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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) constsc::Molecule
atom_label_to_index(const char *label) constsc::Molecule
atom_to_uniq_ (defined in sc::Molecule)sc::Molecule [protected]
atom_to_unique(int iatom) constsc::Molecule [inline]
atom_to_unique_offset(int iatom) constsc::Molecule
atominfo() constsc::Molecule [inline]
atominfo_ (defined in sc::Molecule)sc::Molecule [protected]
center_of_mass() constsc::Molecule
charge(int iatom) constsc::Molecule
charges() constsc::Molecule
charges_ (defined in sc::Molecule)sc::Molecule [protected]
class_desc() constsc::DescribedClass
class_name() constsc::DescribedClass
class_version() constsc::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) constsc::Molecule [inline]
geometry_units_ (defined in sc::Molecule)sc::Molecule [protected]
has_inversion(SCVector3 &origin, double tol=1.0e-8) constsc::Molecule
highest_point_group(double tol=1.0e-8) constsc::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) constsc::Molecule
is_linear(double tolerance=1.0e-5) constsc::Molecule
is_linear_planar(int &linear, int &planar, double tol=1.0e-5) constsc::Molecule
is_planar(double tolerance=1.0e-5) constsc::Molecule
is_plane(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) constsc::Molecule
key_restore_state(StateIn &si, const char *keyword)sc::SavableState [static]
label(int atom) constsc::Molecule
labels_ (defined in sc::Molecule)sc::Molecule [protected]
lock_ptr() constsc::RefCount
managed() const (defined in sc::RefCount)sc::RefCount [inline]
managed() constsc::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() constsc::Molecule [inline]
natoms_ (defined in sc::Molecule)sc::Molecule [protected]
nequiv_ (defined in sc::Molecule)sc::Molecule [protected]
nequivalent(int iuniq) constsc::Molecule [inline]
nreference() constsc::RefCount [inline]
nuclear_charge() constsc::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() constsc::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() constsc::Molecule
principal_moments_of_inertia(double *evals, double **evecs=0) constsc::Molecule
print(std::ostream &=ExEnv::out0()) constsc::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) constsc::Molecule [inline]
unlock_ptr() constsc::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]

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