RNA graph construction and KNN representation about graphein HOT 4 CLOSED

Hey, thanks for this Ryan! Looks exciting!

So, I think we should keep RNA secondary structure & 3D structure separate for now. The secondary structure is functional as a standalone piece of functionality (though it would be really nice to hook it up to Nussinov or bpRNA - the largest database I know of).

With respect to 3D graphs - I had a quick look at this. I think it's actually quite straightforward as most of the components are implemented for protein structure graphs. Essentially, we can use the low-level API in graphein as building blocks and make a function more or less identical to the construct_graphs we use for proteins. The main things I saw so far that need changing:

We need some granularity options for RNA graphs

Then, we simply add a new function convert_structure_to_rna in this block eg.

RNA_ATOMS = [
    "C1'",
    "C2",
    "C2'",
    "C3'",
    "C4",
    "C4'",
    "C5",
    "C5'",
    "C6",
    "C8",
    "N1",
    "N2",
    "N3",
    "N4",
    "N6",
    "N7",
    "N9",
    "O2",
    "O2'",
    "O3'",
    "O4",
    "O4'",
    "O5'",
    "O6",
    "OP1",
    "OP2",
    "P",
]


def subset_structure_to_rna(
    df: pd.DataFrame,
) -> pd.DataFrame:
    """
    Return a subset of atomic dataframe that contains only certain atom names relevant for RNA structures.

    :param df: Protein Structure dataframe to subset
    :type df: pd.DataFrame
    :returns: Subsetted protein structure dataframe
    :rtype: pd.DataFrame
    """
    return filter_dataframe(
        df, by_column="atom_name", list_of_values=RNA_ATOMS, boolean=True
    )

but more flexible (not keeping the RNA_ATOMS fixed so users can subset as they wish)

The only other line that breaks is this one and we easily fix it by removing the three_to_1 call if we're constructing an RNA graph. Then we're good to go essentially. The graph has been populated with the nodes and we write whatever edge functions we like to go on top as per the protein API.

What I'm unfamiliar with is how we coarsen the RNA graphs. E.g. all atom is what I've described above. For proteins it's obviously very normal to consider the alpha carbon trace as representative of a residue-level graph. I'm not sure what the standard for RNA is. In any case, we can leave this open to users with the granularity param. What do you think?

from graphein.

Implemented in 1.5.0

from graphein.

Came across this today: https://www.biorxiv.org/content/10.1101/2022.03.14.484334v1

Might be of interest to you @rg314

from graphein.

Just to follow up on this... we found that the nussinov.py algo isn't great at predicting the dot-bracket notation. I suggest that we create a container running https://github.com/rg314/centroid-rna-package and ping it to get the centroid secondary structure. What do you think @a-r-j ?

from graphein.