+ and - means pro and con of the tool!
The conclusion: MDTraj seems a powerful tools, but once in a while it still feel troublesome.
MDTraj
+ convert files are awesome
- most of it is coded by python
- suck for xml (e.g. can't read image)
- the rotation utilities is hard to use.
MDAnalysis
- Python2 only
CPPTRAJ
- for Amber
ST-analyzer
+ with GUI
LOOS
+ OO
- for structural analysis
Pteros
- developed by only one person
Python Tools for Machine Learning
- scikit-learn: SVM and others
- Deep learning: Theano
