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Table 1 List of all flags used to configure Ambit-SMIRKS

From: Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation

  Flag and description Default value
1. FlagSSMode
Defines substructure searching (mapping) mode and how all found sites for reaction application in the target molecule are combined by function applyReaction(). The following modes are supported: SSM_SINGLE, SSM_NON_OVERLAPPING, SSM_NON_IDENTICAL, SSM_NON_EQUIVALENT, SSM_ALL, SSM_NON_IDENTICAL_FIRST
SSM_NON_OVERLAPPING
2. FlagCheckResultStereo
If true, the stereo elements within the obtained product molecules are verified and incorrect ones are removed. This flag does not define whether the stereo transformation should be applied
True
3. FlagFilterEquivalentMappings
Defines whether to filter topologically equivalent sites (mappings) for reaction application
False
4. FlagProcessResultStructures
If true, the result molecules (products) are processed according to the configurations defined by other flags below
False
5. FlagClearHybridizationBeforeResultProcess
If set true, the atom hybridization types are cleared in the product molecule. Typically this flag should be true in order to correctly detect the new atom types of transformed molecules
True
6. FlagClearAromaticityBeforeResultProcess
If true, aromaticity information for all atoms and bonds in the obtained products is cleared. Typically this flag should be true since the aromaticity should be detected for all new products due to possible changes in the aromatic systems
True
7. FlagClearImplicitHAtomsBeforeResultProcess
Defines whether to clear implicit H atoms before result product processing
True
8. FlagClearExcplicitHAtomsBeforeResultProcess
Defines whether to clear explicit H atoms before result product processing
False
9. FlagAddImplicitHAtomsOnResultProcess
Defines whether to add implicit H atoms on product molecule processing
False
10. FlagConvertAddedImplicitHToExplicitOnResultProcess
Defines whether to convert the added implicit H atoms to explicit. This flag is used only if implicit H atoms are added (see previous flag 9)
False
11. FlagCheckAromaticityOnResultProcess
Defines whether to apply aromaticity detection algorithm for the new products
True
12. FlagConvertExplicitHToImplicitOnResultProcess
Defines whether to convert explicit H atoms to implicit ones. Typically if this flag is true, it is expected that FlagAddImlicitHAtomsOnResultProcess = false
False
13. FlagApplyStereoTransformation
Determines whether to perform stereo transformation of the target molecules according to the defined SMIRKS. If this flag is not set, stereo elements of the molecule are preserved when possible (e.g. when they are not changed or deleted). If the flag is true, full stereo transformation is applied in accordance with the defined SMIRKS
False
14. FlagHAtomsTransformation
Defines whether to apply H atom transformation according to the used atom expressions in the SMIRKS
False
15. FlagHAtomsTransformationMode
Defines H atoms transformation mode: IMPLICIT or EXPLICIT. This flags is used only when previous one is set
Implicit
16. FlagAromaticityTransformation
Defines whether to apply post transformation additional aromaticity setting within obtained products based on the SMIRKS expression
False