Biomol/ControlParameter.hpp File Reference

Definition of constants in namespace CDPL::Biomol::ControlParameter. More...

#include "CDPL/Biomol/APIPrefix.hpp"

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Namespaces
	CDPL
	The namespace of the Chemical Data Processing Library.
	CDPL::Base
	Contains core framework classes and functions.
	CDPL::Biomol
	Contains classes and functions related to biological macromolecules.
	CDPL::Biomol::ControlParameter
	Provides keys for built-in control-parameters.

Variables
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::STRICT_ERROR_CHECKING
	Specifies whether non-fatal recoverable I/O errors should be ignored or cause an I/O operation to fail. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::CHECK_LINE_LENGTH
	Specifies whether to check if data lines exceed the maximum allowed line length when reading or writing data in PDB [PDB] format. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::RESIDUE_DICTIONARY
	Specifies the residue dictionary consulted during PDB and mmCIF I/O when looking up canonical residue atom names, bonding, atom types, or formal charges. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES
	Specifies whether to apply the formal atom charges provided by the residue dictionary during input data post-processing. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES
	Specifies whether to apply the atom types provided by the residue dictionary during input data post-processing. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES
	Specifies whether to calculate formal atomic charges for atoms whose charge could not be obtained from the input data or the residue dictionary. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS
	Specifies whether to perceive bond orders for bonds whose order could not be obtained from the input data or the residue dictionary. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES
	Specifies whether to merge alternative residue conformers whose atoms overlap in space (see Biomol::combineInterferingResidueCoordinates()). More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES
	Specifies whether to use the residue dictionary to derive atom-bonding for atoms of non-standard residues when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES
	Specifies whether to use the residue dictionary to derive atom-bonding for atoms of standard residues when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES
	Specifies whether to apply the residue-dictionary bond orders to bonds of non-standard residues when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES
	Specifies whether to apply the residue-dictionary bond orders to bonds of standard residues when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS
	Specifies whether to skip CONECT records when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS
	Specifies whether to deduce bond orders from the duplication pattern of bonded atom pairs in CONECT records when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD
	Specifies whether to ignore the formal-charge field of ATOM/HETATM records when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD
	Specifies whether to verify the record counts in the PDB MASTER record against the actual numbers observed during input. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_TRUNCATE_LINES
	Specifies whether to truncate output PDB data lines that exceed the maximum allowed line length instead of failing the write operation. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES
	Specifies whether to write the formal-charge field of ATOM/HETATM records when generating PDB output. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS
	Specifies whether to write CONECT records when generating PDB output. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS
	Specifies whether CONECT records shall be written for all bonds (and not only for non-standard ones) when generating PDB output. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER
	Specifies whether CONECT records shall encode the bond order via the duplication count of bonded atom pairs when generating PDB output. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::PDB_FORMAT_VERSION
	Specifies the PDB format version to use when generating PDB output (see Biomol::PDBFormatVersion). More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING
	Specifies whether to use the residue dictionary to derive atom-bonding when reading mmCIF data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS
	Specifies whether to apply the residue-dictionary bond orders when reading mmCIF data. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP
	Specifies whether to emit biopolymer residues using the chem_comp data category (instead of the regular polymer-residue encoding) when generating mmCIF output. More...
CDPL_BIOMOL_API const Base::LookupKey	CDPL::Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION
	Specifies a post-processing function that is applied to the constructed mmCIF data record before it is written to the output stream. More...

Detailed Description

Definition of constants in namespace CDPL::Biomol::ControlParameter.