Update TM-align so that it can read all alternate location
indicators and residue insertions
Add an option '-I align.txt' to allow user to STICK TO the
inital alignment. This is different from '-i align.txt' where
initial alignment can be optimized.
2012/05/07: Improved RMSD calculation subroutine which speeds up TM-algin
program by 10%.
2012/04/19: Add additional output file 'TM.sup_atm' for showing all-atom
superposition while 'TM.sup' and 'TM.sup_all' are only for C-alpha traces
2012/04/17: Add an option '-m matrix.txt' to output the rotation matrix
in separate file, drop-off secondary-structure smooth
procedure, and add one iteration in initial5. This change
increases the alignment accuracy (TM-score) by 2%.
2011/10/11: Distance cutoff for gap is increased from 3.85A to 4.25A.
Added 'TMalign -v' to allow user to check version number.
2011/10/11: A new scale (d0) was introduced for alignment search. This
is to mainly improve alignment selection for small proteins
(e.g. L<50 residues) but also increase alignment coverage
of larger proteins. Second, TM-align output format is changed
and two TM-scores normalized by both chains are reported.
2011/09/03: A new option "-d" is added to allow users to change
TM-score normalization scale. A version number is attached
to the program from now on