Class: PDBParser

parser~PDBParser

This class allows the parsing of the PDB file format version 3.30

Constructor

new PDBParser()

Constructor

Author:
  • Jean-Christophe Taveau
Example
parser = new PDBParser();
parser.parse(myText);
var mol = parser.getStructure();

Methods

getStructure() → {Structure}

Return the PDB structure

Returns:
  • The 3D structure of the molecule
Type
Structure

parse()

Trigger the parsing of the PDB file

parseAtom()

Parse ATOM and HETATM row - Private method

COLUMNS DATA TYPE FIELD DEFINITION
01 - 06 Record name "ATOM "
07 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
18 - 20 Residue name resName Residue name.
22 Character chainID Chain identifier.
23 - 26 Integer resSeq Residue sequence number.
27 AChar iCode Code for insertion of residues.
31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
77 - 78 LString(2) element Element symbol, right-justified.
79 - 80 LString(2) charge Charge on the atom.

parseHeader()

Parse HEADER row - Private method

COLUMNS DATA TYPE FIELD DEFINITION
01 - 06 Record name "HEADER"
11 - 50 String(40) classification Classifies the molecule(s).
51 - 59 Date depDate Deposition date. This is the date the coordinates were received at the PDB.
63 - 66 IDcode idCode This identifier is unique within the PDB.

parseHelix()

Parse HELIX rows - Private method

COLUMNS DATA TYPE FIELD DEFINITION
01 - 06 Record name "HELIX
08 - 10 Integer serNum Serial number of the helix. This starts at 1 and increases incrementally.
12 - 14 LString(3) helixID 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.

parseSheet()

Parse SHEET rows - Private method - TODO

COLUMNS DATA TYPE FIELD DEFINITION
01 - 06 Record name "SHEET "
08 - 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. 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.

parseTitle()

Parse TITLE rows - Private method - TODO

COLUMNS DATA TYPE FIELD DEFINITION
01 - 6 Record name "TITLE "
09 - 10 Continuation continuation Allows concatenation of multiple records.
11 - 80 String title Title of the experiment.