#200 Support for the MaterialsProject

open
Bob Hanson
5
2013-12-04
2013-01-27
Shyue Ping Ong
No

Hi there,

I would like to request for support for the Materials Project (www.materialsproject.org) to be built into Jmol, similar to the current support for PDB. The Materials Project is an initiative to make publicly available the computed data of all known inorganic compounds. Today, it already has more than 30,000 compounds in the database. CIF files from the materials project can be obtained by the following url form:

www.materialsproject.org/materials/{material_id}/cif

where {material_id} is an integer identifier.

Related

Feature Requests: #200

Discussion

  • Bob Hanson
    Bob Hanson
    2013-01-28

    superb idea! I have checked in:

    load =mp/id

    for example:

    load =mp/547211

    What about searching? Is there a REST-like interface for searching the MaterialsProject?

     
  • Bob Hanson
    Bob Hanson
    2013-09-01

    Shyue Ping Ong,

    I would like to do some more with this. Are you still interested?

    I note that load =mp/547211

    no longer works with Java 1.7 because there is a but in Java 1.7. Could you please allow http access instead of https? There seems to be no good reason for https as far as I can tell.

    I was going to present this to a group tomorrow, but I can't because of that. We need to look more into how to integrate this into Jmol.

    Bob

     
  • Shyue Ping Ong
    Shyue Ping Ong
    2013-09-02

    Hi Bob,

    The Materials Project recently switched form using int ids to string ids. THe reason is that we are planning ahead to support user sandboxes where the ids will also indicate which sandbox a structure belongs to.

    The url is now https://www.materialsproject.org/materials/mp-66/cif

    The reason why we use https is because for a lot of the REST API, we need the user to supply an API key. I am not sure if I can switch it to http. I do know that Java does support https, but it does require more setup. I google this: http://radu.cotescu.com/java-https-rest-services-apache-cxf/

    Regards,
    Shyue Ping

    On Sunday, September 1, 2013 at 2:15 PM, Bob Hanson wrote:

    Shyue Ping Ong,
    I would like to do some more with this. Are you still interested?
    I note that load =mp/547211
    no longer works with Java 1.7 because there is a but in Java 1.7. Could you please allow http access instead of https? There seems to be no good reason for https as far as I can tell.
    I was going to present this to a group tomorrow, but I can't because of that. We need to look more into how to integrate this into Jmol.
    Bob
    [feature-requests:#200] (http://sourceforge.net/p/jmol/feature-requests/200/) Support for the MaterialsProject
    Status: open
    Labels: New IO Format
    Created: Sun Jan 27, 2013 11:53 PM UTC by Shyue Ping Ong
    Last Updated: Sun Jan 27, 2013 11:53 PM UTC
    Owner: Bob Hanson
    Hi there,
    I would like to request for support for the Materials Project (www.materialsproject.org (http://www.materialsproject.org)) to be built into Jmol, similar to the current support for PDB. The Materials Project is an initiative to make publicly available the computed data of all known inorganic compounds. Today, it already has more than 30,000 compounds in the database. CIF files from the materials project can be obtained by the following url form:
    www.materialsproject.org/materials/{material_id}/cif (http://www.materialsproject.org/materials/{material_id}/cif)
    where {material_id} is an integer identifier.
    Sent from sourceforge.net (http://sourceforge.net) because you indicated interest in https://sourceforge.net/p/jmol/feature-requests/200/
    To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

     

    Related

    Feature Requests: #200

  • Bob Hanson
    Bob Hanson
    2013-09-02

    I saw the change to string ID; that's not the issue. It's https and the fact that your server is sending a warning that Java 1.7 is flagging as an error instead of a warning and shutting down the connection. Here's the problem, I think. Something with your server:

    http://stackoverflow.com/questions/7615645/ssl-handshake-alert-unrecognized-name-error-since-upgrade-to-java-1-7-0

    If you are going to require user log in for the REST API, there's nothing that we can do with it in Jmol, sorry. If that's the case, I think I should remove the =mp/ short-cut. It doesn't really help, because if you have the ID already, users might as well add https://www.materialsproject.org/materials/ themselves. I suppose one might know the ID, but it's not like PDB IDs, I think. And if you can't search to get information about IDs using Jmol the way you can at RCSB, then that seems not that useful. (But I think you can, because I did.)

    Perhaps you can consider changing your position on that.

    Feel free to give reasons to keep it.

    Bob

     
  • Shyue Ping Ong
    Shyue Ping Ong
    2013-09-02

    Hi Bob,

    Let me discuss this with my colleagues at the Materials Project. You can indeed search for information about ids using the REST interface. For example,

    https://www.materialsproject.org/rest/v1/materials/Fe2O3/mids

    Returns all the ids with a formula of Fe2O3.

    We don't need https for a lot of operations, just those that require an API key (e.g., we also allow people to submit structures to be computed via the Materials Project, but since that eats up compute time, we'd like a way to track back submissions to the actual user). I can try to see if we can allow non-SSL for the operations that do not require an API key, which is most of the basic functions.

    Regards,
    Shyue Ping

    On Monday, September 2, 2013 at 2:38 PM, Bob Hanson wrote:

    I saw the change to string ID; that's not the issue. It's https and the fact that your server is sending a warning that Java 1.7 is flagging as an error instead of a warning and shutting down the connection. Here's the problem, I think. Something with your server:
    http://stackoverflow.com/questions/7615645/ssl-handshake-alert-unrecognized-name-error-since-upgrade-to-java-1-7-0
    If you are going to require user log in for the REST API, there's nothing that we can do with it in Jmol, sorry. If that's the case, I think I should remove the =mp/ short-cut. It doesn't really help, because if you have the ID already, users might as well add https://www.materialsproject.org/materials/ themselves. I suppose one might know the ID, but it's not like PDB IDs, I think. And if you can't search to get information about IDs using Jmol the way you can at RCSB, then that seems not that useful. (But I think you can, because I did.)
    Perhaps you can consider changing your position on that.
    Feel free to give reasons to keep it.
    Bob
    [feature-requests:#200] (http://sourceforge.net/p/jmol/feature-requests/200/) Support for the MaterialsProject
    Status: open
    Labels: New IO Format
    Created: Sun Jan 27, 2013 11:53 PM UTC by Shyue Ping Ong
    Last Updated: Sun Sep 01, 2013 09:15 PM UTC
    Owner: Bob Hanson
    Hi there,
    I would like to request for support for the Materials Project (www.materialsproject.org (http://www.materialsproject.org)) to be built into Jmol, similar to the current support for PDB. The Materials Project is an initiative to make publicly available the computed data of all known inorganic compounds. Today, it already has more than 30,000 compounds in the database. CIF files from the materials project can be obtained by the following url form:
    www.materialsproject.org/materials/{material_id}/cif (http://www.materialsproject.org/materials/{material_id}/cif)
    where {material_id} is an integer identifier.
    Sent from sourceforge.net (http://sourceforge.net) because you indicated interest in https://sourceforge.net/p/jmol/feature-requests/200/
    To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

     

    Related

    Feature Requests: #200

    • Shyue Ping Ong
      Shyue Ping Ong
      2013-12-04

      Hi Bob,

      Sorry for the delay in getting back to you. It took some time to get all the security stuff settled.

      We have removed the requirement for https for the API calls that do not require a user’s API key. These are the key functions that you may be interested in.

      http://materialsproject.org/rest/v1/materials/formulas - provides a list of all formulas available in the Materials Project

      http://materialsproject.org/rest/v1/materials/Fe2O3/mids - provides a list of all material ids related to a specific formula.

      http://materialsproject.org/rest/v1/materials/mp-24972/cif - provides the CIF for a specific material id. We provide three CIFs - Primitive, Refined, and Conventional Standard. This is because people may want different ones depending on what they are doing. For visualization, the Conventional_standard is typically what people are used to. The Primitive version (if different) is usually for electronic structure calculations when you want to minimize the number of atoms.

      Please let me know if there are any other clarifications needed.

      Regards,
      Shyue Ping

      On Monday, September 2, 2013 at 14:49, Shyue Ping Ong wrote:

      Hi Bob,

      Let me discuss this with my colleagues at the Materials Project. You can indeed search for information about ids using the REST interface. For example,

      https://www.materialsproject.org/rest/v1/materials/Fe2O3/mids

      Returns all the ids with a formula of Fe2O3.

      We don't need https for a lot of operations, just those that require an API key (e.g., we also allow people to submit structures to be computed via the Materials Project, but since that eats up compute time, we'd like a way to track back submissions to the actual user). I can try to see if we can allow non-SSL for the operations that do not require an API key, which is most of the basic functions.

      Regards,
      Shyue Ping

      On Monday, September 2, 2013 at 2:38 PM, Bob Hanson wrote:

      I saw the change to string ID; that's not the issue. It's https and the fact that your server is sending a warning that Java 1.7 is flagging as an error instead of a warning and shutting down the connection. Here's the problem, I think. Something with your server:
      http://stackoverflow.com/questions/7615645/ssl-handshake-alert-unrecognized-name-error-since-upgrade-to-java-1-7-0
      If you are going to require user log in for the REST API, there's nothing that we can do with it in Jmol, sorry. If that's the case, I think I should remove the =mp/ short-cut. It doesn't really help, because if you have the ID already, users might as well add https://www.materialsproject.org/materials/ themselves. I suppose one might know the ID, but it's not like PDB IDs, I think. And if you can't search to get information about IDs using Jmol the way you can at RCSB, then that seems not that useful. (But I think you can, because I did.)
      Perhaps you can consider changing your position on that.
      Feel free to give reasons to keep it.
      Bob
      [feature-requests:#200] (http://sourceforge.net/p/jmol/feature-requests/200/) Support for the MaterialsProject
      Status: open
      Labels: New IO Format
      Created: Sun Jan 27, 2013 11:53 PM UTC by Shyue Ping Ong
      Last Updated: Sun Sep 01, 2013 09:15 PM UTC
      Owner: Bob Hanson
      Hi there,
      I would like to request for support for the Materials Project (www.materialsproject.org (http://www.materialsproject.org)) to be built into Jmol, similar to the current support for PDB. The Materials Project is an initiative to make publicly available the computed data of all known inorganic compounds. Today, it already has more than 30,000 compounds in the database. CIF files from the materials project can be obtained by the following url form:
      www.materialsproject.org/materials/{material_id}/cif (http://www.materialsproject.org/materials/{material_id}/cif)
      where {material_id} is an integer identifier.
      Sent from sourceforge.net (http://sourceforge.net) because you indicated interest in https://sourceforge.net/p/jmol/feature-requests/200/
      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Feature Requests: #200

  • Bob Hanson
    Bob Hanson
    2013-12-04

    Send me some examples of the sorts of Jmol scripting that you would imagine, and we can go from there.