6.14. PDBQT structure files in MDAnalysis — MDAnalysis.coordinates.PDBQT

MDAnalysis reads coordinates from PDBQT files and additional optional data such as B-factors, partial charge and AutoDock atom types. It is also possible to substitute a PDBQT file for a PSF file in order to define the list of atoms (but no connectivity information will be available in this case).

class MDAnalysis.coordinates.PDBQT.PDBQTReader(filename, convert_units=None, n_atoms=None, **kwargs)[source]

PDBQTReader that reads a PDBQT-formatted file, no frills.

Records read:
  • CRYST1 for unitcell A,B,C, alpha,beta,gamm
  • ATOM. HETATM for x,y,z

Original PDB format documentation with AutoDOCK extensions

COLUMNS DATA TYPE FIELD DEFINITION
1 - 6 Record name “CRYST1”  
7 - 15 Real(9.3) a a (Angstroms).
16 - 24 Real(9.3) b b (Angstroms).
25 - 33 Real(9.3) c c (Angstroms).
34 - 40 Real(7.2) alpha alpha (degrees).
41 - 47 Real(7.2) beta beta (degrees).
48 - 54 Real(7.2) gamma gamma (degrees).
1 - 6 Record name “ATOM “  
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator. IGNORED
18 - 21 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. IGNORED
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.
67 - 76 Real(10.4) partialChrg Gasteiger PEOE partial charge q.
79 - 80 LString(2) atomType AutoDOCK atom type t.

We ignore torsion notation and just pull the partial charge and atom type columns:

COMPND    NSC7810
REMARK  3 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: A7_7  and  C22_23
REMARK    2  A    between atoms: A9_9  and  A11_11
REMARK    3  A    between atoms: A17_17  and  C21_21
ROOT
123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)
ATOM      1  A1  INH I           1.054   3.021   1.101  0.00  0.00     0.002 A
ATOM      2  A2  INH I           1.150   1.704   0.764  0.00  0.00     0.012 A
ATOM      3  A3  INH I          -0.006   0.975   0.431  0.00  0.00    -0.024 A
ATOM      4  A4  INH I           0.070  -0.385   0.081  0.00  0.00     0.012 A
ATOM      5  A5  INH I          -1.062  -1.073  -0.238  0.00  0.00     0.002 A
ATOM      6  A6  INH I          -2.306  -0.456  -0.226  0.00  0.00     0.019 A
ATOM      7  A7  INH I          -2.426   0.885   0.114  0.00  0.00     0.052 A
ATOM      8  A8  INH I          -1.265   1.621   0.449  0.00  0.00     0.002 A
ATOM      9  A9  INH I          -1.339   2.986   0.801  0.00  0.00    -0.013 A
ATOM     10  A10 INH I          -0.176   3.667   1.128  0.00  0.00     0.013 A
ENDROOT
BRANCH   9  11
ATOM     11  A11 INH I          -2.644   3.682   0.827  0.00  0.00    -0.013 A
ATOM     12  A16 INH I          -3.007   4.557  -0.220  0.00  0.00     0.002 A
ATOM     13  A12 INH I          -3.522   3.485   1.882  0.00  0.00     0.013 A
ATOM     14  A15 INH I          -4.262   5.209  -0.177  0.00  0.00    -0.024 A
ATOM     15  A17 INH I          -2.144   4.784  -1.319  0.00  0.00     0.052 A
ATOM     16  A14 INH I          -5.122   4.981   0.910  0.00  0.00     0.012 A
ATOM     17  A20 INH I          -4.627   6.077  -1.222  0.00  0.00     0.012 A
ATOM     18  A13 INH I          -4.749   4.135   1.912  0.00  0.00     0.002 A
ATOM     19  A19 INH I          -3.777   6.285  -2.267  0.00  0.00     0.002 A
ATOM     20  A18 INH I          -2.543   5.650  -2.328  0.00  0.00     0.019 A
BRANCH  15  21
ATOM     21  C21 INH I          -0.834   4.113  -1.388  0.00  0.00     0.210 C
ATOM     22  O1  INH I          -0.774   2.915  -1.581  0.00  0.00    -0.644 OA
ATOM     23  O3  INH I           0.298   4.828  -1.237  0.00  0.00    -0.644 OA
ENDBRANCH  15  21
ENDBRANCH   9  11
BRANCH   7  24
ATOM     24  C22 INH I          -3.749   1.535   0.125  0.00  0.00     0.210 C
ATOM     25  O2  INH I          -4.019   2.378  -0.708  0.00  0.00    -0.644 OA
ATOM     26  O4  INH I          -4.659   1.196   1.059  0.00  0.00    -0.644 OA
ENDBRANCH   7  24
TORSDOF 3
123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789. (column reference)

Changed in version 0.11.0: Frames now 0-based instead of 1-based

Writer(filename, **kwargs)[source]

Returns a permissive (simple) PDBQTWriter for filename.

Parameters:filename (str) – filename of the output PDBQT file
Returns:
Return type:PDBQTWriter
class MDAnalysis.coordinates.PDBQT.PDBQTWriter(filename, **kwargs)[source]

PDBQT writer that implements a subset of the PDB 3.2 standard and the PDBQT spec.

close()[source]

Close the trajectory file.

write(selection, frame=None)[source]

Write selection at current trajectory frame to file.

Parameters:
  • selection (AtomGroup) – The selection to be written
  • frame (int (optional)) – optionally move to frame index frame before writing; the default is to write the current trajectory frame

Note

The first letter of the segid is used as the PDB chainID.

Changed in version 0.11.0: Frames now 0-based instead of 1-based