Path: csiph.com!v102.xanadu-bbs.net!xanadu-bbs.net!feeder.erje.net!eu.feeder.erje.net!newsfeed.xs4all.nl!newsfeed3a.news.xs4all.nl!xs4all!post.news.xs4all.nl!not-for-mail Return-Path: X-Original-To: python-list@python.org Delivered-To: python-list@mail.python.org X-Spam-Status: OK 0.009 X-Spam-Evidence: '*H*': 0.98; '*S*': 0.00; '12px;': 0.05; 'automate': 0.07; 'failing': 0.07; 'parser': 0.07; 'chime': 0.09; 'subject:files': 0.09; '\xe2\x80\x94': 0.09; 'cc:addr:python- list': 0.11; 'python': 0.11; 'itself.': 0.14; 'biochemistry': 0.16; 'cleaned': 0.16; 'emeritus': 0.16; 'empty.': 0.16; 'etc.),': 0.16; 'feeding': 0.16; 'from:addr:python': 0.16; 'i\xe2\x80\x99m': 0.16; 'mainstream': 0.16; 'read?': 0.16; 'underline;': 0.16; 'subject:python': 0.16; 'helvetica;': 0.16; 'do,': 0.16; 'wrote:': 0.18; 'do.': 0.18; 'library': 0.18; 'trying': 0.19; 'written': 0.21; 'feb': 0.22; 'cc:addr:python.org': 0.22; 'parse': 0.24; 'subject: .': 0.24; 'cc:2**0': 0.24; 'header:In-Reply-To:1': 0.27; 'url:mailman': 0.30; 'that.': 0.31; 'loading': 0.31; 'searches': 0.31; 'compatible': 0.32; 'another': 0.32; 'url:python': 0.33; 'entirely': 0.33; 'not.': 0.33; 'could': 0.34; 'received:209.85': 0.35; 'convert': 0.35; 'but': 0.35; 'received:google.com': 0.35; 'there': 0.35; 'much.': 0.36; 'url:listinfo': 0.36; 'possible': 0.36; 'subject:?': 0.36; 'url:org': 0.36; 'skip:- 20': 0.37; 'received:209': 0.37; 'auto;': 0.38; 'thank': 0.38; 'problems': 0.38; 'files': 0.38; 'pm,': 0.38; 'does': 0.39; 'itself': 0.39; 'structure': 0.39; 'subject:can': 0.39; 'sure': 0.39; 'url:mail': 0.40; 'read': 0.60; 'most': 0.60; 'hope': 0.61; 'mentioned': 0.61; 'offer': 0.62; 'header:Message-Id:1': 0.63; 'show': 0.63; 'pick': 0.64; 'capable': 0.67; 'inline': 0.74; 'goal': 0.75; 'chemical': 0.84; 'i\xe2\x80\x99ll': 0.84; 'subject:handle': 0.84; 'capture': 0.91; 'don\xe2\x80\x99t': 0.91; 'you\xe2\x80\x99re': 0.91; 'wanting': 0.93; 'assess': 0.96 X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:content-type:mime-version:subject:from :in-reply-to:date:cc:message-id:references:to; bh=0cSwJ146vTuFJ+/e07rOi7cKOfrJwleWT7mtDkFzO04=; b=Dfu3xogj1yeLNfF9MOaUvxJ5xyQzC8QRHROl6TpEvWh3NSsZZuyWZZGvFg3tjLnWsz afnBWsbzICeNla99nm2L/1OSbOM3CvGkT6SFDWZk6J0F2fGCR5u2xjbv7RXA4DAVM75/ 7o+RdtTy3j/8tJ/kXSXws/8WSFI6/rbxg3ohjV2PxB1+02AumA30qj8sO7Tm9vWoXpsd aFeGeLf26gxYJCeR+VD/Axx+h7LXhkhHoRx29TSo+hnfRrzxwx/mlLg3sz5N3ONiIc4f 6/PVMgjB+vyXIuFW2aVQX18/S/o5B1j4QWQYp5ZVeGwDQOOwUceOI+2cXJWfL+0qf/sE ufvw== X-Gm-Message-State: ALoCoQkssQizGKBQ7sr21O/KRmysTDYJ2VbnBD2HHSHmNwF8qT8aS39XjJL7N0C/4f8pUzId19PN X-Received: by 10.182.103.232 with SMTP id fz8mr922791obb.59.1424296506727; Wed, 18 Feb 2015 13:55:06 -0800 (PST) Content-Type: multipart/alternative; boundary="Apple-Mail=_EADFFAD8-A090-4ED7-83CB-B715C9E2D1E3" Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2070.6\)) Subject: Re: can python handle CHIME .spt files? From: Davin Potts In-Reply-To: <26AE89FA3A4C214D9E3F06D0AEA41A4083009639@EXCH10MBX01.CAMPUS.CU.CLEMSON.EDU> Date: Wed, 18 Feb 2015 15:55:03 -0600 References: <26AE89FA3A4C214D9E3F06D0AEA41A4083009639@EXCH10MBX01.CAMPUS.CU.CLEMSON.EDU> To: James Zimmerman X-Mailer: Apple Mail (2.2070.6) Cc: "python-list@python.org" X-BeenThere: python-list@python.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: General discussion list for the Python programming language List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Newsgroups: comp.lang.python Message-ID: Lines: 144 NNTP-Posting-Host: 2001:888:2000:d::a6 X-Trace: 1424296516 news.xs4all.nl 2959 [2001:888:2000:d::a6]:49979 X-Complaints-To: abuse@xs4all.nl Xref: csiph.com comp.lang.python:85822 --Apple-Mail=_EADFFAD8-A090-4ED7-83CB-B715C9E2D1E3 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi James =E2=80=94 I=E2=80=99m not entirely sure I understand what you=E2=80=99re wanting = to do, but my ears perked up when you mentioned Jmol and Chime so I=E2=80=99= ll try to offer some pointers: * If you want to assess which .spt files are failing when trying to read = them with Jmol, then yes, Python can be used to automate the feeding of = files to Jmol and can capture whether the loading is successful or not. * If you want a way to parse problematic .spt files that can no longer = be read in using Jmol or MDL Chime, it is possible to create an .spt = parser in Python capable of reading your files though my quick searches = for an existing .spt parser library in Python came up empty. If this is = your goal (to read those problematic .spt files), have you considered = using OpenBabel to read them and convert them to another mainstream = chemical structure format (SDF, MOL, etc.), cleaned up and ready for = reading by any of a variety of other tools? You may already be aware but just in case it isn=E2=80=99t evident, = Python itself does not ship with capabilities for reading/writing = chemical structure formats but there are lots of chemistry tools built = on top of Python that do. You may well find it most productive to pick = up one of those tools in lieu of Python itself. Hope this helps, Davin > On Feb 18, 2015, at 2:56 PM, James Zimmerman = wrote: >=20 > I have a lot of old files that were written in Chime, then made = compatible with Jmol. Now there are problems with that. Will Python = give me a way to be able to show the .spt files that Chime could read? = I don=E2=80=99t want to start learning Python unless I know there is a = way. > =20 > Thank you very much. > =20 > James Zimmerman > Emeritus Professor of Biochemistry > --=20 > https://mail.python.org/mailman/listinfo/python-list = --Apple-Mail=_EADFFAD8-A090-4ED7-83CB-B715C9E2D1E3 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Hi James =E2=80=94

I=E2=80=99m not entirely sure I = understand what you=E2=80=99re wanting to do, but my ears perked up when = you mentioned Jmol and Chime so I=E2=80=99ll try to offer some = pointers:

* If = you want to assess which .spt files are failing when trying to read them = with Jmol, then yes, Python can be used to automate the feeding of files = to Jmol and can capture whether the loading is successful or = not.

* If you = want a way to parse problematic .spt files that can no longer be read in = using Jmol or MDL Chime, it is possible to create an .spt parser in = Python capable of reading your files though my quick searches for an = existing .spt parser library in Python came up empty.  If this is = your goal (to read those problematic .spt files), have you considered = using OpenBabel to read them and convert them to another mainstream = chemical structure format (SDF, MOL, etc.), cleaned up and ready for = reading by any of a variety of other tools?


You = may already be aware but just in case it isn=E2=80=99t evident, Python = itself does not ship with capabilities for reading/writing chemical = structure formats but there are lots of chemistry tools built on top of = Python that do.  You may well find it most productive to pick up = one of those tools in lieu of Python itself.


Hope= this helps,

Davin



On = Feb 18, 2015, at 2:56 PM, James Zimmerman <JKZMM@clemson.edu> = wrote:

I have a lot of old files that were written in Chime, then = made compatible with Jmol.  Now there are problems with that.  = Will Python give me a way to be able to show the .spt files that  = Chime could read?  I don=E2=80=99t want to start learning Python = unless I know there is a way.
 
          &nb= sp;     Thank you very much.
 
James = Zimmerman
Emeritus Professor of Biochemistry
-- 
https://mail.python.org/mailman/listinfo/python-list
<= /blockquote>

= --Apple-Mail=_EADFFAD8-A090-4ED7-83CB-B715C9E2D1E3--