BALL::AromaticityProcessor Class Reference
This processor provides methods for detection and assignment of aromaticity. More...
#include <BALL/QSAR/aromaticityProcessor.h>
Classes | |
| struct | Default |
| Default values for options. More... | |
| struct | Option |
| Option names. More... | |
Public Member Functions | |
Constructors and Destructors | |
| AromaticityProcessor () | |
| AromaticityProcessor (const AromaticityProcessor &aro) | |
| virtual | ~AromaticityProcessor () |
Assignment | |
| AromaticityProcessor & | operator= (const AromaticityProcessor &aro) |
Accessors | |
| void | aromatize (const vector< vector< Atom * > > &sssr, AtomContainer &ac) |
| void | aromatizeSimple (vector< vector< Atom * > > &sssr) |
Processor-related methods | |
| Processor::Result | operator() (AtomContainer &ac) |
| virtual bool | start () |
Protected Member Functions | |
Predicates | |
| bool | isValid_ (const AtomContainer &ac) |
Private Member Functions | |
| bool | simpleCanBeAromatic_ (const HashSet< Atom * > &ring) |
| bool | simpleCanBeAromaticWeaker_ (const HashSet< Atom * > &ring) |
| void | extendAromaticSystem_ (vector< HashSet< Atom * > > &sssr, HashSet< Atom * > ring) |
| bool | hasConjugatedDoubleBonds_ (HashSet< Atom * > ring) |
| Size | countPiElectrons_ (HashSet< Atom * > &ring) |
Private Attributes | |
| bool | overwrite_bond_orders_ |
Public Attributes | |
|
| |
| Options | options |
| options | |
| void | setDefaultOptions () |
Detailed Description
This processor provides methods for detection and assignment of aromaticity.
Aromaticity Processor
Processor method to detect aromaticity of AtomContainers. If it is called as a processor with the operator (), the RingPerceptionProcessor is called before, to calculate a ring set. It can be called explicitely with aromatize with a ringset as parameter.
Definition at line 28 of file aromaticityProcessor.h.
Constructor & Destructor Documentation
| BALL::AromaticityProcessor::AromaticityProcessor | ( | ) |
Default constructor
| BALL::AromaticityProcessor::AromaticityProcessor | ( | const AromaticityProcessor & | aro | ) |
Copy constructor
| virtual BALL::AromaticityProcessor::~AromaticityProcessor | ( | ) | [virtual] |
Destrcutor
Member Function Documentation
| void BALL::AromaticityProcessor::aromatize | ( | const vector< vector< Atom * > > & | sssr, | |
| AtomContainer & | ac | |||
| ) |
Calculated the aromaticity of the molcule and sets the properties "IsAromatic" for aromatic atoms, and Bond::ORDER__AROMATIC for bonds which are aromatic.
- Parameters:
-
SSSR ring set as vector<vector<Atom*> >, (vector of rings in vector<Atom*>) after the processing this variable holds all aromatic systems, which are not necessarily single rings!
| void BALL::AromaticityProcessor::aromatizeSimple | ( | vector< vector< Atom * > > & | sssr | ) |
Method to set aromaticity with the use of simple rules. Each ring from the given SSSR set (which needs just to be a set of rings) is examined for itself. (needed for the implementation of the MMFF94 force field which does not agree with the advanced araomtaticity definition of the default method.).
- It does not set any aromaticity flags, neither at the atoms nor bonds to bond order aromatic! sssr is the set to be examined, only aromatic rings will stay
| void BALL::AromaticityProcessor::extendAromaticSystem_ | ( | vector< HashSet< Atom * > > & | sssr, | |
| HashSet< Atom * > | ring | |||
| ) | [private] |
| bool BALL::AromaticityProcessor::isValid_ | ( | const AtomContainer & | ac | ) | [protected] |
| Processor::Result BALL::AromaticityProcessor::operator() | ( | AtomContainer & | ) | [virtual] |
operator ()
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
| AromaticityProcessor& BALL::AromaticityProcessor::operator= | ( | const AromaticityProcessor & | aro | ) |
Assignment operator
| void BALL::AromaticityProcessor::setDefaultOptions | ( | ) |
reset the options to default values
| bool BALL::AromaticityProcessor::simpleCanBeAromaticWeaker_ | ( | const HashSet< Atom * > & | ring | ) | [private] |
| virtual bool BALL::AromaticityProcessor::start | ( | ) | [virtual] |
start method
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
Member Data Documentation
options
Definition at line 83 of file aromaticityProcessor.h.
Should we set the bond orders to aromatic or merely store the information as a property of the bond? This value depends on the value of the option OVERWRITE_BOND_ORDERS
Definition at line 166 of file aromaticityProcessor.h.
