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Molecule Member List

This is the complete list of members for Molecule, including all inherited members.

• add_atom(int Z, double x, double y, double z, const char *=0, double mass=0.0, int have_charge=0, double charge=0.0)
• atom_at_position(double *, double tol=0.05) const
• atom_label_to_index(const char *label) const
• atom_to_uniq_ (defined in Molecule) [protected]
• atom_to_unique(int iatom) const [inline]
• atom_to_unique_offset(int iatom) const
• atominfo() const [inline]
• atominfo_ (defined in Molecule) [protected]
• center_of_mass() const
• charge(int iatom) const
• charges() const
• charges_ (defined in Molecule) [protected]
• class_desc() const
• class_name() const
• class_version() const
• cleanup_molecule(double tol=0.1)
• clear() (defined in Molecule) [protected]
• clear_symmetry_info() (defined in Molecule) [protected]
• dereference() [inline]
• DescribedClass() (defined in DescribedClass)
• DescribedClass(const DescribedClass &) (defined in DescribedClass)
• dir_restore_state(StateIn &si, const char *objectname, const char *keyword=0) (defined in SavableState) [static]
• equiv_ (defined in Molecule) [protected]
• equivalent(int iuniq, int j) const [inline]
• geometry_units_ (defined in Molecule) [protected]
• has_inversion(SCVector3 &origin, double tol=1.0e-8) const
• highest_point_group(double tol=1.0e-8) const
• identifier() [inline]
• init_symmetry_info(double tol=0.5) (defined in Molecule) [protected]
• is_axis(SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const
• is_linear(double tolerance=1.0e-5) const
• is_linear_planar(int &linear, int &planar, double tol=1.0e-5) const
• is_planar(double tolerance=1.0e-5) const
• is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const
• key_restore_state(StateIn &si, const char *keyword) [static]
• label(int atom) const (defined in Molecule)
• labels_ (defined in Molecule) [protected]
• lock_ptr() const
• managed() const [inline]
• managed() const [inline]
• mass(int atom) const (defined in Molecule)
• mass_ (defined in Molecule) [protected]
• max_z()
• Molecule() (defined in Molecule)
• Molecule(const Molecule &) (defined in Molecule)
• Molecule(StateIn &) (defined in Molecule)
• Molecule(const Ref< KeyVal > &input)
• move_to_com() (defined in Molecule)
• n_core_electrons()
• natom() const [inline]
• natoms_ (defined in Molecule) [protected]
• nequiv_ (defined in Molecule) [protected]
• nequivalent(int iuniq) const [inline]
• nreference() const [inline]
• nuclear_charge() const
• nuclear_charge_efield(const double *charges, const double *position, double *efield)
• nuclear_efield(const double *position, double *efield)
• nuclear_repulsion_1der(int center, double xyz[3])
• nuclear_repulsion_energy()
• nuniq_ (defined in Molecule) [protected]
• nunique() const [inline]
• operator=(const Molecule &) (defined in Molecule)
• operator=(const SavableState &) (defined in SavableState)
• operator=(const DescribedClass &) (defined in DescribedClass)
• operator=(const RefCount &) (defined in RefCount) [inline, protected]
• pg_ (defined in Molecule) [protected]
• point_group() const
• principal_moments_of_inertia(double *evals, double **evecs=0) const
• print(std::ostream &=ExEnv::out()) const [virtual]
• print_parsedkeyval(std::ostream &=ExEnv::out(), int print_pg=1, int print_unit=1, int number_atoms=1) const (defined in Molecule) [virtual]
• print_pdb(std::ostream &=ExEnv::out(), char *title=0) const (defined in Molecule)
• r(int atom, int xyz) (defined in Molecule) [inline]
• r(int atom, int xyz) const (defined in Molecule) [inline]
• r(int atom) (defined in Molecule) [inline]
• r(int atom) const (defined in Molecule) [inline]
• r_ (defined in Molecule) [protected]
• read_pdb(const char *filename) (defined in Molecule)
• RefCount() (defined in RefCount) [inline, protected]
• RefCount(const RefCount &) (defined in RefCount) [inline, protected]
• reference() [inline]
• restore_state(StateIn &si) [static]
• SavableState() (defined in SavableState) [protected]
• SavableState(const SavableState &) (defined in SavableState) [protected]
• SavableState(StateIn &) [protected]
• save_data_state(StateOut &) [virtual]
• save_object_state(StateOut &)
• save_state(StateOut &)
• save_state(SavableState *s, StateOut &) (defined in SavableState) [static]
• save_vbase_state(StateOut &) [virtual]
• set_point_group(const Ref< PointGroup > &, double tol=1.0e-7)
• symmetrize(double tol=0.5)
• symmetrize(const Ref< PointGroup > &pg, double tol=0.5)
• transform_to_principal_axes(int trans_frame=1) (defined in Molecule)
• transform_to_symmetry_frame() (defined in Molecule)
• translate(const double *r) (defined in Molecule)
• unique(int iuniq) const [inline]
• unlock_ptr() const
• unmanage() [inline]
• use_locks(bool inVal)
• Z(int atom) const (defined in Molecule) [inline]
• Z_ (defined in Molecule) [protected]
• ~DescribedClass() (defined in DescribedClass) [virtual]
• ~Identity() (defined in Identity) [virtual]
• ~Molecule() (defined in Molecule) [virtual]
• ~RefCount() (defined in RefCount) [virtual]
• ~SavableState() (defined in SavableState) [virtual]

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