molstar
Version:
A comprehensive macromolecular library.
217 lines (216 loc) • 13.3 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Kim Juho <juho_kim@outlook.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseHelix = parseHelix;
exports.parseSheet = parseSheet;
const cif_1 = require("../../../mol-io/reader/cif.js");
const db_1 = require("../../../mol-data/db.js");
const 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', // TODO or left-handed???
10: 'helx_rh_pp_p', // TODO or left-handed???
};
function getStructConfTypeId(type) {
return HelixTypes[type] || 'helx_p';
}
function parseHelix(lines, lineStart, lineEnd) {
const helices = [];
const getLine = (n) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
for (let i = lineStart; i < lineEnd; i++) {
const 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 - 19 Residue name initResName Name of the initial residue.
// PDB spec defines 3-letter for residue name,
// but 4-letter are commonly used
// 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 - 31 Residue name endResName Name of the terminal residue of the helix.
// PDB spec defines 3-letter for residue name,
// but 4-letter are commonly used
// 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.substring(7, 10).trim(),
helixID: line.substring(11, 14).trim(),
initResName: line.substring(15, 19).trim(),
initChainID: line.substring(19, 20).trim(),
initSeqNum: line.substring(21, 25).trim(),
initICode: line.substring(25, 26).trim(),
endResName: line.substring(27, 31).trim(),
endChainID: line.substring(31, 34).trim(),
endSeqNum: line.substring(33, 37).trim(),
endICode: line.substring(37, 38).trim(),
helixClass: line.substring(38, 40).trim(),
comment: line.substring(40, 70).trim(),
length: line.substring(71, 76).trim()
});
}
const beg_auth_asym_id = cif_1.CifField.ofStrings(helices.map(h => h.initChainID));
const beg_auth_comp_id = cif_1.CifField.ofStrings(helices.map(h => h.initResName));
const end_auth_asym_id = cif_1.CifField.ofStrings(helices.map(h => h.endChainID));
const end_auth_comp_id = cif_1.CifField.ofStrings(helices.map(h => h.endResName));
const 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_comp_id,
beg_auth_seq_id: cif_1.CifField.ofStrings(helices.map(h => h.initSeqNum)),
conf_type_id: cif_1.CifField.ofStrings(helices.map(h => getStructConfTypeId(h.helixClass))),
details: cif_1.CifField.ofStrings(helices.map(h => 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_comp_id,
end_auth_seq_id: cif_1.CifField.ofStrings(helices.map(h => h.endSeqNum)),
id: cif_1.CifField.ofStrings(helices.map(h => h.serNum)),
pdbx_beg_PDB_ins_code: cif_1.CifField.ofStrings(helices.map(h => h.initICode)),
pdbx_end_PDB_ins_code: cif_1.CifField.ofStrings(helices.map(h => h.endICode)),
pdbx_PDB_helix_class: cif_1.CifField.ofStrings(helices.map(h => h.helixClass)),
pdbx_PDB_helix_length: cif_1.CifField.ofStrings(helices.map(h => h.length)),
pdbx_PDB_helix_id: cif_1.CifField.ofStrings(helices.map(h => h.helixID)),
};
return cif_1.CifCategory.ofFields('struct_conf', struct_conf);
}
function parseSheet(lines, lineStart, lineEnd) {
const sheets = [];
const getLine = (n) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
for (let i = lineStart; i < lineEnd; i++) {
const 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 - 21 Residue name initResName Residue name of initial residue.
// PDB spec defines 3-letter for residue name,
// but 4-letter are commonly used
// 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 - 32 Residue name endResName Residue name of terminal residue.
// PDB spec defines 3-letter for residue name,
// but 4-letter are commonly used
// 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 - 49 Residue name curResName Registration. Residue name in current strand
// PDB spec defines 3-letter for residue name,
// but 4-letter are commonly used
// 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 - 64 Residue name prevResName Registration. Residue name in
// previous strand.
// PDB spec defines 3-letter for residue name,
// but 4-letter are commonly used
// 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.substring(7, 10).trim(),
sheetID: line.substring(11, 14).trim(),
numStrands: line.substring(14, 16).trim(),
initResName: line.substring(17, 21).trim(),
initChainID: line.substring(21, 22).trim(),
initSeqNum: line.substring(22, 26).trim(),
initICode: line.substring(26, 27).trim(),
endResName: line.substring(28, 32).trim(),
endChainID: line.substring(32, 33).trim(),
endSeqNum: line.substring(33, 37).trim(),
endICode: line.substring(37, 38).trim(),
sense: line.substring(38, 40).trim(),
curAtom: line.substring(41, 45).trim(),
curResName: line.substring(45, 49).trim(),
curChainId: line.substring(49, 50).trim(),
curResSeq: line.substring(50, 54).trim(),
curICode: line.substring(54, 55).trim(),
prevAtom: line.substring(56, 60).trim(),
prevResName: line.substring(60, 64).trim(),
prevChainId: line.substring(64, 65).trim(),
prevResSeq: line.substring(65, 69).trim(),
prevICode: line.substring(69, 70).trim(),
});
}
const beg_auth_asym_id = cif_1.CifField.ofStrings(sheets.map(s => s.initChainID));
const beg_auth_comp_id = cif_1.CifField.ofStrings(sheets.map(s => s.initResName));
const beg_auth_seq_id = cif_1.CifField.ofStrings(sheets.map(s => s.initSeqNum));
const end_auth_asym_id = cif_1.CifField.ofStrings(sheets.map(s => s.endChainID));
const end_auth_comp_id = cif_1.CifField.ofStrings(sheets.map(s => s.endResName));
const end_auth_seq_id = cif_1.CifField.ofStrings(sheets.map(s => s.endSeqNum));
const 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_comp_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_comp_id,
end_auth_seq_id,
id: cif_1.CifField.ofStrings(sheets.map(s => s.strand)),
sheet_id: cif_1.CifField.ofStrings(sheets.map(s => s.sheetID)), // TODO wrong, needs to point to _struct_sheet.id
pdbx_beg_PDB_ins_code: cif_1.CifField.ofStrings(sheets.map(s => s.initICode)),
pdbx_end_PDB_ins_code: cif_1.CifField.ofStrings(sheets.map(s => s.endICode)),
};
return cif_1.CifCategory.ofFields('struct_sheet_range', struct_sheet_range);
}