5 #ifndef BALL_STRUCTURE_HBONDPROCESSOR_H
6 #define BALL_STRUCTURE_HBONDPROCESSOR_H
8 #ifndef BALL_CONCEPT_PROCESSOR_H
12 #ifndef BALL_KERNEL_RESIDUE_H
16 #ifndef BALL_MATHS_VECTOR3_H
20 #ifndef BALL_DATATYPE_OPTIONS_H
114 HBond(
Atom const* acceptor,
Atom const* donor,
bool donor_is_hydrogen=
false)
115 {acceptor_ = acceptor; donor_ = donor; donor_is_hydrogen_ = donor_is_hydrogen;}
123 float getLength() {
return acceptor_->getDistance(*donor_); }
240 const std::vector< HBond>&
getHBonds()
const {
return h_bonds_;}
Mutable bidirectional iterator.
Computation of hydrogen bonds from topology information.
BALL_CREATE(HBondProcessor)
const std::vector< std::vector< Position > > & getBackboneHBondPattern() const
computes the HBond pattern as needed, e.g. by the SecondaryStructureProcessor
bool finishWishartEtAl_()
static float ALPHA_PROTON_OXYGEN_SEPARATION_DISTANCE
const std::vector< ResidueData > & getResidueData() const
void preComputeBonds_(ResidueIterator &data)
static float BOND_LENGTH_C_O
std::vector< HBond > h_bonds_
store HBond
const std::vector< HBond > & getHBonds() const
HBondProcessor()
Default constructor.
std::vector< Atom * > acceptors_
static float AMIDE_PROTON_OXYGEN_SEPARATION_DISTANCE
std::vector< std::vector< Position > > backbone_h_bond_pairs_
HBondProcessor(Options &new_options)
Detailed constructor.
std::vector< ResidueData > residue_data_
static float BOND_LENGTH_N_H
std::vector< Atom * > donors_
std::vector< HBond > getHBonds()
std::map< Residue *, Position > residue_ptr_to_position_
bool finishKabschSander_()
virtual ~HBondProcessor()
virtual bool finish()
Finish computes all hbonds of the composite according.
float getLength()
Return distance between donor and acceptor.
HBond(Atom const *acceptor, Atom const *donor, bool donor_is_hydrogen=false)
Atom const * getAcceptor()
bool donorIsHydrogen()
Return flag indicating what HBond definition was used.
static const String KABSCH_SANDER_ENERGY_CUTOFF
static const String ADD_HBONDS
static const String PREDICTION_METHOD
Default values for options.
static const String PREDICTION_METHOD
static const bool ADD_HBONDS
static const float KABSCH_SANDER_ENERGY_CUTOFF
Default values for options.
static const String KABSCH_SANDER
static const String WISHART_ET_AL
bool is_complete
sometimes there are defect residues around...