molstar
Version:
A comprehensive macromolecular library.
130 lines • 6.57 kB
JavaScript
;
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.addAnisotropic = exports.getAnisotropic = exports.getAnisotropicTemplate = void 0;
var cif_1 = require("../../../mol-io/reader/cif");
var tokenizer_1 = require("../../../mol-io/reader/common/text/tokenizer");
var util_1 = require("../util");
var number_parser_1 = require("../../../mol-io/reader/common/text/number-parser");
function getAnisotropicTemplate(data, count) {
var str = function () { return []; };
var float = function () { return new Float32Array(count); };
var ts = function () { return tokenizer_1.TokenBuilder.create(data, 2 * count); };
return {
index: 0,
count: count,
id: str(),
type_symbol: ts(),
pdbx_label_atom_id: ts(),
pdbx_label_alt_id: ts(),
pdbx_label_comp_id: ts(),
pdbx_label_asym_id: ts(),
pdbx_label_seq_id: ts(),
pdbx_PDB_ins_code: ts(),
'U[1][1]': float(),
'U[2][2]': float(),
'U[3][3]': float(),
'U[1][2]': float(),
'U[1][3]': float(),
'U[2][3]': float(),
pdbx_auth_seq_id: ts(),
pdbx_auth_comp_id: ts(),
pdbx_auth_asym_id: ts(),
pdbx_auth_atom_id: ts(),
};
}
exports.getAnisotropicTemplate = getAnisotropicTemplate;
function getAnisotropic(sites) {
var pdbx_auth_seq_id = cif_1.CifField.ofTokens(sites.pdbx_auth_seq_id);
var pdbx_auth_comp_id = cif_1.CifField.ofTokens(sites.pdbx_auth_comp_id);
var pdbx_auth_asym_id = cif_1.CifField.ofTokens(sites.pdbx_auth_asym_id);
var pdbx_auth_atom_id = cif_1.CifField.ofTokens(sites.pdbx_auth_atom_id);
var fields = {
id: cif_1.CifField.ofStrings(sites.id),
type_symbol: cif_1.CifField.ofTokens(sites.type_symbol),
pdbx_label_atom_id: pdbx_auth_atom_id,
pdbx_label_alt_id: cif_1.CifField.ofTokens(sites.pdbx_label_alt_id),
pdbx_label_comp_id: pdbx_auth_comp_id,
pdbx_label_asym_id: pdbx_auth_asym_id,
pdbx_label_seq_id: pdbx_auth_seq_id,
pdbx_PDB_ins_code: cif_1.CifField.ofTokens(sites.pdbx_PDB_ins_code),
pdbx_auth_seq_id: pdbx_auth_seq_id,
pdbx_auth_comp_id: pdbx_auth_comp_id,
pdbx_auth_asym_id: pdbx_auth_asym_id,
pdbx_auth_atom_id: pdbx_auth_atom_id,
};
fields['U[1][1]'] = cif_1.CifField.ofNumbers(sites['U[1][1]']);
fields['U[2][2]'] = cif_1.CifField.ofNumbers(sites['U[2][2]']);
fields['U[3][3]'] = cif_1.CifField.ofNumbers(sites['U[3][3]']);
fields['U[1][2]'] = cif_1.CifField.ofNumbers(sites['U[1][2]']);
fields['U[1][3]'] = cif_1.CifField.ofNumbers(sites['U[1][3]']);
fields['U[2][3]'] = cif_1.CifField.ofNumbers(sites['U[2][3]']);
return fields;
}
exports.getAnisotropic = getAnisotropic;
function addAnisotropic(sites, model, data, s, e) {
var str = data.data;
var length = e - s;
// COLUMNS DATA TYPE FIELD DEFINITION
// -----------------------------------------------------------------
// 1 - 6 Record name "ANISOU"
// 7 - 11 Integer serial Atom serial number.
tokenizer_1.Tokenizer.trim(data, s + 6, s + 11);
sites.id[sites.index] = str.substring(data.tokenStart, data.tokenEnd);
// 13 - 16 Atom name Atom name.
tokenizer_1.TokenBuilder.addToken(sites.pdbx_auth_atom_id, tokenizer_1.Tokenizer.trim(data, s + 12, s + 16));
// 17 Character altLoc Alternate location indicator
if (str.charCodeAt(s + 16) === 32) { // ' '
tokenizer_1.TokenBuilder.add(sites.pdbx_label_alt_id, 0, 0);
}
else {
tokenizer_1.TokenBuilder.add(sites.pdbx_label_alt_id, s + 16, s + 17);
}
// 18 - 20 Residue name resName Residue name.
tokenizer_1.TokenBuilder.addToken(sites.pdbx_auth_comp_id, tokenizer_1.Tokenizer.trim(data, s + 17, s + 20));
// 22 Character chainID Chain identifier.
tokenizer_1.TokenBuilder.add(sites.pdbx_auth_asym_id, s + 21, s + 22);
// 23 - 26 Integer resSeq Residue sequence number.
tokenizer_1.TokenBuilder.addToken(sites.pdbx_auth_seq_id, tokenizer_1.Tokenizer.trim(data, s + 22, s + 26));
// 27 AChar iCode Insertion code.
if (str.charCodeAt(s + 26) === 32) { // ' '
tokenizer_1.TokenBuilder.add(sites.pdbx_PDB_ins_code, 0, 0);
}
else {
tokenizer_1.TokenBuilder.add(sites.pdbx_PDB_ins_code, s + 26, s + 27);
}
// 29 - 35 Integer u[0][0] U(1,1)
sites['U[1][1]'][sites.index] = (0, number_parser_1.parseIntSkipLeadingWhitespace)(str, s + 28, s + 35) / 10000;
// 36 - 42 Integer u[1][1] U(2,2)
sites['U[2][2]'][sites.index] = (0, number_parser_1.parseIntSkipLeadingWhitespace)(str, s + 35, s + 42) / 10000;
// 43 - 49 Integer u[2][2] U(3,3)
sites['U[3][3]'][sites.index] = (0, number_parser_1.parseIntSkipLeadingWhitespace)(str, s + 42, s + 49) / 10000;
// 50 - 56 Integer u[0][1] U(1,2)
sites['U[1][2]'][sites.index] = (0, number_parser_1.parseIntSkipLeadingWhitespace)(str, s + 49, s + 56) / 10000;
// 57 - 63 Integer u[0][2] U(1,3)
sites['U[1][3]'][sites.index] = (0, number_parser_1.parseIntSkipLeadingWhitespace)(str, s + 56, s + 63) / 10000;
// 64 - 70 Integer u[1][2] U(2,3)
sites['U[2][3]'][sites.index] = (0, number_parser_1.parseIntSkipLeadingWhitespace)(str, s + 63, s + 70) / 10000;
// 77 - 78 LString(2) element Element symbol, right-justified.
if (length >= 78) {
tokenizer_1.Tokenizer.trim(data, s + 76, s + 78);
if (data.tokenStart < data.tokenEnd) {
tokenizer_1.TokenBuilder.addToken(sites.type_symbol, data);
}
else {
(0, util_1.guessElementSymbolTokens)(sites.type_symbol, str, s + 12, s + 16);
}
}
else {
(0, util_1.guessElementSymbolTokens)(sites.type_symbol, str, s + 12, s + 16);
}
// 79 - 80 LString(2) charge Charge on the atom.
// TODO
sites.index++;
}
exports.addAnisotropic = addAnisotropic;
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