[Octave-cvsupdate] octave-forge/extra/pdb plotpdb.m.in,NONE,1.1 README,1.1,1.2 plotpdb.m,1.3,NONE write_pdb_quick.m,1.2,NONE

[Teemu I. <tpi...@us...>]

Update of /cvsroot/octave/octave-forge/extra/pdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv21812

Modified Files:
	README 
Added Files:
	plotpdb.m.in 
Removed Files:
	plotpdb.m write_pdb_quick.m 
Log Message:
Made plotpdb.m use the rasmol script installed at XPATH.


--- write_pdb_quick.m DELETED ---

--- NEW FILE: plotpdb.m.in ---
function plotpdb(pdb)
#function plotpdb(pdb)
#    
# Visualizes a pdb-file or a pdb-struct with rasmol.

## Created: 3.8.2001
## Author: Teemu Ikonen <tpi...@pc...>

# FIXME: redirecting input for rasmol works by opening a free pseudo-tty
# which isn't (hopefully) attached to anything. Is there a better way?

RASMOL = "@OFORGEXPATH@/rasmol.sh";

ptybase = "/dev/ptyz";
startno = toascii("0");

# This is a hack to get a static -like variable in the function
#global plotpdb_static_ptynum;
#if (! exist ("plotpdb_static_ptynum"))
#    plotpdb_static_ptynum = startno - 1;
#endif

# FIXME: this allows only ten rasmol windows open at one moment
plotpdb_static_ptynum = startno - 1;
do
    ++plotpdb_static_ptynum;
    ptyname = sprintf("%s%c", ptybase, plotpdb_static_ptynum);
    ptyfid = fopen(ptyname, "r");
until(ptyfid > 0)
fclose(ptyfid);

#++plotpdb_static_ptynum;
#ptyname = sprintf("%s%c", ptybase, plotpdb_static_ptynum)

if(isstr(pdb))
    fname = pdb;
    [forkstat, fmsg] = fork();
    if(forkstat == 0),
      exec_args = [fname; ptyname];
      exec(RASMOL, exec_args);
      exit;
    elseif(forkstat < 0)
      error(fmsg);
    endif	
elseif(is_struct(pdb))
    fname = tmpnam;
    write_pdb(pdb, fname, true);
    [forkstat, fmsg] = fork();
    if(forkstat == 0),        
        exec_args = [fname; ptyname];
        exec(RASMOL, exec_args);
        exit;
    elseif(forkstat < 0)
        error(fmsg);
    endif	
else
    error("pdb must be a valid pdb-struct or a file name");
endif

endfunction

--- plotpdb.m DELETED ---

Index: README
===================================================================
RCS file: /cvsroot/octave/octave-forge/extra/pdb/README,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- README	18 Nov 2001 22:54:51 -0000	1.1
+++ README	15 Oct 2004 13:34:24 -0000	1.2
@@ -19,6 +19,9 @@
 read_pdb.m reads a structure from a pdb-file to an Octave structure. See the
 function file for more details
 
+creadpdb.oct is the underlying c++ implementation of read_pdb.m. Use this if
+you do not need the conversion of element names to atomic numbers.
+
 write_pdb.m tries to write as complete pdb-file as possible given an Octave
 pdb-structure as an argument
 
@@ -28,9 +31,38 @@
 plotpdb.m displays a protein structrure with Rasmol. The input can be either
 a pdb-file or an Octave pdb-structure.
 
+strtoz.m converts strings of chemical stoichiometries of the type "H2O" to
+the atomic numbers of the elements, and their amounts in the compound. You
+can generate a test dataset for this function with the script appended below.
+
 References:
 [1] http://www.rcsb.org/pdb/
 [2] http://www.octave.org/
 [3] http://www.openrasmol.org/
 [4] http://www.gnu.org/copyleft/gpl.html
 
+mktestset.m:
+
+function testset = mktestset(N, M)
+#function testset = mktestset(N, M)  
+# 
+# Return a N rows long array of stoichiometries, each M elements long.
+# For testing strtoz.m
+
+# Teemu Ikonen 22.4.2004
+
+  tabfile = file_in_loadpath("elements.mat");
+  load("-force", tabfile);
+  
+  testset = char(toascii(" ").*ones(N, 4.*M));
+  
+  for i = 1:N,
+    s = ""; 
+    for j = 1:M, 
+      s = strcat(s, deblank(elements((floor(length(elements)*rand())+1),:)), \
+                 sprintf("%d", 99.9.*rand()));
+    endfor;
+    testset(i,1:length(s)) = s;
+  endfor
+  
+endfunction