divelab/DIG

Type of atoms

YanjingLiLi opened this issue · 6 comments

YanjingLiLi commented

I am wondering where I can find a detailed description of the atom types here in the get_atom_pos function in
https://github.com/divelab/DIG/blob/dig-stable/dig/threedgraph/dataset/FOLDdataset.py:

N, CA, CB, _G/_G1, _D/_D1, _E/_E1, _Z, NH1

limei0307 commented

Hi @YanjingLiLi, the get_atom_pos function here only get the coordinates of atoms that are used to compute side chain torsion angles. Specifically, the atoms for side chain torsion angle computation are listed in Table 7 of our paper.
N, CA, CB, _G/_G1, _D/_D1, _E/_E1, _Z, NH1: A means alpha, B means beta, G means gamma, D means delta, E means epsilon, Z means zeta, and H means eta.

Thanks.

YanjingLiLi commented

In your code, you have pos_n, pos_ca, pos_c, pos_cb, what is c here, if ca is carbon alpha, cb is carbon beta?

limei0307 commented

Yes. c means carbon, n means nitrogen, and o means oxygen.

YanjingLiLi commented

Thanks! But I am wondering what is pos_c mean here since it doesn't have any index. (pos_ca is for alpha carbon, pos_cb is for beta carbon)

limei0307 commented

Hi, pos_c is another carbon atom in an amino acid (the c in the -COOH group).

YanjingLiLi commented

Get it. Thanks.