#include <haatom.h>
Inheritance diagram for HaAtom:
Public Member Functions | |
| HaAtom (HaResidue *new_phost_res) | |
| bool | SetParamFrom (const HaAtom &atom_ref) |
| int | GetElemNo () const |
| Get atom element. | |
| void | SetElemNo (const int new_elem_no) |
| Set element of the atom. | |
| int | SetName (const char *AtName) |
| Set atom name. | |
| const char * | GetName () const |
| Get the name of the atom. | |
| HaString | GetStdSymbol () const |
| Get Std Symbol of the atom. | |
| bool | operator== (const HaAtom &rhs) const |
| bool | operator< (const HaAtom &rhs) const |
| virtual void | Select () |
| Select atom. | |
| virtual void | UnSelect () |
| Unselect atom. | |
| virtual int | Selected () const |
| Check if atom is selected. | |
| bool | IsDrawSphere () const |
| void | SetDrawSphere (bool set_mode) |
| void | SetDisplayed (bool set_mode) |
| Set Displayed in Wireframe model. | |
| bool | IsDisplayed () const |
| (cross if no bonds attached) | |
| virtual bool | IsAtom () const |
| check the mat point is an atom | |
| virtual bool | IsHydrogen () const |
| check if the point is hydrogen | |
| bool | IsHBDonor () const |
| Check if the atom if Hydrogen bond donor. | |
| bool | IsHBAcceptor () const |
| Check if the atom if Hydrogen bond donor. | |
| void | SetHBDonor (bool set_mode) |
| Set hydrogen bond donor flag for the atom. | |
| void | SetHBAcceptor (bool set_mode) |
| Set hydrogen bond acceptor flag for the atom. | |
| int | SetHBStatus (const char *hb_status_str) |
| Set donor/acceptor. | |
| int | GetHBStatusTextStr (HaString &hb_status_str) |
| HaResidue * | GetHostRes () |
| Get the residue Atom belongs to. | |
| const HaResidue * | GetHostRes () const |
| HaChain * | GetHostChain () |
| const HaChain * | GetHostChain () const |
| ChemGroup * | GetHostChemGroup () |
| HaMolecule * | GetHostMol () |
| const HaMolecule * | GetHostMol () const |
| HaMolSet * | GetHostMolSet () |
| const HaMolSet * | GetHostMolSet () const |
| void | SetHostRes (HaResidue *new_phost_res) |
| int | GetBondedAtoms (AtomList &bonded_atoms) |
| return set of atoms bonded to the given atom | |
| bool | IsBonded (HaAtom &at2) |
| bool | IsSameName (const HaAtom *aptr_ref) const |
| Check if atom has the same name. | |
| bool | Print_info (ostream &sout, const int level) const |
| virtual bool | FillRef (char *buf, int ref_type=ATOMREF_FULL) const |
| Fill Atom Reference. | |
| int | GetSerNo () const |
| Get Serial number of the atom in the Molecular Set. | |
| bool | IsAlphaCarbon () const |
| bool | IsSugarPhosphate () const |
| bool | IsAminoBackbone () const |
| bool | IsShapelyBackbone () const |
| bool | IsNucleicBackbone () const |
| bool | IsShapelySpecial () const |
| bool | IsCysteineSulfur () const |
| HYBRIDIZATION | GetHybrid () const |
| int | GetHybridTextStr (HaString &hybrid_str) const |
| int | SetHybrid (HaString hybrid_str) |
| Set Atom Hybridization. | |
Static Public Member Functions | |
| int | CreateBond (HaAtom *aptr1, HaAtom *aptr2) |
| Create bond between 2 atoms. | |
| int | DeleteBond (HaAtom *aptr1, HaAtom *aptr2) |
| Delete bond between 2 atoms. | |
| int | GetReachableAtoms (AtomList &block_atoms, HaAtom *aptr2, AtomList &reach_atoms, int &loop) |
| Get Atoms Accessible by bond graph from a given atom. | |
| void | FillStdAtomTypes () |
| Fill list of names of atoms with standard names. | |
| int | AtTypeFromLbl (HaString &Label) |
| Determine atom element number from the atom label. | |
| int | NewAtomType (const char *ptr) |
| int | GetElemNoFromName (const HaString at_name, const HaResidue *pres=NULL) |
| Get Element Number from element Symbol. | |
| const char * | GetStdSymbolElem (int elem) |
| Get Standard symbol of the element. | |
| double | ElemVDWRadius (int elem, bool united_atom_flag=false) |
| Get Standard Van der Waals radius of the Element. | |
| double | StdElemMass (int elem) |
| Get Atomic mass of the Element from the periodical table. | |
| double | ElemDuttonRadius (int elem) |
| Get Atom Radii used in Dutton ET model. | |
| double | StdBondLen (const HaAtom *aptr1, const HaAtom *aptr2) |
| Get Standard Bond length (in Ang) for two atoms. | |
Public Attributes | |
| short | x |
| short | y |
| short | z |
| Image Co-ordinates. | |
| double | tempf |
| Temperature Factor used also to pass misc atom properties. | |
| short | col |
| Atom Colour. | |
| HaString | label |
| Atom Label format. | |
| Byte | elemno |
| Atomic Number. | |
| int | refno |
| ElemDesc index number. | |
| unsigned int | flag |
| Database flags. | |
| char | altl |
| Alternate Location. | |
| double | radius |
| Atom Radius in Bohr! to use in Electrostatics calculations. | |
| double | image_radius |
| Atom Radius in Bohr! for plotting on the screen. | |
| short | irad |
| Atom Image Radius in pixels. | |
| short | mbox |
| Shadow Casting NOnce. | |
| double | solv_access_surf |
| Solvent accessible surface of the atom. | |
| HYBRIDIZATION | hybrid |
| Hybridization of the atom. | |
| int | nbonds |
| number of bonds of with this atom | |
Static Public Attributes | |
| StrVec | ElemDesc |
| list of names of atoms | |
Protected Member Functions | |
| void | SetDefaultParam () |
Protected Attributes | |
| HaResidue * | phost_res |
| the residue atom belongs to | |
|
|
Return Position of the atom type given by string ptr in ElemDesc[] array, if such type don't exist add new type to the ElemDesc[] |
1.3.6