This software is a poorly tested and bug-ridden stand-alone version
for disulfide connectivity prediction.
The tarball contains three files:
- ModuleABC_standalone.py
- runNetOxState
- runNetConnectivity
The first one is a python script, the second is the C executable that runs
the oxidation state prediction neural network, the third is the executable
that runs the conectivity prediction NN. The python script runs blast and
psipred, makes a system
call to the two C executables, and writes the output on screen.
The usage is the following:
$ ModuleABC_standalone.py inputSequenceFile 1/2[1:Oxidation State
Prediction; 2:Connectivity prediction]
The input sequence should be in fasta format, but the script checks wether
there is the ">" header in the first line. Then you can select wether you
want only the oxidation state prediction, or the full connectivity
prediction.
In order to run the software, you need to install:
- python 2.3 or higher
- blast
- psipred
Then, you need to edit ModuleABC_standalone.py lines 24-34 in order to
instruct the sofware about the blast and psipred folder pathways.
And the first line should point to the python executable.
If you find any bugs, or you have suggestions/comments, please contact
Fabrizio Ferre.
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