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

Variables
CDPL_CHEM_API const Base::LookupKey	ORDINARY_HYDROGEN_DEPLETE
	Specifies whether the calculation of a molecular property has to be performed for the ordinary hydrogen deplete input structure. More...

CDPL_CHEM_API const Base::LookupKey	COORDINATES_DIMENSION
	Specifies the dimension of atom coordinates. More...

CDPL_CHEM_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_CHEM_API const Base::LookupKey	RECORD_SEPARATOR
	Specifies the separator for SMILES, SMARTS, JME and InChI output data records [SMILES, SMARTS, JME, INCHI]. More...

CDPL_CHEM_API const Base::LookupKey	BOND_MEMBER_SWAP_STEREO_FIX
	Specifies whether unsupported reverse stereo bonds shall be converted to regular stereo bonds by swapping bond start and end atoms. More...

CDPL_CHEM_API const Base::LookupKey	MDL_CTAB_VERSION
	Specifies the desired version of the connection table data format for the output of molecular graphs in MDL SD- or Mol-File format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_IGNORE_PARITY
	Specifies whether the stereo parity of atoms shall be ignored when reading or writing data in a MDL CTFile based format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_UPDATE_TIMESTAMP
	Specifies whether to update the timestamp of Mol- and Rxn-File header blocks when writing data in a MDL CTFile based format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_TRIM_STRINGS
	Specifies whether to remove leading and trailing whitespace from string values when reading or writing data in a MDL CTFile based format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_TRIM_LINES
	Specifies whether to remove leading and trailing whitespace from data lines when reading or writing data in a MDL CTFile based format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_TRUNCATE_STRINGS
	Specifies whether string values that exceed the size of an output data field may be truncated when writing data in a MDL CTFile based format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_TRUNCATE_LINES
	Specifies whether data lines that exceed the maximum allowed line length may be truncated when writing data in a MDL CTFile based format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD

CDPL_CHEM_API const Base::LookupKey	MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY

CDPL_CHEM_API const Base::LookupKey	MDL_CONF_ENERGY_SD_TAG

CDPL_CHEM_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 a MDL [CTFILE] format. More...

CDPL_CHEM_API const Base::LookupKey	MDL_RXN_FILE_VERSION
	Specifies the desired data format version for the output of reactions in MDL Rxn- or RD-File format [CTFILE]. More...

CDPL_CHEM_API const Base::LookupKey	JME_SEPARATE_COMPONENTS
	Specifies for the output of data in JME format [JME] whether the components of a molecular graph shall be written separately or all together as a single JME component. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_RECORD_FORMAT
	Specifies the format of SMILES molecular graph or reaction data records [SMILES]. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_CANONICAL_FORM
	Specifies whether to generate canonical SMILES strings [SMILES]. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_KEKULE_FORM
	Specifies whether to generate SMILES strings [SMILES] with kekulized aromatic rings. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_ATOM_STEREO
	Specifies whether to generate SMILES strings [SMILES] with atom parity specifications. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_BOND_STEREO
	Specifies whether to generate SMILES strings [SMILES] that include directional bonds for the definition of double bond geometries. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_RING_BOND_STEREO
	Specifies whether to generate SMILES strings [SMILES] that also include directional bonds for the definition of ring double bond geometries. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_MIN_STEREO_BOND_RING_SIZE
	Specifies the minimum ring size that is required for the specification of ring double bond geometries in generated SMILES strings [SMILES]. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_ISOTOPE
	Specifies whether to generate SMILES strings [SMILES] with isotopic mass specifications. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_MOL_WRITE_ATOM_MAPPING_ID
	Specifies whether to generate molecule SMILES strings [SMILES] that contain reaction atom-atom mapping numbers. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_RXN_WRITE_ATOM_MAPPING_ID
	Specifies whether to generate reaction SMILES strings [SMILES] that contain reaction atom-atom mapping numbers. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_SINGLE_BONDS
	Specifies whether to generate SMILES strings [SMILES] with explicit single bond specifications. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_WRITE_AROMATIC_BONDS
	Specifies whether to generate SMILES strings [SMILES] with explicit aromatic bond specifications. More...

CDPL_CHEM_API const Base::LookupKey	SMILES_NO_ORGANIC_SUBSET
	Specifies whether to generate SMILES strings [SMILES] where all atom symbols are enclosed in brackets. More...

CDPL_CHEM_API const Base::LookupKey	INCHI_INPUT_OPTIONS
	Specifies options for the input of InChI strings [INCHI]. More...

CDPL_CHEM_API const Base::LookupKey	INCHI_OUTPUT_OPTIONS
	Specifies options for the output of InChI strings [INCHI]. More...

CDPL_CHEM_API const Base::LookupKey	MULTI_CONF_IMPORT
	Specifies whether to check for and import multi-conformer molecules. Value Type: `bool`. More...

CDPL_CHEM_API const Base::LookupKey	MULTI_CONF_EXPORT
	Specifies whether to write all molecule conformations on output. Value Type: `bool`. More...

CDPL_CHEM_API const Base::LookupKey	OUTPUT_CONF_ENERGY_AS_COMMENT

CDPL_CHEM_API const Base::LookupKey	CONF_INDEX_NAME_SUFFIX_PATTERN

CDPL_CHEM_API const Base::LookupKey	MULTI_CONF_INPUT_PROCESSOR
	Specifies an instance of Chem::MultiConfMoleculeInputProcessor that implements the logic of multi-conformer molecule detection and conformational data processing. Value Type: `Chem::MultiConfMoleculeInputProcessor::SharedPointer`. More...

CDPL_CHEM_API const Base::LookupKey	CDF_WRITE_SINGLE_PRECISION_FLOATS

CDPL_CHEM_API const Base::LookupKey	MOL2_ENABLE_EXTENDED_ATOM_TYPES

CDPL_CHEM_API const Base::LookupKey	MOL2_ENABLE_AROMATIC_BOND_TYPES

CDPL_CHEM_API const Base::LookupKey	MOL2_CALC_FORMAL_CHARGES

CDPL_CHEM_API const Base::LookupKey	MOL2_CHARGE_TYPE

CDPL_CHEM_API const Base::LookupKey	MOL2_MOLECULE_TYPE

CDPL_CHEM_API const Base::LookupKey	MOL2_OUTPUT_SUBSTRUCTURES

CDPL_CHEM_API const Base::LookupKey	XYZ_COMMENT_IS_NAME

CDPL_CHEM_API const Base::LookupKey	XYZ_PERCEIVE_CONNECTIVITY

CDPL_CHEM_API const Base::LookupKey	XYZ_PERCEIVE_BOND_ORDERS

CDPL_CHEM_API const Base::LookupKey	XYZ_CALC_FORMAL_CHARGES

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_XML_DECLARATION

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_ELEMENT_NAMESPACE

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_ATOM_PARITY

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_SINGLE_BOND_STEREO

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_DOUBLE_BOND_STEREO

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_KEKULE_FORM

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_MOLECULE_NAME

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_STRUCTURE_DATA

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_ISOTOPE

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_SPIN_MULTIPLICITY

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_COMPACT_ATOM_DATA

CDPL_CHEM_API const Base::LookupKey	CML_OUTPUT_COMPACT_BOND_DATA

Detailed Description

Provides keys for built-in control-parameters.

Variable Documentation

◆ ORDINARY_HYDROGEN_DEPLETE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE

extern

Specifies whether the calculation of a molecular property has to be performed for the ordinary hydrogen deplete input structure.

If the control-parameter is set to true, the calculation result will be equivalent to the result that would have been obtained for the ordinary hydrogen deplete input structure. If the control-parameter is set to false, the calculation will be performed for the unmodified molecular graph.

Value Type: bool

See also: Chem::AtomProperty::IS_ORDINARY_H for the definition of ordinary hydrogens.

◆ COORDINATES_DIMENSION

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::COORDINATES_DIMENSION

extern

Specifies the dimension of atom coordinates.

A control-parameter value of 2 specifies 2D-coordinates and a value of 3 3D-coordinates. Other values trigger the selection of an implementation defined default dimension.

Value Type: std::size_t

◆ STRICT_ERROR_CHECKING

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::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

◆ RECORD_SEPARATOR

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::RECORD_SEPARATOR

extern

Specifies the separator for SMILES, SMARTS, JME and InChI output data records [SMILES, SMARTS, JME, INCHI].

Typical separators are, for example, space (" "), tab ("\t") or newline ("\n").

Value Type: std::string

◆ BOND_MEMBER_SWAP_STEREO_FIX

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX

extern

Specifies whether unsupported reverse stereo bonds shall be converted to regular stereo bonds by swapping bond start and end atoms.

Most molecule storage formats do not support the concept of reverse stereo bonds (see Chem::BondStereoFlag). To allow the output of such bonds without loss of the provided spatial information, an implicit conversion of the reverse stereo bonds to sterically equivalent regular stereo bonds is required. This may be done either by replacing the reverse stereo specification with a regular stereo specification of the opposite type (e.g. Chem::BondStereoFlag::REVERSE_UP is equivalent to Chem::BondStereoFlag::DOWN), or by swapping the start and end atom of the bond and replacing the reverse stereo flag by a regular stereo flag of the same type (e.g. Chem::BondStereoFlag::REVERSE_UP is equivalent to Chem::BondStereoFlag::UP when the start and end atoms are exchanged).

The value of this control-parameter specifies which method of conversion shall be used. If the control-parameter is set to true the latter method will be used, and the former method otherwise.

Value Type: bool

◆ MDL_CTAB_VERSION

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_CTAB_VERSION

extern

Specifies the desired version of the connection table data format for the output of molecular graphs in MDL SD- or Mol-File format [CTFILE].

The desired data format version is specified by one of the constants defined in namespace CDPL::Chem::MDLDataFormatVersion. If MDL_CTAB_VERSION has not been set or the parameter value equals CDPL::Chem::MDLDataFormatVersion::UNDEF, the format specified by the Chem::MolecularGraph property Chem::MolecularGraphProperty::MDL_CTAB_VERSION will take effect.

If, after all, both the control-parameter and the property do not specify a particular connection table format version, a suitable output format is chosen as follows:

if both the atom and bond count of the molecular graph is less than 1000, data will be written in the V2000 format
and in the format V3000 otherwise

Value Type: unsigned int

◆ MDL_IGNORE_PARITY

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_IGNORE_PARITY

extern

Specifies whether the stereo parity of atoms shall be ignored when reading or writing data in a MDL CTFile based format [CTFILE].

If the control-parameter is set to true, the stereo parity of atoms will be ignored both on reading (i.e. the read MDL parity of an input atom will not be converted to the corresponding Chem::StereoDescriptor object and stored in the Chem::Atom property Chem::AtomProperty::STEREO_DESCRIPTOR) and writing (i.e. the property Chem::AtomProperty::MDL_PARITY is not written to the corresponding connection table data field).

Value Type: bool

◆ MDL_UPDATE_TIMESTAMP

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_UPDATE_TIMESTAMP

extern

Specifies whether to update the timestamp of Mol- and Rxn-File header blocks when writing data in a MDL CTFile based format [CTFILE].

If the control-parameter is set to true, the timestamp of molecule and reaction data records will specify the time of their writing. If MDL_UPDATE_TIMESTAMP is false, the time specified by one of the properties Chem::MolecularGraphProperty::MDL_TIMESTAMP (for molecular graph output) or Chem::ReactionProperty::MDL_TIMESTAMP (for reaction output) will be used. If the output data object does not provide a value for the timestamp property, the current time will be used as a fallback.

Value Type: bool

◆ MDL_TRIM_STRINGS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_TRIM_STRINGS

extern

Specifies whether to remove leading and trailing whitespace from string values when reading or writing data in a MDL CTFile based format [CTFILE].

If the control-parameter is set to true, leading and trailing whitespace of string data field values will be removed before processing continues. Otherwise, whitespace is considered to be significant and will be preserved.

Value Type: bool

◆ MDL_TRIM_LINES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_TRIM_LINES

extern

Specifies whether to remove leading and trailing whitespace from data lines when reading or writing data in a MDL CTFile based format [CTFILE].

If the control-parameter is set to true, leading and trailing whitespace of data lines will be removed before processing continues. Otherwise, whitespace is considered to be significant and will be preserved.

Value Type: bool

◆ MDL_TRUNCATE_STRINGS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_TRUNCATE_STRINGS

extern

Specifies whether string values that exceed the size of an output data field may be truncated when writing data in a MDL CTFile based format [CTFILE].

If the control-parameter is set to true, output string values whose length exceeds the size of the target data field are silently truncated to the respective field size. If MDL_TRUNCATE_STRINGS is false, the attempt to write a string value which is too large for the target data field is considered as an error condition and causes the output operation to fail.

Value Type: bool

◆ MDL_TRUNCATE_LINES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_TRUNCATE_LINES

extern

Specifies whether data lines that exceed the maximum allowed line length may be truncated when writing data in a MDL CTFile based format [CTFILE].

If the control-parameter is set to true, output data lines which exceed the maximum allowed line length (according to the MDL CTFile specification) are silently truncated before they get written. If MDL_TRUNCATE_LINES is false, an attempt to write a data line that exceeds maximum line length is considered as an error condition and causes the output operation to fail.

Value Type: bool

Note: The setting has only an effect if the control-parameter Chem::ControlParameter::IGNORE_LINE_LENGTH_LIMIT is false.

◆ MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD

extern

◆ MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY

extern

◆ MDL_CONF_ENERGY_SD_TAG

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_CONF_ENERGY_SD_TAG

extern

◆ CHECK_LINE_LENGTH

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CHECK_LINE_LENGTH

extern

Specifies whether to check if data lines exceed the maximum allowed line length when reading or writing data in a MDL [CTFILE] 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

◆ MDL_RXN_FILE_VERSION

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MDL_RXN_FILE_VERSION

extern

Specifies the desired data format version for the output of reactions in MDL Rxn- or RD-File format [CTFILE].

The desired data format version is specified by one of the constants defined in namespace CDPL::Chem::MDLDataFormatVersion. If MDL_RXN_FILE_VERSION has not been set or the parameter value equals CDPL::Chem::MDLDataFormatVersion::UNDEF, the format specified by the Chem::Reaction property Chem::ReactionProperty::MDL_RXN_FILE_VERSION will take effect.

If, after all, both the control-parameter and the property do not specify a particular Rxn-File format version, a suitable output format is chosen as follows:

if both the reactant and product count of the output reaction is less than 1000, data will be written in the V2000 format
and in the format V3000 otherwise

Value Type: unsigned int

◆ JME_SEPARATE_COMPONENTS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::JME_SEPARATE_COMPONENTS

extern

Specifies for the output of data in JME format [JME] whether the components of a molecular graph shall be written separately or all together as a single JME component.

If the control-parameter is set to true, each component of a molecular graph will be represented by a corresponding JME molecule component in the output data record. If JME_SEPARATE_COMPONENTS is false, the components of the output molecular graph are written all together as a single JME component.

Value Type: bool

◆ SMILES_RECORD_FORMAT

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_RECORD_FORMAT

extern

Specifies the format of SMILES molecular graph or reaction data records [SMILES].

The data record format is specified by one of the two following format strings:

"S"
"SN"

The character 'S' denotes the SMILES representation of the molecular graph or reaction, and 'N' the name of the molecular graph/reaction (see Chem::MolecularGraphProperty::NAME and Chem::ReactionProperty::NAME).

Value Type: std::string

◆ SMILES_WRITE_CANONICAL_FORM

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_CANONICAL_FORM

extern

Specifies whether to generate canonical SMILES strings [SMILES].

If the control-parameter is set to true, canonical SMILES strings will be generated. A canonical SMILES string is unique for a given chemical structure and is always identical regardless of the atom and bond order in the Chem::MolecularGraph object that describes the structure. If the value of SMILES_WRITE_CANONICAL_FORM is false, the form of a generated SMILES string depends on the order of the atoms and bonds in the output molecular graph and thus may differ across a set of Chem::MolecularGraph objects that otherwise represent the same chemical structure.

Value Type: bool

◆ SMILES_WRITE_KEKULE_FORM

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_KEKULE_FORM

extern

Specifies whether to generate SMILES strings [SMILES] with kekulized aromatic rings.

If the control-parameter is set to true, aromatic rings will be represented as Kekulé structures with standard (non-lowercase) atom element symbols and localized bond orders. If the value of SMILES_WRITE_KEKULE_FORM is false, the order of localized aromatic bonds is left unspecified and aromatic atoms of type C, N, O, S, Se, Te or As will be indicated by lowercase atom element symbols.

Value Type: bool

◆ SMILES_WRITE_ATOM_STEREO

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_ATOM_STEREO

extern

Specifies whether to generate SMILES strings [SMILES] with atom parity specifications.

If the control-parameter is set to true, the generated SMILES string will specify the parity of terahedral stereogenic atoms. If the value of the control-parameter is false, the parity of stereogenic atoms is left unspecified.

Value Type: bool

◆ SMILES_WRITE_BOND_STEREO

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_BOND_STEREO

extern

Specifies whether to generate SMILES strings [SMILES] that include directional bonds for the definition of double bond geometries.

If the control-parameter is set to true, the generated SMILES string will contain directional bonds for the specification of chain double bond geometries. If the value of the control-parameter is false, the geometry of double bonds is left unspecified.

Value Type: bool

◆ SMILES_WRITE_RING_BOND_STEREO

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_RING_BOND_STEREO

extern

Specifies whether to generate SMILES strings [SMILES] that also include directional bonds for the definition of ring double bond geometries.

If the control-parameter is set to true, the generated SMILES string will specify the geometry of any double bond that is not a member of a ring which is smaller than the size specified by Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE. If the value of the control-parameter is false, the geometry of ring double bonds will not be specified.

Value Type: bool

Note: The setting of this control-parameter has only an effect if Chem::ControlParameter::SMILES_WRITE_BOND_STEREO is set to true.

◆ SMILES_MIN_STEREO_BOND_RING_SIZE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE

extern

Specifies the minimum ring size that is required for the specification of ring double bond geometries in generated SMILES strings [SMILES].

Value Type: std::size_t

See also: Chem::ControlParameter::SMILES_WRITE_RING_BOND_STEREO

◆ SMILES_WRITE_ISOTOPE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_ISOTOPE

extern

Specifies whether to generate SMILES strings [SMILES] with isotopic mass specifications.

If the control-parameter is set to true, the generated SMILES string will specify the isotopic mass of of atoms (if non-standard). If the value of SMILES_WRITE_ISOTOPE is false, the isotopic mass is left unspecified.

Value Type: bool

◆ SMILES_MOL_WRITE_ATOM_MAPPING_ID

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_MOL_WRITE_ATOM_MAPPING_ID

extern

Specifies whether to generate molecule SMILES strings [SMILES] that contain reaction atom-atom mapping numbers.

If the control-parameter is set to true, the generated SMILES string will specify reaction atom-atom mapping numbers (see Chem::AtomProperty::REACTION_ATOM_MAPPING_ID). If the value of SMILES_WRITE_ATOM_MAPPING_ID is false, atom-atom mapping numbers will not be specified.

Value Type: bool

◆ SMILES_RXN_WRITE_ATOM_MAPPING_ID

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_RXN_WRITE_ATOM_MAPPING_ID

extern

Specifies whether to generate reaction SMILES strings [SMILES] that contain reaction atom-atom mapping numbers.

If the control-parameter is set to true, the generated SMILES string will specify reaction atom-atom mapping numbers (see Chem::AtomProperty::REACTION_ATOM_MAPPING_ID). If the value of SMILES_WRITE_ATOM_MAPPING_ID is false, atom-atom mapping numbers will not be specified.

Value Type: bool

◆ SMILES_WRITE_SINGLE_BONDS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_SINGLE_BONDS

extern

Specifies whether to generate SMILES strings [SMILES] with explicit single bond specifications.

If the control-parameter is set to true, generated SMILES strings will not only specify double and triple bonds, but also single bonds. If the value of SMILES_WRITE_SINGLE_BONDS is false, single bonds are left unspecified.

Value Type: bool

◆ SMILES_WRITE_AROMATIC_BONDS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_WRITE_AROMATIC_BONDS

extern

Specifies whether to generate SMILES strings [SMILES] with explicit aromatic bond specifications.

If the control-parameter is set to true, generated SMILES strings will explicitly specify aromatic bonds. If the value of SMILES_WRITE_AROMATIC_BONDS is false, aromatic bonds are left unspecified.

Value Type: bool

Note: The setting of this control-parameter has only an effect if Chem::ControlParameter::SMILES_WRITE_KEKULE_FORM is set to false.

◆ SMILES_NO_ORGANIC_SUBSET

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET

extern

Specifies whether to generate SMILES strings [SMILES] where all atom symbols are enclosed in brackets.

If the control-parameter is set to true, SMILES strings will be generated where all atoms are enclosed in square brackets regardless of their atom type and the necessity to specify additional atom properties. If the value of SMILES_NO_ORGANIC_SUBSET is false, only those atoms will be enclosed in brackets that require the specification of additional atomic properties (charge, hydrogen count, isotope, ...) or are not part of the organic subset (i.e. C, N, O, S, P, F, Cl, Br and I).

Value Type: bool

◆ INCHI_INPUT_OPTIONS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::INCHI_INPUT_OPTIONS

extern

Specifies options for the input of InChI strings [INCHI].

Please refer to the InChI C-API documentation [INCHI] for further information about the syntax and meaning of the available options.

Value Type: std::string

◆ INCHI_OUTPUT_OPTIONS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::INCHI_OUTPUT_OPTIONS

extern

Specifies options for the output of InChI strings [INCHI].

Please refer to the InChI C-API documentation [INCHI] for further information about the syntax and meaning of the available options.

Value Type: std::string

◆ MULTI_CONF_IMPORT

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MULTI_CONF_IMPORT

extern

Specifies whether to check for and import multi-conformer molecules. Value Type: bool.

◆ MULTI_CONF_EXPORT

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MULTI_CONF_EXPORT

extern

Specifies whether to write all molecule conformations on output. Value Type: bool.

◆ OUTPUT_CONF_ENERGY_AS_COMMENT

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COMMENT

extern

◆ CONF_INDEX_NAME_SUFFIX_PATTERN

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CONF_INDEX_NAME_SUFFIX_PATTERN

extern

◆ MULTI_CONF_INPUT_PROCESSOR

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR

extern

Specifies an instance of Chem::MultiConfMoleculeInputProcessor that implements the logic of multi-conformer molecule detection and conformational data processing. Value Type: Chem::MultiConfMoleculeInputProcessor::SharedPointer.

◆ CDF_WRITE_SINGLE_PRECISION_FLOATS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CDF_WRITE_SINGLE_PRECISION_FLOATS

extern

◆ MOL2_ENABLE_EXTENDED_ATOM_TYPES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MOL2_ENABLE_EXTENDED_ATOM_TYPES

extern

◆ MOL2_ENABLE_AROMATIC_BOND_TYPES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MOL2_ENABLE_AROMATIC_BOND_TYPES

extern

◆ MOL2_CALC_FORMAL_CHARGES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MOL2_CALC_FORMAL_CHARGES

extern

◆ MOL2_CHARGE_TYPE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MOL2_CHARGE_TYPE

extern

◆ MOL2_MOLECULE_TYPE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MOL2_MOLECULE_TYPE

extern

◆ MOL2_OUTPUT_SUBSTRUCTURES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::MOL2_OUTPUT_SUBSTRUCTURES

extern

◆ XYZ_COMMENT_IS_NAME

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::XYZ_COMMENT_IS_NAME

extern

◆ XYZ_PERCEIVE_CONNECTIVITY

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::XYZ_PERCEIVE_CONNECTIVITY

extern

◆ XYZ_PERCEIVE_BOND_ORDERS

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::XYZ_PERCEIVE_BOND_ORDERS

extern

◆ XYZ_CALC_FORMAL_CHARGES

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::XYZ_CALC_FORMAL_CHARGES

extern

◆ CML_OUTPUT_XML_DECLARATION

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_XML_DECLARATION

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_ELEMENT_NAMESPACE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_ELEMENT_NAMESPACE

extern

Value Type: std::string

Since: 1.2

◆ CML_OUTPUT_ATOM_PARITY

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_ATOM_PARITY

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_SINGLE_BOND_STEREO

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_SINGLE_BOND_STEREO

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_DOUBLE_BOND_STEREO

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_DOUBLE_BOND_STEREO

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_KEKULE_FORM

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_KEKULE_FORM

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_MOLECULE_NAME

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_MOLECULE_NAME

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_STRUCTURE_DATA

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_STRUCTURE_DATA

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_ISOTOPE

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_ISOTOPE

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_SPIN_MULTIPLICITY

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_SPIN_MULTIPLICITY

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_COMPACT_ATOM_DATA

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_COMPACT_ATOM_DATA

extern

Value Type: bool

Since: 1.2

◆ CML_OUTPUT_COMPACT_BOND_DATA

CDPL_CHEM_API const Base::LookupKey CDPL::Chem::ControlParameter::CML_OUTPUT_COMPACT_BOND_DATA

extern

Value Type: bool

Since: 1.2

Variables

Detailed Description

Variable Documentation

◆ ORDINARY_HYDROGEN_DEPLETE

◆ COORDINATES_DIMENSION

◆ STRICT_ERROR_CHECKING

◆ RECORD_SEPARATOR

◆ BOND_MEMBER_SWAP_STEREO_FIX

◆ MDL_CTAB_VERSION

◆ MDL_IGNORE_PARITY

◆ MDL_UPDATE_TIMESTAMP

◆ MDL_TRIM_STRINGS

◆ MDL_TRIM_LINES

◆ MDL_TRUNCATE_STRINGS

◆ MDL_TRUNCATE_LINES

◆ MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD

◆ MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY

◆ MDL_CONF_ENERGY_SD_TAG

◆ CHECK_LINE_LENGTH

◆ MDL_RXN_FILE_VERSION

◆ JME_SEPARATE_COMPONENTS

◆ SMILES_RECORD_FORMAT

◆ SMILES_WRITE_CANONICAL_FORM

◆ SMILES_WRITE_KEKULE_FORM

◆ SMILES_WRITE_ATOM_STEREO

◆ SMILES_WRITE_BOND_STEREO

◆ SMILES_WRITE_RING_BOND_STEREO

◆ SMILES_MIN_STEREO_BOND_RING_SIZE

◆ SMILES_WRITE_ISOTOPE

◆ SMILES_MOL_WRITE_ATOM_MAPPING_ID

◆ SMILES_RXN_WRITE_ATOM_MAPPING_ID

◆ SMILES_WRITE_SINGLE_BONDS

◆ SMILES_WRITE_AROMATIC_BONDS

◆ SMILES_NO_ORGANIC_SUBSET

◆ INCHI_INPUT_OPTIONS

◆ INCHI_OUTPUT_OPTIONS

◆ MULTI_CONF_IMPORT

◆ MULTI_CONF_EXPORT

◆ OUTPUT_CONF_ENERGY_AS_COMMENT

◆ CONF_INDEX_NAME_SUFFIX_PATTERN

◆ MULTI_CONF_INPUT_PROCESSOR

◆ CDF_WRITE_SINGLE_PRECISION_FLOATS

◆ MOL2_ENABLE_EXTENDED_ATOM_TYPES

◆ MOL2_ENABLE_AROMATIC_BOND_TYPES

◆ MOL2_CALC_FORMAL_CHARGES

◆ MOL2_CHARGE_TYPE

◆ MOL2_MOLECULE_TYPE

◆ MOL2_OUTPUT_SUBSTRUCTURES

◆ XYZ_COMMENT_IS_NAME

◆ XYZ_PERCEIVE_CONNECTIVITY

◆ XYZ_PERCEIVE_BOND_ORDERS

◆ XYZ_CALC_FORMAL_CHARGES

◆ CML_OUTPUT_XML_DECLARATION

◆ CML_OUTPUT_ELEMENT_NAMESPACE

◆ CML_OUTPUT_ATOM_PARITY

◆ CML_OUTPUT_SINGLE_BOND_STEREO

◆ CML_OUTPUT_DOUBLE_BOND_STEREO

◆ CML_OUTPUT_KEKULE_FORM

◆ CML_OUTPUT_MOLECULE_NAME

◆ CML_OUTPUT_STRUCTURE_DATA

◆ CML_OUTPUT_ISOTOPE

◆ CML_OUTPUT_SPIN_MULTIPLICITY

◆ CML_OUTPUT_COMPACT_ATOM_DATA

◆ CML_OUTPUT_COMPACT_BOND_DATA