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Open Babel
3.0
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#include <openbabel/reactionfacade.h>
Public Member Functions | |
Constructor | |
| OBReactionFacade (OBMol *mol) | |
| ~OBReactionFacade () | |
Low-level methods | |
These are convenience functions that set/get reaction-related data on individual atoms. The actual data is stored in the underlying OBMol as OBPairInteger data with the keys "rxnrole" or "rxncomp" (reaction role, reaction component). The other methods of this class are implemented using these methods. Care should be taken using the setter functions, as (unlike the other methods) their use can result in an inconsistent state. IsValid() may be used to check whether this is the case. | |
| void | AssignComponentIds (bool wipe=true) |
| OBReactionRole | GetRole (OBAtom *atom) |
| unsigned int | GetComponentId (OBAtom *atom) |
| void | SetRole (OBAtom *atom, OBReactionRole rxnrole) |
| void | SetComponentId (OBAtom *atom, unsigned int compid) |
Check validity of reaction data | |
| bool | IsValid () |
High-level methods | |
These are a set of methods that manipulate reactions at the component level. If you use these high-level methods, and subsequently modify the underlying OBMol or its reaction data, you may need to clear cached information on the reaction components via ClearInternalState(). | |
| void | AddComponent (OBMol *mol, OBReactionRole rxnrole) |
| void | ClearInternalState () |
| bool | GetComponent (OBMol *mol, OBReactionRole rxnrole, unsigned int num) |
| unsigned int | NumComponents (OBReactionRole rxnrole) |
| bool | ReassignComponent (OBReactionRole oldrole, unsigned int num, OBReactionRole newrole) |
Facade to simplify manipulation of reactions stored as OBMol objects.
All of the information defining a reaction is stored as part of an OBMol. This information is:
Everything that may need to be done with reactions can be implemented using this information. The purpose of this class is simply to provide convenience functions that cover a range of likely use cases. If your use case is not included, it should still be straightforward for you to manipulate the underlying information to achieve your goal.
| OBReactionFacade | ( | OBMol * | mol | ) |
The constructor requires an OBMol. Member functions retrieve or manipulate reaction data stored in this molecule.
| ~OBReactionFacade | ( | ) |
| void AssignComponentIds | ( | bool | wipe = true | ) |
Assigns a component Id to every atom in the molecule based on connected components. If wipe is false, then any atoms that already have a component Id are skipped.
| OBReactionRole GetRole | ( | OBAtom * | atom | ) |
Return the reaction role of an atom.
| unsigned int GetComponentId | ( | OBAtom * | atom | ) |
Return the component Id of an atom.
| void SetRole | ( | OBAtom * | atom, |
| OBReactionRole | rxnrole | ||
| ) |
Set the reaction role of an atom.
| void SetComponentId | ( | OBAtom * | atom, |
| unsigned int | compid | ||
| ) |
Set the component Id of an atom.
| bool IsValid | ( | ) |
Check whether this OBMol is in a valid state to represent a reaction.
Note, first of all, that this does not check whether a reaction is chemically valid. It simply checks whether the OBMol has the following properties:
If (a) is not true, while it does not affect any of the methods of the OBReactionFacade, the reaction may not be written appropriately by an output format.
If (b), (c) or (d) is not true, then the behavior of the toolkit is undefined when handling this molecule.
While not checked by this function, it is also a good idea to avoid reusing the same component Id for different reaction roles, e.g. having a reactant with component Id 1 as well as a product with component Id 1. If you reassign roles, then the duplication of component Ids may cause two components to be merged into one.
| void AddComponent | ( | OBMol * | mol, |
| OBReactionRole | rxnrole | ||
| ) |
Add a new component to the reaction
| void ClearInternalState | ( | ) |
Clear the list of found components.
On first use any of the high-level methods, the number of components for each reaction role is determined and each is assigned a number from 0 to the number of components. This information is cached for future accesses. If you modify the underlying OBMol in a way that invalidates this information (e.g. using the low-level methods), you should call ClearInternalState() or create a new OBReactionFacade.
| bool GetComponent | ( | OBMol * | mol, |
| OBReactionRole | rxnrole, | ||
| unsigned int | num | ||
| ) |
Copy a component from the reaction into the provided OBMol.
Note that all reaction data is copied, and so this may be useful for building up a new reaction composed of just some of the components of the original reaction. If copying components from multiple reactions into a single one, to avoid duplicate component Ids it may be easier to copy into an empty OBMol, and then use AddComponent() to add this OBMol into the new reaction.
| unsigned int NumComponents | ( | OBReactionRole | rxnrole | ) |
Return the number of reaction components with a particular reaction role.
| bool ReassignComponent | ( | OBReactionRole | oldrole, |
| unsigned int | num, | ||
| OBReactionRole | newrole | ||
| ) |
Reassign the reaction role of a given component. If assigned to NO_REACTIONROLE, this may be used to hide the reaction component when writing to a reaction output format.
It should be noted that reassigning a component changes the numbers assigned. For example, in a reaction with 2 reactants and 2 products (each numbered from 0 to 1), if you reassign reactant number 0 to be a product, it will now be product number 2 while former reactant number 1 will now be reactant number 0.
1.8.13