Convert trace->tjet, maxhalftracepchalftracecvhalfcvpc->max
and ssjetormax->sstjetormax in ESGEMME.

Since we are not using SC2 and SC3 calculations anymore in SGEMME, I decided to remove them. They were making the computations quite slow due to multiple external calls to JET. In addition, I updated the bash script in the examples directory. We have an example to calculate all possible single point mutations. Besides, we have an example to calculate only mutations of interest given in a blah-blah.mut file.

Added maxhalftracepchalftracecvhalfcvpc maxtracehalftracecvhalfcvpc.
In addition, increased java memory request from -Xmx2048m to -Xmx4096m.

SC3 calculation options to JET2 calls.

Changed N=20000 to N=40000. Increased CPU load to 2000000 in default.config
file. Finally, modified jetcmd in gemmeAnal.py file so that we can calculate
SC1, SC2 and SC3.

Once upon a time, we tested the idea of changing the weight
of epistatic (0.6) and independent (1-0.6) component depending
on the residue features such as frequency of aa in the MSA.
Therefore, I had made alpha a list instead of a single value.
Now, I reverted it back to a single value (0.6).