| altl | HaAtom | |
| AtTypeFromLbl(HaString &Label) | HaAtom | [static] |
| CalcAngle(const Vec3D *atm1, const Vec3D *atm2, const Vec3D *atm3) | Vec3D | [static] |
| CalcDihedral(const Vec3D *atm1, const Vec3D *atm2, const Vec3D *atm3, const Vec3D *atm4) | Vec3D | [static] |
| CalcDistance(const Vec3D *atm1, const Vec3D *atm2, const CoordUnits units=BOHR_U) | Vec3D | [static] |
| CalcHlxParams(const Vec3D &c0_1, const Vec3D &v1_1, const Vec3D &v2_1, const Vec3D &v3_1, const Vec3D &c0_2, const Vec3D &v1_2, const Vec3D &v2_2, const Vec3D &v3_2, double &shift, double &slide, double &rise, double &tilt, double &roll, double &twist, int idir=1) | Vec3D | [static] |
| CalcTorsion(const Vec3D *atm1, const Vec3D *atm2, const Vec3D *atm3, const Vec3D *atm4) | Vec3D | [static] |
| charge | MatPoint | |
| col | HaAtom | |
| CreateBond(HaAtom *aptr1, HaAtom *aptr2) | HaAtom | [static] |
| DeleteBond(HaAtom *aptr1, HaAtom *aptr2) | HaAtom | [static] |
| diff(Vec3D &c, const Vec3D &vec1, const Vec3D &vec2) | Vec3D | [static] |
| DotProduct(const Vec3D &vec1, const Vec3D &vec2) | Vec3D | [static] |
| ElemDesc | HaAtom | [static] |
| ElemDuttonRadius(int elem) | HaAtom | [static] |
| elemno | HaAtom | |
| ElemVDWRadius(int elem, bool united_atom_flag=false) | HaAtom | [static] |
| ew | MatPoint | |
| FFSymbol | MatPoint | |
| FillRef(char *buf, int ref_type=ATOMREF_FULL) const | HaAtom | [virtual] |
| FillStdAtomTypes() | HaAtom | [static] |
| flag | HaAtom | |
| GetBondedAtoms(AtomList &bonded_atoms) | HaAtom | |
| GetCharge() const | MatPoint | [inline] |
| GetElemNo() const | HaAtom | |
| GetElemNoFromName(const HaString at_name, const HaResidue *pres=NULL) | HaAtom | [static] |
| GetFFSymbol() const | MatPoint | [inline] |
| GetHBStatusTextStr(HaString &hb_status_str) (defined in HaAtom) | HaAtom | |
| GetHostChain() (defined in HaAtom) | HaAtom | |
| GetHostChain() const (defined in HaAtom) | HaAtom | |
| GetHostChemGroup() (defined in HaAtom) | HaAtom | |
| GetHostMol() (defined in HaAtom) | HaAtom | |
| GetHostMol() const (defined in HaAtom) | HaAtom | |
| GetHostMolSet() (defined in HaAtom) | HaAtom | |
| GetHostMolSet() const (defined in HaAtom) | HaAtom | |
| GetHostRes() | HaAtom | |
| GetHostRes() const (defined in HaAtom) | HaAtom | |
| GetHybrid() const (defined in HaAtom) | HaAtom | [inline] |
| GetHybridTextStr(HaString &hybrid_str) const (defined in HaAtom) | HaAtom | |
| GetMass() const | MatPoint | [inline] |
| GetName() const | HaAtom | |
| GetReachableAtoms(AtomList &block_atoms, HaAtom *aptr2, AtomList &reach_atoms, int &loop) | HaAtom | [static] |
| GetRef(int ref_type=ATOMREF_FULL) const | MatPoint | |
| GetSerNo() const | HaAtom | |
| GetStdSymbol() const | HaAtom | |
| GetStdSymbolElem(int elem) | HaAtom | [static] |
| GetX() const | Vec3D | [inline] |
| GetY() const | Vec3D | [inline] |
| GetZ() const | Vec3D | [inline] |
| HaAtom() (defined in HaAtom) | HaAtom | |
| HaAtom(HaResidue *new_phost_res) (defined in HaAtom) | HaAtom | |
| hybrid | HaAtom | |
| image_radius | HaAtom | |
| irad | HaAtom | |
| IsAlphaCarbon() const (defined in HaAtom) | HaAtom | |
| IsAminoBackbone() const (defined in HaAtom) | HaAtom | |
| IsAtom() const | HaAtom | [inline, virtual] |
| IsBonded(HaAtom &at2) (defined in HaAtom) | HaAtom | |
| IsCysteineSulfur() const (defined in HaAtom) | HaAtom | |
| IsDisplayed() const | HaAtom | |
| IsDrawSphere() const (defined in HaAtom) | HaAtom | |
| IsHBAcceptor() const | HaAtom | |
| IsHBDonor() const | HaAtom | |
| IsHydrogen() const | HaAtom | [virtual] |
| IsNucleicBackbone() const (defined in HaAtom) | HaAtom | |
| IsSameName(const HaAtom *aptr_ref) const | HaAtom | |
| IsShapelyBackbone() const (defined in HaAtom) | HaAtom | |
| IsShapelySpecial() const (defined in HaAtom) | HaAtom | |
| IsSugarPhosphate() const (defined in HaAtom) | HaAtom | |
| label | HaAtom | |
| length() const | Vec3D | |
| length2() const | Vec3D | |
| mass | MatPoint | |
| MatPoint() (defined in MatPoint) | MatPoint | |
| mbox | HaAtom | |
| nbonds | HaAtom | |
| NewAtomType(const char *ptr) | HaAtom | [static] |
| normalize() | Vec3D | |
| operator *(const double factor, const Vec3D &v) | Vec3D | [friend] |
| operator+(const Vec3D &v1, const Vec3D &v2) | Vec3D | [friend] |
| operator-(const Vec3D &v1, const Vec3D &v2) | Vec3D | [friend] |
| operator<(const HaAtom &rhs) const (defined in HaAtom) | HaAtom | |
| operator=(const Vec3D &ref_vec) (defined in Vec3D) | Vec3D | |
| operator==(const HaAtom &rhs) const (defined in HaAtom) | HaAtom | |
| operator[](int i) | Vec3D | [inline] |
| operator[](int i) const | Vec3D | [inline] |
| phost_res | HaAtom | [protected] |
| Print_info(ostream &sout, const int level) const (defined in HaAtom) | HaAtom | |
| radius | HaAtom | |
| refno | HaAtom | |
| Rotate(Vec3D &n, double cosa, double sina) | Vec3D | |
| RotatePt(Vec3D &still_pt, Vec3D &n, double cosa, double sina) | Vec3D | |
| ScaleCoord(double scale) | Vec3D | |
| Select() | HaAtom | [virtual] |
| Selected() const | HaAtom | [virtual] |
| SetAtomPos(Vec3D *pptr, const Vec3D *ptr1, const Vec3D *pptr2, const Vec3D *pptr3, double dist, double val_angle, double dih_angle) | Vec3D | [static] |
| SetCharge(double new_charge) | MatPoint | [inline] |
| SetDefaultParam() (defined in HaAtom) | HaAtom | [protected] |
| SetDisplayed(bool set_mode) | HaAtom | |
| SetDrawSphere(bool set_mode) (defined in HaAtom) | HaAtom | |
| SetElemNo(const int new_elem_no) | HaAtom | |
| SetFFSymbol(HaString new_ff_symbol) | MatPoint | [inline] |
| SetFromStr(const char *str) | Vec3D | |
| SetHBAcceptor(bool set_mode) | HaAtom | |
| SetHBDonor(bool set_mode) | HaAtom | |
| SetHBStatus(const char *hb_status_str) | HaAtom | |
| SetHostRes(HaResidue *new_phost_res) (defined in HaAtom) | HaAtom | |
| SetHybrid(HaString hybrid_str) | HaAtom | |
| SetMass(double new_mass) | MatPoint | [inline] |
| SetName(const char *AtName) | HaAtom | |
| SetParamFrom(const HaAtom &atom_ref) (defined in HaAtom) | HaAtom | |
| MatPoint::SetParamFrom(const MatPoint &pt_ref) | MatPoint | |
| SetX(const double x_new) | Vec3D | |
| SetY(const double y_new) | Vec3D | |
| SetZ(const double z_new) | Vec3D | |
| solv_access_surf | HaAtom | |
| StdBondLen(const HaAtom *aptr1, const HaAtom *aptr2) | HaAtom | [static] |
| StdElemMass(int elem) | HaAtom | [static] |
| sum(Vec3D &c, const Vec3D &vec1, const Vec3D &vec2) | Vec3D | [static] |
| tempf | HaAtom | |
| UnSelect() | HaAtom | [virtual] |
| vdw_rad | MatPoint | |
| Vec3D() (defined in Vec3D) | Vec3D | |
| VecProduct(Vec3D &vprod, const Vec3D &vec1, const Vec3D &vec2) | Vec3D | [static] |
| x (defined in HaAtom) | HaAtom | |
| y (defined in HaAtom) | HaAtom | |
| z | HaAtom | |
| ~HaAtom() (defined in HaAtom) | HaAtom | [virtual] |
| ~MatPoint() (defined in MatPoint) | MatPoint | [virtual] |
| ~Vec3D() (defined in Vec3D) | Vec3D | [virtual] |
