#include <BALL/STRUCTURE/atomTyper.h>
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.
Usage:
typer.
setup(parameter_file_name);
void setRings(const vector< HashSet< Atom * > > &rings)
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)
Definition at line 40 of file atomTyper.h.
◆ AtomTyper() [1/2]
BALL::AtomTyper::AtomTyper |
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◆ AtomTyper() [2/2]
BALL::AtomTyper::AtomTyper |
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const AtomTyper & |
t | ) |
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◆ ~AtomTyper()
virtual BALL::AtomTyper::~AtomTyper |
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inlinevirtual |
◆ assignSpecificValues_()
virtual void BALL::AtomTyper::assignSpecificValues_ |
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Atom & |
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inlineprotectedvirtual |
To be overloaded in derived classes to add support for additional properties e.g. charges
Definition at line 78 of file atomTyper.h.
◆ assignTo() [1/2]
void BALL::AtomTyper::assignTo |
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Molecule & |
mol | ) |
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protected |
◆ assignTo() [2/2]
virtual void BALL::AtomTyper::assignTo |
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System & |
s | ) |
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virtual |
◆ setAromaticRings()
void BALL::AtomTyper::setAromaticRings |
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const vector< HashSet< Atom * > > & |
rings | ) |
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inline |
◆ setRings()
void BALL::AtomTyper::setRings |
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const vector< HashSet< Atom * > > & |
rings | ) |
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inline |
◆ setup()
bool BALL::AtomTyper::setup |
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const String & |
filename | ) |
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Setup with the given line based file with SMARTS expressions.
◆ specificSetup_()
virtual bool BALL::AtomTyper::specificSetup_ |
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inlineprotectedvirtual |
To be overloaded in derived classes to add support for additional properties e.g. charges
Definition at line 83 of file atomTyper.h.
◆ aromatic_rings_
vector<HashSet<Atom*> > BALL::AtomTyper::aromatic_rings_ |
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protected |
◆ atoms_
◆ element_to_rules_
◆ fields_
vector<vector<String> > BALL::AtomTyper::fields_ |
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◆ names_
vector<String> BALL::AtomTyper::names_ |
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◆ number_expected_fields_
Size BALL::AtomTyper::number_expected_fields_ |
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protected |
◆ rings_
◆ rule_times
◆ rules_
vector<String> BALL::AtomTyper::rules_ |
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protected |
◆ types_
vector<Index> BALL::AtomTyper::types_ |
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protected |