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5 #ifndef BALL_STRUCTURE_BUILDBONDSPROCESSOR_H
6 #define BALL_STRUCTURE_BUILDBONDSPROCESSOR_H
8 #ifndef BALL_CONCEPT_PROCESSOR_H
12 #ifndef BALL_KERNEL_ATOMCONTAINER_H
16 #ifndef BALL_DATATYPE_HASHMAP_H
20 #ifndef BALL_KERNEL_BOND_H
24 #ifndef BALL_DATATYPE_OPTIONS_H
127 Size getNumberOfBondsBuilt();
213 #endif // BALL_STRUCTURE_BUILDBONDSPROCESSOR_H
void deleteOverestimatedBonds_(AtomContainer &ac)
deletes bonds, like from multiple bonded hydrogens or halogens
static const bool REESTIMATE_BONDORDERS_RINGS
this option is off by default
static const bool DELETE_EXISTING_BONDS
this option is off by default
HashMap< Size, HashMap< Size, HashMap< int, float > > > bond_lengths_
structure where bond order distances are stored in
BuildBondsProcessor(const BuildBondsProcessor &bbp)
copy construcor
virtual ~BuildBondsProcessor()
destructor
HashMap class based on the STL map (containing serveral convenience functions)
Size num_bonds_
number of bonds, which are created during the processor call
void estimateBondOrders_(AtomContainer &ac)
after the bonds are built, the orders are estimated
void setBondLengths(const String &file_name)
static const char * BONDLENGTHS_FILENAME
void readBondLengthsFromFile_(const String &file_name="")
HashMap< Size, HashMap< Size, float > > min_bond_lengths_
structure were the bond minima stored in (used in buildBonds_)
virtual bool start()
processor method which is called before the operator () call
static const char * BONDLENGTHS_FILENAME
default file name for the bond lengths
static const bool DELETE_OVERESTIMATED_BONDS
this option is off by default
static const char * DELETE_OVERESTIMATED_BONDS
BuildBondsProcessor()
default constructor
float max_length_
parameter which holds the longest possible bond
bool getMaxBondLength_(float &length, Size an1, Size an2)
void reestimateBondOrdersRings_(AtomContainer &ac)
reestimate the bond orders of rings, as aromatic rings are often detected wrong
HashMap< Size, HashMap< Size, float > > max_bond_lengths_
structure were the bond maxima stored in (used in buildBonds_)
static const char * REESTIMATE_BONDORDERS_RINGS
BuildBondsProcessor(const String &file_name)
bool getMinBondLength_(float &length, Size an1, Size an2)
Bond::BondOrder getNearestBondOrder_(float length, Size e1, Size e2)
BALL_CREATE(BuildBondsProcessor)
static const char * DELETE_EXISTING_BONDS
Default values for options.
HashMap< Size, HashMap< Size, HashMap< int, float > > > getBondMap()
Return the bond length Hashmap.
Size buildBondsHashGrid3_(AtomContainer &ac)
builds bonds, based on atom distances read from parameter file using a 3D hash grid