Constructor
new PDBParser()
Constructor
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. |