Configuration information for PDB2PQR.

pdb2pqr.config.AA_DEF_PATH = 'AA.xml'

Expected location for amino acid topology definition file

pdb2pqr.config.AA_NAMES = ['ALA', 'ARG', 'ASH', 'ASN', 'ASP', 'CYS', 'CYM', 'GLN', 'GLU', 'GLH', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'LYN', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'TYM', 'VAL']

Standard amino acid names

pdb2pqr.config.ANGLE_CUTOFF = 20.0

Cutoff for A - D - H(D) hydrogen bond angle

pdb2pqr.config.AVOGADRO = 6.02214076e+23

Avogadro’s number

pdb2pqr.config.BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']

Standard backbone atom names

pdb2pqr.config.BOLTZMANN = 1.380649e-23

Boltzmann constant (in J/K)

pdb2pqr.config.BONDED_SS_LIMIT = 2.5

Disulfide bond distance limit

pdb2pqr.config.BUMP_HEAVY_SIZE = 1.0

Debumping heavy atom size

pdb2pqr.config.BUMP_HYDROGEN_SIZE = 0.5

Debumping hydrogen size

pdb2pqr.config.CELL_SIZE = 2

Size of cells used for neighbor lookups

pdb2pqr.config.CHARGE_ERROR = 0.001

Charge deviation considered to be non-integer

pdb2pqr.config.CITATIONS = ['Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).', 'Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).']

Citation strings for PDB2PQR

pdb2pqr.config.DEBUMP_ANGLE_STEPS = 72

Number of angle steps to scan when debumping

pdb2pqr.config.DEBUMP_ANGLE_STEP_SIZE = 5.0

Size of debumping step

pdb2pqr.config.DEBUMP_ANGLE_TEST_COUNT = 10

Debump angle test

pdb2pqr.config.DIST_CUTOFF = 3.3

Cutoff for H(D) to A hydrogen bond distance

pdb2pqr.config.ELEC_CHARGE = 1.602176634e-19

Electron charge (in C)

pdb2pqr.config.FILTER_WARNINGS = ['Skipped atom during water optimization', 'The best donorH was not picked', 'Multiple occupancies found', 'Tetrahedral hydrogen reconstruction', 'Unable to find amino or nucleic acid definition for']

The start of warning strings to be filtered.

pdb2pqr.config.FILTER_WARNINGS_LIMIT = 10

Number of times warning string is printed before supressing further output

pdb2pqr.config.FORCE_FIELDS = ['amber', 'charmm', 'parse', 'tyl06', 'peoepb', 'swanson']

Standard force field names

pdb2pqr.config.HYD_DEF_PATH = 'HYDROGENS.xml'

Expected location for hydrogens topology definition file

pdb2pqr.config.IGNORED_PROPKA_OPTIONS = {'alignment': None, 'chains': None, 'keep_protons': False, 'mutations': None, 'mutator': None, 'mutator_options': None, 'protonate_all': False, 'reuse_ligand_mol2_file': False, 'thermophiles': None}

Options for PROPKA that PDB2PQR cannot handle

pdb2pqr.config.NA_DEF_PATH = 'NA.xml'

Expected location for nucleic acid topology definition file

pdb2pqr.config.NA_NAMES = ['A', 'A5', 'A3', 'C', 'C5', 'C3', 'G', 'G5', 'G3', 'T', 'T5', 'T3', 'U', 'U5', 'U3', 'RA', 'RG', 'RC', 'RU', 'DA', 'DG', 'DC', 'DT']

Standard nucleic acid names

pdb2pqr.config.PATCH_DEF_PATH = 'PATCHES.xml'

Expected location for topology patch definition file

pdb2pqr.config.PEPTIDE_DIST = 1.7

Peptide bond distance limit

pdb2pqr.config.RADIANS_TO_DEGREES = 57.2958

Convert radians to degrees

pdb2pqr.config.REPAIR_LIMIT = 0.1

Limit on fraction of molecule missing before giving up on repairs

pdb2pqr.config.RNA_MAPPING = {'A': 'RA', 'C': 'RC', 'G': 'RG', 'U': 'RU'}



Rename RNA residues to match PDB nomenclature (https

pdb2pqr.config.SMALL_NUMBER = 1e-07

A small number used by some math routines.

pdb2pqr.config.TITLE_STR = 'PDB2PQR v3.6.2: biomolecular structure conversion software.'

How to format PDB2PQR title in output

pdb2pqr.config.TOPOLOGY_DEF_PATH = 'TOPOLOGY.xml'

Expected location for topology definition file

pdb2pqr.config.VACUUM_PERMIT = 8.8541878128e-12

Vacuum permittivity (in F/m)

pdb2pqr.config.VERSION = '3.6.2'

PDB2PQR version number.