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On Wednesday 25 February 2004 20:44, Daniel Zaharevitz wrote:
> On Feb 24, 2004, at 6:42 PM, Miguel Howard wrote:
> > DanZ wrote:
> >> it seems that CML and loadInLine
> >> are not yet supported. Is this true and if so what are the issues?
> >
> > CML
DanZ wrote:
> Our web pages get ~1.5 million hits/year from ~40K disitinct IP
> addresses.
OK, broad user base running a wide variety of systems.
> We recognize that using CML (and
> XML in general) can have resource and performance issues, but I haven't
> seen any other technology that
> will get
On Feb 24, 2004, at 6:42 PM, Miguel Howard wrote:
DanZ wrote:
it seems that CML and loadInLine
are not yet supported. Is this true and if so what are the issues?
CML
===
CML is probably a good thing for Egon to work on. We have code to
support it in previous versions of Jmol and in the CDK (Chemis
DanZ wrote:
> it seems that CML and loadInLine
> are not yet supported. Is this true and if so what are the issues?
CML
===
CML is probably a good thing for Egon to work on. We have code to
support it in previous versions of Jmol and in the CDK (Chemistry
Development Kit).
One of the major barrie
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On Monday 23 February 2004 15:27, Daniel Zaharevitz wrote:
> On Monday, February 9, 2004, at 04:09 PM, Daniel Zaharevitz wrote:
> > Our software development efforts (See
> > http://dtp.nci.nih.gov/dw/dw_main.html) have reached the point where
> > we ar
On Monday, February 9, 2004, at 04:09 PM, Daniel Zaharevitz wrote:
Our software development efforts (See
http://dtp.nci.nih.gov/dw/dw_main.html) have reached the point where
we are likely to get more involved in the current JMol efforts and we
want to make our efforts be as broadly useful as pos
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Hi Dan,
thank you very much for your interesting emails. I'm sorry that I had not
replied to your first email, but will try to make up now.
On Tuesday 10 February 2004 21:40, Daniel Zaharevitz wrote:
> > Certainly if you felt that there was a place
I think I sent this only to Miguel and I meant it to go to the list as
well
Begin forwarded message:
On Monday, February 9, 2004, at 05:09 PM, Miguel Howard wrote:
First of all let me point out that this is
especially timely considering the new NIH roadmap initiatives (See
http://nihroadmap.ni
> First of all let me point out that this is
> especially timely considering the new NIH roadmap initiatives (See
> http://nihroadmap.nih.gov). The particularly applicable group is the
> Molecular Libraries and Imaging one.
I am very interested in having NIH use Jmol as part of this effort.
[snip
On Sunday, February 1, 2004, at 11:20 AM, Peter Murray-Rust wrote:
[lots of stuff deleted]
Great. I'm guessing that this can be program independent and that
anyone can access this nameserver whatever the platform and OS,
providing they have a WWW library of equivalent (obviously this is
bui
On Sunday 01 February 2004 10:54, Miguel Howard wrote:
> > CAS is short for CAS rigestry number... it's a simple index used for a
> > very big database of published structures, I think... see:
> >
> > http://www.cas.org/EO/regsys.html
>
> This is *very* helpful.
> As I understand it, this is the '
On Sunday, February 1, 2004, at 07:19 AM, Egon Willighagen wrote:
On Sunday 01 February 2004 10:54, Miguel Howard wrote:
CAS is short for CAS rigestry number... it's a simple index used for
a
very big database of published structures, I think... see:
http://www.cas.org/EO/regsys.html
This is *v
This sounds great. Shouldn't be too difficult. We have parsed a number of
pages for chemical content. And I know that Henry has. So we could put
together a collaborative list of sites that we can scrape for chemistry.
The results would all be in CML with appropriate metadata. This would solve
m
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On Monday 02 February 2004 10:17, Peter Murray-Rust wrote:
> At 22:23 01/02/2004 +0100, Egon Willighagen wrote:
> >dadml://pdb/?1CRN
> >
> >or dadml://any/pdbid?1CRN
> >
> >The second will try any mirror that can return information based on the
> >pdbi
At 22:23 01/02/2004 +0100, Egon Willighagen wrote:
On Sunday 01 February 2004 17:28, Egon Willighagen wrote:
> dadml://nist/cas?50-00-0
>
> This would allow things in Java like:
>
> URI uri = new URI("dadml://nist/cas?50-00-0")
> String protocol = uri.getScheme();
> String service = uri.getAuthorit
On Sunday 01 February 2004 17:28, Egon Willighagen wrote:
> dadml://nist/cas?50-00-0
>
> This would allow things in Java like:
>
> URI uri = new URI("dadml://nist/cas?50-00-0")
> String protocol = uri.getScheme();
> String service = uri.getAuthority();
> String index = uri.getPath();
> String query
> This would allow things in Java like:
>
> URI uri = new URI("dadml://nist/cas?50-00-0")
> String protocol = uri.getScheme();
> String service = uri.getAuthority();
> String index = uri.getPath();
> String query = uri.getQuery();
Good idea ... let Java do the parsing.
Miguel
--
At 16:40 01/02/2004 +0100, Egon Willighagen wrote:
On Sunday 01 February 2004 13:22, Peter Murray-Rust wrote:
> At 06:26 31/01/2004 -0500, timothy driscoll wrote:
> >at 9.26a EDT on 2004 January 29 Thursday Peter Murray-Rust said:
> > > At 00:06 29/01/2004 +0100, Miguel Howard wrote:
> > > >I am lo
At 12:01 31/01/2004 +0100, Miguel Howard wrote:
> I am sure you know that Egon has done something like this in CDK/JCP.
While I was aware of the RSS and plug-in work, I did not make the
association between the two ... Thanks!
> So it's important to keep consistency...
Agreed.
> I favour the use
On Sunday 01 February 2004 13:22, Peter Murray-Rust wrote:
> At 06:26 31/01/2004 -0500, timothy driscoll wrote:
> >at 9.26a EDT on 2004 January 29 Thursday Peter Murray-Rust said:
> > > At 00:06 29/01/2004 +0100, Miguel Howard wrote:
> > > >I am looking for a standard syntax for pulling data from r
On Sunday 01 February 2004 00:34, Egon Willighagen wrote:
> Alternatively, we could do:
>
> dadml://nist/cas/50-00-0
>
> where the syntax is as follows:
>
> PROTOCOL://SERVICE[/INDEXTYPE]/INDEX
>
> where the index type is optional...
>
> think of it as a kind of subdirectory in HTTP or FTP URL's...
At 06:26 31/01/2004 -0500, timothy driscoll wrote:
at 9.26a EDT on 2004 January 29 Thursday Peter Murray-Rust said:
> At 00:06 29/01/2004 +0100, Miguel Howard wrote:
> >
> >I am looking for a standard syntax for pulling data from remote databases.
> >The idea is that we would store the exact URL o
>> Q: Are there other large, publically available databases on the web?
>
> Yes, see:
>
> http://www.woc.sci.kun.nl/super.xml
>
> This lists 9 databases... All links refer to URL+database.xml, e.g.
>
> http://www.woc.sci.kun.nl/database.xml for the first entry...
Very good.
>> Q: Is this 'NSC' nu
> CAS is short for CAS rigestry number... it's a simple index used for a
> very big database of published structures, I think... see:
>
> http://www.cas.org/EO/regsys.html
This is *very* helpful.
As I understand it, this is the 'registry' only.
I see that the cactus database (http://cactus.nci.n
On Saturday 31 January 2004 22:54, timothy driscoll wrote:
> > > DADML has support for any syntax for any service... But maybe we
> > > should just restrict to one index type... experience has shown that
> > > this ok. CAS is for small molecules widely accepted...
> >
> > Alternatively, we could do
> where the syntax is as follows:
>
> PROTOCOL://SERVICE[/INDEXTYPE]/INDEX
I should have read ahead :-)
Miguel
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See the bread
>> unless 'pdb' in the above context refers to the actual db from whence
>> the structure cometh?
>
> My intention was indeed that pdb was denoting the actual PDB database...
> The DADML protocol would know how to resolve it into a URL and as such
> into a HTTP request...
I agree.
- //pdb/ was i
at 12.34a EDT on 2004 February 01 Sunday Egon Willighagen said:
> On Sunday 01 February 2004 00:30, Egon Willighagen wrote:
> > On Saturday 31 January 2004 22:14, timothy driscoll wrote:
> > > at 4.15p EDT on 2004 January 31 Saturday Miguel Howard said:
> > > > > maybe it could better be then:
>
On Sunday 01 February 2004 00:30, Egon Willighagen wrote:
> On Saturday 31 January 2004 22:14, timothy driscoll wrote:
> > at 4.15p EDT on 2004 January 31 Saturday Miguel Howard said:
> > > > maybe it could better be then:
> > > >
> > > > dadml://pdb/1crn
> > > >
> > > > where DADML is they wat thi
On Saturday 31 January 2004 22:14, timothy driscoll wrote:
> at 4.15p EDT on 2004 January 31 Saturday Miguel Howard said:
> > > maybe it could better be then:
> > >
> > > dadml://pdb/1crn
> > >
> > > where DADML is they wat things are resolved, and pdb the service...
> >
> > I like this *much* bett
at 4.15p EDT on 2004 January 31 Saturday Miguel Howard said:
> > maybe it could better be then:
> >
> > dadml://pdb/1crn
> >
> > where DADML is they wat things are resolved, and pdb the service...
>
> I like this *much* better.
>
> Miguel
>
how about using 'mol' instead of 'pdb'? it's a litt
> I don't think Peter is refering to the RSS work... JCP also has a system
> called DADML: database access definition markup language...
I wasn't aware of that.
> It uses XML files to download from databases, and is very well suited
> for downloading from databases like the PDB...
>
> See CDK's
On Saturday 31 January 2004 12:01, Miguel Howard wrote:
> > I am sure you know that Egon has done something like this in CDK/JCP.
>
> While I was aware of the RSS and plug-in work, I did not make the
> association between the two ... Thanks!
I don't think Peter is refering to the RSS work... JCP a
> I like the URL syntax, too. the only trouble I can see is if a
> structure DB changes the syntax for remote apps accessing their DB.
Regardless of what syntax we choose (even if it looks like a URL), we will
pull out the key components and substitute them into a pattern to
construct the 'true'
at 9.26a EDT on 2004 January 29 Thursday Peter Murray-Rust said:
> At 00:06 29/01/2004 +0100, Miguel Howard wrote:
> >
> >I am looking for a standard syntax for pulling data from remote databases.
> >The idea is that we would store the exact URL outside the scripts (and in
> >a configuration file)
> I am sure you know that Egon has done something like this in CDK/JCP.
While I was aware of the RSS and plug-in work, I did not make the
association between the two ... Thanks!
> So it's important to keep consistency...
Agreed.
> I favour the use of symbolic addresses which are set in configu
At 00:06 29/01/2004 +0100, Miguel Howard wrote:
>> Q: Do you think that there is value in specifying a 'standard' syntax
>> for pulling files from the pdb? Something like: 'load [pdb]1ezn'
>>
>> That way, you could externalize the location of the server (and the
>> specific URL) and get it out of t
> how about
>
> load someID(someDB,someFlag)
>
> instead? I think of the ID as the central element here, and I'd like to
> be able to say simply
>
> load someID
>
> and have Jmol use the default database from its pref file.
Well, you have an interesting point. But I am concerned that it would
res
at 12.06a EDT on 2004 January 29 Thursday Miguel Howard said:
> >> Q: Do you think that there is value in specifying a 'standard' syntax
> >> for pulling files from the pdb? Something like: 'load [pdb]1ezn'
> >>
> >> That way, you could externalize the location of the server (and the
> >> specifi
>> Q: Do you think that there is value in specifying a 'standard' syntax
>> for pulling files from the pdb? Something like: 'load [pdb]1ezn'
>>
>> That way, you could externalize the location of the server (and the
>> specific URL) and get it out of the RasMol script.
>>
>yes - esp if there is also
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