On Fri, Jan 12, 2001 at 10:46:36AM -0800, Kenward Vaughan wrote:
...
Though you ask for a sh script, this problem is easily solved with a
higher level scripting language like Perl or Python. As I can't get
my mind to grog Perl, I'll go ahead with Python:
#/usr/bin/python
# expected use cleanup hup.m3d hup.pdb
# to replace 'Du' with "O " inline.
# MIND YOU, THIS IS UNTESTED CODE, SO TAKE CARE AND BACKUP FIRST
import sys, fileinput
name = sys.argv[1]
### Input files: <name>.m3d output files: <name>.pdb
### In each file, individual atoms take up a line each.
# let us start by reading the input file
# and store it internally as a list of lines
m3d = open(name+".pdb").readlines()
# the second file is input and output, so we use a smart Python module
# to easy coping with this. A backup is created and changes made to lines
# can be preserved in the file simply by writing to stdout.
pdb = fileinput.input(name+".pdb", inplace=1, backup=1)
### The list of atoms in the input file always start on the 3rd line, and the
# so let's get rid ot those first 2 lines
m3d = m3d[2:]
### labels cover columns 7 and 8 (one or two letters/symbol, space if no 2nd
### letter). I have yet to see an improperly constructed file.
# let's get rid of all unneeded chars
m3d = map(lambda x: x[6,8], m3d)
### The list begins on line 3 in the output file, with symbols in col. 14,15.
# ^? but the example shows 3 leading lines!
# anyway, let's save those lines firs?t
while pdb.filelineno()!=3: #or 2????
sys.stdout(pdb.readline())
### This format is definitely consistent, coming out of the converter app.
###
### Other lines follow the list in both files. So...
### input file: output file:
### .......... ........
### .......... ........
### ......O .... ........
### ......H .... ATOM.........Du.... <-- needs to change to "O "
### ......H .... ATOM.........H ....
### ........ ATOM.........H ....
### .........
for atom in m3d:
line = pdb.readline()
if line[13:15] == "Du":
line[13:15] = m3d
sys.stdout(line)
--
groetjes, carel
