From owner-chemistry@ccl.net Wed Oct 22 03:03:00 2014 From: "benoit benoit ablux13|*|gmail.com" To: CCL Subject: CCL: Critical energy Message-Id: <-50623-141022030151-2573-ggSUbLwqKNnxTUQE7yTpPQ{}server.ccl.net> X-Original-From: "benoit benoit" Date: Wed, 22 Oct 2014 03:01:50 -0400 Sent to CCL by: "benoit benoit" [ablux13{:}gmail.com] Hello, I would like to enquire about critical energy. Is it treated as the same manner as activation energy? In other words, the less is the critical energy the more favorable is the channel (kinetically). Reegrads Benoit From owner-chemistry@ccl.net Wed Oct 22 05:21:01 2014 From: "Georg Lefkidis lefkidis^-^physik.uni-kl.de" To: CCL Subject: CCL: Boys function Message-Id: <-50624-141022045848-4584-H8zwSEHiorl8bVIFdA2/7Q!^!server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 22 Oct 2014 10:59:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis-$-physik.uni-kl.de] Dear all, I am looking for an effective algorithm to calculate the Boys function (preferably but not necessarily in fortran). Looking into the literature leaves me more perplexed than helps, every paper says what is not good, but what to actually do. Can someone give me one paper where the complete algorithm is listed? I do not need to entirely understand it but to actually code it. Best regards George From owner-chemistry@ccl.net Wed Oct 22 05:55:00 2014 From: "Robin Shannon R.Shannon++leeds.ac.uk" To: CCL Subject: CCL: Critical energy Message-Id: <-50625-141022052349-6440-VCM3LvqFtjKCqophItxdlA*server.ccl.net> X-Original-From: Robin Shannon Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 22 Oct 2014 10:20:42 +0100 MIME-Version: 1.0 Sent to CCL by: Robin Shannon [R.Shannon%leeds.ac.uk] Dear Benoit Perhaps it would be most instructive for you to actually carry out an RRKM calculation. MESMER (www.chem.leeds.ac.uk/mesmer.html) is easy to use and the manual describes all the relevant parameters. Regards Robin ________________________________________ > From: owner-chemistry+chmrsh==leeds.ac.uk===ccl.net [owner-chemistry+chmrsh==leeds.ac.uk===ccl.net] On Behalf Of benoit benoit ablux13|*|gmail.com [owner-chemistry===ccl.net] Sent: 22 October 2014 08:01 To: Shannon, Robin J Subject: CCL: Critical energy Sent to CCL by: "benoit benoit" [ablux13{:}gmail.com] Hello, I would like to enquire about critical energy. Is it treated as the same manner as activation energy? In other words, the less is the critical energy the more favorable is the channel (kinetically). Reegrads Benoithttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Oct 22 06:31:01 2014 From: "Adedapo Adeyinka u11335132.:.tuks.co.za" To: CCL Subject: CCL: Conformational analysis challenge Message-Id: <-50626-141022055921-21981-9I4OrvW01sFjQY0hFNRuaQ{:}server.ccl.net> X-Original-From: Adedapo Adeyinka Content-Type: multipart/alternative; boundary=001a113647d8202488050600002d Date: Wed, 22 Oct 2014 11:59:15 +0200 MIME-Version: 1.0 Sent to CCL by: Adedapo Adeyinka [u11335132(!)tuks.co.za] --001a113647d8202488050600002d Content-Type: text/plain; charset=UTF-8 Dear Colleagues, I have generated a number of conformers for a particular polyamine molecule that I am currently studying which has multiple minima. Can anyone suggest to me a free software that I can use to group the set of conformers into clusters so that I can select a representative conformer from each cluster? Thanks in advance for your help and suggestions -- Adedapo Adeyinka -- This message and attachments are subject to a disclaimer. Please refer to http://www.it.up.ac.za/documentation/governance/disclaimer/ for full details. --001a113647d8202488050600002d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
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<= div>
Thanks in advance for your help and suggestions=C2=A0

--
Adedapo Adeyinka

This message and attachments are subject to= a disclaimer. Please refer to=20 http://www.it.u= p.ac.za/documentation/governance/disclaimer/ for full details. --001a113647d8202488050600002d-- From owner-chemistry@ccl.net Wed Oct 22 08:24:00 2014 From: "Michel Petitjean petitjean.chiral[*]gmail.com" To: CCL Subject: CCL: Conformational analysis challenge Message-Id: <-50627-141022082226-5647-wzHwJ910l/xuGMiz83G3GA[*]server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=UTF-8 Date: Wed, 22 Oct 2014 14:22:20 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral%gmail.com] Please have a look at DIVCF: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF (uses the MCG clustering algorithm, same web page). Ref: Meslamani JE, Andre F, Petitjean M. Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion. J. Chem. Inf. Model., 2009, 49[2], 330-337. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral,gmail.com (preferred), michel.petitjean,univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2014-10-22 11:59 GMT+02:00 Adedapo Adeyinka u11335132.:.tuks.co.za : > Dear Colleagues, > I have generated a number of conformers for a > particular polyamine molecule that I am currently studying which has > multiple minima. Can anyone suggest to me a free software that I can use to > group the set of conformers into clusters so that I can select a > representative conformer from each cluster? > > Thanks in advance for your help and suggestions > > -- > Adedapo Adeyinka > > This message and attachments are subject to a disclaimer. Please refer to > http://www.it.up.ac.za/documentation/governance/disclaimer/ for full > details. From owner-chemistry@ccl.net Wed Oct 22 09:28:01 2014 From: "Gerald Knizia knizia{=}theochem.uni-stuttgart.de" To: CCL Subject: CCL: Boys function Message-Id: <-50628-141022092441-10838-rbCtq7yNQjC1F+YtCPp25Q]*[server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 22 Oct 2014 15:24:35 +0200 Mime-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia_+_theochem.uni-stuttgart.de] Dear Georg, a simple, efficient, and highly accurate method is to just tabulate Taylor expanions of the values and derivatives in the near-region (for low T) and use the asymptotic expansion in the long region. The ir/wmme program which's source is available at http://www.theochem.uni-stuttgart.de/~knizia/ under "Program Downloads" has an (as I personally think) excellent implementation of this, which is accurate to < 1e-16 over the entire range of Ts. If you are terribly interested I can also get you the Python script which computes the tables built into the C++ program (by brute force upward recursion with arbitrary precision arithmetic). Best wishes, Gerald On Wed, 2014-10-22 at 10:59 +0200, Georg Lefkidis lefkidis^-^physik.uni-kl.de wrote: > Sent to CCL by: "Georg Lefkidis" [lefkidis-$-physik.uni-kl.de] > Dear all, > > I am looking for an effective algorithm to calculate the Boys function > (preferably but not necessarily in fortran). Looking into the literature > leaves me more perplexed than helps, every paper says what is not good, but > what to actually do. Can someone give me one paper where the complete > algorithm is listed? I do not need to entirely understand it but to actually > code it. > > Best regards > George> > From owner-chemistry@ccl.net Wed Oct 22 10:15:01 2014 From: "Marcin Makowski makowskm _ chemia.uj.edu.pl" To: CCL Subject: CCL: Boys function Message-Id: <-50629-141022071411-10309-btwG2ZYQ1cazFIAFesY5Bg**server.ccl.net> X-Original-From: "Marcin Makowski" Content-Transfer-Encoding: 8bit Content-Type: text/plain Date: Wed, 22 Oct 2014 13:14:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Marcin Makowski" [makowskm . chemia.uj.edu.pl] Take a look at Appendix to Ishida's paper: IJQC, 59(3) 1996, pp. 209-218. Generally, the efficient algorithms will be based on Taylor expansion on grid of points for not so large arguments + asymptotic expression for large arguments + downward(upward) recursion to get all F_0(x) to F_n(x) quickly. Regards, Marcin > Sent to CCL by: "Georg Lefkidis" [lefkidis-$-physik.uni-kl.de] > Dear all, > > > I am looking for an effective algorithm to calculate the Boys function > (preferably but not necessarily in fortran). Looking into the literature > leaves me more perplexed than helps, every paper says what is not good, > but what to actually do. Can someone give me one paper where the complete > algorithm is listed? I do not need to entirely understand it but to > actually code it. > > Best regards > George From owner-chemistry@ccl.net Wed Oct 22 12:32:01 2014 From: "Jozsef Csontos jcsontos.lists*o*gmail.com" To: CCL Subject: CCL: reaction database Message-Id: <-50630-141022071022-7139-klLzgQ8t/R86nwJL4UpC3w ~~ server.ccl.net> X-Original-From: Jozsef Csontos Content-Type: multipart/alternative; boundary="------------080504010303060206080500" Date: Wed, 22 Oct 2014 13:10:13 +0200 MIME-Version: 1.0 Sent to CCL by: Jozsef Csontos [jcsontos.lists[*]gmail.com] This is a multi-part message in MIME format. --------------080504010303060206080500 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Dear list members, I'd like to hear your opinions. I'm about to implement a database that contains chemical reactions (SMILES and SMARTS) with some literature data, like publication date, journal, authors, and a few properties of them. I'm thinking about a web service with a few hundred users. Registered users are able to upload/download and search reactions based on reactants and/or products, etc. I've done some digging and the following setup seems promising: a postgresql webserver with the rdkit cartridge and web2py. Basically, I've two requirements 1, every component should be open source and free 2, the python language is considered to be the glue between them Please, share your experience and thoughts; I'm going to summarize and post them back in this list. All the best, Jozsef --------------080504010303060206080500 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear list members,

I'd like to hear your opinions.
I'm about to implement a database that contains chemical reactions (SMILES and SMARTS) with some literature data, like publication date, journal, authors, and a few properties of them.  I'm thinking about a web service with a few hundred users.
Registered users are able to upload/download and search reactions based on reactants and/or products, etc.

I've done some digging and the following setup seems promising:

a postgresql webserver with the rdkit cartridge and web2py.

Basically, I've two requirements
1, every component should be open source and free
2, the python language is considered to be the glue between them

Please, share your experience and thoughts; I'm going to summarize and post them back in this list.

All the best,

Jozsef


 --------------080504010303060206080500-- From owner-chemistry@ccl.net Wed Oct 22 13:55:01 2014 From: "Chris Swain swain%a%mac.com" To: CCL Subject: CCL: reaction database Message-Id: <-50631-141022135400-26438-DKwUDmLUpsr5uDvFVFM7BQ * server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Apple-Mail=_ED6AED43-246B-44CD-9D9D-D013ECEE1FF1" Date: Wed, 22 Oct 2014 18:53:39 +0100 MIME-version: 1.0 (Mac OS X Mail 8.0 \(1990.1\)) Sent to CCL by: Chris Swain [swain.^.mac.com] --Apple-Mail=_ED6AED43-246B-44CD-9D9D-D013ECEE1FF1 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Will you effectively only have starting material and product or will you = be implementing some kind of atom mapping? Cheers Chris > On 22 Oct 2014, at 12:10, Jozsef Csontos jcsontos.lists*o*gmail.com = wrote: >=20 > Dear list members, >=20 > I'd like to hear your opinions. > I'm about to implement a database that contains chemical reactions = (SMILES and SMARTS) with some literature data, like publication date, = journal, authors, and a few properties of them. I'm thinking about a = web service with a few hundred users. > Registered users are able to upload/download and search reactions = based on reactants and/or products, etc. >=20 > I've done some digging and the following setup seems promising: >=20 > a postgresql webserver with the rdkit cartridge and web2py. >=20 > Basically, I've two requirements=20 > 1, every component should be open source and free > 2, the python language is considered to be the glue between them >=20 > Please, share your experience and thoughts; I'm going to summarize and = post them back in this list. >=20 > All the best, >=20 > Jozsef >=20 >=20 --Apple-Mail=_ED6AED43-246B-44CD-9D9D-D013ECEE1FF1 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii Will you effectively only have starting material and product or will you be implementing some kind of atom mapping?

Cheers

Chris
On 22 Oct 2014, at 12:10, Jozsef Csontos jcsontos.lists*o*gmail.com <owner-chemistry^ccl.net> wrote:

Dear list members,

I'd like to hear your opinions.
I'm about to implement a database that contains chemical reactions (SMILES and SMARTS) with some literature data, like publication date, journal, authors, and a few properties of them.  I'm thinking about a web service with a few hundred users.
Registered users are able to upload/download and search reactions based on reactants and/or products, etc.

I've done some digging and the following setup seems promising:

a postgresql webserver with the rdkit cartridge and web2py.

Basically, I've two requirements
1, every component should be open source and free
2, the python language is considered to be the glue between them

Please, share your experience and thoughts; I'm going to summarize and post them back in this list.

All the best,

Jozsef

--Apple-Mail=_ED6AED43-246B-44CD-9D9D-D013ECEE1FF1-- From owner-chemistry@ccl.net Wed Oct 22 14:30:01 2014 From: "James Buchwald buchwj_+_rpi.edu" To: CCL Subject: CCL: reaction database Message-Id: <-50632-141022131552-13021-ov8zyDGw+p7SJkV9dgawtA() server.ccl.net> X-Original-From: James Buchwald Content-Type: multipart/alternative; boundary="------------000705090704070501020906" Date: Wed, 22 Oct 2014 13:15:44 -0400 MIME-Version: 1.0 Sent to CCL by: James Buchwald [buchwj .. rpi.edu] This is a multi-part message in MIME format. --------------000705090704070501020906 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Jozsef, If you're developing a Python-based web interface with the requirement that the backend libraries be open source, you might also consider the Django package. It introduces a model-view architecture that gives you good abstraction and reusability, and you may find development using it to be faster than with other packages. It's fully compatible with Postgre, along with many other database servers. There's also a lot of modular packages already available for it (again open source), including user management (included in the main package), user registration, etc. For these reasons, you may find that Django significantly speeds up your development process. Best, James On 10/22/2014 07:10 AM, Jozsef Csontos jcsontos.lists*o*gmail.com wrote: > Dear list members, > > I'd like to hear your opinions. > I'm about to implement a database that contains chemical reactions > (SMILES and SMARTS) with some literature data, like publication date, > journal, authors, and a few properties of them. I'm thinking about a > web service with a few hundred users. > Registered users are able to upload/download and search reactions > based on reactants and/or products, etc. > > I've done some digging and the following setup seems promising: > > a postgresql webserver with the rdkit cartridge and web2py. > > Basically, I've two requirements > 1, every component should be open source and free > 2, the python language is considered to be the glue between them > > Please, share your experience and thoughts; I'm going to summarize and > post them back in this list. > > All the best, > > Jozsef > > -- James R. Buchwald Graduate Student, Dept. of Chemistry and Chemical Biology Rensselaer Polytechnic Institute Graduate Research Assistant, Dinolfo Laboratory Teaching Assistant, Experimental Chemistry III --------------000705090704070501020906 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Jozsef,

If you're developing a Python-based web interface with the requirement that the backend libraries be open source, you might also consider the Django package.  It introduces a model-view architecture that gives you good abstraction and reusability, and you may find development using it to be faster than with other packages.  It's fully compatible with Postgre, along with many other database servers. 

There's also a lot of modular packages already available for it (again open source), including user management (included in the main package), user registration, etc.  For these reasons, you may find that Django significantly speeds up your development process.

Best,
James

On 10/22/2014 07:10 AM, Jozsef Csontos jcsontos.lists*o*gmail.com wrote:
Dear list members,

I'd like to hear your opinions.
I'm about to implement a database that contains chemical reactions (SMILES and SMARTS) with some literature data, like publication date, journal, authors, and a few properties of them.  I'm thinking about a web service with a few hundred users.
Registered users are able to upload/download and search reactions based on reactants and/or products, etc.

I've done some digging and the following setup seems promising:

a postgresql webserver with the rdkit cartridge and web2py.

Basically, I've two requirements
1, every component should be open source and free
2, the python language is considered to be the glue between them

Please, share your experience and thoughts; I'm going to summarize and post them back in this list.

All the best,

Jozsef


 

-- 
James R. Buchwald
Graduate Student, Dept. of Chemistry and Chemical Biology
Rensselaer Polytechnic Institute
Graduate Research Assistant, Dinolfo Laboratory
Teaching Assistant, Experimental Chemistry III
--------------000705090704070501020906-- From owner-chemistry@ccl.net Wed Oct 22 15:05:01 2014 From: "Susi Lehtola susi.lehtola:alumni.helsinki.fi" To: CCL Subject: CCL: Boys function Message-Id: <-50633-141022133532-19908-bdq0JDAV4heSV8GMhZU1Bw * server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 22 Oct 2014 10:35:20 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola-$-alumni.helsinki.fi] On 10/22/2014 01:59 AM, Georg Lefkidis lefkidis^-^physik.uni-kl.de wrote: > > Sent to CCL by: "Georg Lefkidis" [lefkidis-$-physik.uni-kl.de] > Dear all, > > I am looking for an effective algorithm to calculate the Boys function > (preferably but not necessarily in fortran). Looking into the literature > leaves me more perplexed than helps, every paper says what is not good, but > what to actually do. Can someone give me one paper where the complete > algorithm is listed? I do not need to entirely understand it but to actually > code it. What many codes do is use Taylor expansion, which has been described in Helgaker's book. Here, you pretabulate the function on a grid, and then evaluating the function simplifies to table lookup and interpolation. Now, you still need to get the reference values. As you know, the Boys' function is given by F_m (x) = \int_0^1 t^(2m) e^(-xt^2) dt [1] You can actually show that you can also write it in another form that I've found much easier to work with: F_m (x) = 1/2 x^(-m-1/2) Gamma(m+1/2) gamma(m+1/2; x) [2] where Gamma and gamma are Eulers complete and incomplete gamma functions, respectively, which are available as part of many mathematical function libraries, e.g., the GSL. The library functions are typically accurate to numerical precision, which makes one happy. Naturally eqn [1] doesn't work for small values of x, but for this case you can evaluate the original integral by Taylor expansion to a polynomial that you can integrate analytically. For instance, if x To: CCL Subject: CCL: Boys function Message-Id: <-50634-141022150801-6214-oRX/Z90C31m27zPSkQ0Tgw(!)server.ccl.net> X-Original-From: JC Womack Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Wed, 22 Oct 2014 20:07:50 +0100 MIME-Version: 1.0 Sent to CCL by: JC Womack [jw5533-x-my.bristol.ac.uk] Dear George, Having recently dealt with writing Boys function code myself, I would suggest that the book "Molecular Electronic-Structure Theory" by T. Helgaker, P. Jørgensen & J.Olsen is a good place to start. The book provides a clear account of an efficient method for computationally evaluating the Boys function. As already mentioned, this involves a combination of methods (Taylor expansion, recursion and an asymptotic expression). The relevant section is 9.8, which in my copy is pp.365--367. Hope this helps, James On 22/10/14 09:59, Georg Lefkidis lefkidis^-^physik.uni-kl.de wrote: > Sent to CCL by: "Georg Lefkidis" [lefkidis-$-physik.uni-kl.de] > Dear all, > > I am looking for an effective algorithm to calculate the Boys function > (preferably but not necessarily in fortran). Looking into the literature > leaves me more perplexed than helps, every paper says what is not good, but > what to actually do. Can someone give me one paper where the complete > algorithm is listed? I do not need to entirely understand it but to actually > code it. > > Best regards > George> > -- James C. Womack PhD research student Centre for Computational Chemistry School of Chemistry University of Bristol BRISTOL BS8 1TS Email: jw5533*|*my.bristol.ac.uk Web: http://jcwomack.uk From owner-chemistry@ccl.net Wed Oct 22 18:05:00 2014 From: "Michael Sluydts michael.sluydts|a|ugent.be" To: CCL Subject: CCL: reaction database Message-Id: <-50635-141022163613-1840-ht0dyurEnJR2VyPJHQunJw . server.ccl.net> X-Original-From: Michael Sluydts Content-Type: multipart/alternative; boundary="------------010508020402040809000501" Date: Wed, 22 Oct 2014 22:35:58 +0200 MIME-Version: 1.0 Sent to CCL by: Michael Sluydts [michael.sluydts]_[ugent.be] This is a multi-part message in MIME format. --------------010508020402040809000501 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hey, I may be a bit late in the discussion but I'd recommend using technologies which were designed for websites. The concept seems fairly simple so it would not be too hard to develop it from scratch. I recommend using PHP rather than Python for the code, a MySQL database and for ease of use but a modern layout something based on http://www.initializr.com/ using the twitter bootstrap layout (responds to screen resolution). How to use the layout can be found here: http://getbootstrap.com/components/ . Depending on the needs and ideas I might be able to offer some help/infrastructure if needed. Feel free to send me a direct email if so. Best regards, Michael Sluydts Chris Swain swain%a%mac.com schreef op 22/10/2014 19:53: > Will you effectively only have starting material and product or will > you be implementing some kind of atom mapping? > > Cheers > > Chris >> On 22 Oct 2014, at 12:10, Jozsef Csontos jcsontos.lists*o*gmail.com >> > > wrote: >> >> Dear list members, >> >> I'd like to hear your opinions. >> I'm about to implement a database that contains chemical reactions >> (SMILES and SMARTS) with some literature data, like publication date, >> journal, authors, and a few properties of them. I'm thinking about a >> web service with a few hundred users. >> Registered users are able to upload/download and search reactions >> based on reactants and/or products, etc. >> >> I've done some digging and the following setup seems promising: >> >> a postgresql webserver with the rdkit cartridge and web2py. >> >> Basically, I've two requirements >> 1, every component should be open source and free >> 2, the python language is considered to be the glue between them >> >> Please, share your experience and thoughts; I'm going to summarize >> and post them back in this list. >> >> All the best, >> >> Jozsef >> >> > --------------010508020402040809000501 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Hey,

I may be a bit late in the discussion but I'd recommend using technologies which were designed for websites. The concept seems fairly simple so it would not be too hard to develop it from scratch.

I recommend using PHP rather than Python for the code, a MySQL database and for ease of use but a modern layout something based on http://www.initializr.com/ using the twitter bootstrap layout (responds to screen resolution). How to use the layout can be found here: http://getbootstrap.com/components/ .

Depending on the needs and ideas I might be able to offer some help/infrastructure if needed. Feel free to send me a direct email if so.


Best regards,

Michael Sluydts

Chris Swain swain%a%mac.com schreef op 22/10/2014 19:53:
Will you effectively only have starting material and product or will you be implementing some kind of atom mapping?

Cheers

Chris
On 22 Oct 2014, at 12:10, Jozsef Csontos jcsontos.lists*o*gmail.com <owner-chemistry]-[ccl.net> wrote:

Dear list members,

I'd like to hear your opinions.
I'm about to implement a database that contains chemical reactions (SMILES and SMARTS) with some literature data, like publication date, journal, authors, and a few properties of them.  I'm thinking about a web service with a few hundred users.
Registered users are able to upload/download and search reactions based on reactants and/or products, etc.

I've done some digging and the following setup seems promising:

a postgresql webserver with the rdkit cartridge and web2py.

Basically, I've two requirements
1, every component should be open source and free
2, the python language is considered to be the glue between them

Please, share your experience and thoughts; I'm going to summarize and post them back in this list.

All the best,

Jozsef


--------------010508020402040809000501-- From owner-chemistry@ccl.net Wed Oct 22 18:40:00 2014 From: "Igors Mihailovs igors.mihailovs0!^!gmail.com" To: CCL Subject: CCL:G: Problems with multiple constrains in Gaussian Message-Id: <-50636-141022164725-6441-+Yghi6/82995dVNDTnYIqQ===server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a11c3db00be49620506090dbb Date: Wed, 22 Oct 2014 23:46:58 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0(0)gmail.com] --001a11c3db00be49620506090dbb Content-Type: text/plain; charset=UTF-8 Hello Tobias, I think we have had similar problem to Yours recently. It was connected with ModRedundant keyword which we used for conformational barrier calculations. But line 10 1 2 32 -178.422 S 6 30.000 was read as D 10 1 2 32 -178.4 B So we wrote to Gaussian and here is what they answered. Dear Mr. Mihailovs, > This option was changed in Gaussian 09 Rev. C.01. Unfortunately, it was > not > documented in the release notes. > Now the syntax of "ModRedundant" section is only valid when the value of > the coordinate is not set so it uses the value that corresponds with the > input > geometry. For example: > 10 1 2 32 S 6 30.000 > is accepted but > 10 1 2 32 -178.422 S 6 30.000 > is not accepted in Rev. C.01 and higher. In your example, you will need to > position atoms 10, 1, 2 and 32 at the desired starting dihedral in the > input. > The reason why we removed this option can be demonstrated when one > uses the "Bond", "Angle" and "Dihedral" tools in GaussView. There one > has several modes in which this internal coordinate can be modified, > such as rotating groups, rotating atoms, or keeping one side frozen > but rotating only the other side. The fact that a modification of one > internal coordinate can be done in several different ways underscores > why the "old syntax" of allowing modification of the coordinate value > is problematic. Because of the redundancy of the "redundant internal > coordinates", some internal coordinates could be strongly coupled with > others. Thus, a modification of the value in one internal coordinate might > not be possible without modifying the values of other redundant internal > coordinates, therefore becoming a not well-defined problem because > there could be multiple solutions depending on how many other (and which) > internal coordinates are allowed to be modified and by how much. This > was our motivation for disabling the "old syntax". We understand that > the "old syntax" may have worked for users in many cases before but > we considered that this was not reliable enough to be of general use. > Regards, > Gary W. Trucks, Ph.D. > Gaussian, Inc. So I advise that You consider writing to help|,|gaussian.com in case of strange problems. We did several times, and they were indeed very helpful. Best regards, Igors Mihailovs 2014-10-20 16:11 GMT+03:00 Tobias Schindler tschindl^-^uni-potsdam.de < owner-chemistry|,|ccl.net>: > > Sent to CCL by: "Tobias Schindler" [tschindl[*]uni-potsdam.de] > Hello everybody, > > i got a problem with a geometry optimisation in Gaussian. I want to > optimise a structure while fixing two bond lengths and one dihedral. > Unfortunately Gaussian is not able to fix these parameters. If only the > bond lengths are fixed everything is fine. I used Gaussian 09 D.01. With > older versions everything is fine. > > Best> > > --001a11c3db00be49620506090dbb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello Tobias,

I think we have had simil= ar problem to Yours recently.=C2=A0It was connected with ModRedundant keywo= rd which we used for conformational barrier calculations. But line
=C2=A010 1 2 32 -178.422 S 6 30.000
was read as
<= div>=C2=A0D =C2=A0 =C2=A0 =C2=A010 =C2=A0 =C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2= =A0 2 =C2=A0 =C2=A0 =C2=A032 -178.4 B
So we wrote to Gaussi= an and here is what they answered.

Dear Mr. Mihailovs= ,
This option= was changed in Gaussian 09 Rev. C.01. Unfortunately, it was not=C2=A0
<= /span>documente= d in the release notes.
No= w the syntax of=C2=A0 "ModRedundant" section is only valid when t= he value of=C2=A0
the coordinate is not set so it uses the value that correspond= s with the input=C2=A0
geometry. For example:
10 1 2 32 S 6 30.000<= br>is ac= cepted but
10 1 2 32 -178.422 S 6 30.000
<= /font>is= not accepted in Rev. C.01 and higher. In your example, you will need to=C2= =A0
p= osition atoms 10, 1, 2 and 32 at the desired starting dihedral in the input= .
The reason why we remove= d this option can be demonstrated when one=C2=A0
uses the "Bond", &quo= t;Angle" and "Dihedral" tools in GaussView. There one=C2=A0<= br>has s= everal modes in which this internal coordinate can be modified,=C2=A0
such as ro= tating groups, rotating atoms, or keeping one side frozen=C2=A0
<= span style=3D"font-family:arial,sans-serif;font-size:13px">but rotating onl= y the other side. The fact that a modification of one=C2=A0
internal coordinate = can be done in several different ways underscores=C2=A0
why the "old syntax= " of allowing modification of the coordinate value=C2=A0
is problematic. Be= cause of the redundancy of the "redundant internal=C2=A0
coordinates",= some internal coordinates could be strongly coupled with=C2=A0
<= span style=3D"font-family:arial,sans-serif;font-size:13px">others. Thus, a = modification of the value in one internal coordinate might=C2=A0
= not be possible= without modifying the values of other redundant internal=C2=A0
<= span style=3D"font-family:arial,sans-serif;font-size:13px">coordinates, the= refore becoming a not well-defined problem because=C2=A0
there could be multiple= solutions depending on how many other (and which)=C2=A0
internal coordinates ar= e allowed to be modified and by how much. This=C2=A0
was our motivation for dis= abling the "old syntax". We understand that=C2=A0
the "old syntax= " may have worked for users in many cases before but=C2=A0
<= span style=3D"font-family:arial,sans-serif;font-size:13px">we considered th= at this was not reliable enough to be of general use.
Regards,
Gary W. Trucks, Ph.D.
Gaussian, Inc.

<= span style=3D"font-family:arial,sans-serif;font-size:13px">
=C2=A0So I advise that You consider writing to=C2=A0help|,|gaussian.com=C2=A0in case of= strange problems. We did several times, and they were indeed very helpful.=

Best regards,
Igors = Mihailovs


2014-10-20 16:11 GMT+03:00 Tobias Schindler = tschindl^-^uni-potsdam.de <o= wner-chemistry|,|ccl.net>:
Sent to CCL by: "Tobias=C2=A0 Schindler" [tschindl[*]uni-potsdam.de]
Hello everybody,

i got a problem with a geometry optimisation in Gaussian. I want to optimis= e a structure while fixing two bond lengths and one dihedral. Unfortunately= Gaussian is not able to fix these parameters. If only the bond lengths are= fixed everything is fine. I used Gaussian 09 D.01. With older versions eve= rything is fine.

Best



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--001a11c3db00be49620506090dbb-- From owner-chemistry@ccl.net Wed Oct 22 19:15:00 2014 From: "Soren Eustis soreneustis[A]gmail.com" To: CCL Subject: CCL: reaction database Message-Id: <-50637-141022173934-4978-7pjp8BTBTxeOxGAbQOwm+w]^[server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3496844367_666765" Date: Wed, 22 Oct 2014 17:39:20 -0400 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis/a\gmail.com] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3496844367_666765 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Jozsef, I would also recommend MOLDB5 (http://merian.pch.univie.ac.at/~nhaider/cheminf/moldb5.html). It has a version (MOLDB5R) that handles reactions. I used this program to build a very flexible inventory and data repository. All aspects are open source. It uses MySQL, Perl, and a Java structure search tool. Soren On 10/22/14, 1:15 PM, "James Buchwald buchwj_+_rpi.edu" wrote: Jozsef, If you're developing a Python-based web interface with the requirement that the backend libraries be open source, you might also consider the Django package. It introduces a model-view architecture that gives you good abstraction and reusability, and you may find development using it to be faster than with other packages. It's fully compatible with Postgre, along with many other database servers. There's also a lot of modular packages already available for it (again open source), including user management (included in the main package), user registration, etc. For these reasons, you may find that Django significantly speeds up your development process. Best, James On 10/22/2014 07:10 AM, Jozsef Csontos jcsontos.lists*o*gmail.com wrote: > Dear list members, > > I'd like to hear your opinions. > I'm about to implement a database that contains chemical reactions (SMILES > and SMARTS) with some literature data, like publication date, journal, > authors, and a few properties of them. I'm thinking about a web service with > a few hundred users. > Registered users are able to upload/download and search reactions based on > reactants and/or products, etc. > > I've done some digging and the following setup seems promising: > > a postgresql webserver with the rdkit cartridge and web2py. > > Basically, I've two requirements > 1, every component should be open source and free > 2, the python language is considered to be the glue between them > > Please, share your experience and thoughts; I'm going to summarize and post > them back in this list. > > All the best, > > Jozsef > > > -- James R. Buchwald Graduate Student, Dept. of Chemistry and Chemical Biology Rensselaer Polytechnic Institute Graduate Research Assistant, Dinolfo Laboratory Teaching Assistant, Experimental Chemistry III --B_3496844367_666765 Content-type: text/html; charset="US-ASCII" Content-transfer-encoding: quoted-printable
Jozsef,

I would also recommend MOLDB5 (http://merian.pch.univie.ac.at/~nhaider/cheminf/m= oldb5.html).  It has a version (MOLDB5R) that handles reactions.

I used this program to build a very flexible inventor= y and data repository.  All aspects are open source.  It uses MySQ= L, Perl, and a Java structure search tool.

Soren

On 10/22/14, 1:1= 5 PM, "James Buchwald buchwj_+_rpi.edu" <owner-chemistry(~)ccl.net> wrote:

Jozsef,

If you're developing a Python-based web interface with the requirement that the backend libraries be open source, you might also consider the Django package.  It introduces a model-view architecture that gives you good abstraction and reusability, and you may find development using it to be faster than with other packages.  It's fully compatible with Postgre, along with many oth= er database servers. 

There's also a lot of modular packages already available for it (again open source), including user management (included in the main package), user registration, etc.  For these reasons, you may find= that Django significantly speeds up your development process.

Best,
James

On 10/22/2014 07:10 AM, Jozsef Csontos jcsontos.lists*o*gmail.com wrote:
Dear list members,

I'd like to hear your opinions.
I'm about to implement a database that contains chemical reactions (SMILES and SMARTS) with some literature data, like publication date, journal, authors, and a few properties of them.  I'm thinking about a web service with a few hundred users.
Registered users are able to upload/download and search reactions based on reactants and/or products, etc.

I've done some digging and the following setup seems promising:

a postgresql webserver with the rdkit cartridge and web2py.

Basically, I've two requirements
1, every component should be open source and free
2, the python language is considered to be the glue between them
Please, share your experience and thoughts; I'm going to summarize and post them back in this list.

All the best,

Jozsef


 

-- 
James R. Buchwald
Graduate Student, Dept. of Chemistry and Chemical Biology
Rensselaer Polytechnic Institute
Graduate Research Assistant, Dinolfo Laboratory
Teaching Assistant, Experimental Chemistry III
--B_3496844367_666765--