From owner-chemistry@ccl.net Fri Mar 11 13:07:00 2022 From: "Peter Jarowski p.jarowski_._chemalive.com" To: CCL Subject: CCL: ConstruQt-API Alpha Message-Id: <-54626-220311120305-8651-3C5naArYriOXZuSTbGWAww~!~server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary="0000000000009aba3105d9f44c04" Date: Fri, 11 Mar 2022 18:02:33 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [p.jarowski .. chemalive.com] --0000000000009aba3105d9f44c04 Content-Type: text/plain; charset="UTF-8" Dear CCL Community: We are launching the alpha version of our ConstruQt-API and we are inviting CCL subscribers to try it out and tell us when things go wrong or are difficult to understand. ConstruQt is a high throughput cloud software for deploying quantum mechanics (QM) calculations at scale (up to 10,000 molecules per query). Here is more info (go to bottom to download api-docs): https://www.chemalive.com/construqt/ Accessible as a web-API using JSON-RPC, the core engine is a wrapper for a number of open source softwares and libraries (openbabel, RDkit, Nwchem, Cp2k and Gromacs) built over a management and pipeline architecture within a Spark context. The motivation of ConstruQt is to displace classical mechanics approaches to structural chemistry by providing a framework to scale more accurate QM calculations and leverage their predicted energies to prune and prioritize accessible tautomeric, stereoisomeric, protomeric and conformational structures. Thus, from SMILES designation, one can scale structural analysis with a reliable tool having low latency, robust error management, quality control and data storage / look-up. We operate under the principle - know your molecules better. Here are some details about how you can get started submitting and reading quantum chemical results with our API. Firstly, here is the apikey I have assigned to CCL: 56zzA19mxc44faa3 To use this apikey execute a curl command from a csh or bash terminal as follows: curl -d '{"id": "0", "method": "read", "params": {"apiKey": "56zzA19mxc44faa3", "substances": ["Brc1ccc2c(c1)ncs2"], "procedure": "UFF-PM6", "sdf": true, "allTautomers": true, "allConformers": true, "allZwittomers": false, "allProtomers": false, "allDiastereomers": false}, "jsonrpc": "2.0"}' -H "Content-Type: application/json-rpc" -X POST https://api.chemalive.com This command can be readily integrated into a bash script. As written, it will read all the PM6 data for molecule Brc1ccc2c(c1)ncs2 on all its enumerated tautomers with all associated conformers and return the structural data in sdf format as a blob (Hint: pipe it into: sed 's/\\n/\n/g' to get a readable text file). The corollary to this call uses the submit method to request a calculation. curl -d '{"id": "0", "method": "submit", "params": {"apiKey": "56zzA19mxc44faa3", "substances": ["Brc1ccc2c(c1)ncs2"], "procedure": "UFF-PM6", "sdf": true, "allTautomers": true, "allConformers": true, "allZwittomers": false, "allProtomers": false, "allDiastereomers": false}, "jsonrpc": "2.0"}' -H "Content-Type: application/json-rpc" -X POST https://api.chemalive.com This call returns the status for the molecule, submitted, running, exists, failed. So in general, one submits a request and later on will read the results. If you would like a python script just get in touch at info() chemalive.com or for any other question, comments or help Your API key entitles you to run single-point DFT. For example you could deploy the following procedure: UFF-PM6-B3LYP-SP This means ConstruQt will generate initial guesses with the UFF molecular mechanics force field, refine them with semi-empirical PM6 optimization and thermal correction and then will compute the B3LYP single-point on top (default basis is 6-31+g(d)). UFF-PM6-B3LYP-SP-D (with D3 dispersion) UFF-PM6-B3LYP-SP-WATER (with PCM solvent modeling) Here are some more that are currently available UFF-PM6-PBE0-SP UFF-PM6-PBE91-SP UFF-PM6-PW91-SP UFF-PM6-BECKEHANDH-SP UFF-PM6-BLYP-SP UFF-PM6-BHLYP-SP (add 'D' or 'WATER' as needed) If you would like another method or procedure, just ask. We can implement whatever Nwchem can do. We can optimize and frequency correct with ab initio, predict NMR tensors, IR spectra and do TDDFT. It would be great if you could alert us to any issues so we can finalize the launch of this software. Thanks for your time. Best regards, Peter p.s. sdf format is tested with Avogadro (openbabel) and JMol. If you have formatting issues because you use proprietary software we do not have access to, please let us know and we can try to align. *security note: CAREFUL: While the ConstruQt database is not substructure searchable, please be advised that the software does not guarantee the molecules you enter can not be viewed by others assuming that they query the exact same molecule. In this event that molecule is not really a secret anyway. All meta data is private and secure. -- Peter Jarowski, Ph. D. CEO / Co-founder ChemAlive SA - Quantum Chemistry for All Twitter: () SAChemAlive LinkedIn: https://www.linkedin.com/company/chemalive-sa/ Web: http://www.chemalive.com Try our Interface: https://www.app.chemalive.com MassChallenge Switzerland Gold Winners Stage 3 Climate-KIC Winners --0000000000009aba3105d9f44c04 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dea= r CCL Community:

We are launching the alpha v= ersion of=C2=A0 our ConstruQt-API and we are inviting CCL subscribers to tr= y it out and tell us when things go wrong or are difficult to understand.

ConstruQt is a high th= roughput cloud software for deploying quantum mechanics=20 (QM) calculations at scale (up to 10,000 molecules per query). Here is more= info (go to bottom to download api-docs):

https://= www.chemalive.com/construqt/

Accessible as a web-API using JSON-RPC, the core engine is a wrappe= r for a number of open source softwares and libraries (openbabel, RDkit, Nw= chem, Cp2k and Gromacs) built over a=C2=A0 management and pipeline architec= ture within a Spark context.

The motivation of ConstruQt is to displace classical mechanics approach= es to structural chemistry by providing a framework to scale more accurate = QM calculations and leverage their predicted energies to prune and prioriti= ze accessible tautomeric, stereoisomeric, protomeric and conformational str= uctures. Thus, from SMILES designation, one can scale structural analysis w= ith a reliable tool having low latency, robust error management, quality co= ntrol and=20 data storage / look-up. We operate under the principle - know your molecule= s better.

<= /div>Here are some details about how you can get started submitting and rea= ding quantum chemical results with our API.

Firstly, here is the apikey I have assigned to CCL:
<= div class=3D"gmail_default" style=3D"font-size:small">
56zzA19mxc44faa3

To use this apikey execute a curl comm= and from a csh or bash terminal as follows:

curl -d '{"id": "0", "method": "read", "params": {"apiKey": "56zzA19mxc44faa3", "substances": ["Brc1ccc2c(c1)ncs2"], "procedure": "UFF-PM6", "sdf": true, "al= lTautomers": true, "allConformers&= quot;: true, "allZwittomers": fals= e, "allProtomers": false, "allDiastereomers": false}, "jsonrpc": "2.0"}' -H "Content-Type: application/json-rpc" -X POST https://api.chemalive.com


This command can be read= ily integrated into a bash script. As written, it will read all the PM6 dat= a for molecule Brc1ccc2c(c1)ncs2 on all its enumerated tautomers with all associated conformers and=20 return the structural data in sdf format as a blob (Hint: pipe it into: sed= =C2=A0's/\\n/\n/g' to get a readable text file).
<= div style=3D"font-size:small" class=3D"gmail_default">
The corollary to this call uses the s= ubmit method to request a calculation.

curl -d '{"id": "0", "method": "submit", "params": {"apiKey": "56zzA19mxc44faa3", "substances": ["Brc1ccc2c(c1)ncs2"], "procedure": "UFF-PM6", "sdf": true, "al= lTautomers": true, "allConformers&= quot;: true, "allZwittomers": fals= e, "allProtomers": false, "allDiastereomers": false}, "jsonrpc": "2.0"}' -H "Content-Type: application/json-rpc" -X POST https://api.chemalive.com


This call returns the status for the molecule, submitted, running, exists, failed. So in general, one submits a request and later on will read the=20 results.
= If you would like a python script just get in touch at info() chemalive.com or for any other= question, comments or help

Your API key entitles you to run single-point DFT. For e= xample you could deploy the following procedure:

UFF-PM6-B3LYP-SP

This means ConstruQt will generate initial guesses with the= UFF molecular mechanics force field, refine them with semi-empirical PM6 o= ptimization and thermal correction and then will compute the B3LYP single-p= oint on top (default basis is 6-31+g(d)).

UFF-PM6-B3LYP-SP-D (with D3 dispersion)
UFF-PM6-B3LYP-SP-WATER (with = PCM solvent modeling)

Here are some more that are currently available
UFF-PM6-PBE0-SP
UFF-PM6-PBE91-SP
UFF-PM6-PW91-SP
UFF-PM6-BECKEHANDH-SP
UFF-PM6-BLYP-SP
UFF-PM6-BHLYP-SP
(add 'D' or = 9;WATER' as needed)

If you would like another method or procedure, just ask. We can implemen= t whatever Nwchem can do. We can optimize and frequency correct with ab ini= tio, predict NMR tensors, IR spectra and do TDDFT. It would be great if you= could alert us to any issues so we can finalize the launch of this softwar= e. Thanks for your time.

Best regards,

Peter

p.s. sdf format is tested with Avogadro (openbabel) and JMol. If you have=20 formatting issues because you use proprietary software we do not have=20 access to, please let us know and we can try to align.
=
*secu= rity note: CAREFUL:=C2=A0 While the ConstruQt database is not substructure=20 searchable, please be advised that the software does not guarantee the molecules you enter can not be viewed by others=20 assuming=20 that they query the exact same molecule. In this event that molecule is=20 not really a secret anyway. All meta data is private and secure.

--
=
Peter Jarowski, Ph. D.
CEO / Co-founder
ChemAliv= e SA - Quantum Chemistry for All

LinkedIn: https://www.linkedin.com/company/chemalive-sa/

Try our In= terface: https://= www.app.chemalive.com

<= /div>
= Stage 3 Climate-K= IC Winners
--0000000000009aba3105d9f44c04--