5#ifndef BALL_STRUCTURE_SDGENERATOR_H
6#define BALL_STRUCTURE_SDGENERATOR_H
8#ifndef BALL_DATATYPE_OPTIONS_H
12#ifndef BALL_STRUCTURE_RINGANALYSER_H
16#ifndef BALL_KERNEL_PDBATOM_H
42 FIRST_SDGENERATOR_PROPERTY = PDBAtom::NUMBER_OF_PROPERTIES+1,
54 LAST_SDGENERATOR_PROPERTY
130 bool operator() (
Atom const* first,
Atom const* second)
const
135 return first_value < second_value;
unsigned int getUnsignedInt() const
const NamedProperty & getProperty(const std::string &name) const
Methods for the analysis of the structure of ringsystems.
void placeSubstituent_(Atom *seed, Atom *head, Atom *next)
void computeAdjacencyMatrix_(std::vector< Atom * > &chain, std::vector< bool > &result)
Compute adjacency matrix of the given atoms.
SDGenerator(bool show_hydrogens=false)
void computeShelleyPriorities_()
std::priority_queue< Atom *, std::vector< Atom * >, AtomComparator > redraw_queue_
our redraw queue
System * system_
the system we are working on
void pushCFS_(Atom *atom)
Property
Properties, used to describe atoms and their status.
Angle computeAngularSeparation_(Atom *seed)
bool ringIsClockwise_(const RingAnalyser::Ring &ring, Index start_index=0) const
void buildOpenPolygon_(RingAnalyser::Ring &ring, Position first_anchor_index, Position second_anchor_index)
void attachBridged_(Position current_ring, std::vector< RingAnalyser::Ring > ¤t_system)
attach a bridged ring to a (partially) constructed ringsystem
Angle getCFS_(Atom const *atom, bool hi)
std::vector< Atom * > sequenceSubstituents_(Atom *seed)
void buildRegularPolygon_(RingAnalyser::Ring &ring, Position first_anchor_index, bool clockwise)
void depositPFU_(Atom *seed_atom, Atom *next_neighbour)
void attachTemplate_(Position current_ring, std::vector< RingAnalyser::Ring > ¤t_system)
attach a ring template to a (partially) constructed ringsystem (no functionality yet)
void setCFS_(Atom *atom, Angle cfs, bool high)
void generateSD(System &molecule_sys)
Generates a structure Diagram from the input System.
void attachCore_(Position current_ring, std::vector< RingAnalyser::Ring > ¤t_system, float x_start)
construct the core-ring as a regular polygon
void smoothCFSAngle_(Atom *seed)
std::list< std::list< Atom * > > chains_
all chains
void attachSpiro_(Position current_ring, std::vector< RingAnalyser::Ring > ¤t_system)
attach a spiro ring to a (partially) constructed ringsystem
static bool compareChains_(const vector< Atom * > &x, const vector< Atom * > &y)
Comparator for chains of atoms.
void prepare_()
Distinguishes between ring-atoms and core-chain-atoms, removes all H-Atoms from the System.
void treatChains_()
cluster and arrange all chains in the system
Angle getBackupCFS_(Atom const *, bool hi)
Angle computeCFS_(Vector3 const &input)
void checkOverlap_(Atom *atom)
Angle computeAngularDemand_(Atom *seed)
void computeCoreCFS_(RingAnalyser::Ring &ring, bool clockwise)
void constructRingSystem_(Position current_ring_system)
Constructs a ringsystem, providing the atoms with relative 2D-coordinates, starting in the point of o...
void attachFused_(Position current_ring, std::vector< RingAnalyser::Ring > ¤t_system)
attach a fused ring to a (partially) constructed ringsystem
void findFloydWarshallPath_(std::vector< int > &path, std::vector< Index > &next, Size remaining_atoms, Position i, Position j, std::list< Index > &output)
RingAnalyser ring_analyser_
The ring analyser containing all information about ring systems.
static const char * STANDARD_BOND_LENGTH
static const char * SHOW_HYDROGENS
Default values for options.
static const bool SHOW_HYDROGENS
static const float STANDARD_BOND_LENGTH