  3m3r.pdb
1ae5.pdb  1lta.pdb  2dcv.pdb  3m4d.pdb
1ah7.pdb  1ltb.pdb  2dcw.pdb  3m4e.pdb
1am7.pdb  1ltg.pdb  2ddr.pdb  3o44.pdb
1ao6.pdb  1lti.pdb  2dds.pdb  3psm.pdb
1aok.pdb  1lts.pdb  2ddt.pdb  3q76.pdb
1aro.pdb  1ltt.pdb  2dtb.pdb  3q77.pdb
1au8.pdb  1m3i.pdb  2e2f.pdb  3roh.pdb
1ayj.pdb  1m3j.pdb  2ffz.pdb  3sqj.pdb
1b0f.pdb  1md2.pdb  2fgn.pdb  3tdl.pdb
1bah.pdb  1mm0.pdb  2ga4.pdb  3uiv.pdb
1bj5.pdb  1n5u.pdb  2gj0.pdb  3ujo.pdb
1bk8.pdb  1o71.pdb  2gl1.pdb  3ujq.pdb
1bke.pdb  1o72.pdb  2huc.pdb  3uk9.pdb
1bm0.pdb  1o9x.pdb  2i0w.pdb  3ul2.pdb
1bos.pdb  1oba.pdb  2i2z.pdb  3v08.pdb
1brz.pdb  1odb.pdb  2i30.pdb  3vts.pdb
1c01.pdb  1ozz.pdb  2ixu.pdb  3zwg.pdb
1c4q.pdb  1p00.pdb  2ixv.pdb  3zwj.pdb
1ca1.pdb  1p0a.pdb  2j8g.pdb  3zx7.pdb
1cfe.pdb  1p5x.pdb  2k38.pdb  3zxd.pdb
1cgh.pdb  1p6d.pdb  2kam.pdb  3zxg.pdb
1chp.pdb  1p6e.pdb  2kcg.pdb  4dwx.pdb
1chq.pdb  1p9z.pdb  2kgq.pdb  4dyg.pdb
1chv.pdb  1ppf.pdb  2knj.pdb  4fb9.pdb
1cix.pdb  1ppg.pdb  2knm.pdb  4fbb.pdb
1cqf.pdb  1pvl.pdb  2knn.pdb  4fbc.pdb
1cre.pdb  1pzi.pdb  2ks4.pdb  4fbh.pdb
1crf.pdb  1q3j.pdb  2ksg.pdb  4g03.pdb
1ct1.pdb  1qm6.pdb  2kuk.pdb  4g04.pdb
1cxn.pdb  1qmd.pdb  2kyq.pdb  4h56.pdb
1cxo.pdb  1qnu.pdb  2l2b.pdb  4he7.pdb
1cz6.pdb  1qoh.pdb  2l38.pdb  4hgk.pdb
1czg.pdb  1qoy.pdb  2lb7.pdb  4iw2.pdb
1czw.pdb  1r4p.pdb  2lj7.pdb  4iyc.pdb
1d1i.pdb  1r4q.pdb  2lkf.pdb  4iyt.pdb
1d1k.pdb  1rcv.pdb  2lr3.pdb  4izl.pdb
1d9u.pdb  1reo.pdb  2ly5.pdb  4j0o.pdb
1djr.pdb  1rf2.pdb  2ly6.pdb  4jox.pdb
1dkc.pdb  1rgb.pdb  2m8b.pdb  4jta.pdb
1dm0.pdb  1s5b.pdb  2m9g.pdb  4jtc.pdb
1dtc.pdb  1s5c.pdb  2mcw.pdb  4jtd.pdb
1du5.pdb  1s5d.pdb  2mcx.pdb  4k2c.pdb
1e78.pdb  1s5e.pdb  2mp9.pdb  4k71.pdb
1e7a.pdb  1s5f.pdb  2mxz.pdb  4l8u.pdb
1e7b.pdb  1siy.pdb  2mz0.pdb  4l9k.pdb
1e7c.pdb  1t32.pdb  2n0o.pdb  4l9q.pdb
1e7e.pdb  1t5r.pdb  2n2q.pdb  4la0.pdb
1e7f.pdb  1tdk.pdb  2n2r.pdb  4lb2.pdb
1e7g.pdb  1tdn.pdb  2n2z.pdb  4lb9.pdb
1e7h.pdb  1tdo.pdb  2n66.pdb  4m1u.pdb
1e7i.pdb  1tf0.pdb  2n81.pdb  4m3c.pdb
1e8a.pdb  1tgx.pdb  2nrj.pdb  4n0f.pdb
1eef.pdb  1tzq.pdb  2qk7.pdb  4n0u.pdb
1efi.pdb  1ueo.pdb  2rg3.pdb  4oeb.pdb
1fd7.pdb  1ug4.pdb  2uyr.pdb  4om4.pdb
1fgb.pdb  1uor.pdb  2v9u.pdb  4om5.pdb
1fy1.pdb  1ut3.pdb  2vdb.pdb  4or0.pdb
1fy3.pdb  1uun.pdb  2vue.pdb  4p1x.pdb
1g8z.pdb  1xez.pdb  2vuf.pdb  4p1y.pdb
1gni.pdb  1xjt.pdb  2wcd.pdb  4p24.pdb
1gnj.pdb  1xju.pdb  2wcf.pdb  4p2c.pdb
1gps.pdb  1xt3.pdb  2wxt.pdb  4s1y.pdb
1gpt.pdb  1xtc.pdb  2wxu.pdb  4tsy.pdb
1gqm.pdb  1xv3.pdb  2wy6.pdb  4tw1.pdb
1gwy.pdb  1xx1.pdb  2xrq.pdb  4u6v.pdb
1gyg.pdb  1z99.pdb  2xsi.pdb  4ull.pdb
1h09.pdb  1zrv.pdb  2xvq.pdb  4wvm.pdb
1h0j.pdb  1zrw.pdb  2xvu.pdb  4xre.pdb
1h1b.pdb  1zrx.pdb  2xvv.pdb  4yhd.pdb
1h5o.pdb  1zwx.pdb  2xvw.pdb  4z69.pdb
1h9z.pdb  2a9h.pdb  2xw0.pdb  4zgh.pdb
1ha2.pdb  2ap7.pdb  2xw1.pdb  4zpu.pdb
1hk1.pdb  2ap8.pdb  2ydf.pdb  5a09.pdb
1hk2.pdb  2bhi.pdb  2ygt.pdb  5a0a.pdb
1hk3.pdb  2bos.pdb  2ymk.pdb  5a0b.pdb
1hk4.pdb  2brz.pdb  2ymw.pdb  5a0c.pdb
1hk5.pdb  2bx8.pdb  2z7f.pdb  5a8x.pdb
1hne.pdb  2bxa.pdb  3a2e.pdb  5a8y.pdb
1htl.pdb  2bxb.pdb  3a73.pdb  5a8z.pdb
1i02.pdb  2bxc.pdb  3anz.pdb  5aod.pdb
1i2u.pdb  2bxd.pdb  3b07.pdb  5aoe.pdb
1i2v.pdb  2bxe.pdb  3b9l.pdb  5aof.pdb
1iaz.pdb  2bxf.pdb  3b9m.pdb  5dqf.pdb
1iyc.pdb  2bxg.pdb  3bkh.pdb  5ec5.pdb
1jkz.pdb  2bxh.pdb  3bkv.pdb  5fuo.pdb
1jlt.pdb  2bxi.pdb  3chb.pdb  5gaq.pdb
1jqy.pdb  2bxk.pdb  3cx9.pdb  5hoz.pdb
1jr0.pdb  2bxl.pdb  3d3d.pdb  5ifo.pdb
1kbs.pdb  2bxm.pdb  3hc7.pdb  5iih.pdb
1kbt.pdb  2bxn.pdb  3hde.pdb  5iiu.pdb
1kd6.pdb  2bxo.pdb  3i5v.pdb  5iix.pdb
1kho.pdb  2bxp.pdb  3ipv.pdb  5ij5.pdb
1kyn.pdb  2bxq.pdb  3jqz.pdb  5ije.pdb
1lba.pdb  2c5c.pdb  3jry.pdb  5ijf.pdb
1lkf.pdb  2cdx.pdb  3lim.pdb  5k59.pdb
1lt3.pdb  2chb.pdb  3lkf.pdb  7ahl.pdb
1lt4.pdb  2crd.pdb  3lu7.pdb  8tfv.pdb
1lt5.pdb  2crs.pdb  3m2l.pdb

The following do NOT work:

1c48.pdb  3rlg.pdb  4gv5.pdb  4tsp.pdb
1p9g.pdb  3v03.pdb  4i0n.pdb  4tsq.pdb
1rd9.pdb  3v09.pdb  4idj.pdb  4wdc.pdb
1rdp.pdb  3vwi.pdb  4iw1.pdb  4whn.pdb
2anv.pdb  3w9p.pdb  4iya.pdb  4wvp.pdb
2anx.pdb  3weu.pdb  4j0l.pdb  4wx3.pdb
2f9r.pdb  3wev.pdb  4j2v.pdb  4wx5.pdb
2j8f.pdb  3wmu.pdb  4jk4.pdb  4zbq.pdb
2wc8.pdb  3wmv.pdb  4nzl.pdb  4zbr.pdb
2wcb.pdb  4bct.pdb  4ot2.pdb  5abw.pdb
2wce.pdb  4e99.pdb  4pho.pdb  5bpg.pdb
2xrs.pdb  4emx.pdb  4phq.pdb  5cr6.pdb
2xsc.pdb  4f5s.pdb  4po0.pdb  5dby.pdb
3a57.pdb  4f5t.pdb  4q7g.pdb  5elc.pdb
3hdf.pdb  4f5u.pdb  4rw3.pdb  5ele.pdb
3kve.pdb  4f5v.pdb  4rw5.pdb  5elf.pdb
3lu6.pdb  4fba.pdb  4tsl.pdb  5id7.pdb
3lu8.pdb  4fzm.pdb  4tsn.pdb  5id9.pdb
3mxg.pdb  4fzn.pdb  4tso.pdb

Some of this information may be useful for tests & debugging.

test failure: AmberEntropist (precision problem)

FAIL: AmberEntropist.Test.test_amberEntropist

Traceback (most recent call last):
File "/home/raik/data/py/Biskit/AmberEntropist.py", line 811, in test_amberEntropist
self.assertEqual( int(self.r['S_total']), 398 )
AssertionError: 399 != 398

Unclosed files from executor.py

In the execute method of executor.py, lines 501, 503 and 524 write to file without closing it. The open file from line 524 results in a warning being raised upon successful execution of a program.

/home/suliat16/.conda/envs/kaustenv/lib/python3.6/site-packages/biskit-3.0.0a0-py3.6.egg/biskit/exe/executor.py:524: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/rate4site_thq6mf7w.out' mode='wt' encoding='UTF-8'> open( self.f_out, 'wt').writelines( self.output )

failed test(s): DSSP wrapper

Tested on Ubuntu 14.04 with DSSP 2.0.4

ERROR: DSSP.Test.test_DSSP

Traceback (most recent call last):
File "/home/raik/data/py/Biskit/DSSP.py", line 272, in test_DSSP
self.result = self.dssp.run()
File "/home/raik/data/py/Biskit/Executor.py", line 557, in run
self.finish()
File "/home/raik/data/py/Biskit/DSSP.py", line 240, in finish
self.result = self.parse_result( )
File "/home/raik/data/py/Biskit/DSSP.py", line 134, in parse_result
'Dssp result file %s empty'%self.f_out
Dssp_Error: Dssp result file /tmp/dsspcmbi_LaCQ7V.out empty

This also raises another test error in PDBDope: PDBDope.Test.test_addSecondaryStructure

failed test: AmberParmBuilder.Test.test_capIrregular

Tested on: Linux64 (Ubuntu 14.04), with AmberTools 15

ERROR: AmberParmBuilder.Test.test_capIrregular
Traceback (most recent call last):
File "/home/raik/data/py/Biskit/AmberParmBuilder.py", line 680, in test_capIrregular
self.m4 = self.a.capACE( normal, 0 )
File "/home/raik/data/py/Biskit/AmberParmBuilder.py", line 313, in capACE
return cleaner.capACE( model, chain, breaks=True )
File "/home/raik/data/py/Biskit/PDBCleaner.py", line 390, in capACE
if len(c_start) != r.lenChains( breaks=breaks ):
File "/home/raik/data/py/Biskit/PDBModel.py", line 2518, in lenChains
singleRes=singleRes, solvent=solvent))
File "/home/raik/data/py/Biskit/PDBModel.py", line 2796, in chainIndex
solvent=solvent, force=force )
File "/home/raik/data/py/Biskit/PDBModel.py", line 2880, in chainBreaks
bb = self.take( i_bb )
File "/home/raik/data/py/Biskit/PDBModel.py", line 2206, in take
r.residues = self.residues.take( i_res, r )
File "/home/raik/data/py/Biskit/ProfileCollection.py", line 876, in take
raise ProfileError( "Can't take sub-profile %r: %r" % (key,why) )
ProfileError: Can't take sub-profile 'biomol': IndexError('index 2 is out of bounds for size 2',)

DSSP returns KeyError8 on protein 5fb8

Traceback (most recent call last):
  File "1.py", line 11, in <module>
    m = m.compress(m.maskProtein())	
  File "/home/dbmiller/scires/biskit/Biskit/PDBModel.py", line 2309, in compress
    return self.take( N0.nonzero( mask ), *initArgs, **initKw )
  File "/home/dbmiller/scires/biskit/Biskit/PDBModel.py", line 2249, in take
    r.biounit = self.biounit.take(i)
  File "/home/dbmiller/scires/biskit/Biskit/BioUnit.py", line 107, in take
    r.biomol = dict([ (bm , self.biomol[bm]) for bm in remaining_biomols ])
KeyError: 8

	def __init__( self, recDic, ligDic, recPdb=None, ligPdb=None,
	comPdb=None, out='hex_%s', soln=512,
	recChainId=None, ligChainId=None, macDock=None,
	bin='hex', verbose=1 ): ## use ExeConfig instead of bin=...
	"""