sync/ports
1
0
Fork 0
mirror of https://git.freebsd.org/ports.git synced 2025-07-18 17:59:20 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions

update biology/nab: 4.4 -> 4.5.1

Browse source 
PR:		52786
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU> (maintainer)
This commit is contained in:
Daichi GOTO 2003-07-08 11:50:36 +00:00
parent 22507c2d49
commit a1ab1ee112
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=84471
12 changed files with 418 additions and 428 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

30
biology/nab/Makefile
View file

@ -6,24 +6,28 @@
#
PORTNAME= nab
PORTVERSION= 4.4
PORTVERSION= 4.5.1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ \
http://www.scripps.edu/case/
MAINTAINER= bdodson@scms.utmb.edu
COMMENT= This is nab (nucleic acid builder), a language for macromolecules
COMMENT= \
"This is nab (nucleic acid builder), a language for macromolecules"
BUILD_DEPENDS= ucpp:${PORTSDIR}/devel/ucpp
ONLY_FOR_ARCHS= i386
MAKE_ENV+= NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH}
USE_BISON= yes
MAN1= nab.1
MANCOMPRESSED= yes
USE_REINPLACE= yes
BINARIES= matextract matmul teLeap tss_main \
matgen nab transform tss_next \
matmerge nab2c tss_init ucpp
matmerge nab2c tss_init
LIBRARIES= cifparse.a libnab.a libsym.a
@ -44,18 +48,18 @@ pre-install:
${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall
do-install:
@-mkdir -p ${PREFIX}/share/nab
@-mkdir -p ${PREFIX}/share/nab/bin
@-mkdir -p ${PREFIX}/share/nab/include
@-mkdir -p ${PREFIX}/share/nab/lib
@-${MKDIR} ${PREFIX}/share/nab
@-${MKDIR} ${PREFIX}/share/nab/bin
@-${MKDIR} ${PREFIX}/share/nab/include
@-${MKDIR} ${PREFIX}/share/nab/lib
.if !defined(NOPORTDOCS)
@cd ${WRKSRC} && (tar cf - examples test peptide suppose | \
(cd ${PREFIX}/share/nab; tar xf -))
@-mkdir -p ${PREFIX}/share/doc/nab
@cd ${WRKSRC} && (${TAR} cf - examples test peptide suppose | \
(cd ${PREFIX}/share/nab; ${TAR} xf -))
@-${MKDIR} ${PREFIX}/share/doc/nab
${INSTALL_MAN} ${WRKSRC}/doc/NAB.pdf ${PREFIX}/share/doc/nab
.endif
@cd ${WRKSRC} && (tar cf - dgdb reslib fd_data | \
(cd ${PREFIX}/share/nab; tar xf -))
@cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data | \
(cd ${PREFIX}/share/nab; ${TAR} xf -))
@(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}:${SHAREGRP} nab; \
${CHMOD} -R ugo+rX-w nab)
@-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords)

2
biology/nab/distinfo
View file

@ -1 +1 @@
MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474
MD5 (nab-4.5.1.tar.gz) = 650be5581dfe5af1b7edb6da44a221d4

16
biology/nab/files/config.h
View file

@ -79,26 +79,26 @@ SHELL= /bin/sh
#
# For RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
#
# For FreeBSD 4.2-STABLE, there seems to be a dependency
# on bison. Berkeley yacc was very problematic.
CC= cc
#CC=
LEX= flex
YACC= bison -y -t
YACC= yacc
AR= ar
#
# Set the C-preprocessor. Code for a small preprocessor is in
# uccp-0.7; it gets installed as $(NABHOME)/bin/$(ARCH)/ucpp;
# this should generally *not* be changed.
# Changed 14 Feb 2003 to use the ucpp port (FreeBSD). MLD
#
# Again, for FreeBSD 4.2-STABLE, I had problems using the system
# C-preprocessor.
# For FreeBSD 4.x, I had problems using the system C-preprocessor. MLD
#
CPP= ucpp -l
#
# Use these CFLAGS if AVS = 0
#
CFLAGS= -O -pipe
OCFLAGS= -O -pipe
# Pick up initial CFLAGS from /etc/make.conf instead of here
# This is a Berkeley make- (pmake-)specific construct
CFLAGS+=
OCFLAGS= ${CFLAGS}
NABFLAGS=
#
# Use these CFLAGS if AVS = 1

40
biology/nab/files/patch-Makefile Normal file
View file

@ -0,0 +1,40 @@
--- Makefile.orig Mon Oct 23 20:33:23 2000
+++ Makefile Wed Feb 12 16:33:42 2003
@@ -1,15 +1,15 @@
# top-level Makefile for the NAB suite of programs
+all: compiler test
compiler:
-mkdir bin lib include
- (cd ucpp-0.7; make install )
(cd cifparse; make install )
(cd src; make install )
(cd nss; make install )
(cd tleap; make install )
- @echo
- @echo "completed installation of NAB version 4"
- @echo
+# @echo
+# @echo "completed installation of NAB version 4"
+# @echo
# note: "make test" needs to follow "make", since it is very hard to
# tell if the compiler is completely "made" or not.
@@ -18,17 +18,14 @@
(cd nss; make test )
clean:
- (cd ucpp-0.7; make clean )
(cd cifparse; make clean )
(cd src; make clean )
(cd nss; make clean )
(cd tleap; make clean )
uninstall:
- (cd ucpp-0.7; make uninstall )
(cd cifparse; make uninstall )
(cd src; make uninstall )
(cd nss; make uninstall )
(cd tleap; make uninstall )
-/bin/rm config.h
-

32
biology/nab/files/patch-aa
View file

@ -1,32 +0,0 @@
*** Makefile.orig Mon Oct 23 20:01:09 2000
--- Makefile Sun Jan 28 13:36:22 2001
***************
*** 1,5 ****
--- 1,6 ----
# top-level Makefile for the NAB suite of programs
+ all: compiler test
compiler:
-mkdir bin lib include
(cd ucpp-0.7; make install )
***************
*** 7,15 ****
(cd src; make install )
(cd nss; make install )
(cd tleap; make install )
! @echo
! @echo "completed installation of NAB version 4"
! @echo
# note: "make test" needs to follow "make", since it is very hard to
# tell if the compiler is completely "made" or not.
--- 8,16 ----
(cd src; make install )
(cd nss; make install )
(cd tleap; make install )
! # @echo
! # @echo "completed installation of NAB version 4"
! # @echo
# note: "make test" needs to follow "make", since it is very hard to
# tell if the compiler is completely "made" or not.

11
biology/nab/files/patch-nabgrm.y
View file

@ -1,11 +0,0 @@
--- src/nabgrm.y.orig Tue Oct 29 13:04:56 2002
+++ src/nabgrm.y Tue Oct 29 13:40:29 2002
@@ -244,7 +244,7 @@
expr_stmt : expr SYM_SEMICOLON
{ CG_genmain(); CG_genexpr( $1 );
CG_genop( NULL, SYM_SEMICOLON ); } ;
-if_stmt : if_hdr stmt ;
+if_stmt : if_hdr stmt
| if_hdr stmt SYM_ELSE
{ CG_genrword( SYM_ELSE ); } stmt ;
for_stmt : for_hdr stmt ;

10
biology/nab/files/patch-parser.y
View file

@ -1,10 +0,0 @@
--- tleap/parser.y.orig Tue Oct 29 13:46:35 2002
+++ tleap/parser.y Tue Oct 29 13:48:18 2002
@@ -220,6 +220,7 @@
{
return;
}
+ ;
line : LENDOFCOMMAND
| instruct

48
biology/nab/files/patch-src:database.c
View file

@ -1,32 +1,16 @@
*** src/database.c.orig Wed Nov 15 19:46:50 2000
--- src/database.c Sun Jun 2 12:57:50 2002
***************
*** 67,72 ****
--- 67,79 ----
+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
+ #include <sys/param.h>
+ #endif
+
+ #if defined(BSD)
+ #include <math.h>
+ #endif
#include "stdio.h"
***************
*** 979,985 ****
--- 986,996 ----
sDBRemoveLeadingSpaces( sLine );
sDBRemoveFirstString( sLine, sHead );
+ #if defined (linux) || defined(BSD)
+ sscanf( sHead, "%lg", dPDbl );
+ #else
sscanf( sHead, "%lG", dPDbl );
+ #endif
}
--- src/database.c.orig Thu Nov 16 15:37:11 2000
+++ src/database.c Fri Feb 14 12:15:53 2003
@@ -64,6 +64,13 @@
* The TOTAL database name MUST NEVER be longer than
* can be contained in the String object.
*/
+#if (defined(__unix__) || defined(unix)) && !defined(USG)
+#include <sys/param.h>
+#endif
+
+#if defined(BSD)
+#include <math.h>
+#endif

51
biology/nab/files/patch-tleap:database.c
View file

@ -1,35 +1,16 @@
*** tleap/database.c.orig Wed Mar 27 15:41:01 2002
--- tleap/database.c Sun Jun 2 12:59:14 2002
***************
*** 97,102 ****
--- 97,109 ----
+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
+ #include <sys/param.h>
+ #endif
+
+ #if defined(BSD)
+ #include <math.h>
+ #endif
#include "basics.h"
***************
*** 563,569 ****
sRemoveLeadingSpaces( sLine );
sRemoveFirstString( sLine, sHead );
! #ifdef linux
sscanf( sHead, "%lg", dPDbl );
#else
sscanf( sHead, "%lG", dPDbl );
--- 570,576 ----
sRemoveLeadingSpaces( sLine );
sRemoveFirstString( sLine, sHead );
! #if defined(linux) || defined(BSD)
sscanf( sHead, "%lg", dPDbl );
#else
sscanf( sHead, "%lG", dPDbl );
--- tleap/database.c.orig Sat Nov 9 18:36:58 2002
+++ tleap/database.c Wed Jan 29 09:56:46 2003
@@ -185,6 +185,13 @@
}
+#if (defined(__unix__) || defined(unix)) && !defined(USG)
+#include <sys/param.h>
+#endif
+
+#if defined(BSD)
+#include <math.h>
+#endif

10
biology/nab/files/patch-unitio.c Normal file
View file

@ -0,0 +1,10 @@
--- tleap/unitio.c.orig Sat Nov 9 18:37:02 2002
+++ tleap/unitio.c Fri Feb 14 12:20:38 2003
@@ -5958,6 +5958,7 @@
*TODO: Add CAP information
*/
#define AMBERINDEX(i) 3*(i-1)
+#undef INTFORMAT
#define INTFORMAT "%6d"
#define DBLFORMAT "%16.8lE"
#define LBLFORMAT "%-4s"

27
biology/nab/pkg-descr
View file

@ -1,20 +1,23 @@
This is version 4.4 of nab (nucleic acid builder), a computer language that
is intended for use in creating, describing and modifying macromolecules,
especially nucleic acids. Programs written in nab are translated into C,
which in turn is compiled into machine code.
This is version 4.5 of nab (nucleic acid builder), a computer
language that is intended for use in creating, describing and
modifying macromolecules, especially nucleic acids. Programs
written in nab are translated into C, which in turn is compiled
into machine code.
Further general information can be obtained from our web page:
WWW: http://www.scripps.edu/case/
Although we have been using this code for some time now, users should be
aware that bugs may still exist. Please see the file COPYING for the usual
disclaimer of liability. Further enhancements are planned, and will be
announced on the web page.
Although we have been using this code for some time now, users
should be aware that bugs may still exist. Please see the file
COPYING for the usual disclaimer of liability. Further
enhancements are planned, and will be announced on the web page.
Please send comments and suggestions to Tom Macke (macke@scripps.edu) and/or
to Dave Case (case@scripps.edu). If you find the program useful, please
send us a note outlining your applications.
Please send comments and suggestions to Tom Macke
(macke@scripps.edu) and/or to Dave Case (case@scripps.edu). If
you find the program useful, please send us a note outlining your
applications.
This port to FreeBSD by M. L. Dodson, Univ. of Texas Medical Branch, Galveston
This port to FreeBSD by M. L. Dodson, Univ. of Texas Medical
Branch, Galveston
bdodson@scms.utmb.edu

569
biology/nab/pkg-plist
View file

@ -9,7 +9,6 @@ bin/transform
bin/tss_init
bin/tss_main
bin/tss_next
bin/ucpp
include/defreal.h
include/nab.h
include/nabcode.h
@ -19,90 +18,17 @@ lib/libnab.a
lib/libsym.a
share/doc/nab/NAB.pdf
share/nab/bin/matextract
share/nab/bin/matmul
share/nab/bin/teLeap
share/nab/bin/tss_main
share/nab/bin/matgen
share/nab/bin/nab
share/nab/bin/transform
share/nab/bin/tss_next
share/nab/bin/matmerge
share/nab/bin/matmul
share/nab/bin/nab
share/nab/bin/nab2c
share/nab/bin/teLeap
share/nab/bin/transform
share/nab/bin/tss_init
share/nab/bin/ucpp
share/nab/examples/test.pdb
share/nab/examples/ADE.pdb
share/nab/examples/README
share/nab/examples/Makefile
share/nab/examples/program_9.nab
share/nab/examples/gcg10.pdb
share/nab/examples/program_8.nab
share/nab/examples/program_7.nab
share/nab/examples/program_6.nab
share/nab/examples/rna_pseudoknot.pdb
share/nab/examples/THY.pdb
share/nab/examples/program_5.gcg.in
share/nab/examples/program_5.nab
share/nab/examples/getbase.nab
share/nab/examples/program_14.nab
share/nab/examples/program_4.ref
share/nab/examples/program_4.nab
share/nab/examples/acgtacgt.pdb
share/nab/examples/program_5.tat.in
share/nab/examples/program_3.nab
share/nab/examples/program_12.nab
share/nab/examples/program_2.ref
share/nab/examples/program_2.nab
share/nab/examples/program_13.nab
share/nab/examples/program_5.cgc.in
share/nab/examples/program_1.nab
share/nab/examples/program_10.nab
share/nab/examples/program_5.ata.in
share/nab/examples/test.sup.pdb
share/nab/examples/program_11.nab
share/nab/examples/gcg10.pdb.save
share/nab/test/get_sugar_info.nab
share/nab/test/get_pep_info.nab
share/nab/test/read_obs_shifts.nab
share/nab/test/hash.out.check
share/nab/test/ico.sym.out.check
share/nab/test/2.pdb
share/nab/test/sbcoil.nab
share/nab/test/ltest.nab
share/nab/test/prmtop
share/nab/test/reflexive.nab
share/nab/test/reflexive.out
share/nab/test/duplex.in
share/nab/test/hash.in
share/nab/test/gbrna.prmtop
share/nab/test/fd.nab
share/nab/test/gbrna.out.check
share/nab/test/d01.pdb.check
share/nab/test/fd.pdb.check
share/nab/test/d01.lin.check
share/nab/test/swap_shifts.nab
share/nab/test/shifts.h
share/nab/test/ico.sym
share/nab/test/gbrna.pdb
share/nab/test/gbrna.nab
share/nab/test/tbv.60.com.pdb.check
share/nab/test/hash.nab
share/nab/test/5pti.shifts.check
share/nab/test/5pti.obs
share/nab/test/5pti.pdb
share/nab/test/dna.circle.nab
share/nab/test/tbv.com.pdb
share/nab/test/pointplane.nab
share/nab/test/dg_gyrate.nab
share/nab/test/getresid_from_pdb.nab
share/nab/test/get_ring_info.nab
share/nab/test/shifts.nab
share/nab/test/write_sander_inp.nab
share/nab/test/duplex.nab
share/nab/test/ltest.out.check
share/nab/test/dg_gyrate.out.check
share/nab/suppose/suppose.1
share/nab/suppose/suppose.nab
share/nab/bin/tss_main
share/nab/bin/tss_next
share/nab/coords
share/nab/dgdb/adna.basepair.db
share/nab/dgdb/adna.nucleotide.db
share/nab/dgdb/adna.stack.db
@ -120,210 +46,305 @@ share/nab/dgdb/trna.stack.db
share/nab/dgdb/zdna.basepair.db
share/nab/dgdb/zdna.nucleotide.db
share/nab/dgdb/zdna.stack.db
share/nab/peptide/peptide.nab
share/nab/peptide/README
share/nab/reslib/leap.log
share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb
share/nab/reslib/hetatm.amber94/hetatm.amber94.qr
share/nab/reslib/charlie.star.note
share/nab/reslib/axes/Axes.bnd
share/nab/reslib/axes/XYZ.axes
share/nab/reslib/dna3/dna3.qr
share/nab/reslib/dna3/dna3.bnd
share/nab/reslib/dna3/dna3.chi
share/nab/reslib/dna3/dna3.pdb
share/nab/reslib/leap/leap.log
share/nab/reslib/leap/opls_parm.dat
share/nab/reslib/leap/leaprc.stdX
share/nab/reslib/leap/parm91X.ua.dat
share/nab/reslib/leap/parm94.dat
share/nab/reslib/leap/protein.amberua.N.prepin
share/nab/reslib/leap/protein.amberua.C.prepin
share/nab/reslib/leap/leaprc.nmr
share/nab/reslib/leap/leaprc.std
share/nab/reslib/leap/leaprc.rna
share/nab/reslib/leap/water.lib
share/nab/reslib/leap/na.amberua.prepin
share/nab/reslib/leap/0README
share/nab/reslib/leap/protein.opls.lib
share/nab/reslib/leap/protein.amberua.prepin
share/nab/reslib/leap/leaprc.protein.amberua
share/nab/reslib/leap/parm91.lib
share/nab/reslib/leap/parm91X.dat
share/nab/reslib/leap/parm94X.dat
share/nab/reslib/leap/protein.amberua.lib
share/nab/reslib/leap/dna.amberua.lib
share/nab/reslib/leap/rna.amberua.lib
share/nab/reslib/leap/all_aminoct91.lib
share/nab/reslib/leap/all_aminont91.lib
share/nab/reslib/leap/all_nucleic91.lib
share/nab/reslib/leap/dna.amberua.redch.lib
share/nab/reslib/leap/all_amino91.lib
share/nab/reslib/leap/ions94.lib
share/nab/reslib/leap/all_amino94.lib
share/nab/reslib/leap/all_aminoct94.lib
share/nab/reslib/leap/all_aminont94.lib
share/nab/reslib/leap/all_nucleic94.lib
share/nab/reslib/leap/leaprc.dna.amberua.redch
share/nab/reslib/leap/leaprc.rna.amberua
share/nab/reslib/leap/leaprc.dna.amberua
share/nab/reslib/leap/Notes
share/nab/reslib/leap/ions91.lib
share/nab/reslib/leap/pro-dna91.nmr.lib
share/nab/reslib/leap/pro-dna91.nmr.prepin
share/nab/reslib/leap/WW7.lib
share/nab/reslib/bdna.std/bdna.std.bnd
share/nab/reslib/bdna.std/bdna.std.chi
share/nab/reslib/bdna.std/bdna.std.pdb
share/nab/reslib/bdna.std/dna.qr
share/nab/reslib/arna.std/arna.std.bnd
share/nab/reslib/arna.std/arna.std.pdb
share/nab/reslib/adna.std/adna.std.bnd
share/nab/reslib/adna.std/adna.std.pdb
share/nab/reslib/pep1.off
share/nab/reslib/ala.off
share/nab/reslib/protein.opls/protein.opls.bnd
share/nab/reslib/protein.opls/protein.opls.chi
share/nab/reslib/protein.opls/protein.opls.pdb
share/nab/reslib/protein.opls/protein.opls.qr
share/nab/reslib/parm94.star
share/nab/reslib/bdna.std.rlb
share/nab/reslib/adna.std.rlb
share/nab/reslib/arna.std.rlb
share/nab/reslib/bounds.db
share/nab/reslib/off2star
share/nab/reslib/dna3.rlb
share/nab/reslib/axes.rlb
share/nab/reslib/hetatm.amber94.rlb
share/nab/reslib/rna.amber94_nmr.rlb
share/nab/reslib/dna.amber94/dna.amber94_nmr.3.qr
share/nab/reslib/dna.amber94/dna.amber94_nmr.5.qr
share/nab/reslib/dna.amber94/dna.amber94.35.chi
share/nab/reslib/dna.amber94/ade.pdb
share/nab/reslib/dna.amber94/dna.amber94.qr
share/nab/reslib/dna.amber94/dna.amber94.3.qr
share/nab/reslib/dna.amber94/dna.amber94.5.qr
share/nab/reslib/dna.amber94/dna.amber94.3.bnd
share/nab/reslib/dna.amber94/dna.amber94.3.pdb
share/nab/reslib/dna.amber94/dna.amber94.pdb
share/nab/reslib/dna.amber94/dna.amber94.bnd
share/nab/reslib/dna.amber94/dna.amber94.chi
share/nab/reslib/dna.amber94/dna.amber94.5.bnd
share/nab/reslib/dna.amber94/dna.amber94.5.pdb
share/nab/reslib/dna.amber94/dna.amber94_nmr.qr
share/nab/reslib/protein.amber94_nmr.rlb
share/nab/reslib/protein.amber94.C.rlb
share/nab/reslib/rna.amber94/rna.amber94_nmr.3.qr
share/nab/reslib/rna.amber94/rna.amber94_nmr.5.qr
share/nab/reslib/rna.amber94/rna.amber94.3.qr
share/nab/reslib/rna.amber94/rna.amber94.5.qr
share/nab/reslib/rna.amber94/rna.amber94.3.pdb
share/nab/reslib/rna.amber94/rna.amber94.3.bnd
share/nab/reslib/rna.amber94/rna.amber94_nmr.qr
share/nab/reslib/rna.amber94/rna.amber94.pdb
share/nab/reslib/rna.amber94/rna.amber94.bnd
share/nab/reslib/rna.amber94/rna.amber94.chi
share/nab/reslib/rna.amber94/rna.amber94.5.pdb
share/nab/reslib/rna.amber94/rna.amber94.5.bnd
share/nab/reslib/rna.amber94/rna.amber94.qr
share/nab/reslib/rna.amberua/rna.amberua.qr
share/nab/reslib/rna.amberua/rna.amberua.pdb
share/nab/reslib/rna.amberua/rna.amberua.bnd
share/nab/reslib/rna.amberua/rna.amberua.chi
share/nab/reslib/rna.amberua/rna.amberua.3.qr
share/nab/reslib/rna.amberua/rna.amberua.5.qr
share/nab/reslib/rna.amberua/rna.amberua.3.pdb
share/nab/reslib/rna.amberua/rna.amberua.3.bnd
share/nab/reslib/rna.amberua/rna.amberua.5.pdb
share/nab/reslib/rna.amberua/rna.amberua.5.bnd
share/nab/reslib/dna.amberua/dna.amberua.pdb
share/nab/reslib/dna.amberua/dna.amberua.bnd
share/nab/reslib/dna.amberua/dna.amberua.chi
share/nab/reslib/dna.amberua/dna.amberua.3.qr
share/nab/reslib/dna.amberua/dna.amberua.5.qr
share/nab/reslib/dna.amberua/dna.amberua.qr
share/nab/reslib/dna.amberua/dna.amberua.3.bnd
share/nab/reslib/dna.amberua/dna.amberua.3.pdb
share/nab/reslib/dna.amberua/dna.amberua.5.bnd
share/nab/reslib/dna.amberua/dna.amberua.5.pdb
share/nab/reslib/protein.amber94/protein.amber94.NC.chi
share/nab/reslib/protein.amber94/protein.amber94.C.qr
share/nab/reslib/protein.amber94/protein.amber94.N.qr
share/nab/reslib/protein.amber94/protein.amber94.C.pdb
share/nab/reslib/protein.amber94/protein.amber94.C.bnd
share/nab/reslib/protein.amber94/protein.amber94.qr
share/nab/reslib/protein.amber94/protein.amber94.N.pdb
share/nab/reslib/protein.amber94/protein.amber94.N.bnd
share/nab/reslib/protein.amber94/protein.amber94.chi
share/nab/reslib/protein.amber94/protein.amber94.bnd
share/nab/reslib/protein.amber94/protein.amber94.pdb
share/nab/reslib/protein.amber94/protein.amber94_nmr.qr
share/nab/reslib/protein.opls.rlb
share/nab/reslib/conf.lib
share/nab/reslib/pro-dna.nmr/pro-dna.nmr.star
share/nab/reslib/pro-dna.nmr/pro-dna.nmr.input
share/nab/reslib/pro-dna.nmr/pro-dna.nmr.off
share/nab/reslib/dna.amberua.rlb
share/nab/reslib/rna.amberua.rlb
share/nab/reslib/protein.amber94.N.rlb
share/nab/reslib/rna.amber94_nmr.3.rlb
share/nab/reslib/dna.amber94_nmr.3.rlb
share/nab/reslib/syblCDD.lib
share/nab/reslib/dna.amberua.3.rlb
share/nab/reslib/rna.amberua.3.rlb
share/nab/reslib/rna.amber94.3.rlb
share/nab/reslib/dna.amber94.3.rlb
share/nab/reslib/cdd.mol2
share/nab/reslib/rna.amber94_nmr.5.rlb
share/nab/reslib/dna.amber94_nmr.5.rlb
share/nab/reslib/dna.amber94_nmr.rlb
share/nab/reslib/protein.amber94.rlb
share/nab/reslib/rna.amber94.rlb
share/nab/reslib/dna.amber94.rlb
share/nab/reslib/dna.amberua.5.rlb
share/nab/reslib/rna.amberua.5.rlb
share/nab/reslib/rna.amber94.5.rlb
share/nab/reslib/dna.amber94.5.rlb
share/nab/fd_data/adna.dat
share/nab/fd_data/arna.dat
share/nab/fd_data/sbdna.dat
share/nab/examples/ADE.pdb
share/nab/examples/Makefile
share/nab/examples/README
share/nab/examples/THY.pdb
share/nab/examples/acgtacgt.pdb
share/nab/examples/gcg10.pdb
share/nab/examples/gcg10.pdb.save
share/nab/examples/getbase.nab
share/nab/examples/program_1.nab
share/nab/examples/program_10.nab
share/nab/examples/program_11.nab
share/nab/examples/program_12.nab
share/nab/examples/program_13.nab
share/nab/examples/program_14.nab
share/nab/examples/program_2.nab
share/nab/examples/program_2.ref
share/nab/examples/program_3.nab
share/nab/examples/program_4.nab
share/nab/examples/program_4.ref
share/nab/examples/program_5.ata.in
share/nab/examples/program_5.cgc.in
share/nab/examples/program_5.gcg.in
share/nab/examples/program_5.nab
share/nab/examples/program_5.tat.in
share/nab/examples/program_6.nab
share/nab/examples/program_7.nab
share/nab/examples/program_8.nab
share/nab/examples/program_9.nab
share/nab/examples/rna_pseudoknot.pdb
share/nab/examples/test.pdb
share/nab/examples/test.sup.pdb
share/nab/fd_data/abdna.dat
share/nab/fd_data/aprna.dat
share/nab/fd_data/lbdna.dat
share/nab/fd_data/abdna.dat.old
share/nab/coords
share/nab/lib/cifparse.a
share/nab/lib/libnab.a
share/nab/lib/libsym.a
share/nab/fd_data/adna.dat
share/nab/fd_data/aprna.dat
share/nab/fd_data/arna.dat
share/nab/fd_data/lbdna.dat
share/nab/fd_data/sbdna.dat
share/nab/include/defreal.h
share/nab/include/nab.h
share/nab/include/nabcode.h
share/nab/include/nabtypes.h
@dirrm share/doc/nab
@dirrm share/nab/bin
@dirrm share/nab/lib
@dirrm share/nab/include
@dirrm share/nab/examples
share/nab/lib/cifparse.a
share/nab/lib/libnab.a
share/nab/lib/libsym.a
share/nab/peptide/README
share/nab/peptide/peptide.nab
share/nab/reslib/adna.std.rlb
share/nab/reslib/adna.std/adna.std.bnd
share/nab/reslib/adna.std/adna.std.pdb
share/nab/reslib/ala.off
share/nab/reslib/arna.std.rlb
share/nab/reslib/arna.std/arna.std.bnd
share/nab/reslib/arna.std/arna.std.pdb
share/nab/reslib/axes.rlb
share/nab/reslib/axes/Axes.bnd
share/nab/reslib/axes/XYZ.axes
share/nab/reslib/bdna.std.rlb
share/nab/reslib/bdna.std/bdna.std.bnd
share/nab/reslib/bdna.std/bdna.std.chi
share/nab/reslib/bdna.std/bdna.std.pdb
share/nab/reslib/bdna.std/dna.qr
share/nab/reslib/bounds.db
share/nab/reslib/cdd.mol2
share/nab/reslib/charlie.star.note
share/nab/reslib/conf.lib
share/nab/reslib/dna.amber94.3.rlb
share/nab/reslib/dna.amber94.5.rlb
share/nab/reslib/dna.amber94.rlb
share/nab/reslib/dna.amber94/ade.pdb
share/nab/reslib/dna.amber94/dna.amber94.3.bnd
share/nab/reslib/dna.amber94/dna.amber94.3.pdb
share/nab/reslib/dna.amber94/dna.amber94.3.qr
share/nab/reslib/dna.amber94/dna.amber94.35.chi
share/nab/reslib/dna.amber94/dna.amber94.5.bnd
share/nab/reslib/dna.amber94/dna.amber94.5.pdb
share/nab/reslib/dna.amber94/dna.amber94.5.qr
share/nab/reslib/dna.amber94/dna.amber94.bnd
share/nab/reslib/dna.amber94/dna.amber94.chi
share/nab/reslib/dna.amber94/dna.amber94.pdb
share/nab/reslib/dna.amber94/dna.amber94.qr
share/nab/reslib/dna.amber94/dna.amber94_nmr.3.qr
share/nab/reslib/dna.amber94/dna.amber94_nmr.5.qr
share/nab/reslib/dna.amber94/dna.amber94_nmr.qr
share/nab/reslib/dna.amber94_nmr.3.rlb
share/nab/reslib/dna.amber94_nmr.5.rlb
share/nab/reslib/dna.amber94_nmr.rlb
share/nab/reslib/dna.amberua.3.rlb
share/nab/reslib/dna.amberua.5.rlb
share/nab/reslib/dna.amberua.rlb
share/nab/reslib/dna.amberua/dna.amberua.3.bnd
share/nab/reslib/dna.amberua/dna.amberua.3.pdb
share/nab/reslib/dna.amberua/dna.amberua.3.qr
share/nab/reslib/dna.amberua/dna.amberua.5.bnd
share/nab/reslib/dna.amberua/dna.amberua.5.pdb
share/nab/reslib/dna.amberua/dna.amberua.5.qr
share/nab/reslib/dna.amberua/dna.amberua.bnd
share/nab/reslib/dna.amberua/dna.amberua.chi
share/nab/reslib/dna.amberua/dna.amberua.pdb
share/nab/reslib/dna.amberua/dna.amberua.qr
share/nab/reslib/dna3.rlb
share/nab/reslib/dna3/dna3.bnd
share/nab/reslib/dna3/dna3.chi
share/nab/reslib/dna3/dna3.pdb
share/nab/reslib/dna3/dna3.qr
share/nab/reslib/hetatm.amber94.rlb
share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb
share/nab/reslib/hetatm.amber94/hetatm.amber94.qr
share/nab/reslib/leap.log
share/nab/reslib/leap/0README
share/nab/reslib/leap/Notes
share/nab/reslib/leap/all_amino91.lib
share/nab/reslib/leap/all_amino94.lib
share/nab/reslib/leap/all_aminoct91.lib
share/nab/reslib/leap/all_aminoct94.lib
share/nab/reslib/leap/all_aminont91.lib
share/nab/reslib/leap/all_aminont94.lib
share/nab/reslib/leap/all_nucleic91.lib
share/nab/reslib/leap/all_nucleic94.lib
share/nab/reslib/leap/dna.amberua.lib
share/nab/reslib/leap/dna.amberua.redch.lib
share/nab/reslib/leap/ions91.lib
share/nab/reslib/leap/ions94.lib
share/nab/reslib/leap/leap.log
share/nab/reslib/leap/leaprc.dna.amberua
share/nab/reslib/leap/leaprc.dna.amberua.redch
share/nab/reslib/leap/leaprc.nmr
share/nab/reslib/leap/leaprc.protein.amberua
share/nab/reslib/leap/leaprc.rna
share/nab/reslib/leap/leaprc.rna.amberua
share/nab/reslib/leap/leaprc.std
share/nab/reslib/leap/leaprc.stdX
share/nab/reslib/leap/na.amberua.prepin
share/nab/reslib/leap/opls_parm.dat
share/nab/reslib/leap/parm91.lib
share/nab/reslib/leap/parm91X.dat
share/nab/reslib/leap/parm91X.ua.dat
share/nab/reslib/leap/parm94.dat
share/nab/reslib/leap/parm94X.dat
share/nab/reslib/leap/pro-dna91.nmr.lib
share/nab/reslib/leap/pro-dna91.nmr.prepin
share/nab/reslib/leap/protein.amberua.C.prepin
share/nab/reslib/leap/protein.amberua.N.prepin
share/nab/reslib/leap/protein.amberua.lib
share/nab/reslib/leap/protein.amberua.prepin
share/nab/reslib/leap/protein.opls.lib
share/nab/reslib/leap/rna.amberua.lib
share/nab/reslib/leap/water.lib
share/nab/reslib/off2star
share/nab/reslib/parm94.star
share/nab/reslib/pep1.off
share/nab/reslib/pro-dna.nmr/pro-dna.nmr.input
share/nab/reslib/pro-dna.nmr/pro-dna.nmr.off
share/nab/reslib/pro-dna.nmr/pro-dna.nmr.star
share/nab/reslib/protein.amber94.C.rlb
share/nab/reslib/protein.amber94.N.rlb
share/nab/reslib/protein.amber94.rlb
share/nab/reslib/protein.amber94/protein.amber94.C.bnd
share/nab/reslib/protein.amber94/protein.amber94.C.pdb
share/nab/reslib/protein.amber94/protein.amber94.C.qr
share/nab/reslib/protein.amber94/protein.amber94.N.bnd
share/nab/reslib/protein.amber94/protein.amber94.N.pdb
share/nab/reslib/protein.amber94/protein.amber94.N.qr
share/nab/reslib/protein.amber94/protein.amber94.NC.chi
share/nab/reslib/protein.amber94/protein.amber94.bnd
share/nab/reslib/protein.amber94/protein.amber94.chi
share/nab/reslib/protein.amber94/protein.amber94.pdb
share/nab/reslib/protein.amber94/protein.amber94.qr
share/nab/reslib/protein.amber94/protein.amber94_nmr.qr
share/nab/reslib/protein.amber94_nmr.rlb
share/nab/reslib/protein.opls.rlb
share/nab/reslib/protein.opls/protein.opls.bnd
share/nab/reslib/protein.opls/protein.opls.chi
share/nab/reslib/protein.opls/protein.opls.pdb
share/nab/reslib/protein.opls/protein.opls.qr
share/nab/reslib/rna.amber94.3.rlb
share/nab/reslib/rna.amber94.5.rlb
share/nab/reslib/rna.amber94.rlb
share/nab/reslib/rna.amber94/rna.amber94.3.bnd
share/nab/reslib/rna.amber94/rna.amber94.3.pdb
share/nab/reslib/rna.amber94/rna.amber94.3.qr
share/nab/reslib/rna.amber94/rna.amber94.5.bnd
share/nab/reslib/rna.amber94/rna.amber94.5.pdb
share/nab/reslib/rna.amber94/rna.amber94.5.qr
share/nab/reslib/rna.amber94/rna.amber94.bnd
share/nab/reslib/rna.amber94/rna.amber94.chi
share/nab/reslib/rna.amber94/rna.amber94.pdb
share/nab/reslib/rna.amber94/rna.amber94.qr
share/nab/reslib/rna.amber94/rna.amber94_nmr.3.qr
share/nab/reslib/rna.amber94/rna.amber94_nmr.5.qr
share/nab/reslib/rna.amber94/rna.amber94_nmr.qr
share/nab/reslib/rna.amber94_nmr.3.rlb
share/nab/reslib/rna.amber94_nmr.5.rlb
share/nab/reslib/rna.amber94_nmr.rlb
share/nab/reslib/rna.amberua.3.rlb
share/nab/reslib/rna.amberua.5.rlb
share/nab/reslib/rna.amberua.rlb
share/nab/reslib/rna.amberua/rna.amberua.3.bnd
share/nab/reslib/rna.amberua/rna.amberua.3.pdb
share/nab/reslib/rna.amberua/rna.amberua.3.qr
share/nab/reslib/rna.amberua/rna.amberua.5.bnd
share/nab/reslib/rna.amberua/rna.amberua.5.pdb
share/nab/reslib/rna.amberua/rna.amberua.5.qr
share/nab/reslib/rna.amberua/rna.amberua.bnd
share/nab/reslib/rna.amberua/rna.amberua.chi
share/nab/reslib/rna.amberua/rna.amberua.pdb
share/nab/reslib/rna.amberua/rna.amberua.qr
share/nab/reslib/syblCDD.lib
share/nab/suppose/Makefile
share/nab/suppose/PCA_suppose.nab
share/nab/suppose/ccmath.h
share/nab/suppose/eigen.c
share/nab/suppose/housev.c
share/nab/suppose/matutl.h
share/nab/suppose/qrevec.c
share/nab/suppose/suppose.1
share/nab/suppose/suppose.nab
share/nab/suppose/trnm.c
share/nab/test/2.pdb
share/nab/test/5pti.obs
share/nab/test/5pti.pdb
share/nab/test/5pti.shifts.check
share/nab/test/a.exe
share/nab/test/d01.lin.check
share/nab/test/d01.pdb.check
share/nab/test/dg_gyrate.nab
share/nab/test/dg_gyrate.out.check
share/nab/test/dna.circle.nab
share/nab/test/duplex.exe
share/nab/test/duplex.in
share/nab/test/duplex.nab
share/nab/test/fd.nab
share/nab/test/fd.pdb.check
share/nab/test/gbrna.nab
share/nab/test/gbrna.out.check
share/nab/test/gbrna.pdb
share/nab/test/gbrna.prmtop
share/nab/test/gbrna_long.exe
share/nab/test/gbrna_long.nab
share/nab/test/gbrna_long.out
share/nab/test/gbtrx.nab
share/nab/test/gbtrx.out.check
share/nab/test/get_pep_info.nab
share/nab/test/get_ring_info.nab
share/nab/test/get_sugar_info.nab
share/nab/test/getresid_from_pdb.nab
share/nab/test/hash.in
share/nab/test/hash.nab
share/nab/test/hash.out.check
share/nab/test/ico.sym
share/nab/test/ico.sym.out.check
share/nab/test/ltest.nab
share/nab/test/ltest.out.check
share/nab/test/pointplane.nab
share/nab/test/prmtop
share/nab/test/prmtop.gb2
share/nab/test/rattle_md.nab
share/nab/test/rattle_md.out.check
share/nab/test/rattle_min.nab
share/nab/test/rattle_min.out.check
share/nab/test/read_obs_shifts.nab
share/nab/test/reflexive.nab
share/nab/test/reflexive.out
share/nab/test/rembed.nab
share/nab/test/rembed.out.check
share/nab/test/sbcoil.nab
share/nab/test/shifts.h
share/nab/test/shifts.nab
share/nab/test/swap_shifts.nab
share/nab/test/tbv.60.com.pdb.check
share/nab/test/tbv.com.pdb
share/nab/test/trxox.2.4ns.pdb
share/nab/test/trxox.2.4ns.x
share/nab/test/write_sander_inp.nab
@dirrm share/nab/test
@dirrm share/nab/peptide
@dirrm share/nab/suppose
@dirrm share/nab/dgdb
@dirrm share/nab/reslib/hetatm.amber94
@dirrm share/nab/reslib/axes
@dirrm share/nab/reslib/dna3
@dirrm share/nab/reslib/leap
@dirrm share/nab/reslib/bdna.std
@dirrm share/nab/reslib/arna.std
@dirrm share/nab/reslib/adna.std
@dirrm share/nab/reslib/protein.opls
@dirrm share/nab/reslib/dna.amber94
@dirrm share/nab/reslib/rna.amber94
@dirrm share/nab/reslib/rna.amberua
@dirrm share/nab/reslib/dna.amberua
@dirrm share/nab/reslib/rna.amber94
@dirrm share/nab/reslib/protein.opls
@dirrm share/nab/reslib/protein.amber94
@dirrm share/nab/reslib/pro-dna.nmr
@dirrm share/nab/reslib/leap
@dirrm share/nab/reslib/hetatm.amber94
@dirrm share/nab/reslib/dna3
@dirrm share/nab/reslib/dna.amberua
@dirrm share/nab/reslib/dna.amber94
@dirrm share/nab/reslib/bdna.std
@dirrm share/nab/reslib/axes
@dirrm share/nab/reslib/arna.std
@dirrm share/nab/reslib/adna.std
@dirrm share/nab/reslib
@dirrm share/nab/peptide
@dirrm share/nab/lib
@dirrm share/nab/include
@dirrm share/nab/fd_data
@dirrm share/nab/examples
@dirrm share/nab/dgdb
@dirrm share/nab/bin
@dirrm share/nab
@dirrm share/doc/nab