tmalign is a python module (or script) that provides wrappers to TMalign, TMscore and MMalign. The executables can be downloaded from http://zhanglab.ccmb.med.umich.edu/TM-align/ and should be saved to any directory in PATH.
The module also provides the command alignwithanymethod which is useful to quickly test different alignment methods (with their respective default values).
Installation
All dependencies are available from Anaconda Cloud:
conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c speleo3 tmalign
Usage
tmalign mobile, target [, args [, exe [, ter [, transform [, object ]]]]]
tmscore and mmalign usage is equivalent.
alignwithanymethod mobile, target [, methods ]
Examples
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