molstar
Version:
A comprehensive macromolecular library.
205 lines • 12.9 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.parseSheet = exports.parseHelix = void 0;
var cif_1 = require("../../../mol-io/reader/cif");
var db_1 = require("../../../mol-data/db");
var HelixTypes = {
// CLASS NUMBER
// TYPE OF HELIX (COLUMNS 39 - 40)
// --------------------------------------------------------------
// Right-handed alpha (default) 1
// Right-handed omega 2
// Right-handed pi 3
// Right-handed gamma 4
// Right-handed 3 - 10 5
// Left-handed alpha 6
// Left-handed omega 7
// Left-handed gamma 8
// 2 - 7 ribbon/helix 9
// Polyproline 10
1: 'HELX_RH_AL_P',
2: 'HELX_RH_OM_P',
3: 'HELX_RH_PI_P',
4: 'HELX_RH_GA_P',
5: 'HELX_RH_3T_P',
6: 'HELX_LH_AL_P',
7: 'HELX_LH_OM_P',
8: 'HELX_LH_GA_P',
9: 'HELX_RH_27_P',
10: 'HELX_RH_PP_P', // TODO or left-handed???
};
function getStructConfTypeId(type) {
return HelixTypes[type] || 'HELX_P';
}
function parseHelix(lines, lineStart, lineEnd) {
var helices = [];
var getLine = function (n) { return lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]); };
for (var i = lineStart; i < lineEnd; i++) {
var line = getLine(i);
// COLUMNS DATA TYPE FIELD DEFINITION
// -----------------------------------------------------------------------------------
// 1 - 6 Record name "HELIX "
// 8 - 10 Integer serNum Serial number of the helix. This starts
// at 1 and increases incrementally.
// 12 - 14 LString(3) helixID Helix identifier. In addition to a serial
// number, each helix is given an
// alphanumeric character helix identifier.
// 16 - 18 Residue name initResName Name of the initial residue.
// 20 Character initChainID Chain identifier for the chain containing
// this helix.
// 22 - 25 Integer initSeqNum Sequence number of the initial residue.
// 26 AChar initICode Insertion code of the initial residue.
// 28 - 30 Residue name endResName Name of the terminal residue of the helix.
// 32 Character endChainID Chain identifier for the chain containing
// this helix.
// 34 - 37 Integer endSeqNum Sequence number of the terminal residue.
// 38 AChar endICode Insertion code of the terminal residue.
// 39 - 40 Integer helixClass Helix class (see below).
// 41 - 70 String comment Comment about this helix.
// 72 - 76 Integer length Length of this helix.
helices.push({
serNum: line.substr(7, 3).trim(),
helixID: line.substr(11, 3).trim(),
initResName: line.substr(15, 3).trim(),
initChainID: line.substr(19, 1).trim(),
initSeqNum: line.substr(21, 4).trim(),
initICode: line.substr(25, 1).trim(),
endResName: line.substr(27, 3).trim(),
endChainID: line.substr(31, 3).trim(),
endSeqNum: line.substr(33, 4).trim(),
endICode: line.substr(37, 1).trim(),
helixClass: line.substr(38, 2).trim(),
comment: line.substr(40, 30).trim(),
length: line.substr(71, 5).trim()
});
}
var beg_auth_asym_id = cif_1.CifField.ofStrings(helices.map(function (h) { return h.initChainID; }));
var beg_auth_comp_id = cif_1.CifField.ofStrings(helices.map(function (h) { return h.initResName; }));
var end_auth_asym_id = cif_1.CifField.ofStrings(helices.map(function (h) { return h.endChainID; }));
var end_auth_comp_id = cif_1.CifField.ofStrings(helices.map(function (h) { return h.endResName; }));
var struct_conf = {
beg_label_asym_id: beg_auth_asym_id,
beg_label_comp_id: beg_auth_comp_id,
beg_label_seq_id: cif_1.CifField.ofUndefined(helices.length, db_1.Column.Schema.int),
beg_auth_asym_id: beg_auth_asym_id,
beg_auth_comp_id: beg_auth_comp_id,
beg_auth_seq_id: cif_1.CifField.ofStrings(helices.map(function (h) { return h.initSeqNum; })),
conf_type_id: cif_1.CifField.ofStrings(helices.map(function (h) { return getStructConfTypeId(h.helixClass); })),
details: cif_1.CifField.ofStrings(helices.map(function (h) { return h.comment; })),
end_label_asym_id: end_auth_asym_id,
end_label_comp_id: end_auth_comp_id,
end_label_seq_id: cif_1.CifField.ofUndefined(helices.length, db_1.Column.Schema.int),
end_auth_asym_id: end_auth_asym_id,
end_auth_comp_id: end_auth_comp_id,
end_auth_seq_id: cif_1.CifField.ofStrings(helices.map(function (h) { return h.endSeqNum; })),
id: cif_1.CifField.ofStrings(helices.map(function (h) { return h.serNum; })),
pdbx_beg_PDB_ins_code: cif_1.CifField.ofStrings(helices.map(function (h) { return h.initICode; })),
pdbx_end_PDB_ins_code: cif_1.CifField.ofStrings(helices.map(function (h) { return h.endICode; })),
pdbx_PDB_helix_class: cif_1.CifField.ofStrings(helices.map(function (h) { return h.helixClass; })),
pdbx_PDB_helix_length: cif_1.CifField.ofStrings(helices.map(function (h) { return h.length; })),
pdbx_PDB_helix_id: cif_1.CifField.ofStrings(helices.map(function (h) { return h.helixID; })),
};
return cif_1.CifCategory.ofFields('struct_conf', struct_conf);
}
exports.parseHelix = parseHelix;
function parseSheet(lines, lineStart, lineEnd) {
var sheets = [];
var getLine = function (n) { return lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]); };
for (var i = lineStart; i < lineEnd; i++) {
var line = getLine(i);
// COLUMNS DATA TYPE FIELD DEFINITION
// -------------------------------------------------------------------------------------
// 1 - 6 Record name "SHEET "
// 8 - 10 Integer strand Strand number which starts at 1 for each
// strand within a sheet and increases by one.
// 12 - 14 LString(3) sheetID Sheet identifier.
// 15 - 16 Integer numStrands Number of strands in sheet.
// 18 - 20 Residue name initResName Residue name of initial residue.
// 22 Character initChainID Chain identifier of initial residue
// in strand.
// 23 - 26 Integer initSeqNum Sequence number of initial residue
// in strand.
// 27 AChar initICode Insertion code of initial residue
// in strand.
// 29 - 31 Residue name endResName Residue name of terminal residue.
// 33 Character endChainID Chain identifier of terminal residue.
// 34 - 37 Integer endSeqNum Sequence number of terminal residue.
// 38 AChar endICode Insertion code of terminal residue.
// 39 - 40 Integer sense Sense of strand with respect to previous
// strand in the sheet. 0 if first strand,
// 1 if parallel,and -1 if anti-parallel.
// 42 - 45 Atom curAtom Registration. Atom name in current strand.
// 46 - 48 Residue name curResName Registration. Residue name in current strand
// 50 Character curChainId Registration. Chain identifier in
// current strand.
// 51 - 54 Integer curResSeq Registration. Residue sequence number
// in current strand.
// 55 AChar curICode Registration. Insertion code in
// current strand.
// 57 - 60 Atom prevAtom Registration. Atom name in previous strand.
// 61 - 63 Residue name prevResName Registration. Residue name in
// previous strand.
// 65 Character prevChainId Registration. Chain identifier in
// previous strand.
// 66 - 69 Integer prevResSeq Registration. Residue sequence number
// in previous strand.
// 70 AChar prevICode Registration. Insertion code in
// previous strand.
sheets.push({
strand: line.substr(7, 3).trim(),
sheetID: line.substr(11, 3).trim(),
numStrands: line.substr(14, 2).trim(),
initResName: line.substr(17, 3).trim(),
initChainID: line.substr(21, 1).trim(),
initSeqNum: line.substr(22, 4).trim(),
initICode: line.substr(26, 1).trim(),
endResName: line.substr(28, 3).trim(),
endChainID: line.substr(32, 1).trim(),
endSeqNum: line.substr(33, 4).trim(),
endICode: line.substr(37, 1).trim(),
sense: line.substr(38, 2).trim(),
curAtom: line.substr(41, 4).trim(),
curResName: line.substr(45, 3).trim(),
curChainId: line.substr(49, 1).trim(),
curResSeq: line.substr(50, 4).trim(),
curICode: line.substr(54, 1).trim(),
prevAtom: line.substr(56, 4).trim(),
prevResName: line.substr(60, 3).trim(),
prevChainId: line.substr(64, 1).trim(),
prevResSeq: line.substr(65, 4).trim(),
prevICode: line.substr(69, 1).trim(),
});
}
var beg_auth_asym_id = cif_1.CifField.ofStrings(sheets.map(function (s) { return s.initChainID; }));
var beg_auth_comp_id = cif_1.CifField.ofStrings(sheets.map(function (s) { return s.initResName; }));
var beg_auth_seq_id = cif_1.CifField.ofStrings(sheets.map(function (s) { return s.initSeqNum; }));
var end_auth_asym_id = cif_1.CifField.ofStrings(sheets.map(function (s) { return s.endChainID; }));
var end_auth_comp_id = cif_1.CifField.ofStrings(sheets.map(function (s) { return s.endResName; }));
var end_auth_seq_id = cif_1.CifField.ofStrings(sheets.map(function (s) { return s.endSeqNum; }));
var struct_sheet_range = {
beg_label_asym_id: beg_auth_asym_id,
beg_label_comp_id: beg_auth_comp_id,
beg_label_seq_id: beg_auth_seq_id,
beg_auth_asym_id: beg_auth_asym_id,
beg_auth_comp_id: beg_auth_comp_id,
beg_auth_seq_id: beg_auth_seq_id,
end_label_asym_id: end_auth_asym_id,
end_label_comp_id: end_auth_asym_id,
end_label_seq_id: end_auth_seq_id,
end_auth_asym_id: end_auth_asym_id,
end_auth_comp_id: end_auth_comp_id,
end_auth_seq_id: end_auth_seq_id,
id: cif_1.CifField.ofStrings(sheets.map(function (s) { return s.strand; })),
sheet_id: cif_1.CifField.ofStrings(sheets.map(function (s) { return s.sheetID; })),
pdbx_beg_PDB_ins_code: cif_1.CifField.ofStrings(sheets.map(function (s) { return s.initICode; })),
pdbx_end_PDB_ins_code: cif_1.CifField.ofStrings(sheets.map(function (s) { return s.endICode; })),
};
return cif_1.CifCategory.ofFields('struct_sheet_range', struct_sheet_range);
}
exports.parseSheet = parseSheet;
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