freehelix stable port information

Package: freehelix
Version: 98
Revision: 12
Description: Nucleic acid helix analysis program
License: Restrictive

DescDetail: <<
Freehelix is a substantially modified version of Newhelix, designed
specifically for the analysis of radically bent and kinked DNA double
helices.
<<

BuildDepends: gcc44, fink (>= 0.24.12-1)

Source: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/freehel%v.for
Source2: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/sel%v.for
Source3: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/freehel.tex
Source4: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/test.com
Source5: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/test.inp
Source6: ftp://ndbserver.rutgers.edu/NDB/programs/%n%v/README
Source-MD5: 6bd8ecb84a087dfad0d3464e204e1a3f
Source2-MD5: 559cc8a1804a7f583766749bd92bb6f5
Source3-MD5: 2e79bba04111965eb6bf5f0917a6736d
Source4-MD5: 718841fe4ef3a6dce5ab55a60b766b5c
Source5-MD5: e8d854a995ff8cb90c4c49d00b498b1b
Source6-MD5: 655b85d66b4d06de8d6b61393fa444c7

SourceDirectory: .
PatchFile: %n.patch
PatchFile-MD5: 61f00f63de1bb8d794329243259447b9

PatchScript: <<
sed 's|@prefix@|%p|g' <%{PatchFile} | patch -p1
chmod -x README
chmod +x test.com
<<

CompileScript: <<
gfortran -O3 -ffixed-form -w -o freehel98 freehel98.for
gfortran -O3 -ffixed-form -o sel98 sel98.for
<<

InstallScript: <<
mkdir -p %i/bin
mkdir -p %i/share/freehelix/examples
install -c -m 755 freehel98 sel98 %i/bin
install -c -m 755 test.com test.inp %i/share/freehelix/examples
<<

DocFiles: freehel.tex:freehel.txt README

InfoTest: <<
TestScript: ./test.com || exit 2
<<

DescUsage: <<
For instructions on how to use refer to the document 'freehel.txt' found
in your finkdirectory/share/doc/freehelix. There is an example script
installed in your finkdirectory/share/freehelix/examples.
<<

DescPort: <<
2009-09-12
- Patches and fixes to enable compilation with gfortran
- enable testscript
- README added to DocFiles
????-??-??
Use fort77 instead of g77 to build due to sel98 crashing with a bus error
when compiled with g77.
<<

DescPackaging: Originally packaged by Matt Stephenson.
Homepage: http://www.csb.yale.edu/userguides/datamanip/freehelix/freehelix_descrip.html
Maintainer: Karl-Michael Schindler

freehelix stable port .patch

diff -Naur ../freehelix98old/freehel98.for ./freehel98.for
--- ../freehelix98old/freehel98.for 2006-07-28 00:00:00.000000000 +0200
+++ ./freehel98.for 2009-09-12 11:53:38.000000000 +0200
@@ -2350,7 +2350,7 @@
DATA IST/'*'/
READ(*,'(A80)') INP
OPEN(UNIT=L11,FILE=INP(1:(index(INP,' ')-1)),STATUS='OLD',
- * READONLY)
+ * action='read')
C OPEN(UNIT=L11,STATUS='OLD',READONLY)
IB=3
NOCH=6
diff -Naur ../freehelix98old/freehelix.patch ./freehelix.patch
--- ../freehelix98old/freehelix.patch 1970-01-01 01:00:00.000000000 +0100
+++ ./freehelix.patch 2009-09-12 12:36:51.000000000 +0200
@@ -0,0 +1,12 @@
+diff -Naur ../freehelix98old/freehel98.for ./freehel98.for
+--- ../freehelix98old/freehel98.for 2006-07-28 00:00:00.000000000 +0200
++++ ./freehel98.for 2009-09-12 11:53:38.000000000 +0200
+@@ -2350,7 +2350,7 @@
+ DATA IST/'*'/
+ READ(*,'(A80)') INP
+ OPEN(UNIT=L11,FILE=INP(1:(index(INP,' ')-1)),STATUS='OLD',
+- * READONLY)
++ * action='read')
+ C OPEN(UNIT=L11,STATUS='OLD',READONLY)
+ IB=3
+ NOCH=6
diff -Naur ../freehelix98old/sel98.for ./sel98.for
--- ../freehelix98old/sel98.for 2006-07-28 00:00:00.000000000 +0200
+++ ./sel98.for 2009-09-12 12:17:40.000000000 +0200
@@ -59,9 +59,9 @@
C
102 READ(*,1)TNAME
IF(TNAME.NE.' BASE PAIR N')GO TO 102
- READ(*,3)
- READ(*,3)
- READ(*,3)
+ READ(*,333)
+ READ(*,333)
+ READ(*,333)
C
C READ IN X,Y NORMAL COSINES
C
@@ -81,12 +81,12 @@
C
C READ IN NORMAL ANGLE MATRIX
C
- READ(*,3)
- READ(*,3)
- READ(*,3)
+ READ(*,333)
+ READ(*,333)
+ READ(*,333)
READ(*,452)(NJAY(J),J=1,NBPR)
452 FORMAT(8X,50I4)
- READ(*,3)
+ READ(*,333)
DO 453 I=1,NBPR
READ(*,452)(IANGALL(I,J),J=1,NBPR)
453 CONTINUE
@@ -101,12 +101,12 @@
C
C READ IN 1ST HALF OF NORMAL ANGLE MATRIX
C
- READ(*,3)
- READ(*,3)
- READ(*,3)
+ READ(*,333)
+ READ(*,333)
+ READ(*,333)
READ(*,852)(NJAY(J),J=1,25)
852 FORMAT(8X,50I4)
- READ(*,3)
+ READ(*,333)
DO 853 I=1,NBPR
READ(*,852)(IANGALL(I,J),J=1,25)
853 CONTINUE
@@ -120,12 +120,12 @@
C
C READ IN 2ND HALF OF NORMAL ANGLE MATRIX
C
- READ(*,3)
- READ(*,3)
- READ(*,3)
+ READ(*,333)
+ READ(*,333)
+ READ(*,333)
READ(*,952)(NJAY(J),J=26,NBPR)
952 FORMAT(8X,50I4)
- READ(*,3)
+ READ(*,333)
DO 953 I=1,NBPR
READ(*,952)(IANGALL(I,J),J=26,NBPR)
953 CONTINUE
@@ -138,8 +138,9 @@
1 FORMAT(A12)
IF(TNAME.NE.' BEST PLANE')GO TO 2
DO 10 J=1,3
-10 READ(*,3)
+10 READ(*,333)
3 FORMAT(1H )
+333 FORMAT(1X)
C
C READ IN TABLES OF BASE STEPS AND BASE PAIRS FROM BROLL
C
@@ -158,7 +159,7 @@
6 READ(*,1)TNAME
IF(TNAME.NE.' ROTATION ')GO TO 6
DO 7 K=1,5
-7 READ(*,3)
+7 READ(*,333)
C
C READ IN FIRST TABLES FROM CYLIN
C
@@ -171,7 +172,7 @@
C
11 READ(*,1)TNAME
IF(TNAME.NE.' STRAND 2')GO TO 11
- READ(*,3)
+ READ(*,333)
C
C READ IN SECOND TABLES FROM CYLIN
C
@@ -186,7 +187,7 @@
C
14 READ(*,1)TNAME
IF(TNAME.NE.' ALPHA ')GO TO 14
- READ(*,3)
+ READ(*,333)
C
C READ FIRST TORAN LIST
C
@@ -199,7 +200,7 @@
C
47 READ(*,1)TNAME
IF(TNAME.NE.' ALPHA ')GO TO 47
- READ(*,3)
+ READ(*,333)
C
C READ SECOND TORAN LIST
C
@@ -212,7 +213,7 @@
C
50 READ(*,1)TNAME
IF(TNAME.NE.' V0 ')GO TO 50
- READ(*,3)
+ READ(*,333)
C
C READ FIRST PSEUDO VALUES
C
@@ -225,7 +226,7 @@
C
60 READ(*,1)TNAME
IF(TNAME.NE.' V0 ')GO TO 60
- READ(*,3)
+ READ(*,333)
C
C READ SECOND PSEUDO VALUES
C
diff -Naur ../freehelix98old/test.com ./test.com
--- ../freehelix98old/test.com 2006-07-28 00:00:00.000000000 +0200
+++ ./test.com 2009-09-12 11:27:44.000000000 +0200
@@ -1,10 +1,10 @@
-#command file for freehel97 on UNIX machines tkc 1/23/98
-#for meaning of keywords, refer to freehel98.tex
+#command file for freehel98 on UNIX machines tkc 1/23/98
+#for meaning of keywords, refer to freehel98.txt
#*.dat, *.PDB, & *.po4 files have the pdb filename (represented as *) as prefix
#******* enter the pdb file name on the line after the 'END' keyword *******
#
-echo "Executing newhel98 ..."
-freehel97.exe<test.freehelix
+echo "Executing freehel98 ..."
+freehel98 <test.freehelix
TITL TBPJ C-G-T-A-T-A-T-A-T-A-C-G Juo & Dickerson--Human TBP/DNA
CELL 1., 1., 1., 90., 90., 90.
BRKH
@@ -25,7 +25,7 @@
test.inp
eof
#
-echo "freehel97 finished and output as *.out, *.PDB, *.dat, and *.po4 "
+echo "freehel98 finished and output as *.out, *.PDB, *.dat, and *.po4 "
echo "Executing sel98 ..."
-sel98.exe test.sel
+sel98 test.sel
echo "sel98 finished. "

freehelix _unstable_ port .patch