Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
I must be missing something here...
load $caffeine
x = http://webbook.nist.gov/cgi/cbook.cgi?Mask=80; + script(show
chemical inchi)
y = http://webbook.nist.gov/cgi/cbook.cgi?Spec=; +
load(x).split(Spec=)[2].split('')[1].replace(amp;,)
background image @y
At this point y =
http://webbook.nist.gov/cgi/cbook.cgi?Spec=C58082Index=0Type=IR
Right?
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Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
got blocked because of the image. It's an interesting script. Best with
background white but also kind of cool with background black
On Wed, Jul 4, 2012 at 7:26 PM, Robert Hanson hans...@stolaf.edu wrote:
I must be missing something here...
load $caffeine
x = http://webbook.nist.gov/cgi/cbook.cgi?Mask=80; + script(show
chemical inchi)
y = http://webbook.nist.gov/cgi/cbook.cgi?Spec=; +
load(x).split(Spec=)[2].split('')[1].replace(amp;,)
background image @y
At this point y =
http://webbook.nist.gov/cgi/cbook.cgi?Spec=C58082Index=0Type=IR
Right?
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
I tried to test Bob's script, and it seems that the space after 80 must be removed x = http://webbook.nist.gov/cgi/cbook.cgi?Mask=80; + script(show chemical inchi) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
those aren't actual links -- that is just Jmol script that is being messed with by your browser. On Thu, Jul 5, 2012 at 11:38 AM, Angel Herráez angel.herr...@uah.es wrote: I tried to test Bob's script, and it seems that the space after 80 must be removed x = http://webbook.nist.gov/cgi/cbook.cgi?Mask=80; + script(show chemical inchi) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
Otis, What about this? http://webbook.nist.gov/cgi/cbook.cgi?Mask=80InChI=1S/C2H5NO2/c3-1-2%284%295/h1,3H2,%28H,4,5%29 That's the escaped INCHI there, or: [ http://webbook.nist.gov/cgi/cbook.cgi?Mask=80InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)] Mask=80 says you want the IR spectrum information. - Not specified, most likely a prism, grating, or hybrid spectrometer.; (NO SPECTRUM, ONLY SCANNED IMAGE IS AVAILABLE)http://webbook.nist.gov/cgi/cbook.cgi?ID=C56406Type=IR-SPECIndex=0#IR-SPEC - SOLID (MULL, KBr DISC) $$INACTIVE KBr PLATES AROUND 300-200 CM-1; PERKIN-ELMER 521 (GRATING); DIGITIZED BY COBLENTZ SOCIETY (BATCH I) FROM HARD COPY; 2 cm-1 resolutionhttp://webbook.nist.gov/cgi/cbook.cgi?ID=C56406Type=IR-SPECIndex=1#IR-SPEC So there's your index 0 and index 1 business. I'm not sure how much more than that we could expect from NIST. I don't think you want to be blindly using those indexes. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
Bob, On our end, this all started with a request from one of Tom's colleagues. He's using the VMK in a service outreach lecture series to discuss, among other things, how chemists know what molecules look like. We thought it would be neat to be able to discuss this with a series of edited molecules in the VMK window - ethane, ethene, ethyne, ethanol, ethanal, etc. The ability to instantaneously display the IR's of these molecules would allow a discussion of peak meaning. Since the technical details of the IR methodology were not a real issue in the non-major discussion, we wanted the presentational power of wham, here's the IR spectrum for each model used in the lecture. This is the reason that I wanted to load the SVG directly: http://webbook.nist.gov/cgi/cbook.cgi?Spec=C56406Index=1Type=IRLarge=onSVG=on I plan to display them on our image panel right next to the corresponding model. I knew that the indexes were a zero based system. After some extensive playing, however, I noticed that there was no pattern. Evidently, the zero and other indexes can disappear. I guess a deleted spectrum does not lose it's index number. It's just eliminated from display. Still, I'm convinced I can make some sense out of the indexes for our purposes. A while back, we moved our db search operations for the virtual model kit to our AKA application, and what you suggest is a good idea for the NIST IR on the AKA page. For presentational neat, however, I'm going to take a closer look at getting the direct display of the NIST SVG files under control - just like NMRDB.ORG display. Otis On 7/4/2012 5:26 PM, Robert Hanson wrote: Otis, What about this? http://webbook.nist.gov/cgi/cbook.cgi?Mask=80InChI=1S/C2H5NO2/c3-1-2%284%295/h1,3H2,%28H,4,5%29 That's the escaped INCHI there, or: [ http://webbook.nist.gov/cgi/cbook.cgi?Mask=80InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) http://webbook.nist.gov/cgi/cbook.cgi?Mask=80InChI=1S/C2H5NO2/c3-1-2%284%295/h1,3H2,%28H,4,5%29 ] Mask=80 says you want the IR spectrum information. * Not specified, most likely a prism, grating, or hybrid spectrometer.; (NO SPECTRUM, ONLY SCANNED IMAGE IS AVAILABLE) http://webbook.nist.gov/cgi/cbook.cgi?ID=C56406Type=IR-SPECIndex=0#IR-SPEC * SOLID (MULL, KBr DISC) $$INACTIVE KBr PLATES AROUND 300-200 CM^-1 ; PERKIN-ELMER 521 (GRATING); DIGITIZED BY COBLENTZ SOCIETY (BATCH I) FROM HARD COPY; 2 cm^-1 resolution http://webbook.nist.gov/cgi/cbook.cgi?ID=C56406Type=IR-SPECIndex=1#IR-SPEC So there's your index 0 and index 1 business. I'm not sure how much more than that we could expect from NIST. I don't think you want to be blindly using those indexes. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
Interesting. OK, so with NIH resolver you can get the CAS number from a
SMILES, as used in Jmol with:
$ show chemical cas
71701-02-5
95789-13-2
58-08-2
or
x = script(show chemical cas)
or
var jsvar = Jmol.evaluate(appid, script('show chemical cas'))
And then you can just use that, I think. Right?
Bob
On Tue, Jul 3, 2012 at 12:25 PM, Otis Rothenberger osrot...@chemagic.comwrote:
All-
The real problem here, however, is the Jmol SMILES to the Spec= id
required above. This id is the CAS number with a leading C.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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threat landscape has changed and how IT managers can respond. Discussions
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Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
Bob,
Almost, but not quite. ACS makes money from CAS numbers, so there are several
(often many) CAS numbers for a given compound. As far as unique identification
is concerned, this is irritating. NIST seems to use one of these numbers for a
given compound. NIST, therefore, seems to use a single CAS number uniquely
inside NIST.
By making Google do the resolution, I'm picking up Google hits exclusive to the
NIST site, thus the captured CAS number is the one that NIST uniquely uses. So,
here's what I'm doing:
1) ChemSpider InChI API for SMILES to InChI
2) Advanced Google Search using InChI, spectrum, and NIST web site
3) Parse the CAS Number from the returned search HTML page - painful, but
doable with consistent results because the extracted info is a URL - not broken
up in the HTML.
With the NIST CAS number, I can construct the proper image URL, except for the
spectrum index= query.
At first, I though I could go directly to NIST with the InChI to parse the CAS
#. Unfortunately, such a query often returns an intervening options page that
has no CAS numbers.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jul 3, 2012, at 2:49 PM, Robert Hanson wrote:
Interesting. OK, so with NIH resolver you can get the CAS number from a
SMILES, as used in Jmol with:
$ show chemical cas
71701-02-5
95789-13-2
58-08-2
or
x = script(show chemical cas)
or
var jsvar = Jmol.evaluate(appid, script('show chemical cas'))
And then you can just use that, I think. Right?
Bob
On Tue, Jul 3, 2012 at 12:25 PM, Otis Rothenberger osrot...@chemagic.com
wrote:
All-
The real problem here, however, is the Jmol SMILES to the Spec= id required
above. This id is the CAS number with a leading C.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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threat landscape has changed and how IT managers can respond. Discussions
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Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
I have to say, that's pretty wild.
Why don't you start a conversation with NIST and see if they could add an
InChI interface. Explain how nearly impossible it is to user their current
interface with the CAS numbers and how this would benefit the world.
Also, there are only 16,000 compounds there for IR. We could almost just
catalog them. Maybe Markus can add them to the Resolver.
Do you need an introduction?
Bob
On Tue, Jul 3, 2012 at 2:07 PM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
Almost, but not quite. ACS makes money from CAS numbers, so there are
several (often many) CAS numbers for a given compound. As far as unique
identification is concerned, this is irritating. NIST seems to use one of
these numbers for a given compound. NIST, therefore, seems to use a single
CAS number uniquely inside NIST.
By making Google do the resolution, I'm picking up Google hits exclusive
to the NIST site, thus the captured CAS number is the one that NIST
uniquely uses. So, here's what I'm doing:
1) ChemSpider InChI API for SMILES to InChI
2) Advanced Google Search using InChI, spectrum, and NIST web site
3) Parse the CAS Number from the returned search HTML page - painful, but
doable with consistent results because the extracted info is a URL - not
broken up in the HTML.
With the NIST CAS number, I can construct the proper image URL, except for
the spectrum index= query.
At first, I though I could go directly to NIST with the InChI to parse the
CAS #. Unfortunately, such a query often returns an intervening options
page that has no CAS numbers.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jul 3, 2012, at 2:49 PM, Robert Hanson wrote:
Interesting. OK, so with NIH resolver you can get the CAS number from a
SMILES, as used in Jmol with:
$ show chemical cas
71701-02-5
95789-13-2
58-08-2
or
x = script(show chemical cas)
or
var jsvar = Jmol.evaluate(appid, script('show chemical cas'))
And then you can just use that, I think. Right?
Bob
On Tue, Jul 3, 2012 at 12:25 PM, Otis Rothenberger
osrot...@chemagic.comwrote:
All-
The real problem here, however, is the Jmol SMILES to the Spec= id
required above. This id is the CAS number with a leading C.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
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threat landscape has changed and how IT managers can respond. Discussions
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Re: [Jmol-users] Google as an InChI to CAS Resolver for NIST Spectra
Bob,
I'm willing to give it a try. An introduction to NIST by you might be
useful. I'm just an old guy who lives in Florida. You're the Jmol boss.
Markus is a different. I know him. I'll write to him to see what he
thinks about the idea re Resolver.
Otis
On 7/3/2012 5:15 PM, Robert Hanson wrote:
I have to say, that's pretty wild.
Why don't you start a conversation with NIST and see if they could add
an InChI interface. Explain how nearly impossible it is to user their
current interface with the CAS numbers and how this would benefit the
world.
Also, there are only 16,000 compounds there for IR. We could almost
just catalog them. Maybe Markus can add them to the Resolver.
Do you need an introduction?
Bob
On Tue, Jul 3, 2012 at 2:07 PM, Otis Rothenberger
osrot...@chemagic.com mailto:osrot...@chemagic.com wrote:
Bob,
Almost, but not quite. ACS makes money from CAS numbers, so there
are several (often many) CAS numbers for a given compound. As far
as unique identification is concerned, this is irritating. NIST
seems to use one of these numbers for a given compound. NIST,
therefore, seems to use a single CAS number uniquely inside NIST.
By making Google do the resolution, I'm picking up Google hits
exclusive to the NIST site, thus the captured CAS number is the
one that NIST uniquely uses. So, here's what I'm doing:
1) ChemSpider InChI API for SMILES to InChI
2) Advanced Google Search using InChI, spectrum, and NIST web site
3) Parse the CAS Number from the returned search HTML page -
painful, but doable with consistent results because the extracted
info is a URL - not broken up in the HTML.
With the NIST CAS number, I can construct the proper image URL,
except for the spectrum index= query.
At first, I though I could go directly to NIST with the InChI to
parse the CAS #. Unfortunately, such a query often returns an
intervening options page that has no CAS numbers.
Otis
--
Otis Rothenberger
o...@chemagic.com mailto:o...@chemagic.com
http://chemagic.com
On Jul 3, 2012, at 2:49 PM, Robert Hanson wrote:
Interesting. OK, so with NIH resolver you can get the CAS number
from a SMILES, as used in Jmol with:
$ show chemical cas
71701-02-5
95789-13-2
58-08-2
or
x = script(show chemical cas)
or
var jsvar = Jmol.evaluate(appid, script('show chemical cas'))
And then you can just use that, I think. Right?
Bob
On Tue, Jul 3, 2012 at 12:25 PM, Otis Rothenberger
osrot...@chemagic.com mailto:osrot...@chemagic.com wrote:
All-
The real problem here, however, is the Jmol SMILES to the
Spec= id required above. This id is the CAS number with a
leading C.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond.
Discussions
will include endpoint security, mobile security and the latest in
malware
threats.
http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___
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Jmol-users@lists.sourceforge.net
mailto:Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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threat landscape has changed and how IT managers can respond.
Discussions
will include endpoint security, mobile security and the latest in
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___
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https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and
