Case closed.
Thanks to Hongbo Zhu for a solution.
Best
Troels
2011/12/12 Troels Emtekær Linnet <tlin...@gmail.com>
> Hi guys.
>
> I am trying to use the plugin: MSMS<http://www.pymolwiki.org/index.php/Msms>
> on
> a win machine.
> The plugin is dependent on a shell script: pdb_to_xyzrn
> But I cant execute it on a win machine, and I won't install cygwin.
>
> Can someone help me convert the shell script to a python script?
> Or know if it exist somewhere in .py script?
>
> The script is:
> --------------------
> #! /bin/sh
> # extract x,y,z from PDB file, generate radius of each atom
> # Hydrogens are presumed to be missing ("united atom" approach) unless -h
> given
> # later: options for alternate radius and pattern files
> # --- Mike Pique, The Scripps Research Institute
> #
> # input: pdb file as argument or stdin
> # output: new xyzr file to stdout
> #
> # Options:
> #
> # -h: use explicit hydrogen radii instead of default united atom radii
> #
> # examples:
> # pdb_to_xyzr crambin.pdb > crambin.xyzr
> #
> # foo_to_pdb -h mol.foo | pdb_to_xyzr > mol.xyzr
> #
> # foo_to_pdb mol.foo | pdb_to_xyzr | awk '{print $4}' > mol.r
> #
> #
>
> # set which field to use for radii:
> h_select=5
> if test $# -ge 1 ;then
> if test $1 = "-h" ; then
> h_select=4
> shift
> fi
> fi
> nawk 'BEGIN{
> # read radius table and patterns from supplied file
> npats=0
> numfile = "./atmtypenumbers"
> while ((getline < numfile) > 0) {
> if(NF==0||substr($1,1,1)=="#") continue;
> if($1=="radius") {
> n=$2 # atom number key
> explicit_rad[$2] = $4
>
> if(NF<=4 || substr($5,1,1)=="#") united_rad[n]=explicit_rad[n]
> else united_rad[n] = $5
> continue;
> }
> respat[npats] = $1
> if(respat[npats] == "*") respat[npats] = ".*"
> respat[npats] = "^"respat[npats]"$"
> atmpat[npats] = "^"$2"$"
> gsub("_", " ",atmpat[npats])
> atmnum[npats] = $3
> if( ! (atmnum[npats] in explicit_rad) ) {
> # the key has no radius --- complain and fake one
> print "pdb_to_xyzr: error in library file",numfile,
> "entry ",$1,$2,$3, "has no corresponding radius value" \
> | "cat 1>&2" # write to stderr
> explicit_rad[atmnum[npats]] = 0.01
> united_rad[atmnum[npats]] = 0.01
> }
> npats++
> }
> # for(pat=0;pat<npats;pat++) print pat,respat[pat],atmpat[pat],atmnum[pat]
> }
>
> $1=="ATOM"||$1=="atom"||$1=="HETATM"||$1=="hetatm"{
> x = substr($0,31,8)
> y = substr($0,39,8)
> z = substr($0,47,8)
> resname=substr($0,18,3)
>
> aname = substr($0,13,4)
> # special handling needed for hydrogens in PDB files: they start with
> # digits not the letter "H"
> #
> if(substr(aname,1,2) ~ /[ 0-9][HhDd]/) aname="H"
> # However, some bogus PDP files have the H in column 13 so we allow
> # those too, which means we will treat as Hydrogen helium and hafnium
> # but we protect HG ... ... mp
> #
> if(substr(aname,1,2) ~ /[Hh][^Gg]/ ) aname="H"
>
>
> resnum=substr($0,23,4);
>
> # trim any blanks
> gsub(" ", "", resname);
> gsub(" ", "", aname);
>
> for(pat=0;pat<npats;pat++) {
> if( aname ~ atmpat[pat] && resname ~ respat[pat] ) break
> }
> if(pat==npats) {
> # Not found
> print "pdb_to_xyzr: error, file",FILENAME,"line",NR,"residue",
> resnum,
> "atom pattern",resname, aname,"was not found in " numfile \
> | "cat 1>&2" # write to stderr
> print x,y,z,0.01
> }
> else printf("%f %f %f %f %d %s_%s_%d\n", x, y, z, \
> ('$h_select'== 5 ? united_rad[atmnum[pat]]:explicit_rad[atmnum[pat]]),
> 1, aname, resname, resnum);
> next;
> }' $*
>
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