In Avogadro v1.x, we had a set of common molecular fragments and a crystal library. I used a custom Qt class to give an outline view of the subdirectories with a search form that responded to various names.
The big drawback was that it wasn’t easy (or in some cases possible) to add your own common fragments to the list.
I haven’t used MongoChem much and I’m wondering if the right approach for Avogadro v2 is to have the “insert fragment” to use MongoChem integration. We’d ship with a default database much like we did in v1. The advantage is that the search form could execute more complex queries, since formulas and other properties would be in the Mongo DB.
Users would also be able to add files to MongoChem fairly easily as a personal or group-level repository.
My question is two-fold:
- Should “insert fragment” (which is a fairly common use case) require MongoChem
- Does MongoChem support having a custom hierarchy - that is, can we easily categorize 2-3 levels of files?
I guess a minor question is CIF vs. non-crystalline files, but that seems like an easy filter.
-Geoff
Sorry about the delay, too much work travel…
On Fri, Jun 5, 2015 at 12:50 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:
In Avogadro v1.x, we had a set of common molecular fragments and a crystal library. I used a custom Qt class to give an outline view of the subdirectories with a search form that responded to various names.
The big drawback was that it wasn’t easy (or in some cases possible) to add your own common fragments to the list.
I haven’t used MongoChem much and I’m wondering if the right approach for Avogadro v2 is to have the “insert fragment” to use MongoChem integration. We’d ship with a default database much like we did in v1. The advantage is that the search form could execute more complex queries, since formulas and other properties would be in the Mongo DB.
Would we want to add a dependence on MongoDB? I had spoken with Peter
about this, and wondered about using CML (or our JSON format) to store
fragments along with other useful metadata, reading those in and
querying them.
Users would also be able to add files to MongoChem fairly easily as a personal or group-level repository.
My question is two-fold:
- Should “insert fragment” (which is a fairly common use case) require MongoChem
Seems a little heavy, if we offered this I wonder if something simpler
in addition (that perhaps was harder to edit, but easier to
distribute) might be appropriate.
- Does MongoChem support having a custom hierarchy - that is, can we easily categorize 2-3 levels of files?
No, could be added, but it wasn’t there.
Marcus