Re: [Jmol-users] PubChem SDF

2011-01-19 Thread Otis Rothenberger
Hanson hans...@stolaf.edu Sent: Wednesday, January 19, 2011 1:26 AM To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] PubChem SDF yup, that's what I was thinking you might do. OK, I will implement that. see http://chemapps.stolaf.edu/jmol/docs/examples-12

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Angel Herráez
Just my 2 cents: Evidently, a fair number of PubChem's sdf's have partial charge data. I see aproblem here. The format shown in your example is not according to SDF spec (I think it does not suppor partial charge, only formal charge). They shouldbe using a different format, like MOL2. So

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Otis Rothenberger
@lists.sourceforge.net Subject: Re: [Jmol-users] PubChem SDF Just my 2 cents: Evidently, a fair number of PubChem's sdf's have partial charge data. I see aproblem here. The format shown in your example is not according to SDF spec (I think it does not suppor partial charge, only formal charge

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Robert Hanson
University Normal, IL 61790-4160 http://chemagic.org -- *From*: Angel Herráez angel.herr...@uah.es *Sent*: Tuesday, January 18, 2011 5:18 AM *To*: osrot...@chemagic.com, jmol-users@lists.sourceforge.net *Subject*: Re: [Jmol-users] PubChem SDF Just my 2 cents

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Robert Hanson
Of course, Otis is so good at JavaScript, he could easily write a little JavaScript parser for this;) -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them.

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Otis Rothenberger
-4160 http://chemagic.org From: Robert Hanson hans...@stolaf.edu Sent: Tuesday, January 18, 2011 6:55 PM To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] PubChem SDF Of course, Otis is so good at JavaScript, he could

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Egon Willighagen
2011/1/18 Angel Herráez angel.herr...@uah.es: Just my 2 cents: Evidently, a fair number of PubChem's sdf's have partial charge data. I see aproblem here. The format shown in your example is not according to SDF spec (I think it does not suppor partial charge, only formal charge). How so?

Re: [Jmol-users] PubChem SDF

2011-01-18 Thread Robert Hanson
yup, that's what I was thinking you might do. OK, I will implement that. see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107

[Jmol-users] PubChem SDF

2011-01-17 Thread Otis Rothenberger
Bob, Evidently, a fair number of PubChem's sdf's have partial charge data. I know that I can parse the data with JavaScript and apply the charge results, including implied zeros, to the model with Jmol script, but I want to make sure I'm not reinventing the wheel. I've pasted the data for