ccpro-1.0: library for computing mathematical properties of the congruence coefficient 

Reference publication: 

P. Di Lena, P. Baldi. Fold recognition by scoring protein map similarities using the congruence coefficient. Submitted to Bioinformatics

Requires: gsl library

Compile:
make
make test 

Test (optional) tests the library against brute force algorithms on small
maps. If the compilation is ok no error message is shown

Typical usage:

- Compute cc mean over all alignments (-M), cc sampling mean and standard deviation (-S)
  for predicted target T0960RR106 and native ECOD template 000138669.

  bash$ ./bin/ccpro examples/map/T0960RR106.map.simp.txt examples/map/000138669.map.simp.txt -MS
  E[cc]: 0.0031 ES[cc]: 0.0031 SdS[cc]: 0.0018 

  Automatically recognizes casp contact format.

  bash$ ./bin/ccpro examples/map/T0960RR106.map.casp.txt examples/map/000138669.map.casp.txt -MS
  E[cc]: 0.0031 ES[cc]: 0.0031 SdS[cc]: 0.0018 

- Compute cc for predicted target T0960RR106 and native ECOD template 000138669 with respect
  to the alignment T0960RR106.000138669.AlEigen.aln.simp.txt

  bash$ ./bin/ccpro examples/map/T0960RR106.map.simp.txt examples/map/000138669.map.simp.txt -A examples/aln/T0960RR106.000138669.AlEigen.aln.simp.txt -C
  cc: 0.3524 P-val1: 0.00e+00  P-val2: 3.13e-09

  Automatically recognizes fasta alignment format.

  bash$ ./bin/ccpro examples/map/T0960RR106.map.simp.txt examples/map/000138669.map.simp.txt -A examples/aln/T0960RR106.000138669.AlEigen.aln.fasta.txt -C
  cc: 0.3524 P-val1: 0.00e+00  P-val2: 3.13e-09

  P-val1 is p-value with known target T0960RR106, P-val2 with known target 000138669

- Compute cc for predicted target T0960RR106 and native ECOD template 000138669 with respect
  to the alignment T0960RR106.000138669.AlEigen.aln.fasta.txt along with alignment Z-score
  (note, we use sampling mean and standard deviation, since true sd computation is unfeasible for
   T0960RR106 target)

  bash$ ./bin/ccpro examples/map/T0960RR106.map.simp.txt examples/map/000138669.map.simp.txt -A examples/aln/T0960RR106.000138669.AlEigen.aln.fasta.txt -CS
  cc: 0.3524 P-val1: 0.00e+00  P-val2: 3.13e-09  ES[cc]: 0.0031 SdS[cc]: 0.0018 Z-scoreS: 194.7589

- Create expectation matrix for target size 384 (i.e. size of target T0960RR106)

  bash$ ./bin/ccmap examples/map/000138669.map.simp.txt 384 -v -o 000138669.emap384.txt 

  Expectation matrix saved in 000138669.emap384.txt file

- Compute the mean cc by using the pre-computed expectation matrix

  bash$ ./bin/ccpro examples/map/T0960RR106.map.simp.txt examples/map/000138669.map.simp.txt -E 000138669.emap384.txt -M
  E[cc]: 0.0031 

- Create variance-covariance matrix for target size 30 (384 size is unfeasible)

  bash$ ./bin/ccmap examples/map/000138669.map.simp.txt 30 -v -o 000138669.vmap30.txt -t vmap

  Variance-covariance matrix saved in 000138669.vmap30.txt