6.16. 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).
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class
MDAnalysis.coordinates.PDBQT.PDBQTReader(filename, convert_units=True, 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
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Writer(filename, **kwargs)[source]¶ Returns a permissive (simple) PDBQTWriter for filename.
Parameters: filename (str) – filename of the output PDBQT file Returns: Return type: PDBQTWriter
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class
MDAnalysis.coordinates.PDBQT.PDBQTWriter(filename, **kwargs)[source]¶ PDBQT writer that implements a subset of the PDB 3.2 standard and the PDBQT spec.