README

INSTALLING
----------

a) making the pre-processor

depends on lapack, and 
assumes it is installed in /usr/lib/ 
(sudo apt-get install liblapack-dev)
also depends stride, which is included

> cd $STRUCT_HOME/05_preproc/stride
> make
> make clean

> cd ..
> make
> make clean

the executable called preproc should appear in $STRUCT_HOME
both give usage statements if ran without arguments

b) making struct proper

also depends on lapack

> cd ../10_objects/
> make
> make clean

the executable called struct should now be in $STRUCT_HOME




TEST CASES
----------

a) 1-on-1 comparison

> cd $STRUCT_HOME/11_tests/01_1d4xG_2d8bA/

preprocessing:
> $STRUCT_HOME/preproc 1d4xG 1d4xG.pdb 1d4xG.db
> $STRUCT_HOME/preproc 2d8bA 2d8bA.pdb 2d8bA.db

comparing 1d4xG("target") and 2d8bA("query")
> $STRUCT_HOME/struct 1d4xG 2d8bA params

in the params file, the exclamation mark (!)
is the comment sign - comment it out to get a silent run
(only the output file with the score is produced)


b) 1-to-many comparison

> cd $STRUCT_HOME/11_tests/00_kolodny

the presprocessing already done (db files
for the target are concatenated in all.db)

> $STRUCT_HOME/struct all.db  cathdbdir/1a02N01.db params
(any other dbfile from cathdbdir/1a02N01.db can be used)

postprocessing - producing a match on the backbone level 
for the top 10 (substitute your own number) best hits:

> $STRUCT_HOME/15_postproc/perlscr/postp_3.pl 1a02N01.struct_out params 10
1a02N01.struct_out will be moved (by the script) to 1a02N01.struct_out.full