BALL::HybridisationProcessor Class Reference
[Miscellaneous]
#include <BALL/STRUCTURE/hybridisationProcessor.h>
Classes | |
| struct | AtomNames_ |
| struct | Default |
| Default values for options. More... | |
| struct | Elements_ |
| struct | Method |
| struct | Option |
| Option names. More... | |
Public Member Functions | |
Constructors and Destructors | |
| BALL_CREATE (HybridisationProcessor) | |
| HybridisationProcessor () | |
| default constructor | |
| HybridisationProcessor (const HybridisationProcessor &hp) | |
| copy construcor | |
| HybridisationProcessor (const String &smarts_file_name, const String &ff_file_name) throw (Exception::FileNotFound) | |
| virtual | ~HybridisationProcessor () |
| destructor | |
Processor-related methods | |
| virtual bool | start () |
| processor method which is called before the operator () call | |
| virtual Processor::Result | operator() (AtomContainer &ac) |
| operator () for the processor | |
Accessors | |
| Size | getNumberOfHybridisationStatesSet () |
| Return the number of hybridisation states set during the last application. | |
| void | setAtomTypeSmarts (const String &file_name) throw (Exception::FileNotFound) |
| sets the parameters file | |
| vector< std::pair< String, Size > > | getHybridisationMap () |
| Return the atom_types--hybridisation Hashmap. | |
Assignment | |
| HybridisationProcessor & | operator= (const HybridisationProcessor &hp) |
| assignment operator | |
Protected Member Functions | |
| bool | readAtomTypeSmartsFromFile_ (const String &file_name="") throw (Exception::FileNotFound) |
| method to read the paramter file | |
| bool | readAndInitBondAnglesFromFile_ (const String &file_name="") throw (Exception::FileNotFound) |
| double | AverageBondAngle_ (Atom *a) |
| computes the averaged bond angle for the given Atom | |
Protected Attributes | |
| Size | num_hybridisation_states_ |
| number of bonds, which are created during the processor call | |
| vector< std::pair< String, Size > > | atom_type_smarts_ |
| structure where atom type smarts and the corresponding hybridisation states are stored in | |
| StringHashMap< StringHashMap < StringHashMap< std::multimap < float, AtomNames_ > > > > | bond_angles_ |
| StringHashMap< Elements_ > | elements_ |
| bool | valid_ |
| the Processors state | |
Public Attributes | |
|
| |
| Options | options |
| options | |
| void | setDefaultOptions () |
Detailed Description
Hybridisation processor
Definition at line 42 of file hybridisationProcessor.h.
Constructor & Destructor Documentation
| BALL::HybridisationProcessor::HybridisationProcessor | ( | ) |
default constructor
| BALL::HybridisationProcessor::HybridisationProcessor | ( | const HybridisationProcessor & | hp | ) |
copy construcor
| BALL::HybridisationProcessor::HybridisationProcessor | ( | const String & | smarts_file_name, | |
| const String & | ff_file_name | |||
| ) | throw (Exception::FileNotFound) |
Constructor with parameter filename for the smarts based algorithm and parameter filename for the force field based method
| virtual BALL::HybridisationProcessor::~HybridisationProcessor | ( | ) | [virtual] |
destructor
Member Function Documentation
computes the averaged bond angle for the given Atom
| BALL::HybridisationProcessor::BALL_CREATE | ( | HybridisationProcessor | ) |
Return the atom_types--hybridisation Hashmap.
Definition at line 146 of file hybridisationProcessor.h.
| Size BALL::HybridisationProcessor::getNumberOfHybridisationStatesSet | ( | ) |
Return the number of hybridisation states set during the last application.
| virtual Processor::Result BALL::HybridisationProcessor::operator() | ( | AtomContainer & | ac | ) | [virtual] |
operator () for the processor
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
| HybridisationProcessor& BALL::HybridisationProcessor::operator= | ( | const HybridisationProcessor & | hp | ) |
assignment operator
| bool BALL::HybridisationProcessor::readAndInitBondAnglesFromFile_ | ( | const String & | file_name = "" |
) | throw (Exception::FileNotFound) [protected] |
| bool BALL::HybridisationProcessor::readAtomTypeSmartsFromFile_ | ( | const String & | file_name = "" |
) | throw (Exception::FileNotFound) [protected] |
method to read the paramter file
| void BALL::HybridisationProcessor::setAtomTypeSmarts | ( | const String & | file_name | ) | throw (Exception::FileNotFound) |
sets the parameters file
| void BALL::HybridisationProcessor::setDefaultOptions | ( | ) |
reset the options to default values
| virtual bool BALL::HybridisationProcessor::start | ( | ) | [virtual] |
processor method which is called before the operator () call
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
Member Data Documentation
vector< std::pair<String, Size> > BALL::HybridisationProcessor::atom_type_smarts_ [protected] |
structure where atom type smarts and the corresponding hybridisation states are stored in
Definition at line 198 of file hybridisationProcessor.h.
StringHashMap<StringHashMap<StringHashMap<std::multimap<float, AtomNames_> > > > BALL::HybridisationProcessor::bond_angles_ [protected] |
Contains the bond angles and their atom types. The bond angles are stored in 'rad'.
Definition at line 203 of file hybridisationProcessor.h.
Maps the atom types onto their elements
Definition at line 209 of file hybridisationProcessor.h.
number of bonds, which are created during the processor call
Definition at line 195 of file hybridisationProcessor.h.
options
Definition at line 160 of file hybridisationProcessor.h.
bool BALL::HybridisationProcessor::valid_ [protected] |
the Processors state
Definition at line 213 of file hybridisationProcessor.h.
