During instalation of Py contact in LinuxMint 2019.1 getting error. Installed all liberaries but still int installing.Plz help

Question

During instalation of Py contact in LinuxMint 2019.1 getting error. Installed all liberaries but still int installing.Plz help

debanjansen48 opened this issue 5 years ago · 5 comments

python2.7 -m pip install pycontact
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Defaulting to user installation because normal site-packages is not writeable
Collecting pycontact
Using cached pycontact-1.0.1.tar.gz (8.2 MB)
Requirement already satisfied: cython in /home/debanjan/.local/lib/python2.7/site-packages (from pycontact) (0.29.17)
Requirement already satisfied: matplotlib in /usr/lib/python2.7/dist-packages (from pycontact) (2.1.1)
Collecting mdanalysis<0.16
Using cached MDAnalysis-0.15.0.tar.gz (2.2 MB)
Requirement already satisfied: numpy in /home/debanjan/.local/lib/python2.7/site-packages (from pycontact) (1.16.6)
Requirement already satisfied: GridDataFormats>=0.3.2 in /home/debanjan/.local/lib/python2.7/site-packages (from mdanalysis<0.16->pycontact) (0.5.0)
Requirement already satisfied: biopython>=1.59 in /usr/lib/python2.7/dist-packages (from mdanalysis<0.16->pycontact) (1.70)
Requirement already satisfied: networkx>=1.0 in /home/debanjan/.local/lib/python2.7/site-packages (from mdanalysis<0.16->pycontact) (2.2)
Requirement already satisfied: six>=1.4.0 in /home/debanjan/.local/lib/python2.7/site-packages (from mdanalysis<0.16->pycontact) (1.14.0)
Requirement already satisfied: scipy in /home/debanjan/.local/lib/python2.7/site-packages (from GridDataFormats>=0.3.2->mdanalysis<0.16->pycontact) (1.2.3)
Requirement already satisfied: decorator>=4.3.0 in /home/debanjan/.local/lib/python2.7/site-packages (from networkx>=1.0->mdanalysis<0.16->pycontact) (4.4.2)
Building wheels for collected packages: pycontact, mdanalysis
Building wheel for pycontact (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ai7V51/pycontact/setup.py'"'"'; file='"'"'/tmp/pip-install-ai7V51/pycontact/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-9caFpX
cwd: /tmp/pip-install-ai7V51/pycontact/
Complete output (79 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/PyContact
copying PyContact/pycontact.py -> build/lib.linux-x86_64-2.7/PyContact
copying PyContact/init.py -> build/lib.linux-x86_64-2.7/PyContact
creating build/lib.linux-x86_64-2.7/tests
copying tests/test_basic.py -> build/lib.linux-x86_64-2.7/tests
copying tests/map_animate.py -> build/lib.linux-x86_64-2.7/tests
copying tests/init.py -> build/lib.linux-x86_64-2.7/tests
creating build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/exampleData/init.py -> build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/exampleData/datafiles.py -> build/lib.linux-x86_64-2.7/PyContact/exampleData
creating build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/detail_ui.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/VMDControlPanel.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/TrackCanvas.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/sasa_gui.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/Canvas.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/ExportTabWidget.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/MainWindow.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/statistics_ui.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/MoleculeTracker.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/DetailWidget.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/LabelView.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/HelpButton.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/MainQtGui.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/ErrorBox.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/Statistics.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/init.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/TableModels.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/track_mol_gui.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/Dialogues.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/SasaWidgets.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/Plotters.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/Preferences.py -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/gui/ErrorMessages.py -> build/lib.linux-x86_64-2.7/PyContact/gui
creating build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/Scripting.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/LoadConfiguration.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/ContactAnalyzer.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/aroundPatch.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/LogPool.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/init.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/multi_accumulation.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/DataHandler.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/Biochemistry.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/multi_trajectory.py -> build/lib.linux-x86_64-2.7/PyContact/core
copying PyContact/core/ContactFilters.py -> build/lib.linux-x86_64-2.7/PyContact/core
creating build/lib.linux-x86_64-2.7/PyContact/cy_modules
copying PyContact/cy_modules/init.py -> build/lib.linux-x86_64-2.7/PyContact/cy_modules
creating build/lib.linux-x86_64-2.7/PyContact/db
copying PyContact/db/init.py -> build/lib.linux-x86_64-2.7/PyContact/db
copying PyContact/db/DbReader.py -> build/lib.linux-x86_64-2.7/PyContact/db
copying PyContact/exampleData/defaultsession -> build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/exampleData/rpn11_ubq.psf -> build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/exampleData/rpn11_ubq.dcd -> build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/exampleData/md.tpr -> build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/exampleData/md_noPBC.xtc -> build/lib.linux-x86_64-2.7/PyContact/exampleData
copying PyContact/gui/remote_ctl.tcl -> build/lib.linux-x86_64-2.7/PyContact/gui
copying PyContact/db/aa.db -> build/lib.linux-x86_64-2.7/PyContact/db
copying PyContact/cy_modules/cy_gridsearch.pyx -> build/lib.linux-x86_64-2.7/PyContact/cy_modules
creating build/lib.linux-x86_64-2.7/PyContact/cy_modules/src
copying PyContact/cy_modules/src/ResizeArray.h -> build/lib.linux-x86_64-2.7/PyContact/cy_modules/src
copying PyContact/cy_modules/src/vmdstream.h -> build/lib.linux-x86_64-2.7/PyContact/cy_modules/src
copying PyContact/cy_modules/src/gridsearch.C -> build/lib.linux-x86_64-2.7/PyContact/cy_modules/src
running build_ext
building 'PyContact.cy_modules.cy_gridsearch' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/PyContact
creating build/temp.linux-x86_64-2.7/PyContact/cy_modules
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-UKCoZ3/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -IPyContact/cy_modules -I. -IPyContact/cy_modules/src -I/usr/include/python2.7 -c PyContact/cy_modules/cy_gridsearch.cpp -o build/temp.linux-x86_64-2.7/PyContact/cy_modules/cy_gridsearch.o -std=c++0x
PyContact/cy_modules/cy_gridsearch.cpp:28:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

ERROR: Failed building wheel for pycontact
Running setup.py clean for pycontact
Building wheel for mdanalysis (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ai7V51/mdanalysis/setup.py'"'"'; file='"'"'/tmp/pip-install-ai7V51/mdanalysis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-awfeCz
cwd: /tmp/pip-install-ai7V51/mdanalysis/
Complete output (158 lines):
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Will not attempt to use Cython.
running bdist_wheel
The [wheel] section is deprecated. Use [bdist_wheel] instead.
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/version.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/KDTree.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-2.7/MDAnalysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
creating build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/ten2eleven.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
creating build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/parallel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/Selection.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/qcprot.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/Timeseries.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
creating build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PrimitivePDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/hole.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/x3dna.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
running build_ext
building 'coordinates._dcdmodule' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/MDAnalysis
creating build/temp.linux-x86_64-2.7/MDAnalysis/coordinates
creating build/temp.linux-x86_64-2.7/MDAnalysis/coordinates/src
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-UKCoZ3/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/debanjan/.local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/coordinates/include -I/usr/include/python2.7 -c MDAnalysis/coordinates/src/dcd.c -o build/temp.linux-x86_64-2.7/MDAnalysis/coordinates/src/dcd.o
MDAnalysis/coordinates/src/dcd.c:21:10: fatal error: Python.h: No such file or directory
#include <Python.h>
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

ERROR: Failed building wheel for mdanalysis
Running setup.py clean for mdanalysis
Failed to build pycontact mdanalysis
Installing collected packages: mdanalysis, pycontact
Running setup.py install for mdanalysis ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ai7V51/mdanalysis/setup.py'"'"'; file='"'"'/tmp/pip-install-ai7V51/mdanalysis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-3fZGYt/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/debanjan/.local/include/python2.7/mdanalysis
cwd: /tmp/pip-install-ai7V51/mdanalysis/
Complete output (157 lines):
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Will not attempt to use Cython.
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/authors.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/version.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/KDTree.py -> build/lib.linux-x86_64-2.7/MDAnalysis
copying MDAnalysis/exceptions.py -> build/lib.linux-x86_64-2.7/MDAnalysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/jmol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/vmd.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/gromacs.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/charmm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
copying MDAnalysis/selections/pymol.py -> build/lib.linux-x86_64-2.7/MDAnalysis/selections
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
copying MDAnalysis/lib/mdamath.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib
creating build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
copying MDAnalysis/visualization/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/visualization
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/ten2eleven.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration
creating build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/log.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/units.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/parallel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/Selection.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/qcprot.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/transformations.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/util.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
copying MDAnalysis/core/Timeseries.py -> build/lib.linux-x86_64-2.7/MDAnalysis/core
creating build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-x86_64-2.7/MDAnalysis/coordinates
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GROParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/core.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/tables.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/PrimitivePDBParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/base.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/hole.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/x3dna.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/align.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/gnm.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/helanal.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rms.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/distances.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/rdf.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/contacts.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/polymer.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/psa.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/density.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis
creating build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
copying MDAnalysis/tests/datafiles.py -> build/lib.linux-x86_64-2.7/MDAnalysis/tests
creating build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats
copying MDAnalysis/lib/formats/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/lib/formats
creating build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.linux-x86_64-2.7/MDAnalysis/migration/fixes
creating build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-x86_64-2.7/MDAnalysis/topology/tpr
creating build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
copying MDAnalysis/analysis/hbonds/init.py -> build/lib.linux-x86_64-2.7/MDAnalysis/analysis/hbonds
running build_ext
building 'coordinates._dcdmodule' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/MDAnalysis
creating build/temp.linux-x86_64-2.7/MDAnalysis/coordinates
creating build/temp.linux-x86_64-2.7/MDAnalysis/coordinates/src
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-UKCoZ3/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/debanjan/.local/lib/python2.7/site-packages/numpy/core/include -IMDAnalysis/coordinates/include -I/usr/include/python2.7 -c MDAnalysis/coordinates/src/dcd.c -o build/temp.linux-x86_64-2.7/MDAnalysis/coordinates/src/dcd.o
MDAnalysis/coordinates/src/dcd.c:21:10: fatal error: Python.h: No such file or directory
#include <Python.h>
^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ai7V51/mdanalysis/setup.py'"'"'; file='"'"'/tmp/pip-install-ai7V51/mdanalysis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-3fZGYt/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/debanjan/.local/include/python2.7/mdanalysis Check the logs for full command output.

Answer 1 · 2020-05-09T07:50:37.000Z

Python2 is not supported, PyContact will only work with Python3.
The version on pip is a bit old, so it's best do clone/download the code from the repository,
then run

python setup.py build_ext -i
python setup.py install

Answer 2 · 2020-05-09T15:47:04.000Z

Thanks for your reply.... requesting you kindly provide me some info that u can resolve my issues... 1. you advised "so it's best do clone/download the code from the repository," are you talking about cloning pycontact from github or it's about pip? 2. I am a linuxmint 19.1 user shall I use sudo apt-get python .... to install new setup.py 3. to day afternoon I am able to install pycontact using conda.. that is after installing anaconda for python 2.7. it shows success. but from a new terminal when I call pycontact it returns nothing. if I issue whereis pycontact it shows nothing. 4. can u plz tell me how get updated pip, as I found in the tutorial it supports python 2.7 . Now requesting you plz provide me... the exact repository info, and how to execute after installation. is there any changes required in bashrc? thanking you with regards Debanjan

…

On Sat, 9 May 2020, 1:20 pm Maximilian Scheurer, ***@***.***> wrote: Python2 is not supported, PyContact will only work with Python3. The version on pip is a bit old, so it's best do clone/download the code from the repository, then run python setup.py build_ext -i python setup.py install — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#69 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4T6SRPKHBIS6UMA753RQUDNRANCNFSM4M4THDRA> .

Answer 3 · 2020-05-10T05:12:15.000Z

i installed pip3 sudo apt-get install python3-pip then pip install pycontact returns Failed building wheel for mdanalysis Running setup.py clean for mdanalysis Failed to build pycontact mdanalysis in red colour ---------------------------------------- Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-v80pjutl/mdanalysis/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-ssgl4xqp-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-v80pjutl/mdanalysis/

…

On Sat, May 9, 2020 at 1:20 PM Maximilian Scheurer ***@***.***> wrote: Python2 is not supported, PyContact will only work with Python3. The version on pip is a bit old, so it's best do clone/download the code from the repository, then run python setup.py build_ext -i python setup.py install — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#69 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4T6SRPKHBIS6UMA753RQUDNRANCNFSM4M4THDRA> .

Answer 4 · 2020-05-10T05:34:32.000Z

After issuing following comands sudo apt-get install python3 pip install -U pi pip install seaborn python setup.py build_ext -i sudo python setup.py install pip install mdanalysis=== 0.15 python3 -m pip install pycontact sudo apt-get install qgis python-qgis qgis-plugin-grass sudo apt-get install python3-pyqt5.qtsvg i am able to install pycontact but when i call from terminal encountered by the error given bellow Traceback (most recent call last): File "/usr/local/bin/pycontact", line 11, in <module> load_entry_point('pycontact==1.0.3.dev0', 'console_scripts', 'pycontact')() File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 480, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2693, in load_entry_point return ep.load() File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2324, in load return self.resolve() File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2330, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/usr/local/lib/python2.7/dist-packages/pycontact-1.0.3.dev0-py2.7-linux-x86_64.egg/PyContact/pycontact.py", line 11, in <module> from .gui.MainWindow import MainWindow File "/usr/local/lib/python2.7/dist-packages/pycontact-1.0.3.dev0-py2.7-linux-x86_64.egg/PyContact/gui/MainWindow.py", line 13, in <module> from PyQt5.QtSvg import QSvgGenerator ImportError: No module named QtSvg

…

On Sat, May 9, 2020 at 1:20 PM Maximilian Scheurer ***@***.***> wrote: Python2 is not supported, PyContact will only work with Python3. The version on pip is a bit old, so it's best do clone/download the code from the repository, then run python setup.py build_ext -i python setup.py install — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#69 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4T6SRPKHBIS6UMA753RQUDNRANCNFSM4M4THDRA> .

Answer 5 · 2020-05-10T07:34:57.000Z

after a long try and error able to install pycontact but new issue is NotImplementedError: Your tpx version is 116, which this parser does not support, yet Aborted (core dumped) i performed md simulation with gromacs 2019.05

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On Sat, May 9, 2020 at 1:20 PM Maximilian Scheurer ***@***.***> wrote: Python2 is not supported, PyContact will only work with Python3. The version on pip is a bit old, so it's best do clone/download the code from the repository, then run python setup.py build_ext -i python setup.py install — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#69 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4T6SRPKHBIS6UMA753RQUDNRANCNFSM4M4THDRA> .