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sc::Molecule Member List This is the complete list of members for sc::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) sc::Molecule atom_at_position(double *, double tol=0.05) const sc::Molecule atom_label_to_index(const char *label) const sc::Molecule atom_to_uniq_ (defined in sc::Molecule) sc::Molecule [protected] atom_to_unique(int iatom) const sc::Molecule [inline] atom_to_unique_offset(int iatom) const sc::Molecule atominfo() const sc::Molecule [inline] atominfo_ (defined in sc::Molecule) sc::Molecule [protected] center_of_mass() const sc::Molecule charge(int iatom) const sc::Molecule charges() const sc::Molecule charges_ (defined in sc::Molecule) sc::Molecule [protected] class_desc() const sc::DescribedClass class_name() const sc::DescribedClass class_version() const sc::DescribedClass cleanup_molecule(double tol=0.1) sc::Molecule clear() (defined in sc::Molecule) sc::Molecule [protected] clear_symmetry_info() (defined in sc::Molecule) sc::Molecule [protected] dereference() sc::RefCount [inline] DescribedClass() (defined in sc::DescribedClass) sc::DescribedClass DescribedClass(const DescribedClass &) (defined in sc::DescribedClass) sc::DescribedClass dir_restore_state(StateIn &si, const char *objectname, const char *keyword=0) (defined in sc::SavableState) sc::SavableState [static] equiv_ (defined in sc::Molecule) sc::Molecule [protected] equivalent(int iuniq, int j) const sc::Molecule [inline] geometry_units_ (defined in sc::Molecule) sc::Molecule [protected] has_inversion(SCVector3 &origin, double tol=1.0e-8) const sc::Molecule highest_point_group(double tol=1.0e-8) const sc::Molecule identifier() sc::Identity [inline] init_symmetry_info(double tol=0.5) (defined in sc::Molecule) sc::Molecule [protected] is_axis(SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const sc::Molecule is_linear(double tolerance=1.0e-5) const sc::Molecule is_linear_planar(int &linear, int &planar, double tol=1.0e-5) const sc::Molecule is_planar(double tolerance=1.0e-5) const sc::Molecule is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const sc::Molecule key_restore_state(StateIn &si, const char *keyword) sc::SavableState [static] label(int atom) const sc::Molecule labels_ (defined in sc::Molecule) sc::Molecule [protected] lock_ptr() const sc::RefCount managed() const (defined in sc::RefCount) sc::RefCount [inline] managed() const sc::RefCount [inline] mass(int atom) const (defined in sc::Molecule) sc::Molecule mass_ (defined in sc::Molecule) sc::Molecule [protected] max_z() sc::Molecule Molecule() (defined in sc::Molecule) sc::Molecule Molecule(const Molecule &) (defined in sc::Molecule) sc::Molecule Molecule(StateIn &) (defined in sc::Molecule) sc::Molecule Molecule(const Ref< KeyVal > &input) sc::Molecule move_to_com() (defined in sc::Molecule) sc::Molecule n_core_electrons() sc::Molecule natom() const sc::Molecule [inline] natoms_ (defined in sc::Molecule) sc::Molecule [protected] nequiv_ (defined in sc::Molecule) sc::Molecule [protected] nequivalent(int iuniq) const sc::Molecule [inline] nreference() const sc::RefCount [inline] nuclear_charge() const sc::Molecule nuclear_charge_efield(const double *charges, const double *position, double *efield) sc::Molecule nuclear_efield(const double *position, double *efield) sc::Molecule nuclear_repulsion_1der(int center, double xyz[3]) sc::Molecule nuclear_repulsion_energy() sc::Molecule nuniq_ (defined in sc::Molecule) sc::Molecule [protected] nunique() const sc::Molecule [inline] operator=(const Molecule &) (defined in sc::Molecule) sc::Molecule operator=(const SavableState &) (defined in sc::SavableState) sc::SavableState operator=(const DescribedClass &) (defined in sc::DescribedClass) sc::DescribedClass operator=(const RefCount &) (defined in sc::RefCount) sc::RefCount [inline, protected] pg_ (defined in sc::Molecule) sc::Molecule [protected] point_group() const sc::Molecule principal_moments_of_inertia(double *evals, double **evecs=0) const sc::Molecule print(std::ostream &=ExEnv::out0()) const sc::Molecule [virtual] print_parsedkeyval(std::ostream &=ExEnv::out0(), int print_pg=1, int print_unit=1, int number_atoms=1) const (defined in sc::Molecule) sc::Molecule [virtual] print_pdb(std::ostream &=ExEnv::out0(), char *title=0) const (defined in sc::Molecule) sc::Molecule r(int atom, int xyz) (defined in sc::Molecule) sc::Molecule [inline] r(int atom, int xyz) const (defined in sc::Molecule) sc::Molecule [inline] r(int atom) (defined in sc::Molecule) sc::Molecule [inline] r(int atom) const (defined in sc::Molecule) sc::Molecule [inline] r_ (defined in sc::Molecule) sc::Molecule [protected] read_pdb(const char *filename) (defined in sc::Molecule) sc::Molecule RefCount() (defined in sc::RefCount) sc::RefCount [inline, protected] RefCount(const RefCount &) (defined in sc::RefCount) sc::RefCount [inline, protected] reference() sc::RefCount [inline] restore_state(StateIn &si) sc::SavableState [static] SavableState() (defined in sc::SavableState) sc::SavableState [protected] SavableState(const SavableState &) (defined in sc::SavableState) sc::SavableState [protected] SavableState(StateIn &) sc::SavableState [protected] save_data_state(StateOut &) sc::Molecule [virtual] save_object_state(StateOut &) sc::SavableState save_state(StateOut &) sc::SavableState save_state(SavableState *s, StateOut &) (defined in sc::SavableState) sc::SavableState [static] save_vbase_state(StateOut &) sc::SavableState [virtual] set_point_group(const Ref< PointGroup > &, double tol=1.0e-7) sc::Molecule symmetrize(double tol=0.5) sc::Molecule symmetrize(const Ref< PointGroup > &pg, double tol=0.5) sc::Molecule transform_to_principal_axes(int trans_frame=1) (defined in sc::Molecule) sc::Molecule transform_to_symmetry_frame() (defined in sc::Molecule) sc::Molecule translate(const double *r) (defined in sc::Molecule) sc::Molecule unique(int iuniq) const sc::Molecule [inline] unlock_ptr() const sc::RefCount unmanage() sc::RefCount [inline] use_locks(bool inVal) sc::RefCount Z(int atom) const (defined in sc::Molecule) sc::Molecule [inline] Z_ (defined in sc::Molecule) sc::Molecule [protected] ~DescribedClass() (defined in sc::DescribedClass) sc::DescribedClass [virtual] ~Identity() (defined in sc::Identity) sc::Identity [virtual] ~Molecule() (defined in sc::Molecule) sc::Molecule [virtual] ~RefCount() (defined in sc::RefCount) sc::RefCount [virtual] ~SavableState() (defined in sc::SavableState) sc::SavableState [virtual]