6.17. PQR file format — MDAnalysis.coordinates.PQR

Read atoms with charges from a PQR file (as written by PDB2PQR). The following is adopted from the description of the PQR format as used by APBS:

MDAnalysis reads very loosely-formatted PQR files: all fields are whitespace-delimited rather than the strict column formatting mandated by the PDB format. This more liberal formatting allows coordinates which are larger/smaller than ±999 Å.

MDAnalysis reads data on a per-line basis from PQR files using the following format:

recordName serial atomName residueName chainID residueNumber X Y Z charge radius

If this fails it is assumed that the chainID was omitted and the shorter format is read:

recordName serial atomName residueName residueNumber X Y Z charge radius

Anything else will raise a ValueError.

The whitespace is the most important feature of this format: fields must be separated by at least one space or tab character. The fields are:

recordName

A string which specifies the type of PQR entry and should either be ATOM or HETATM.

serial

An integer which provides the atom index (but note that MDAnalysis renumbers atoms so one cannot rely on the serial)

atomName

A string which provides the atom name.

residueName

A string which provides the residue name.

chainID

An optional string which provides the chain ID of the atom.

residueNumber

An integer which provides the residue index.

X Y Z

Three floats which provide the atomic coordiantes.

charge

A float which provides the atomic charge (in electrons).

radius

A float which provides the atomic radius (in Å).

Clearly, this format can deviate wildly from PDB due to the use of whitespaces rather than specific column widths and alignments. This deviation can be particularly significant when large coordinate values are used.

Output should look like this (although the only real requirement is whitespace separation between all entries). The chainID is optional and can be omitted:

ATOM      1  N    MET     1     -11.921   26.307   10.410 -0.3000 1.8500
ATOM     36  NH1  ARG     2      -6.545   25.499    3.854 -0.8000 1.8500
ATOM     37 HH11  ARG     2      -6.042   25.480    4.723  0.4600 0.2245

Warning

Fields must be white-space separated or data are read incorrectly. PDB formatted files are not guaranteed to be white-space separated so extra care should be taken when quickly converting PDB files into PQR files using simple scripts.

For example, PQR files created with PDB2PQR and the –whitespace option are guaranteed to conform to the above format:

pdb2pqr --ff=charmm --whitespace 4ake.pdb 4ake.pqr

Notes

The PQR format does not provide a means by which to provide box information. In all cases the dimensions attribute will be set to None.

class MDAnalysis.coordinates.PQR.PQRReader(filename, convert_units=True, n_atoms=None, **kwargs)

Read a PQR file into MDAnalysis.

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

Writer(filename, **kwargs)

Returns a PQRWriter for filename.

Parameters:

filename (str) – filename of the output PQR file

Return type:

PQRWriter

units = {'length': 'Angstrom', 'time': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

class MDAnalysis.coordinates.PQR.PQRWriter(filename, convert_units=True, **kwargs)

Write a single coordinate frame in whitespace-separated PQR format.

Charges (“Q”) are taken from the MDAnalysis.core.groups.Atom.charge attribute while radii are obtaine from the MDAnalysis.core.groups.Atom.radius attribute.

• If the segid is ‘SYSTEM’ then it will be set to the empty string. Otherwise the first letter will be used as the chain ID.

• The serial number always starts at 1 and increments sequentially for the atoms.

The output format is similar to pdb2pqr --whitespace.

New in version 0.9.0.

Changed in version 2.6.0: Files are now written in wt mode, and keep extensions, allowing for files to be written under compressed formats

Set up a PQRWriter with full whitespace separation.

Parameters:

• filename (str) – output filename

• convert_units (bool (optional)) – units are converted to the MDAnalysis base format; [True]

• remarks (str (optional)) – remark lines (list of strings) or single string to be added to the top of the PQR file

units = {'length': 'Angstrom', 'time': None}

dict with units of of time and length (and velocity, force, … for formats that support it)

write(selection, frame=None)

Write selection at current trajectory frame to file.

Parameters:

• selection (AtomGroup or Universe) – MDAnalysis AtomGroup or Universe

• frame (int (optional)) – optionally move to frame index frame; by default, write the current frame

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