BALL
1.4.1
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#include <BALL/STRUCTURE/atomTyper.h>
Public Member Functions | |
AtomTyper () | |
AtomTyper (const AtomTyper &t) | |
virtual | ~AtomTyper () |
bool | setup (const String &filename) |
Setup with the given line based file with SMARTS expressions. | |
virtual void | assignTo (System &s) |
void | setAromaticRings (const vector< HashSet< Atom * > > &rings) |
void | setRings (const vector< HashSet< Atom * > > &rings) |
Static Public Attributes | |
static StringHashMap< float > | rule_times |
Protected Member Functions | |
void | assignTo (Molecule &mol) |
virtual void | assignSpecificValues_ (Atom &) |
virtual bool | specificSetup_ () |
Protected Attributes | |
vector< String > | names_ |
vector< String > | rules_ |
vector< Index > | types_ |
vector< vector< String > > | fields_ |
Size | number_expected_fields_ |
vector< HashSet< Atom * > > | rings_ |
vector< HashSet< Atom * > > | aromatic_rings_ |
StringHashMap< vector< Position > > | element_to_rules_ |
HashSet< Atom * > | atoms_ |
Base class for a programable Atom typer. The types are assigned by using a line based file with SMARTS expressions. For usage have a look at the derived class MMFF94AtomTyper.
AtomTyper typer; typer.setRings(...); typer.setAromaticRings(...); typer.setup(parameter_file_name); typer.assignTo(system);
Definition at line 40 of file atomTyper.h.
BALL::AtomTyper::AtomTyper | ( | const AtomTyper & | t | ) |
virtual BALL::AtomTyper::~AtomTyper | ( | ) | [inline, virtual] |
Definition at line 53 of file atomTyper.h.
virtual void BALL::AtomTyper::assignSpecificValues_ | ( | Atom & | ) | [inline, protected, virtual] |
To be overloaded in derived classes to add support for additional properties e.g. charges
Definition at line 78 of file atomTyper.h.
virtual void BALL::AtomTyper::assignTo | ( | System & | s | ) | [virtual] |
Reimplemented in BALL::MMFF94AtomTyper.
void BALL::AtomTyper::assignTo | ( | Molecule & | mol | ) | [protected] |
void BALL::AtomTyper::setAromaticRings | ( | const vector< HashSet< Atom * > > & | rings | ) | [inline] |
Definition at line 62 of file atomTyper.h.
void BALL::AtomTyper::setRings | ( | const vector< HashSet< Atom * > > & | rings | ) | [inline] |
Definition at line 65 of file atomTyper.h.
bool BALL::AtomTyper::setup | ( | const String & | filename | ) |
Setup with the given line based file with SMARTS expressions.
virtual bool BALL::AtomTyper::specificSetup_ | ( | ) | [inline, protected, virtual] |
To be overloaded in derived classes to add support for additional properties e.g. charges
Definition at line 83 of file atomTyper.h.
vector<HashSet<Atom*> > BALL::AtomTyper::aromatic_rings_ [protected] |
Definition at line 93 of file atomTyper.h.
HashSet<Atom*> BALL::AtomTyper::atoms_ [protected] |
Definition at line 95 of file atomTyper.h.
StringHashMap<vector<Position> > BALL::AtomTyper::element_to_rules_ [protected] |
Definition at line 94 of file atomTyper.h.
vector<vector<String> > BALL::AtomTyper::fields_ [protected] |
Definition at line 89 of file atomTyper.h.
vector<String> BALL::AtomTyper::names_ [protected] |
Definition at line 85 of file atomTyper.h.
Size BALL::AtomTyper::number_expected_fields_ [protected] |
Definition at line 91 of file atomTyper.h.
vector<HashSet<Atom*> > BALL::AtomTyper::rings_ [protected] |
Definition at line 92 of file atomTyper.h.
StringHashMap<float> BALL::AtomTyper::rule_times [static] |
Definition at line 68 of file atomTyper.h.
vector<String> BALL::AtomTyper::rules_ [protected] |
Definition at line 86 of file atomTyper.h.
vector<Index> BALL::AtomTyper::types_ [protected] |
Definition at line 87 of file atomTyper.h.