delete column content

Hi: How to replace with blank the single-character in column 21 of a pdb file (in pdb numbering it is column 22). Attached is an incomplete exercise with slices. I am unable to get real plain text with gmail. Thanks for help francesco pietra # Sample line # Slice indexes cut to the left of the

reposition a column

complete the script. Much obliged for help. francesco pietra # Sample line # Slice indexes cut to the left of the corrresponding item index # 1 2 3 4 5 6 # 012345678901234567890123456789012345678901234567890123456789012345 ... # ATOM 1 W

Fwd: Extract value and average

her blocks in the output file is the same. francesco ------ Forwarded message -- From: Francesco Pietra Date: Mon, Jun 8, 2009 at 11:55 PM Subject: Re: Extract value and average To: Tim Chase On Mon, Jun 8, 2009 at 8:54 PM, Tim Chase wrote: >> Of the various suggestions, of which I am most gra

Extract value and average

would like to extract values corresponding to variable DIHED (here 4660.1650) and getting also the mean value from all DIHED. Thanks for giving a possible attack francesco pietra NSTEP = 1000 TIME(PS) = 152.000 TEMP(K) = 298.54 PRESS =89.4 Etot = -134965.2

strip part of string

Hi: I would like to delete everything from column 54 on for each line beginning with "ATOM". In the example in the attachment (sorry for the attachment; I found no way with Google mail to have plain text mail) the new line would become: ATOM 49 NH1 ARG84 84.628 41.570 44.395 witho

value error

hi: with script data = open('134-176_rectified_edited.pdb', 'r') outp = open('134-176_renumbered.pdb', 'w') for L in data: if L[3] == 'M': L = L[:24] + "%4d" % (int(L[24-28])+133) + L[28:] outp.write(L) i wanted to modify lines of the type: ATOM 1 HH31 ACE 1 1.573 1.

Renumbering

different for the same name in column 4. For example, LEU can have a different number of lines depending on the position of this amino acid (leucine). I was unable to set non-proportional characters, sorry. Thanks for help francesco pietra -- http://mail.python.org/mailman/listinfo/python-list

Insert string into string

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 a

Re: Insert character at a fixed position of lines

File xxx.pdb is opened by the command: when I forgot the single quote ' after [23:] the error answer was: SynthaxError: EOL while scanning single-quoted string. Thanks francesco On Sat, Jul 26, 2008 at 1:10 PM, Lie <[EMAIL PROTECTED]> wrote: > On Jul 26, 5:42 pm, "Francesco Pietra

Re: Insert character at a fixed position of lines

scripts I am lost about the filename for the pdb file to modify, francesco On Sat, Jul 26, 2008 at 11:35 AM, Lie <[EMAIL PROTECTED]> wrote: > On Jul 26, 2:41 pm, "Francesco Pietra" <[EMAIL PROTECTED]> wrote: >> How to insert letter "A" on each line (of a ver

Insert character at a fixed position of lines

How to insert letter "A" on each line (of a very long list of lines) 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"ATOM" is c

Strip lines from files

. grep -v WAT trp.pdb.n Unless you can think better to remove that pervasive molecule of water, to avoid performing the calculation ex novo. Thanks francesco pietra Be a better frien

Re: Delete lines containing a specific word

As I said I am no expert in OS and commands, except on what concerns mechanical statistical and quantum mechanical calculations. Therefore, better for me (and for all guys here) if I stop on this matter. My reply is only to say that I did the job with: f=open("prod1-3_no_wat_pop.pdb", "r") for lin

Re: Delete lines containing a specific word

--- Steven D'Aprano <[EMAIL PROTECTED]> wrote: > On Sun, 06 Jan 2008 13:33:52 -0800, Francesco Pietra wrote: > > > Steven: > > Thanks. See below please (of very marginal interest) > > > > --- Steven D'Aprano <[EMAIL PROTECTED]> wrote: >

Re: Delete lines containing a specific word

Steven: Thanks. See below please (of very marginal interest) --- Steven D'Aprano <[EMAIL PROTECTED]> wrote: > On Sun, 06 Jan 2008 09:21:33 -0800, Francesco Pietra wrote: > > > Please, how to adapt the following script (to delete blank lines) to > > delete lines c

Re: Delete lines containing a specific word

--- Martin Marcher <[EMAIL PROTECTED]> wrote: > On Sunday 06 January 2008 18:21 Francesco Pietra wrote: > > > Please, how to adapt the following script (to delete blank lines) to > > delete lines containing a specific word, or words? > > > > f=open(

Fwd: Delete lines containing a specific word

econd script would be useful where the line that follow the block are renumbered, e.g, line "HETATM 7010" following the above block renumbered "HEATM 7006". thanks francesco --- Francesco Pietra <[EMAIL PROTECTED]> wrote: > Date: Sun, 6 Jan 2008 09:21:33 -0800 (PST

Delete lines containing a specific word

beginning with # as comment lines, please also a script to comment lines containing a specific word, or words, and back, to remove #. Thanks francesco pietra Looking for last minute shopping deals? Find

Donloadin mail on the background

. That I found easy with web-based email. I do not maintain locally on any machine any mail for longer than working on. I am sure you have, or can devise, a better strategy to the same purpose. I am not an expert in software. Regards francesco pietra

Re: Science list

ts. f. --- nmp <[EMAIL PROTECTED]> wrote: > Bjoern Schliessmann wrote: > > > Francesco Pietra wrote: > >> Nonetheless, this extremely useful list is so crowded that if checking > >> email is not carried out every few hours, it is difficult to detect > >>

Re: Science list

I was trying to suggest a more specific mail-list in order not to be floaded. I am the opinion that python-list@python.org is very informative and useful, though it is hard to find the time for so many mails. f. --- Bjoern Schliessmann <[EMAIL PROTECTED]> wrote: > Francesco Pie

Science list

resent list they are not. Thanks francesco pietra Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs -- http://mail.python.org/mailman/listinfo/python-list

Re: Recursive insertion of a line

--- Dennis Lee Bieber <[EMAIL PROTECTED]> wrote: > On Tue, 20 Nov 2007 01:16:53 -0800 (PST), Francesco Pietra > <[EMAIL PROTECTED]> declaimed the following in comp.lang.python: > > > > > > Now, "file .out" had "TER" inserted where I wan

Re: Recursive insertion of a line

Please, see below. --- Gabriel Genellina <[EMAIL PROTECTED]> wrote: > En Mon, 19 Nov 2007 21:15:16 -0300, Henry <[EMAIL PROTECTED]> > escribió: > > > On 19/11/2007, Francesco Pietra <[EMAIL PROTECTED]> wrote: > >> > >> How to insert "

Recursive insertion of a line

3.835 26.423 1.00 0.00 W20 H ATOM 27402 H2 WAT 4178 21.173 4.237 26.554 1.00 0.00 W20 H TER Thanks francesco pietra Get easy, one-click access to your favorites. Make Yahoo!