API Reference
The pdb2pqr command provides a command-line interface to PDB2PQR’s functionality.
It is built on classes and functions in the pdb2pqr
module.
The API of pdb2pqr
is documented here for developers who might want to directly use the PDB2PQR code.
Note
The API is still changing and there is currently no guarantee that it will remain stable between minor releases.
Forcefield support modules
Molecular structure modules
I/O modules
cif
io
inputgen
pdb
ANISOU
ATOM
AUTHOR
BaseRecord
CAVEAT
CISPEP
COMPND
CONECT
CRYST1
DBREF
END
ENDMDL
EXPDTA
FORMUL
HEADER
HELIX
HET
HETATM
HETNAM
HETSYN
HYDBND
JRNL
KEYWDS
LINK
MASTER
MODEL
MODRES
MTRIX1
MTRIX2
MTRIX3
MTRIXn
NUMMDL
OBSLTE
ORIGX1
ORIGX2
ORIGX3
ORIGXn
REMARK
REVDAT
SCALE1
SCALE2
SCALE3
SCALEn
SEQADV
SEQRES
SHEET
SIGATM
SIGUIJ
SITE
SLTBRG
SOURCE
SPRSDE
SSBOND
TER
TITLE
TURN
TVECT
read_atom()
read_pdb()
register_line_parser()
Other modules
cells
config
AA_DEF_PATH
AA_NAMES
ANGLE_CUTOFF
AVOGADRO
BACKBONE
BOLTZMANN
BONDED_SS_LIMIT
BUMP_HEAVY_SIZE
BUMP_HYDROGEN_SIZE
CELL_SIZE
CHARGE_ERROR
CITATIONS
DEBUMP_ANGLE_STEPS
DEBUMP_ANGLE_STEP_SIZE
DEBUMP_ANGLE_TEST_COUNT
DIST_CUTOFF
ELEC_CHARGE
FILTER_WARNINGS
FILTER_WARNINGS_LIMIT
FORCE_FIELDS
HYD_DEF_PATH
IGNORED_PROPKA_OPTIONS
NA_DEF_PATH
NA_NAMES
PATCH_DEF_PATH
PEPTIDE_DIST
RADIANS_TO_DEGREES
REPAIR_LIMIT
RNA_MAPPING
SMALL_NUMBER
TITLE_STR
TOPOLOGY_DEF_PATH
VACUUM_PERMIT
VERSION
debump
main
psize
quatfit
run
utilities