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ContactStore indexing and definition
Hello
I'm trying to extract all interactions from the ContactStore object. However, the numbers from index1 and index2 do not seem to correspond to the atom numbering from atomStore?
E.g. for PDB 1CRN, some of the indexes are larger than the number of atoms in the protein. Total atom count is 327.
struc.reprList[5].repr.bufferList[0].picking.contacts.contactStore.index1
Int32Array(256) [1, 7, 7, 9, 10, 11, 13, 13, 14, 16, 17, 18, 18, 19, 20, 21, 22, 24, 26, 29, 29, 30, 30, 32, 36, 36, 38, 39, 42, 43, 43, 44, 45, 46, 46, 52, 53, 55, 56, 56, 58, 60, 66, 74, 74, 75, 76, 339, 340, 341, 352, 357, 372, 372, 375, 387, 392, 393, 394, 394, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …]
struc.reprList[5].repr.bufferList[0].picking.contacts.contactStore.index2
Int32Array(256) [2, 182, 124, 91, 90, 122, 135, 195, 150, 88, 87, 92, 93, 94, 96, 97, 99, 100, 101, 163, 105, 163, 108, 106, 103, 160, 112, 113, 114, 116, 115, 119, 166, 120, 119, 121, 144, 119, 81, 139, 77, 78, 132, 82, 91, 145, 89, 359, 415, 349, 390, 365, 378, 380, 398, 390, 413, 415, 411, 401, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …]
struc.reprList[5].repr.bufferList[0].picking.contacts.contactStore.type
Int8Array(256) [1, 8, 10, 4, 4, 10, 10, 8, 8, 10, 4, 10, 4, 10, 10, 10, 10, 10, 10, 8, 10, 8, 4, 10, 4, 8, 10, 10, 10, 10, 4, 4, 8, 10, 4, 4, 8, 4, 10, 8, 10, 4, 10, 10, 4, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …]
Could you enlighten me on how the index number is connected to the atom numbering? Many thanks.
those indices are pointers into
contacts.features
@arose ah, thanks so much for this! It finally makes sense now - some interaction donor contains more than 1 atom.