programs for ca binding pdb file shelling


test.prl scans data/*.ent and deletes any files that contain the word
engineered putting their names in toremove.txt 

PROGRAM I

finds convex hull of atom points and progressively removing convex hull

files in program (marked with * are programs called by user): 
processdata.prl	*
genshells.prl	
genqhull.prl 
genshells.prl 
count.prl 
rebuild.prl

results/formatreport.prl  	*
results/shellreport.prl		*
results/shellreportpercent.prl	*
results/calcaverage.prl
results/calcpercent.prl 
results/extractwindow.prl	*
results/pullfirstnum.prl	*
results/pullsecondshell.prl	*
results/pullthirdshell.prl	*

./processdata.prl calls genshells.prl for all pdb files matching *.ent in data subdirecory 

genshells.prl given pdb file name cuts progressive convex hulls of amino
acids away saving in results/<datafilename>/ the intermediate pdb files produced

after running
 genshells.prl pdbXXXX.ent 

results/XXXX.res  has on each line the name of the numerically named intermediate
pdb file in which the ion was eliminated
ie if it was in the first convex hull it would say:
results/XXXX/0.pdb 

there are as many lines as CA ions in that file

XXXX.shell lists the names of the amino acids removed in each shell 
format is shell file name and a space delimited list of the amino acid abbreviation on each line
as many lines as shells


results/formatreport.prl takes all the res files and compiles them into a single report for all protien
res files present  each line is 1 protien record eg for file pdbXXXX.ent result would be
XXXX	2	5 ... 

with a tab delimited integer for each shell that contained a calcium (still starting with 0) 

results/shellreport.prl  creates average hydrophobicity for each shell and puts allthat on one
line of file
xxxx  0 shell0average shell1average etc

results/shellpercentreport.prl  calcs fraction hydrophbic for each shell

results/extractwindow.prl takes local 7 wide window out of average
data, the name of text file which has entry on each line for which shell
to center window around for each protien is hand coded into program

pullfirstnum.prl
pullsecondshell.prl
pullthirdshell.prl
are the files that get the 1,2,3 binding shell number and put's it in a
file suitable for use with extractwindow

CAVEATS 
assumes qhull program is in particular subdirectory where it is

genshells processdata + possibly their called subscripts currently assume
provided filename  will be in data subdirectory off of place script is
(just takes form of regular expresson to extract part of filename that
takes form 'data/..'

also assumes results subdirectory exist to put results in

also genshells +processdata assume files will have name format pdb####.ent

formatreport script has to be in same folder as data files it's going to work on

as mentioned extractwindow.prl has the name of file that tells it where to
center window hard coded, easy enough to change.



PROGRAM II 

Looks at atoms within certain radius of CA ion and finds fraction
hydrophobicity within one radius and then within further radius.

files:
spherecalc2.prl

takes all files from results*.ent does above for all CA in all files and
puts in cirlcereport.txt, they are not seperated in any way by pdb file they came from

CAVEATS same directory/name assumptions may apply 



PROGRAM III

takes only first CA hetam record for each file and build minimal enclosing local convex around CA
ie smalles set of amino acids who's atoms form a convex hull that encloses the CA

files:
calclocalshells.plr
calcalllocalshells.prl 		*
results/localhullreport.prl 	*

calcalllocalshells.plr calls calclocalshells for each .ent in data it finds the minimal shell and
puts its amino acids in a XXXX.localhull

results/localhullreport.prl goes through these and calculates average and fraction hydrophobic for
each as well as producing a count of how many of each amino acid were
present
resutls/localhullaminoacid.txt is the count
results/localhullaveragephobicity.txt is average
results/localhullpercentphobicity.txt is percent
