Support for hierarchical biomolecular fields #396
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…o store biomolecular data.
JPBergsma
commented
Dec 29, 2021
| group_type | ||
| ~~~~~~~~~~ | ||
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| - **Description**: For each type of chemical group/molecule in the system there is a dictionary that describes this group/molecule. |
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Do we want to have some way of indicating that a group is at the top level, i.e. that it is a molecule and not a subgroup?
JPBergsma
commented
Dec 29, 2021
| - **name**: REQUIRED; The name of the group_type; | ||
| - The **name** value MUST be unique in the :property:`group_types` list. | ||
| - Strings of 3 characters or less MUST match the strings belonging to this group as defined by wwPDB at `<ftp://ftp.wwpdb.org/pub/pdb/data/monomers>`_. | ||
| - **molecular_formula**: OPTIONAL; The molecular formula of the molecule/group described in this group type. |
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In the list of groups of wwPDB, the groups are described without taking any bonding to other groups into account. When amino acids are polymerized, each amino acid loses a water molecule.
I am therefore wondering whether I should have different group types for bound and unbound amino acids. In the list of wwPDB there is however just one entry for each type of amino acid.
For now, I am still wondering about how to handle this case.
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This is the second option on how to include biomolecular data within Optimade. It is the second option that is discussed in issue #389. The first option is described in PR #395.
It introduces a
group_typethat represents kinds of molecules or groups of groups and sites.A group of groups is for example a protein, here the individual amino acids are the subgroups of the much larger protein strand.
Properties that are specific for a particular molecule or group of atoms, such as a molecular formula or a mass, can be stored here.
The
groupsproperty is introduced to describe instances of these group_types, i.e. a particular molecule or chemical group.This gives a "top down" data structure, the groups know which atoms belong to the group, but the atoms do not know to which group they belong. I do not think this is a problem, as the client can easily reconstruct this information. If necessary, we could also add a property for each site that describes to which groups the sites belong.
It would be nice if you could tell me which method you prefer, the one described here or the one described in PR #395, and any other remarks about these the options are of course also welcome.
For now, I have placed these fields in the appendix, as I am not sure whether they will be used by many OPTIMADE providers.
They can be moved to the structures section if you think they are general enough.