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_name(int iatom) const | sc::Molecule |
atom_symbol(int iatom) 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_charge() const | sc::Molecule |
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
include_q() const | sc::Molecule | inline
include_q_ (defined in sc::Molecule) | sc::Molecule | protected
include_qq() const | sc::Molecule | inline
include_qq_ (defined in sc::Molecule) | sc::Molecule | protected
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 |
n_non_q_atom() const | sc::Molecule | inline
n_q_atom() const | sc::Molecule | inline
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
non_q_atom(int i) const | sc::Molecule | inline
non_q_atoms_ (defined in sc::Molecule) | sc::Molecule | protected
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 |
q_atom(int i) const | sc::Molecule | inline
q_atoms_ (defined in sc::Molecule) | sc::Molecule | protected
q_Z_ (defined in sc::Molecule) | sc::Molecule | protected
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_include_q(bool iq) | sc::Molecule | inline
set_include_qq(bool iqq) | sc::Molecule | inline
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 |
throw_if_atom_duplicated(int begin=0, double tol=1e-3) (defined in sc::Molecule) | sc::Molecule | protected
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