[60248] trunk/dports/science
jmr at macports.org
jmr at macports.org
Sat Nov 7 01:06:27 PST 2009
Revision: 60248
http://trac.macports.org/changeset/60248
Author: jmr at macports.org
Date: 2009-11-07 01:06:24 -0800 (Sat, 07 Nov 2009)
Log Message:
-----------
New port: mddisplay (#21611)
Added Paths:
-----------
trunk/dports/science/mddisplay/
trunk/dports/science/mddisplay/Portfile
trunk/dports/science/mddisplay/files/
trunk/dports/science/mddisplay/files/patch-displib.c.diff
trunk/dports/science/mddisplay/files/patch-mddisplay.c.diff
trunk/dports/science/mddisplay/files/patch-preproc.c.diff
Added: trunk/dports/science/mddisplay/Portfile
===================================================================
--- trunk/dports/science/mddisplay/Portfile (rev 0)
+++ trunk/dports/science/mddisplay/Portfile 2009-11-07 09:06:24 UTC (rev 60248)
@@ -0,0 +1,45 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem 1.0
+
+name mddisplay
+version 3.0
+categories science
+maintainers yahoo.com:mjhsieh
+description A 3D Stereo Molecular Dynamics Trajectory Visualization Package
+long_description MD Display turns molecular dynamics trajectory data into a \
+ colorful, animated, on-screen movie. Key features include: \
+ Mouse control of translation, rotation, scaling, and \
+ clipping. Half-bond coloring controls. Animation speed and \
+ direction controls. Dynamic monitoring of distances, bond \
+ angles, dihedrals, and hydrogen bonds. Superimposition of \
+ static initial or average reference structures. \
+ Ramachandron plots. Real-time filtering of higher \
+ frequency molecular motions. PDB dump feature, for \
+ extracting movie frames on-the-fly.
+
+homepage http://structbio.vanderbilt.edu/~cmoth/mddisplay/
+master_sites ${homepage}
+distname ${name}
+dist_subdir ${name}/${version}
+platforms darwin
+checksums md5 b4f61a306d321bcdb53870887090c2e0 \
+ sha1 d5586a6b1357d8d42f778b4cf299db28f02190e4
+
+use_configure no
+
+patchfiles patch-mddisplay.c.diff \
+ patch-displib.c.diff \
+ patch-preproc.c.diff
+
+build.args CC=${configure.cc} CFLAGS="${configure.cflags} ${configure.cc_archflags}"
+
+build.target -f makefile.osx default
+
+destroot {
+ xinstall -m 0755 ${worksrcpath}/mddisplay ${destroot}${prefix}/bin
+ xinstall -m 0755 ${worksrcpath}/preproc ${destroot}${prefix}/bin
+ xinstall -d ${destroot}${prefix}/share/doc/${name}
+ xinstall -m 0644 ${worksrcpath}/readme.txt ${destroot}${prefix}/share/doc/${name}
+}
Property changes on: trunk/dports/science/mddisplay/Portfile
___________________________________________________________________
Added: svn:keywords
+ Id
Added: svn:eol-style
+ native
Added: trunk/dports/science/mddisplay/files/patch-displib.c.diff
===================================================================
--- trunk/dports/science/mddisplay/files/patch-displib.c.diff (rev 0)
+++ trunk/dports/science/mddisplay/files/patch-displib.c.diff 2009-11-07 09:06:24 UTC (rev 60248)
@@ -0,0 +1,20 @@
+--- displib.c.orig 2003-08-04 07:50:36.000000000 -0700
++++ displib.c 2009-09-30 11:43:57.000000000 -0700
+@@ -76,7 +76,7 @@
+
+ if ( nread != n )
+ {
+- fprintf(stderr,"Unable to fread(%d elements of size %d). fread() returned %d Error: %s\n",n,size,nread,strerror(errno));
++ fprintf(stderr,"Unable to fread(%ld elements of size %ld). fread() returned %ld Error: %s\n",n,size,nread,strerror(errno));
+ exit(EXIT_FAILURE);
+ }
+ }
+@@ -89,7 +89,7 @@
+
+ if ( nwritten != n )
+ {
+- fprintf(stderr,"Unable to fwrite(%d elements of size %d): %s\n",n,size,strerror(errno));
++ fprintf(stderr,"Unable to fwrite(%ld elements of size %ld): %s\n",n,size,strerror(errno));
+ exit(EXIT_FAILURE);
+ }
+ }
Added: trunk/dports/science/mddisplay/files/patch-mddisplay.c.diff
===================================================================
--- trunk/dports/science/mddisplay/files/patch-mddisplay.c.diff (rev 0)
+++ trunk/dports/science/mddisplay/files/patch-mddisplay.c.diff 2009-11-07 09:06:24 UTC (rev 60248)
@@ -0,0 +1,20 @@
+--- mddisplay.c.orig 2003-08-04 07:48:13.000000000 -0700
++++ mddisplay.c 2009-09-30 11:36:01.000000000 -0700
+@@ -3598,7 +3598,7 @@
+
+ // Write the movie and view structs, which contain transformation matrices,
+ // as well as other info such as scaling
+- printf(" Writing session file %s (%d bytes).\n", sesFileName,sizeof(movie) + sizeof (view));
++ printf(" Writing session file %s (%ld bytes).\n", sesFileName,sizeof(movie) + sizeof (view));
+ f = fopen_or_exit_if_error(sesFileName,"wb");
+ fwrite_or_exit_if_error(&movie,sizeof (movie),1,f);
+ fwrite_or_exit_if_error(&view,sizeof (view),1,f);
+@@ -5225,7 +5225,7 @@
+ sizeof(atomattrib) *
+ fread(&attribs[nat+nres+1],sizeof(atomattrib),1,f);
+
+- printf("%d attribute bytes read (%d attribute records).\n",
++ printf("%d attribute bytes read (%ld attribute records).\n",
+ attribytesread,attribytesread/sizeof(atomattrib));
+
+ /* CHECK FOR BOX COORDS */
Added: trunk/dports/science/mddisplay/files/patch-preproc.c.diff
===================================================================
--- trunk/dports/science/mddisplay/files/patch-preproc.c.diff (rev 0)
+++ trunk/dports/science/mddisplay/files/patch-preproc.c.diff 2009-11-07 09:06:24 UTC (rev 60248)
@@ -0,0 +1,128 @@
+--- preproc.c.orig 2003-08-04 08:48:01.000000000 -0700
++++ preproc.c 2009-09-30 11:42:07.000000000 -0700
+@@ -3205,7 +3205,7 @@
+ goto bin;
+
+ nline++;
+- if (sscanf(line,"%5d",&ntun)!=1)
++ if (sscanf(line,"%5ld",&ntun)!=1)
+ goto bin;
+
+ if (ntun<1 || ntun>3) goto bin;
+@@ -3219,7 +3219,7 @@
+ goto bin;
+
+ nline++;
+- if (sscanf(line,"%5d",&nratt)!=1) /* # of atom types */
++ if (sscanf(line,"%5ld",&nratt)!=1) /* # of atom types */
+
+ goto bin;
+
+@@ -3269,7 +3269,7 @@
+ if (fgets(line,120,filep)==NULL)
+ goto err1;
+
+- if (sscanf(line,"%5d",&nraa2)!=1) /* Number of residues */
++ if (sscanf(line,"%5ld",&nraa2)!=1) /* Number of residues */
+
+ goto err1;
+
+@@ -3293,7 +3293,7 @@
+
+ if (fgets(line,120,filep)==NULL)
+ goto err1;
+- if (sscanf(line,"%5d",&nrp)!=1)
++ if (sscanf(line,"%5ld",&nrp)!=1)
+ goto err1;
+
+ if (nrp<1 || nrp>MAXATM)
+@@ -3347,7 +3347,7 @@
+ /* Skip over the nbty - BUG: Comment what is nbty??? */
+
+
+- if (sscanf(line,"%5d",&nbty)!=1)
++ if (sscanf(line,"%5ld",&nbty)!=1)
+ goto err1;
+
+ n = (nbty+3)/4;
+@@ -3365,7 +3365,7 @@
+ goto err1;
+ /* Read about bonds involving hydrogen */
+
+- if (sscanf(line,"%5d",&nbonh)!=1)
++ if (sscanf(line,"%5ld",&nbonh)!=1)
+ goto err1;
+
+ for (k=0;k<nbonh;k++)
+@@ -3375,7 +3375,7 @@
+ if (fgets(line,120,filep)==NULL)
+ goto err1;
+
+- if (sscanf(line,"%5d%5d",&ibond[k][0],&ibond[k][1])!=2)
++ if (sscanf(line,"%5ld%5ld",&ibond[k][0],&ibond[k][1])!=2)
+ goto err1;
+ }
+
+@@ -3390,7 +3390,7 @@
+
+ /* seem to throw around bonds involving H */
+
+- if (sscanf(line,"%5d",&nbond)!=1)
++ if (sscanf(line,"%5ld",&nbond)!=1)
+ goto err1;
+
+ {
+@@ -3405,7 +3405,7 @@
+ if (fgets(line,120,filep)==NULL)
+ goto err1;
+
+- if (sscanf(line,"%5d%5d",&ibond[k][0],&ibond[k][1])!=2)
++ if (sscanf(line,"%5ld%5ld",&ibond[k][0],&ibond[k][1])!=2)
+ goto err1;
+ }
+
+@@ -3425,7 +3425,7 @@
+
+
+ filep = fopen_or_exit_if_error("bond.dat","w");
+- fprintf(filep,"%5d %5d\n",nbonh,nbond);
++ fprintf(filep,"%5ld %5ld\n",nbonh,nbond);
+ for (k=0;k<nbonh+nbond+1;k++)
+ fprintf(filep,"%5d %5d %5d\n",ib[k][0],ib[k][1],ib[k][2]);
+ fclose_or_exit_if_error("bond.dat",filep);
+@@ -3536,7 +3536,7 @@
+ goto write;
+
+ err1:
+- printf("\n Error reading gromos formatted molecular topology file at line %d\n\n",nline);
++ printf("\n Error reading gromos formatted molecular topology file at line %ld\n\n",nline);
+ fclose(filep);
+
+
+@@ -3914,7 +3914,7 @@
+ bufptr = getuflong(buff,&nattyp,1);
+ if (nattyp>MAXATP)
+ {
+- printf("\nError: (# of atom types) NATTYP=%d exceeds (Max # atom types) MAXATP=%d\n",nattyp,MAXATP);
++ printf("\nError: (# of atom types) NATTYP=%ld exceeds (Max # atom types) MAXATP=%d\n",nattyp,MAXATP);
+ exit(EXIT_FAILURE);
+ }
+
+@@ -3966,7 +3966,7 @@
+ bufptr = getuflong(bufptr,&natmov,1);
+ if (natmov>natom)
+ {
+- printf("NATMOV=%d > NATOM=%d??\n\n",natmov,natom);
++ printf("NATMOV=%ld > NATOM=%ld??\n\n",natmov,natom);
+ exit(EXIT_FAILURE);
+ }
+
+@@ -4020,7 +4020,7 @@
+ getuflong(buff,&nbond,1);
+ if (nbond>MAXBND)
+ {
+- printf("\nError: NBOND=%d exceeds MAXBND=%d\n\n",nbond,MAXBND);
++ printf("\nError: NBOND=%ld exceeds MAXBND=%d\n\n",nbond,MAXBND);
+ exit(EXIT_FAILURE);
+ }
+
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