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

Inheritance diagram for CDPL.Chem.ControlParameter:

Static Public Attributes
	COORDINATES_DIMENSION = CDPL.Base.LookupKey('COORDINATES_DIMENSION')
	Specifies the dimension of atom coordinates. More...

	ORDINARY_HYDROGEN_DEPLETE = CDPL.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...

	STRICT_ERROR_CHECKING = CDPL.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...

	BOND_MEMBER_SWAP_STEREO_FIX = CDPL.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...

	CHECK_LINE_LENGTH = CDPL.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...

	RECORD_SEPARATOR = CDPL.Base.LookupKey('RECORD_SEPARATOR')
	Specifies the separator for SMILES, SMARTS, JME and InChI output data records [SMILES, SMARTS, JME, INCHI]. More...

	JME_SEPARATE_COMPONENTS = CDPL.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...

	MDL_CTAB_VERSION = CDPL.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...

	MDL_IGNORE_PARITY = CDPL.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...

	MDL_RXN_FILE_VERSION = CDPL.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...

	MDL_TRIM_LINES = CDPL.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...

	MDL_TRIM_STRINGS = CDPL.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...

	MDL_TRUNCATE_LINES = CDPL.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...

	MDL_TRUNCATE_STRINGS = CDPL.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...

	MDL_UPDATE_TIMESTAMP = CDPL.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...

	MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD = CDPL.Base.LookupKey('MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD')

	MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY = CDPL.Base.LookupKey('MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY')

	MDL_CONF_ENERGY_SD_TAG = CDPL.Base.LookupKey('MDL_CONF_ENERGY_SD_TAG')

	SMILES_RECORD_FORMAT = CDPL.Base.LookupKey('SMILES_RECORD_FORMAT')
	Specifies the format of SMILES molecular graph or reaction data records [SMILES]. More...

	SMILES_MIN_STEREO_BOND_RING_SIZE = CDPL.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...

	SMILES_NO_ORGANIC_SUBSET = CDPL.Base.LookupKey('SMILES_NO_ORGANIC_SUBSET')
	Specifies whether to generate SMILES strings [SMILES] where all atom symbols are enclosed in brackets. More...

	SMILES_WRITE_AROMATIC_BONDS = CDPL.Base.LookupKey('SMILES_WRITE_AROMATIC_BONDS')
	Specifies whether to generate SMILES strings [SMILES] with explicit aromatic bond specifications. More...

	SMILES_WRITE_ISOTOPE = CDPL.Base.LookupKey('SMILES_WRITE_ISOTOPE')
	Specifies whether to generate SMILES strings [SMILES] with isotopic mass specifications. More...

	SMILES_MOL_WRITE_ATOM_MAPPING_ID = CDPL.Base.LookupKey('SMILES_MOL_WRITE_ATOM_MAPPING_ID')
	Specifies whether to generate molecule SMILES strings [SMILES] that contain reaction atom-atom mapping numbers. More...

	SMILES_RXN_WRITE_ATOM_MAPPING_ID = CDPL.Base.LookupKey('SMILES_RXN_WRITE_ATOM_MAPPING_ID')
	Specifies whether to generate reaction SMILES strings [SMILES] that contain reaction atom-atom mapping numbers. More...

	SMILES_WRITE_ATOM_STEREO = CDPL.Base.LookupKey('SMILES_WRITE_ATOM_STEREO')
	Specifies whether to generate SMILES strings [SMILES] with atom parity specifications. More...

	SMILES_WRITE_BOND_STEREO = CDPL.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...

	SMILES_WRITE_CANONICAL_FORM = CDPL.Base.LookupKey('SMILES_WRITE_CANONICAL_FORM')
	Specifies whether to generate canonical SMILES strings [SMILES]. More...

	SMILES_WRITE_KEKULE_FORM = CDPL.Base.LookupKey('SMILES_WRITE_KEKULE_FORM')
	Specifies whether to generate SMILES strings [SMILES] with kekulized aromatic rings. More...

	SMILES_WRITE_RING_BOND_STEREO = CDPL.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...

	SMILES_WRITE_SINGLE_BONDS = CDPL.Base.LookupKey('SMILES_WRITE_SINGLE_BONDS')
	Specifies whether to generate SMILES strings [SMILES] with explicit single bond specifications. More...

	INCHI_INPUT_OPTIONS = CDPL.Base.LookupKey('INCHI_INPUT_OPTIONS')
	Specifies options for the input of InChI strings [INCHI]. More...

	INCHI_OUTPUT_OPTIONS = CDPL.Base.LookupKey('INCHI_OUTPUT_OPTIONS')
	Specifies options for the output of InChI strings [INCHI]. More...

	MULTI_CONF_IMPORT = CDPL.Base.LookupKey('MULTI_CONF_IMPORT')
	Specifies whether to check for and import multi-conformer molecules. More...

	MULTI_CONF_EXPORT = CDPL.Base.LookupKey('MULTI_CONF_EXPORT')
	Specifies whether to write all molecule conformations on output. More...

	MULTI_CONF_INPUT_PROCESSOR = CDPL.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. More...

	OUTPUT_CONF_ENERGY_AS_COMMENT = CDPL.Base.LookupKey('OUTPUT_CONF_ENERGY_AS_COMMENT')

	CONF_INDEX_NAME_SUFFIX_PATTERN = CDPL.Base.LookupKey('CONF_INDEX_NAME_SUFFIX_PATTERN')

	CDF_WRITE_SINGLE_PRECISION_FLOATS = CDPL.Base.LookupKey('CDF_WRITE_SINGLE_PRECISION_FLOATS')

	MOL2_ENABLE_EXTENDED_ATOM_TYPES = CDPL.Base.LookupKey('MOL2_ENABLE_EXTENDED_ATOM_TYPES')

	MOL2_ENABLE_AROMATIC_BOND_TYPES = CDPL.Base.LookupKey('MOL2_ENABLE_AROMATIC_BOND_TYPES')

	MOL2_CALC_FORMAL_CHARGES = CDPL.Base.LookupKey('MOL2_CALC_FORMAL_CHARGES')

	MOL2_CHARGE_TYPE = CDPL.Base.LookupKey('MOL2_CHARGE_TYPE')

	MOL2_OUTPUT_SUBSTRUCTURES = CDPL.Base.LookupKey('MOL2_OUTPUT_SUBSTRUCTURES')

	MOL2_MOLECULE_TYPE = CDPL.Base.LookupKey('MOL2_MOLECULE_TYPE')

	COMMENT_IS_NAME = CDPL.Base.LookupKey('XYZ_COMMENT_IS_NAME')

	XYZ_PERCEIVE_CONNECTIVITY = CDPL.Base.LookupKey('XYZ_PERCEIVE_CONNECTIVITY')

	XYZ_PERCEIVE_BOND_ORDERS = CDPL.Base.LookupKey('XYZ_PERCEIVE_BOND_ORDERS')

	XYZ_CALC_FORMAL_CHARGES = CDPL.Base.LookupKey('XYZ_CALC_FORMAL_CHARGES')

Detailed Description

Provides keys for built-in control-parameters.

Member Data Documentation

◆ COORDINATES_DIMENSION

CDPL.Chem.ControlParameter.COORDINATES_DIMENSION = CDPL.Base.LookupKey('COORDINATES_DIMENSION')

static

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

◆ ORDINARY_HYDROGEN_DEPLETE

CDPL.Chem.ControlParameter.ORDINARY_HYDROGEN_DEPLETE = CDPL.Base.LookupKey('ORDINARY_HYDROGEN_DEPLETE')

static

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.

◆ STRICT_ERROR_CHECKING

CDPL.Chem.ControlParameter.STRICT_ERROR_CHECKING = CDPL.Base.LookupKey('STRICT_ERROR_CHECKING')

static

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

◆ BOND_MEMBER_SWAP_STEREO_FIX

CDPL.Chem.ControlParameter.BOND_MEMBER_SWAP_STEREO_FIX = CDPL.Base.LookupKey('BOND_MEMBER_SWAP_STEREO_FIX')

static

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

◆ CHECK_LINE_LENGTH

CDPL.Chem.ControlParameter.CHECK_LINE_LENGTH = CDPL.Base.LookupKey('CHECK_LINE_LENGTH')

static

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

◆ RECORD_SEPARATOR

CDPL.Chem.ControlParameter.RECORD_SEPARATOR = CDPL.Base.LookupKey('RECORD_SEPARATOR')

static

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

◆ JME_SEPARATE_COMPONENTS

CDPL.Chem.ControlParameter.JME_SEPARATE_COMPONENTS = CDPL.Base.LookupKey('JME_SEPARATE_COMPONENTS')

static

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

◆ MDL_CTAB_VERSION

CDPL.Chem.ControlParameter.MDL_CTAB_VERSION = CDPL.Base.LookupKey('MDL_CTAB_VERSION')

static

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.ControlParameter.MDL_IGNORE_PARITY = CDPL.Base.LookupKey('MDL_IGNORE_PARITY')

static

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_RXN_FILE_VERSION

CDPL.Chem.ControlParameter.MDL_RXN_FILE_VERSION = CDPL.Base.LookupKey('MDL_RXN_FILE_VERSION')

static

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

◆ MDL_TRIM_LINES

CDPL.Chem.ControlParameter.MDL_TRIM_LINES = CDPL.Base.LookupKey('MDL_TRIM_LINES')

static

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_TRIM_STRINGS

CDPL.Chem.ControlParameter.MDL_TRIM_STRINGS = CDPL.Base.LookupKey('MDL_TRIM_STRINGS')

static

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_TRUNCATE_LINES

CDPL.Chem.ControlParameter.MDL_TRUNCATE_LINES = CDPL.Base.LookupKey('MDL_TRUNCATE_LINES')

static

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_TRUNCATE_STRINGS

CDPL.Chem.ControlParameter.MDL_TRUNCATE_STRINGS = CDPL.Base.LookupKey('MDL_TRUNCATE_STRINGS')

static

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_UPDATE_TIMESTAMP

CDPL.Chem.ControlParameter.MDL_UPDATE_TIMESTAMP = CDPL.Base.LookupKey('MDL_UPDATE_TIMESTAMP')

static

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

◆ SMILES_RECORD_FORMAT

CDPL.Chem.ControlParameter.SMILES_RECORD_FORMAT = CDPL.Base.LookupKey('SMILES_RECORD_FORMAT')

static

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_MIN_STEREO_BOND_RING_SIZE

CDPL.Chem.ControlParameter.SMILES_MIN_STEREO_BOND_RING_SIZE = CDPL.Base.LookupKey('SMILES_MIN_STEREO_BOND_RING_SIZE')

static

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_NO_ORGANIC_SUBSET

CDPL.Chem.ControlParameter.SMILES_NO_ORGANIC_SUBSET = CDPL.Base.LookupKey('SMILES_NO_ORGANIC_SUBSET')

static

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

◆ SMILES_WRITE_AROMATIC_BONDS

CDPL.Chem.ControlParameter.SMILES_WRITE_AROMATIC_BONDS = CDPL.Base.LookupKey('SMILES_WRITE_AROMATIC_BONDS')

static

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_WRITE_ISOTOPE

CDPL.Chem.ControlParameter.SMILES_WRITE_ISOTOPE = CDPL.Base.LookupKey('SMILES_WRITE_ISOTOPE')

static

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.ControlParameter.SMILES_MOL_WRITE_ATOM_MAPPING_ID = CDPL.Base.LookupKey('SMILES_MOL_WRITE_ATOM_MAPPING_ID')

static

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.ControlParameter.SMILES_RXN_WRITE_ATOM_MAPPING_ID = CDPL.Base.LookupKey('SMILES_RXN_WRITE_ATOM_MAPPING_ID')

static

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_ATOM_STEREO

CDPL.Chem.ControlParameter.SMILES_WRITE_ATOM_STEREO = CDPL.Base.LookupKey('SMILES_WRITE_ATOM_STEREO')

static

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.ControlParameter.SMILES_WRITE_BOND_STEREO = CDPL.Base.LookupKey('SMILES_WRITE_BOND_STEREO')

static

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_CANONICAL_FORM

CDPL.Chem.ControlParameter.SMILES_WRITE_CANONICAL_FORM = CDPL.Base.LookupKey('SMILES_WRITE_CANONICAL_FORM')

static

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.ControlParameter.SMILES_WRITE_KEKULE_FORM = CDPL.Base.LookupKey('SMILES_WRITE_KEKULE_FORM')

static

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_RING_BOND_STEREO

CDPL.Chem.ControlParameter.SMILES_WRITE_RING_BOND_STEREO = CDPL.Base.LookupKey('SMILES_WRITE_RING_BOND_STEREO')

static

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_WRITE_SINGLE_BONDS

CDPL.Chem.ControlParameter.SMILES_WRITE_SINGLE_BONDS = CDPL.Base.LookupKey('SMILES_WRITE_SINGLE_BONDS')

static

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

◆ INCHI_INPUT_OPTIONS

CDPL.Chem.ControlParameter.INCHI_INPUT_OPTIONS = CDPL.Base.LookupKey('INCHI_INPUT_OPTIONS')

static

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.ControlParameter.INCHI_OUTPUT_OPTIONS = CDPL.Base.LookupKey('INCHI_OUTPUT_OPTIONS')

static

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.ControlParameter.MULTI_CONF_IMPORT = CDPL.Base.LookupKey('MULTI_CONF_IMPORT')

static

Specifies whether to check for and import multi-conformer molecules.

Value Type: bool.

◆ MULTI_CONF_EXPORT

CDPL.Chem.ControlParameter.MULTI_CONF_EXPORT = CDPL.Base.LookupKey('MULTI_CONF_EXPORT')

static

Specifies whether to write all molecule conformations on output.

Value Type: bool.

◆ MULTI_CONF_INPUT_PROCESSOR

CDPL.Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR = CDPL.Base.LookupKey('MULTI_CONF_INPUT_PROCESSOR')

static

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

Value Type: Chem.MultiConfMoleculeInputProcessor.SharedPointer.

Static Public Attributes

Detailed Description

Member Data Documentation

◆ COORDINATES_DIMENSION

◆ ORDINARY_HYDROGEN_DEPLETE

◆ STRICT_ERROR_CHECKING

◆ BOND_MEMBER_SWAP_STEREO_FIX

◆ CHECK_LINE_LENGTH

◆ RECORD_SEPARATOR

◆ JME_SEPARATE_COMPONENTS

◆ MDL_CTAB_VERSION

◆ MDL_IGNORE_PARITY

◆ MDL_RXN_FILE_VERSION

◆ MDL_TRIM_LINES

◆ MDL_TRIM_STRINGS

◆ MDL_TRUNCATE_LINES

◆ MDL_TRUNCATE_STRINGS

◆ MDL_UPDATE_TIMESTAMP

◆ SMILES_RECORD_FORMAT

◆ SMILES_MIN_STEREO_BOND_RING_SIZE

◆ SMILES_NO_ORGANIC_SUBSET

◆ SMILES_WRITE_AROMATIC_BONDS

◆ SMILES_WRITE_ISOTOPE

◆ SMILES_MOL_WRITE_ATOM_MAPPING_ID

◆ SMILES_RXN_WRITE_ATOM_MAPPING_ID

◆ SMILES_WRITE_ATOM_STEREO

◆ SMILES_WRITE_BOND_STEREO

◆ SMILES_WRITE_CANONICAL_FORM

◆ SMILES_WRITE_KEKULE_FORM

◆ SMILES_WRITE_RING_BOND_STEREO

◆ SMILES_WRITE_SINGLE_BONDS

◆ INCHI_INPUT_OPTIONS

◆ INCHI_OUTPUT_OPTIONS

◆ MULTI_CONF_IMPORT

◆ MULTI_CONF_EXPORT

◆ MULTI_CONF_INPUT_PROCESSOR