On Jul 26, 6:32 pm, Mensanator <[EMAIL PROTECTED]> wrote:
> On Jul 26, 4:40�pm, "Francesco Pietra" <[EMAIL PROTECTED]> wrote:
>
>
>
>
>
> > I am posting ex novo as it became confusing to me. I take the
> > opportunity to ask advice for a second problem.
>
> > FIRST PROBLEM
> > For file xxx.pdb, insert letter "A" into each line that starts with
> > "ATOM". "A" should be inserted at position 22, i.e., one space after
> > "LEU", leaving all other characters at the same position as in the
> > original example:
>
> > ATOM � � �1 �N � LEU � � 1 � � 146.615 �40.494 103.776 �1.00 73.04 � � �
> > 1SG � 2
>
> > In all lines starting with "ATOM", "LEU" is constant as to position
> > only (18-20), i.e., "LEU" may be replaced by
> > three different uppercase letters. Therefore, the most direct
> > indication would be position 22. If specifying line starting with
> > "ATOM" makes complication, forget about that as most lines begin with
> > "ATOM" so that hand correction will be easy.
>
> > Script
> > f = open("xxx.pdb", "w")
> > import sys
>
> > for line in sys.stdin:
> > � � line = line[:22] + "A" + line[23:]
> > � � sys.stdout.write(line)
>
> > destroys the xxxx.pdb file and python exits witha non zero exit status.
>
> > The same occurs with script
>
> > f = open("hASIC1a.B99990003.pdb", "w")
> > f.write(' line = line[:22] + "A" + line[23:]')
> > f.close()
>
> > I must have misunderstood the suggestion I received on previous posting.
> > ____________________________________
> > SECOND PROBLEM
> > File xxx.pdb above has 426 lines stating with "ATOM", this serial
> > number occupying positions 7-11, right justified (Thus 1, as in the
> > line example above, means first line). A second, similar file yyy.pdb
> > has to be concatenated to xxx.pdb. Before that it should be added of
> > "A" as above and renumbered at position 7-11, starting from 428 (there
> > is an intermediate line to add). How should a script look like for
> > this string insertion into string with recursive +1?
>
> > Thanks
> > francesco
>
> I don't know why you're using stdin if you're reading from a file.
>
> Also, the serial number isn't 7-11, it's 6-10 (remember to
> count from 0, so character 1 is position 0, etc.)
>
> fx = open('xxx.pdb','r') # first input file
> fy = open('yyy.pdb','r') # second input file
> fz = open('zzz.pdb','w') # output file (to be created)
>
> for xline in fx: # read input one line at a time
> if len(xline) >= 80: # don't process invalid lines
> line_index = int(xline[7:12]) # keep track of this
Forgot to fix this after I discovered your error.
S/b int(xline[6:11])
> if xline[:4]=='ATOM':
> fz.write(xline[:22] + 'A' + xline[23:])
> else:
> fz.write(xline)
>
> fx.close() # done with first file
>
> fz.write('the extra line \n')
> line_index += 1 # don't forget to count it
>
> for yline in fy: # read second file
> if len(yline) >= 80: # again, valid only
> line_index += 1 # ignore serial number, use
> # where we left off from
> # from first file
> if yline[:4]=='ATOM':
> # note use of .rjust(5) to creat new serial number
> fz.write(yline[:6] + \
> str(line_index).rjust(5) + \
> yline[11:22] + 'A' + yline[23:])
> else:
> fz.write(yline[:6] + \
> str(line_index).rjust(5) + yline[11:])
>
> fy.close() # done with second file
>
> fz.close() # done with output file
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