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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Provides keys for built-in control-parameters. More...
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| 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. 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. 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 an MDL CTFile-based format. 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 an MDL CTFile-based format. 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 an MDL CTFile-based format. 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 an MDL CTFile-based format. 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 an MDL CTFile-based format. 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 an MDL CTFile-based format. More... | |
| CDPL_CHEM_API const Base::LookupKey | MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD |
| Specifies whether to output conformer energies into the energy field of the molecule header block when writing data in an MDL CTFile-based format. More... | |
| CDPL_CHEM_API const Base::LookupKey | MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY |
| Specifies whether to output the energy of conformers as an MDL SD-File structure data entry when writing data in an MDL CTFile-based format. More... | |
| CDPL_CHEM_API const Base::LookupKey | MDL_CONF_ENERGY_SD_TAG |
| Specifies the MDL SD-File structure data entry header used for the conformer energy. More... | |
| CDPL_CHEM_API const Base::LookupKey | MDL_ENABLE_AROMATIC_BOND_TYPES |
Specifies whether to output the 'aromatic' bond type value (4) in the type field of aromatic bonds when writing molecular graph data in an MDL CTFile-based format. On data reading, the aromaticity flag property of bonds having this type will be set to true and to false if the bond type specifies a defined bond order. More... | |
| 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. 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. More... | |
| CDPL_CHEM_API const Base::LookupKey | JME_SEPARATE_COMPONENTS |
| Specifies for the output of data in JME format 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. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_CANONICAL_FORM |
| Specifies whether to generate canonical SMILES strings. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_KEKULE_FORM |
| Specifies whether to generate SMILES strings with kekulized aromatic rings. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_ATOM_STEREO |
| Specifies whether to generate SMILES strings with atom configuration specifications. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_BOND_STEREO |
| Specifies whether to generate SMILES strings that include directional bonds for the definition of double bond configurations. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_RING_BOND_STEREO |
| Specifies whether to generate SMILES strings that also include directional bonds for the definition of ring double bond configurations. 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 configurations in generated SMILES strings. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_ISOTOPE |
| Specifies whether to generate SMILES strings with isotopic mass specifications. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_HYDROGEN_COUNT |
| Specifies whether to generate SMILES strings with implicit hydrogen count specifications. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_MOL_OUTPUT_ATOM_MAPPING_ID |
| Specifies whether to generate molecule SMILES strings that contain atom-atom mapping numbers. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_RXN_OUTPUT_ATOM_MAPPING_ID |
| Specifies whether to generate reaction SMILES strings that contain atom-atom mapping numbers. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_SINGLE_BONDS |
| Specifies whether to generate SMILES strings with explicit single bond specifications. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_OUTPUT_AROMATIC_BONDS |
| Specifies whether to generate SMILES strings with explicit aromatic bond specifications. More... | |
| CDPL_CHEM_API const Base::LookupKey | SMILES_NO_ORGANIC_SUBSET |
| Specifies whether to generate SMILES strings 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. More... | |
| CDPL_CHEM_API const Base::LookupKey | INCHI_OUTPUT_OPTIONS |
| Specifies options for the output of InChI strings. More... | |
| CDPL_CHEM_API const Base::LookupKey | MULTI_CONF_IMPORT |
| Specifies whether to check for and import multi-conformer molecules. More... | |
| CDPL_CHEM_API const Base::LookupKey | MULTI_CONF_EXPORT |
| Specifies whether to write all molecule conformations on output. More... | |
| CDPL_CHEM_API const Base::LookupKey | OUTPUT_CONF_ENERGY_AS_COMMENT |
| Specifies whether to write the conformer energy into the molecule comment field (if supported by the selected data format) on output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CONF_INDEX_NAME_SUFFIX_PATTERN |
| Specifies a format pattern used to derive per-conformer molecule name suffixes from the conformer index. More... | |
| 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. More... | |
| CDPL_CHEM_API const Base::LookupKey | CDF_OUTPUT_SINGLE_PRECISION_FLOATS |
Specifies whether floating-point values shall be output in single-precision (true) or double-precision (false) when writing data in CDF format. More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_ENABLE_EXTENDED_ATOM_TYPES |
| Specifies whether to enable the CDPL-specific extended Sybyl atom type set when reading/writing Sybyl MOL2 data. More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_ENABLE_AROMATIC_BOND_TYPES |
Specifies whether to interpret/write the Sybyl bond type "ar" as aromatic when reading/writing Sybyl MOL2 data. More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_READ_PARTIAL_AS_FORMAL_CHARGES |
| Specifies whether to interpret read partial charges as formal charges (obtained by rounding to the nearest integer value) on Sybyl MOL2 input. More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_CALC_FORMAL_CHARGES |
| Specifies whether to recompute formal charges from atom types when reading Sybyl MOL2 data. More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_CHARGE_TYPE |
Specifies the charge type to write to the @<TRIPOS>MOLECULE block when generating Sybyl MOL2 output (see namespace Chem::MOL2ChargeType). Value Type: unsigned int More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_MOLECULE_TYPE |
Specifies the molecule type to write to the @<TRIPOS>MOLECULE block when generating Sybyl MOL2 output (see namespace Chem::MOL2MoleculeType). More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_OUTPUT_SUBSTRUCTURES |
Specifies whether to write the @<TRIPOS>SUBSTRUCTURE block when generating Sybyl MOL2 output. More... | |
| CDPL_CHEM_API const Base::LookupKey | MOL2_OUTPUT_FORMAL_CHARGES |
Specifies whether to emit formal atomic charges in the partial charge column when generating Sybyl MOL2 output. Value Type: bool. More... | |
| CDPL_CHEM_API const Base::LookupKey | XYZ_COMMENT_IS_NAME |
| Specifies whether to treat the comment line of an XYZ record as the molecule name on data I/O. More... | |
| CDPL_CHEM_API const Base::LookupKey | XYZ_PERCEIVE_CONNECTIVITY |
| Specifies whether to perceive bond connectivity from atom 3D coordinates when reading XYZ data. More... | |
| CDPL_CHEM_API const Base::LookupKey | XYZ_PERCEIVE_BOND_ORDERS |
| Specifies whether to perceive bond orders from the perceived connectivity when reading XYZ data. More... | |
| CDPL_CHEM_API const Base::LookupKey | XYZ_CALC_FORMAL_CHARGES |
| Specifies whether to recompute formal atomic charges after the bond perception step when reading XYZ data. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_XML_DECLARATION |
| Specifies whether to emit an XML declaration at the beginning of CML output records. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_ELEMENT_NAMESPACE |
| Specifies the XML namespace URI emitted with the root element when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_ATOM_PARITY |
| Specifies whether to emit tetrahedral atom parities when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_SINGLE_BOND_STEREO |
| Specifies whether to emit wedge/hash stereo flags for single bonds when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_DOUBLE_BOND_STEREO |
| Specifies whether to emit cis/trans descriptors for double bonds when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_ENABLE_AROMATIC_BOND_TYPES |
Specifies whether to interpret/write CML's aromatic bond type "a" when reading/writing CML data. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_MOLECULE_NAME |
| Specifies whether to emit the title attribute (molecule name) when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_STRUCTURE_DATA |
| Specifies whether to emit attached structure data fields when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_ISOTOPE |
| Specifies whether to emit the isotopic mass number of non-standard isotopes when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_SPIN_MULTIPLICITY |
| Specifies whether to emit the atom spin multiplicity when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_COMPACT_ATOM_DATA |
| Specifies whether to use a compact (array-style) representation for atom data when generating CML output. More... | |
| CDPL_CHEM_API const Base::LookupKey | CML_OUTPUT_COMPACT_BOND_DATA |
| Specifies whether to use a compact (array-style) representation for bond data when generating CML output. More... | |
Provides keys for built-in control-parameters.
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Specifies whether the calculation of a molecular property has to be performed for the ordinary hydrogen deplete input structure.
If the parameter is set to true, the calculation result will be equivalent to the result that would have been obtained for the same input structure with all explicit ordinary hydrogens removed. If the parameter is set to false, the calculation will be performed for the unmodified molecular graph.
Value Type: bool
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Specifies the dimension of atom coordinates.
A parameter value of 2 specifies 2D coordinates and a value of 3 3D coordinates. Other values usually trigger the selection of an implementation defined default dimension.
Value Type: std::size_t
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Specifies whether non-fatal recoverable I/O errors should be ignored or cause an I/O operation to fail.
If the 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 parameter is set to false, I/O operations will proceed even if a non-fatal error has been detected.
Value Type: bool
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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 parameter specifies which method of conversion shall be used. If the parameter is set to true the latter method will be used, and the former method otherwise.
Value Type: bool
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Specifies the desired version of the connection table data format for the output of molecular graphs in MDL SD- or Mol-File format.
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 parameter and the property do not specify a particular connection table format version, a suitable output format is chosen as follows:
Value Type: unsigned int
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Specifies whether the stereo parity of atoms shall be ignored when reading or writing data in an MDL CTFile-based format.
If the 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
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Specifies whether to update the timestamp of Mol- and Rxn-File header blocks when writing data in an MDL CTFile-based format.
If the 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::TIMESTAMP (for molecular graph output) or Chem::ReactionProperty::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
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Specifies whether to remove leading and trailing whitespace from string values when reading or writing data in an MDL CTFile-based format.
If the 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
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Specifies whether to remove leading and trailing whitespace from data lines when reading or writing data in an MDL CTFile-based format.
If the 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
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Specifies whether string values that exceed the size of an output data field may be truncated when writing data in an MDL CTFile-based format.
If the 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
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Specifies whether data lines that exceed the maximum allowed line length may be truncated when writing data in an MDL CTFile-based format.
If the 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
false.
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Specifies whether to output conformer energies into the energy field of the molecule header block when writing data in an MDL CTFile-based format.
Value Type: bool
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Specifies whether to output the energy of conformers as an MDL SD-File structure data entry when writing data in an MDL CTFile-based format.
Value Type: bool
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Specifies the MDL SD-File structure data entry header used for the conformer energy.
Value Type: std::string
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Specifies whether to output the 'aromatic' bond type value (4) in the type field of aromatic bonds when writing molecular graph data in an MDL CTFile-based format. On data reading, the aromaticity flag property of bonds having this type will be set to true and to false if the bond type specifies a defined bond order.
Value Type: bool
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Specifies whether to check if data lines exceed the maximum allowed line length when reading or writing data.
If the 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
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Specifies the desired data format version for the output of reactions in MDL Rxn- or RD-File format.
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 parameter and the property do not specify a particular Rxn-File format version, a suitable output format is chosen as follows:
Value Type: unsigned int
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Specifies for the output of data in JME format whether the components of a molecular graph shall be written separately or all together as a single JME component.
If the 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
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Specifies the format of SMILES molecular graph or reaction data records.
The data record format is specified by one of the two following format strings:
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
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Specifies whether to generate canonical SMILES strings.
If the 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 instance that describes the structure. If the value of SMILES_OUTPUT_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 instances that otherwise represent the same chemical structure.
Value Type: bool
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Specifies whether to generate SMILES strings with kekulized aromatic rings.
If the 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_OUTPUT_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
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Specifies whether to generate SMILES strings with atom configuration specifications.
If the parameter is set to true, the generated SMILES string will specify the configuration of terahedral stereogenic atoms. If the value of the parameter is false, the stereochemistry of atoms is left unspecified.
Value Type: bool
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Specifies whether to generate SMILES strings that include directional bonds for the definition of double bond configurations.
If the parameter is set to true, the generated SMILES string will contain directional bonds for the specification of chain double bond configurations. If the value of the parameter is false, the stereochemistry of double bonds is left unspecified.
Value Type: bool
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Specifies whether to generate SMILES strings that also include directional bonds for the definition of ring double bond configurations.
If the parameter is set to true, the generated SMILES string will specify the configuration (if known) 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 parameter is false, the stereochemistry of ring double bonds will not be specified.
Value Type: bool
true.
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Specifies the minimum ring size that is required for the specification of ring double bond configurations in generated SMILES strings.
Value Type: std::size_t
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Specifies whether to generate SMILES strings with isotopic mass specifications.
If the 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_OUTPUT_ISOTOPE is false, the isotopic mass is left unspecified.
Value Type: bool
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Specifies whether to generate SMILES strings with implicit hydrogen count specifications.
If the parameter is set to true, the generated SMILES string will specify the implicit hydrogen count of atoms (if non-standard). If the value of SMILES_OUTPUT_HYDROGEN_COUNT is false, the implicit hydrogen count is always left unspecified.
Value Type: bool
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Specifies whether to generate molecule SMILES strings that contain atom-atom mapping numbers.
If the parameter is set to true, the generated SMILES string will specify reaction atom-atom mapping numbers (see Chem::AtomProperty::ATOM_MAPPING_ID). If the value of SMILES_OUTPUT_ATOM_MAPPING_ID is false, atom-atom mapping numbers will not be specified.
Value Type: bool
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Specifies whether to generate reaction SMILES strings that contain atom-atom mapping numbers.
If the parameter is set to true, the generated SMILES string will specify reaction atom-atom mapping numbers (see Chem::AtomProperty::ATOM_MAPPING_ID). If the value of SMILES_OUTPUT_ATOM_MAPPING_ID is false, atom-atom mapping numbers will not be specified.
Value Type: bool
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Specifies whether to generate SMILES strings with explicit single bond specifications.
If the 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_OUTPUT_SINGLE_BONDS is false, single bonds are left unspecified.
Value Type: bool
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Specifies whether to generate SMILES strings with explicit aromatic bond specifications.
If the parameter is set to true, generated SMILES strings will explicitly specify aromatic bonds. If the value of SMILES_OUTPUT_AROMATIC_BONDS is false, aromatic bonds are left unspecified.
Value Type: bool
false.
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Specifies whether to generate SMILES strings where all atom symbols are enclosed in brackets.
If the 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
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Specifies options for the input of InChI strings.
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
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Specifies options for the output of InChI strings.
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
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Specifies whether to check for and import multi-conformer molecules.
Value Type: bool
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Specifies whether to write all molecule conformations on output.
Value Type: bool
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Specifies whether to write the conformer energy into the molecule comment field (if supported by the selected data format) on output.
Value Type: bool
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Specifies a format pattern used to derive per-conformer molecule name suffixes from the conformer index.
The placeholder "%I%" in the pattern will be raplaced by the one-based conformer index and the resulting string is then appended to the molecule name. An empty pattern string disables the suffix.
Value Type: std::string
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Specifies an instance of Chem::MultiConfMoleculeInputProcessor that implements the logic of multi-conformer molecule detection and conformational data processing.
Value Type: Chem::MultiConfMoleculeInputProcessor::SharedPointer
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Specifies whether floating-point values shall be output in single-precision (true) or double-precision (false) when writing data in CDF format.
Value Type: bool
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Specifies whether to enable the CDPL-specific extended Sybyl atom type set when reading/writing Sybyl MOL2 data.
Value Type: bool
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Specifies whether to interpret/write the Sybyl bond type "ar" as aromatic when reading/writing Sybyl MOL2 data.
Value Type: bool
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Specifies whether to interpret read partial charges as formal charges (obtained by rounding to the nearest integer value) on Sybyl MOL2 input.
Value Type: bool
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Specifies whether to recompute formal charges from atom types when reading Sybyl MOL2 data.
Value Type: bool
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Specifies the charge type to write to the @<TRIPOS>MOLECULE block when generating Sybyl MOL2 output (see namespace Chem::MOL2ChargeType). Value Type: unsigned int
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Specifies the molecule type to write to the @<TRIPOS>MOLECULE block when generating Sybyl MOL2 output (see namespace Chem::MOL2MoleculeType).
Value Type: unsigned int
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Specifies whether to write the @<TRIPOS>SUBSTRUCTURE block when generating Sybyl MOL2 output.
Value Type: bool
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Specifies whether to emit formal atomic charges in the partial charge column when generating Sybyl MOL2 output. Value Type: bool.
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Specifies whether to treat the comment line of an XYZ record as the molecule name on data I/O.
Value Type: bool
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Specifies whether to perceive bond connectivity from atom 3D coordinates when reading XYZ data.
Value Type: bool
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Specifies whether to perceive bond orders from the perceived connectivity when reading XYZ data.
Value Type: bool
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Specifies whether to recompute formal atomic charges after the bond perception step when reading XYZ data.
Value Type: bool
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Specifies whether to emit an XML declaration at the beginning of CML output records.
Value Type: bool
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Specifies the XML namespace URI emitted with the root element when generating CML output.
Value Type: std::string
|
extern |
Specifies whether to emit tetrahedral atom parities when generating CML output.
Value Type: bool
|
extern |
Specifies whether to emit wedge/hash stereo flags for single bonds when generating CML output.
Value Type: bool
|
extern |
Specifies whether to emit cis/trans descriptors for double bonds when generating CML output.
Value Type: bool
|
extern |
Specifies whether to interpret/write CML's aromatic bond type "a" when reading/writing CML data.
Value Type: bool
|
extern |
Specifies whether to emit the title attribute (molecule name) when generating CML output.
Value Type: bool
|
extern |
Specifies whether to emit attached structure data fields when generating CML output.
Value Type: bool
|
extern |
Specifies whether to emit the isotopic mass number of non-standard isotopes when generating CML output.
Value Type: bool
|
extern |
Specifies whether to emit the atom spin multiplicity when generating CML output.
Value Type: bool
|
extern |
Specifies whether to use a compact (array-style) representation for atom data when generating CML output.
Value Type: bool
|
extern |
Specifies whether to use a compact (array-style) representation for bond data when generating CML output.
Value Type: bool
1.9.1