python_pdb.formats.pdb module
Information and tools for working with PDB file formats.
Range contants for parsing PDB files.
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
COLUMNS |
DATA TYPE |
FIELD |
DEFINITION |
|---|---|---|---|
1 to 6 |
Record name |
“ATOM “ or “HETATM” |
|
7 to 11 |
Integer |
serial |
Atom serial number. |
13 to 16 |
Atom |
name |
Atom name. |
17 |
Character |
altLoc |
Alternate location indicator. |
18 to 20 |
Residue name |
resName |
Residue name. |
22 |
Character |
chainID |
Chain identifier. |
23 to 26 |
Integer |
resSeq |
Residue sequence number. |
27 |
AChar |
iCode |
Code for insertion of residues. |
31 to 38 |
Real(8.3) |
x |
Orthogonal coordinates for X in Angstroms. |
39 to 46 |
Real(8.3) |
y |
Orthogonal coordinates for Y in Angstroms. |
47 to 54 |
Real(8.3) |
z |
Orthogonal coordinates for Z in Angstroms. |
55 to 60 |
Real(6.2) |
occupancy |
Occupancy. |
61 to 66 |
Real(6.2) |
tempFactor |
Temperature factor. |
77 to 78 |
LString(2) |
element |
Element symbol, right-justified. |
79 to 80 |
LString(2) |
charge |
Charge on the atom. |
Eg:
ATOM 13 CA GLU A 3 42.492 -46.706 53.609 1.00 0.00 C
ATOM 10 2HE2 GLN A 2 42.647 -51.666 50.359 1.00 0.00 H
...
- python_pdb.formats.pdb.ALT_LOC_RANGE = (16, 17)
Range indicating the alternate location details (17)
- python_pdb.formats.pdb.ATOM_NAME_RANGE = (12, 16)
Range indicating the atom name (13 - 16)
- python_pdb.formats.pdb.ATOM_NUMBER_RANGE = (6, 11)
Range indicating the atom number (7 - 11)
- python_pdb.formats.pdb.B_FACTOR_RANGE = (60, 66)
Range indicating the B factor (61 - 66)
- python_pdb.formats.pdb.CHAIN_ID_RANGE = (21, 22)
Range indicating the chain ID (22)
- python_pdb.formats.pdb.CHARGE_RANGE = (78, 80)
Range indicating the charge (79 - 80)
- python_pdb.formats.pdb.ELEMENT_RANGE = (76, 78)
Range indicating the element (77 - 78)
- python_pdb.formats.pdb.INSERT_CODE_RANGE = (26, 27)
Range indicating the insert code (27)
- python_pdb.formats.pdb.MODEL_SERIAL_RANGE = (10, 14)
Range for MODEL records serial number.
RECORD formats COLUMNS
DATA TYPE
FIELD
DEFINITION
1 to 6
Record name
“MODEL “
11 - 14
Integer
serial
Model serial number.
- python_pdb.formats.pdb.OCCUPANCY_RANGE = (54, 60)
Range indicating the occupancy (55 - 60)
- python_pdb.formats.pdb.RECORD_TYPE_RANGE = (0, 6)
Range indicating the record type (1 - 6)
- python_pdb.formats.pdb.RESIDUE_NAME_RANGE = (17, 20)
Range indicating the residue name (18 - 20)
- python_pdb.formats.pdb.SEQ_ID_RANGE = (22, 26)
Range indicating the sequence ID (23 - 26)
- python_pdb.formats.pdb.X_POS_RANGE = (30, 38)
Range indicating the X position (31 - 38)
- python_pdb.formats.pdb.Y_POS_RANGE = (38, 46)
Range indicating the Y position (39 - 46)
- python_pdb.formats.pdb.Z_POS_RANGE = (46, 54)
Range indicating the Y position (47 - 54)
- python_pdb.formats.pdb.format_atom_record(chain, residue, atom)
Format information as a record entry for pdb files. Function will handle both ATOM and HETATM entries.
- python_pdb.formats.pdb.format_model_record(model_number)
Format model_number into a MODEL record.