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Welcome to the pytraj wiki!

Install

1. github version (pytraj will take care of installing libcpptraj)

• if using the most updated pytraj version (recommended)
  • git clone https://github.com/pytraj/pytraj
  • cd pytraj
  • python ./setup.py install
• if using specific verion (go to releases to check the most updated and stable version)
  • wget https://github.com/pytraj/pytraj/archive/0.1.beta.8.tar.gz
  • tar -xf 0.1.beta.8.tar.gz
  • cd pytraj-0.1.beta.8
  • python setup.py install
• Done
• Simple test: python -c 'import pytraj as pt; pt.run_tests()'

Note: Possible failure: can not find netcdf.h file. Make sure to install netcdeflib or specify its include path

2. Using pip

• install libcpptraj
  • git clone https://github.com/mojyt/cpptraj
  • cd cpptraj
  • export CPPTRAJHOME=`pwd`
  • ./configure -shared -nomathlib gnu
    • (if you're using Amber, you can do ./configure -shared -nomathlib -amberlib gnu)
  • make libcpptraj
• then install pytraj
  • (make sure to export CPPTRAJHOME=your_cpptraj_dir because pytraj will find header files in $CPPTRAJHOME/src and libcpptraj in $CPPTRAJHOME/lib
  • pip install pytraj

3. Using conda

Not yet

4. run small test after installing

python -c 'import pytraj as pt; pt.run_tests()'

if you install via github, you will get full test runs

• cd tests
• python ./RunAllAndFindFailure.py

Possible errors:

1. "ImportError: libcpptraj.so: cannot open shared object file: No such file or directory"

you need to add libcpptraj.so to LD_LIBRARY_PATH