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Training set for RosettaFold/MPNN etc.
Each PDB entry is represented as a collection of .pt files:
PDBID_CHAINID.pt - contains CHAINID chain from PDBID
PDBID.pt - metadata and information on biological assemblies
PDBID_CHAINID.pt has the following fields:
seq - amino acid sequence (string)
xyz - atomic coordinates [L,14,3]
mask - boolean mask [L,14]
bfac - temperature factors [L,14]
occ - occupancy [L,14] (is 1 for most atoms, <1 if alternative conformations are present)
PDBID.pt:
method - experimental method (str)
date - deposition date (str)
resolution - resolution (float)
chains - list of CHAINIDs (there is a corresponding PDBID_CHAINID.pt file for each of these)
tm - pairwise similarity between chains (TM-score,seq.id.,rmsd from TM-align) [num_chains,num_chains,3]
asmb_ids - biounit IDs as in the PDB (list of str)
asmb_details - how the assembly was identified: author, or software, or smth else (list of str)
asmb_method - PISA or smth else (list of str)
asmb_chains - list of chains which each biounit is composed of (list of str, each str contains comma separated CHAINIDs)
asmb_xformIDX - (one per biounit) xforms to be applied to chains from asmb_chains[IDX], [n,4,4]
[n,:3,:3] - rotation matrices
[n,3,:3] - translation vectors
list.csv:
CHAINID - chain label, PDBID_CHAINID
DEPOSITION - deposition date
RESOLUTION - structure resolution
HASH - unique 6-digit hash for the sequence
CLUSTER - sequence cluster the chain belongs to (clusters were generated at seqID=30%)
SEQUENCE - reference amino acid sequence
valid_clusters.txt - clusters used for validation
test_clusters.txt - clusters used for testing
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