config

Configuration information for PDB2PQR.

class pdb2pqr.config.ApbsCalcType(value)

Enumerate APBS Elec calcuation types.

MG_AUTO = 'mg-auto'

MG_MANUAL = 'mg-manual'

MG_PARA = 'mg-para'

class pdb2pqr.config.AtomType(value)

Enumerate atom types.

ATOM = 'ATOM'

HETATM = 'HETATM'

pdb2pqr.config.BYTES_PER_GRID = 200

Approximate memory usage (in bytes) can be estimated by multiplying the number of grid points by this constant

pdb2pqr.config.BYTES_STORED = 96.0

Number of bytes for stored representation of floating point values

class pdb2pqr.config.Backbone(value)

Standard backbone atom names.

C = 'C'

CA = 'CA'

H = 'H'

HA = 'HA'

HN = 'HN'

N = 'N'

O = 'O'

O2 = 'O2'

TN = 'tN'

class pdb2pqr.config.BaseEnum(value)

Base class for enumerables, defining common methods.

classmethod values() → list

Generates list of the Enum values

Returns

List of enum values

Return type

List[T]

pdb2pqr.config.CL_CHARGE = -1

Charge of a chloride ion

pdb2pqr.config.CL_RADIUS = 1.815

Solvated chloride radius (in ångströms)

pdb2pqr.config.COARSE_GRID_FACTOR = 1.7

The fine grid dimensions are multiplied by this constant to calculate the coarse grid dimensions

class pdb2pqr.config.DuplicateFilter

Filter duplicate messages.

__init__()

Initialize a filter.

Initialize with the name of the logger which, together with its children, will have its events allowed through the filter. If no name is specified, allow every event.

filter(record)

Filter current record.

pdb2pqr.config.FINE_GRID_ADD = 20.0

The number of Ångströms added to the molecular dimensions to determine the find grid dimensions

pdb2pqr.config.FOCUS_FACTOR = 0.25

The maximum factor by which a domain can be “shrunk” during a focusing calculation

class pdb2pqr.config.FilePermission(value)

Enumerate file permissions operations.

READ = 1

WRITE = 2

class pdb2pqr.config.ForceFields(value)

Enumerate built-in forcefield types.

AMBER = 'amber'

CHARMM = 'charmm'

PARSE = 'parse'

PEOEPB = 'peoepb'

SWANSON = 'swanson'

TYL06 = 'tyl06'

pdb2pqr.config.GRID_SPACING = 0.5

Desired fine grid spacing (in Ångströms)

class pdb2pqr.config.LogLevels(value)

Enumerate log levels.

CRITICAL = 'CRITICAL'

DEBUG = 'DEBUG'

ERROR = 'ERROR'

INFO = 'INFO'

WARNING = 'WARNING'

pdb2pqr.config.MAX_PDB_ACCURACY = 0.001

The maximum accuracy of old PDB coordinates (no atom left behind when partitioning).

pdb2pqr.config.MEMORY_CEILING_MB = 400

Maxmimum memory (in MB) to be used for a calculation

pdb2pqr.config.MIN_GRID_POINTS = 33

The minimum number of points in a grid

pdb2pqr.config.MIN_LEVELS = 4

Minimum number of multigrid levels

pdb2pqr.config.MIN_MOL_LENGTH = 0.1

The minimum length of a molecule (in Ångströms) in any direction

pdb2pqr.config.NA_CHARGE = -1

Charge of a sodium ion

pdb2pqr.config.NA_RADIUS = 1.875

Solvated sodium radius (in ångströms)

pdb2pqr.config.PARTITION_OVERLAP = 0.1

The fractional overlap between grid partitions in a parallel focusing calculation

pdb2pqr.config.PREFIX_CONVERT = 1024.0

Byte prefix conversion factor

pdb2pqr.config.ROOM_TEMPERATURE = 298.15

Room temperature (in Kelvin)

pdb2pqr.config.SOLUTE_DIELECTRIC = 2.0

Dielectric of a solute due to only molecular polarizability

pdb2pqr.config.SOLVENT_DIELECTRIC = 78.54

One potential value for the dielectric constant of water under standard conditions

pdb2pqr.config.SOLVENT_RADIUS = 1.4

Solvent (water) molecule radius in Ångströms

pdb2pqr.config.SPLINE_WINDOW = 0.3

Window (in Ångströms) for spline-based dielectric surface definitions

pdb2pqr.config.SURFACE_DENSITY = 10.0

Number of grid points per squared Ångström for dielectric surfaces

pdb2pqr.config.SURFACE_TENSION = 0.105

Surface tension (in kJ mol^{-1} Å^{-2})

pdb2pqr.config.TITLE_STR = 'PDB2PQR v4.0.0: biomolecular structure conversion software.'

How to format PDB2PQR title in output

class pdb2pqr.config.TitrationMethods(value)

Enumerate titration-state methods.

PROPKA = 'propka'

pdb2pqr.config.setup_logger(output_filename, level='DEBUG')

Setup the logger.

Setup logger to output the log file to the same directory as the output file.

Parameters

• output_filename (str) – path to the output file

• level (str) – logging level