CDPL::Biomol::ControlParameter Namespace Reference

Provides keys for built-in control-parameters. More...

Variables
CDPL_BIOMOL_API const Base::LookupKey	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	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	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	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	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	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	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	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	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	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	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	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	PDB_IGNORE_CONECT_RECORDS
	Specifies whether to skip CONECT records when reading PDB data. More...
CDPL_BIOMOL_API const Base::LookupKey	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	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	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	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	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	PDB_OUTPUT_CONECT_RECORDS
	Specifies whether to write CONECT records when generating PDB output. More...
CDPL_BIOMOL_API const Base::LookupKey	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	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	PDB_FORMAT_VERSION
	Specifies the PDB format version to use when generating PDB output (see Biomol::PDBFormatVersion). More...
CDPL_BIOMOL_API const Base::LookupKey	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	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	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	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

Provides keys for built-in control-parameters.

Variable Documentation

STRICT_ERROR_CHECKING

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::STRICT_ERROR_CHECKING

extern

Specifies whether non-fatal recoverable I/O errors should be ignored or cause an I/O operation to fail.

If the control-parameter is set to true, not only severe errors cause an I/O operation to fail, but also non-fatal errors from which a recovery would be possible. If the control-parameter is set to false, I/O operations will proceed even if a non-fatal error has been detected.

Value Type: bool

CHECK_LINE_LENGTH

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::CHECK_LINE_LENGTH

extern

Specifies whether to check if data lines exceed the maximum allowed line length when reading or writing data in PDB [PDB] format.

If the control-parameter is set to true, the length of data lines that were read from or have to be written to data encoded in one of the above mentioned formats will be checked against the maximum allowed line length. Lines that exceeded the line length limit are considered as an error condition and cause the input or output operation to fail. If CHECK_LINE_LENGTH is false, the length of data lines will not be checked and has no impact on the success of the performed I/O operation.

Value Type: bool

RESIDUE_DICTIONARY

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::RESIDUE_DICTIONARY

extern

Specifies the residue dictionary consulted during PDB and mmCIF I/O when looking up canonical residue atom names, bonding, atom types, or formal charges.

Value Type: Biomol::ResidueDictionary::SharedPointer

Since

1.2

APPLY_DICT_FORMAL_CHARGES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::APPLY_DICT_FORMAL_CHARGES

extern

Specifies whether to apply the formal atom charges provided by the residue dictionary during input data post-processing.

Value Type: bool

Since

1.2

APPLY_DICT_ATOM_TYPES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::APPLY_DICT_ATOM_TYPES

extern

Specifies whether to apply the atom types provided by the residue dictionary during input data post-processing.

Value Type: bool

Since

1.2

CALC_MISSING_FORMAL_CHARGES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::CALC_MISSING_FORMAL_CHARGES

extern

Specifies whether to calculate formal atomic charges for atoms whose charge could not be obtained from the input data or the residue dictionary.

Value Type: bool

Since

1.2

PERCEIVE_MISSING_BOND_ORDERS

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PERCEIVE_MISSING_BOND_ORDERS

extern

Specifies whether to perceive bond orders for bonds whose order could not be obtained from the input data or the residue dictionary.

Value Type: bool

Since

1.2

COMBINE_INTERFERING_RESIDUE_COORDINATES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::COMBINE_INTERFERING_RESIDUE_COORDINATES

extern

Specifies whether to merge alternative residue conformers whose atoms overlap in space (see Biomol::combineInterferingResidueCoordinates()).

Value Type: bool

PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_NON_STD_RESIDUES

extern

Specifies whether to use the residue dictionary to derive atom-bonding for atoms of non-standard residues when reading PDB data.

Value Type: bool

PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_ATOM_BONDING_TO_STD_RESIDUES

extern

Specifies whether to use the residue dictionary to derive atom-bonding for atoms of standard residues when reading PDB data.

Value Type: bool

PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_NON_STD_RESIDUES

extern

Specifies whether to apply the residue-dictionary bond orders to bonds of non-standard residues when reading PDB data.

Value Type: bool

PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_APPLY_DICT_BOND_ORDERS_TO_STD_RESIDUES

extern

Specifies whether to apply the residue-dictionary bond orders to bonds of standard residues when reading PDB data.

Value Type: bool

PDB_IGNORE_CONECT_RECORDS

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_IGNORE_CONECT_RECORDS

extern

Specifies whether to skip CONECT records when reading PDB data.

Value Type: bool

PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_DEDUCE_BOND_ORDERS_FROM_CONECT_RECORDS

extern

Specifies whether to deduce bond orders from the duplication pattern of bonded atom pairs in CONECT records when reading PDB data.

Value Type: bool

PDB_IGNORE_FORMAL_CHARGE_FIELD

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_IGNORE_FORMAL_CHARGE_FIELD

extern

Specifies whether to ignore the formal-charge field of ATOM/HETATM records when reading PDB data.

Value Type: bool

PDB_EVALUATE_MASTER_RECORD

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_EVALUATE_MASTER_RECORD

extern

Specifies whether to verify the record counts in the PDB MASTER record against the actual numbers observed during input.

Value Type: bool

PDB_TRUNCATE_LINES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_TRUNCATE_LINES

extern

Specifies whether to truncate output PDB data lines that exceed the maximum allowed line length instead of failing the write operation.

Value Type: bool

PDB_OUTPUT_FORMAL_CHARGES

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_OUTPUT_FORMAL_CHARGES

extern

Specifies whether to write the formal-charge field of ATOM/HETATM records when generating PDB output.

Value Type: bool

Since

1.2

PDB_OUTPUT_CONECT_RECORDS

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS

extern

Specifies whether to write CONECT records when generating PDB output.

Value Type: bool

Since

1.2

PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_FOR_ALL_BONDS

extern

Specifies whether CONECT records shall be written for all bonds (and not only for non-standard ones) when generating PDB output.

Value Type: bool

Since

1.2

PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_OUTPUT_CONECT_RECORDS_REFLECTING_BOND_ORDER

extern

Specifies whether CONECT records shall encode the bond order via the duplication count of bonded atom pairs when generating PDB output.

Value Type: bool

Since

1.2

PDB_FORMAT_VERSION

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::PDB_FORMAT_VERSION

extern

Specifies the PDB format version to use when generating PDB output (see Biomol::PDBFormatVersion).

Value Type: unsigned int

MMCIF_APPLY_DICT_ATOM_BONDING

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::MMCIF_APPLY_DICT_ATOM_BONDING

extern

Specifies whether to use the residue dictionary to derive atom-bonding when reading mmCIF data.

Value Type: bool

Since

1.2

MMCIF_APPLY_DICT_BOND_ORDERS

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::MMCIF_APPLY_DICT_BOND_ORDERS

extern

Specifies whether to apply the residue-dictionary bond orders when reading mmCIF data.

Value Type: bool

Since

1.2

MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::MMCIF_OUTPUT_BIOPOLYMERS_AS_CHEM_COMP

extern

Specifies whether to emit biopolymer residues using the chem_comp data category (instead of the regular polymer-residue encoding) when generating mmCIF output.

Value Type: bool

Since

1.2

MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION

CDPL_BIOMOL_API const Base::LookupKey CDPL::Biomol::ControlParameter::MMCIF_OUTPUT_DATA_POSTPROC_FUNCTION

extern

Specifies a post-processing function that is applied to the constructed mmCIF data record before it is written to the output stream.

Value Type: Biomol::MMCIFDataProcessingFunction

Since

1.2