<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html><head><meta name="robots" content="noindex"> <meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1"> <title>Member List</title> <link href="doxygen.css" rel="stylesheet" type="text/css"> </head><body bgcolor="#ffffff"> <!-- Generated by Doxygen 1.2.5 on Mon Oct 14 14:17:11 2002 --> <center> <a class="qindex" href="index.html">Main Page</a> <a class="qindex" href="hierarchy.html">Class Hierarchy</a> <a class="qindex" href="annotated.html">Compound List</a> <a class="qindex" href="files.html">File List</a> <a class="qindex" href="functions.html">Compound Members</a> <a class="qindex" href="pages.html">Related Pages</a> </center> <hr><h1>sc::Molecule Member List</h1>This is the complete list of members for <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>, including all inherited members.<ul> <li><a class="el" href="class_sc__Molecule.html#a6">add_atom</a>(int Z, double x, double y, double z, const char *=0, double mass=0.0, int have_charge=0, double charge=0.0) <li><a class="el" href="class_sc__Molecule.html#a17">atom_at_position</a>(double *, double tol=0.05) const <li><a class="el" href="class_sc__Molecule.html#a18">atom_label_to_index</a>(const char *label) const <li><b>atom_to_uniq_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a50">atom_to_unique</a>(int iatom) const <code> [inline]</code><li><a class="el" href="class_sc__Molecule.html#a51">atom_to_unique_offset</a>(int iatom) const <li><a class="el" href="class_sc__Molecule.html#a54">atominfo</a>() const <code> [inline]</code><li><b>atominfo_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a31">center_of_mass</a>() const <li><a class="el" href="class_sc__Molecule.html#a20">charge</a>(int iatom) const <li><a class="el" href="class_sc__Molecule.html#a19">charges</a>() const <li><b>charges_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__DescribedClass.html#a4">class_desc</a>() const <li><a class="el" href="class_sc__DescribedClass.html#a5">class_name</a>() const <li><a class="el" href="class_sc__DescribedClass.html#a6">class_version</a>() const <li><a class="el" href="class_sc__Molecule.html#a38">cleanup_molecule</a>(double tol=0.1) <li><b>clear</b>() (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><b>clear_symmetry_info</b>() (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__RefCount.html#a6">dereference</a>() <code> [inline]</code><li><b>DescribedClass</b>() (defined in <a class="el" href="class_sc__DescribedClass.html">sc::DescribedClass</a>)<li><b>DescribedClass</b>(const DescribedClass &) (defined in <a class="el" href="class_sc__DescribedClass.html">sc::DescribedClass</a>)<li><b>dir_restore_state</b>(StateIn &si, const char *objectname, const char *keyword=0) (defined in <a class="el" href="class_sc__SavableState.html">sc::SavableState</a>)<code> [static]</code><li><b>equiv_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a49">equivalent</a>(int iuniq, int j) const <code> [inline]</code><li><b>geometry_units_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a27">has_inversion</a>(SCVector3 &origin, double tol=1.0e-8) const <li><a class="el" href="class_sc__Molecule.html#a24">highest_point_group</a>(double tol=1.0e-8) const <li><a class="el" href="class_sc__Identity.html#a1">identifier</a>() <code> [inline]</code><li><b>init_symmetry_info</b>(double tol=0.5) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a25">is_axis</a>(SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const <li><a class="el" href="class_sc__Molecule.html#a28">is_linear</a>(double tolerance=1.0e-5) const <li><a class="el" href="class_sc__Molecule.html#a30">is_linear_planar</a>(int &linear, int &planar, double tol=1.0e-5) const <li><a class="el" href="class_sc__Molecule.html#a29">is_planar</a>(double tolerance=1.0e-5) const <li><a class="el" href="class_sc__Molecule.html#a26">is_plane</a>(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const <li><a class="el" href="class_sc__SavableState.html#d2">key_restore_state</a>(StateIn &si, const char *keyword) <code> [static]</code><li><a class="el" href="class_sc__Molecule.html#a16">label</a>(int atom) const <li><b>labels_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__RefCount.html#a1">lock_ptr</a>() const <li><a class="el" href="class_sc__RefCount.html#a7">managed</a>() const <code> [inline]</code><li><a class="el" href="class_sc__RefCount.html#a9">managed</a>() const <code> [inline]</code><li><b>mass</b>(int atom) const (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>mass_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a53">max_z</a>() <li><b>Molecule</b>() (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>Molecule</b>(const Molecule &) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>Molecule</b>(StateIn &) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><a class="el" href="class_sc__Molecule.html#a3">Molecule</a>(const Ref< KeyVal > &input) <li><b>move_to_com</b>() (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><a class="el" href="class_sc__Molecule.html#a52">n_core_electrons</a>() <li><a class="el" href="class_sc__Molecule.html#a9">natom</a>() const <code> [inline]</code><li><b>natoms_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><b>nequiv_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a48">nequivalent</a>(int iuniq) const <code> [inline]</code><li><a class="el" href="class_sc__RefCount.html#a4">nreference</a>() const <code> [inline]</code><li><a class="el" href="class_sc__Molecule.html#a21">nuclear_charge</a>() const <li><a class="el" href="class_sc__Molecule.html#a35">nuclear_charge_efield</a>(const double *charges, const double *position, double *efield) <li><a class="el" href="class_sc__Molecule.html#a34">nuclear_efield</a>(const double *position, double *efield) <li><a class="el" href="class_sc__Molecule.html#a33">nuclear_repulsion_1der</a>(int center, double xyz[3]) <li><a class="el" href="class_sc__Molecule.html#a32">nuclear_repulsion_energy</a>() <li><b>nuniq_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a46">nunique</a>() const <code> [inline]</code><li><b>operator=</b>(const Molecule &) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>operator=</b>(const SavableState &) (defined in <a class="el" href="class_sc__SavableState.html">sc::SavableState</a>)<li><b>operator=</b>(const DescribedClass &) (defined in <a class="el" href="class_sc__DescribedClass.html">sc::DescribedClass</a>)<li><b>operator=</b>(const RefCount &) (defined in <a class="el" href="class_sc__RefCount.html">sc::RefCount</a>)<code> [inline, protected]</code><li><b>pg_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a23">point_group</a>() const <li><a class="el" href="class_sc__Molecule.html#a45">principal_moments_of_inertia</a>(double *evals, double **evecs=0) const <li><a class="el" href="class_sc__Molecule.html#a7">print</a>(std::ostream &=ExEnv::out0()) const <code> [virtual]</code><li><b>print_parsedkeyval</b>(std::ostream &=ExEnv::out0(), int print_pg=1, int print_unit=1, int number_atoms=1) const (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [virtual]</code><li><b>print_pdb</b>(std::ostream &=ExEnv::out0(), char *title=0) const (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>r</b>(int atom, int xyz) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [inline]</code><li><b>r</b>(int atom, int xyz) const (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [inline]</code><li><b>r</b>(int atom) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [inline]</code><li><b>r</b>(int atom) const (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [inline]</code><li><b>r_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><b>read_pdb</b>(const char *filename) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>RefCount</b>() (defined in <a class="el" href="class_sc__RefCount.html">sc::RefCount</a>)<code> [inline, protected]</code><li><b>RefCount</b>(const RefCount &) (defined in <a class="el" href="class_sc__RefCount.html">sc::RefCount</a>)<code> [inline, protected]</code><li><a class="el" href="class_sc__RefCount.html#a5">reference</a>() <code> [inline]</code><li><a class="el" href="class_sc__SavableState.html#d1">restore_state</a>(StateIn &si) <code> [static]</code><li><b>SavableState</b>() (defined in <a class="el" href="class_sc__SavableState.html">sc::SavableState</a>)<code> [protected]</code><li><b>SavableState</b>(const SavableState &) (defined in <a class="el" href="class_sc__SavableState.html">sc::SavableState</a>)<code> [protected]</code><li><a class="el" href="class_sc__SavableState.html#b2">SavableState</a>(StateIn &) <code> [protected]</code><li><a class="el" href="class_sc__Molecule.html#a55">save_data_state</a>(StateOut &) <code> [virtual]</code><li><a class="el" href="class_sc__SavableState.html#a3">save_object_state</a>(StateOut &) <li><a class="el" href="class_sc__SavableState.html#a2">save_state</a>(StateOut &) <li><b>save_state</b>(SavableState *s, StateOut &) (defined in <a class="el" href="class_sc__SavableState.html">sc::SavableState</a>)<code> [static]</code><li><a class="el" href="class_sc__SavableState.html#a4">save_vbase_state</a>(StateOut &) <code> [virtual]</code><li><a class="el" href="class_sc__Molecule.html#a22">set_point_group</a>(const Ref< PointGroup > &, double tol=1.0e-7) <li><a class="el" href="class_sc__Molecule.html#a36">symmetrize</a>(double tol=0.5) <li><a class="el" href="class_sc__Molecule.html#a37">symmetrize</a>(const Ref< PointGroup > &pg, double tol=0.5) <li><b>transform_to_principal_axes</b>(int trans_frame=1) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>transform_to_symmetry_frame</b>() (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><b>translate</b>(const double *r) (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<li><a class="el" href="class_sc__Molecule.html#a47">unique</a>(int iuniq) const <code> [inline]</code><li><a class="el" href="class_sc__RefCount.html#a2">unlock_ptr</a>() const <li><a class="el" href="class_sc__RefCount.html#a8">unmanage</a>() <code> [inline]</code><li><a class="el" href="class_sc__RefCount.html#a3">use_locks</a>(bool inVal) <li><b>Z</b>(int atom) const (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [inline]</code><li><b>Z_</b> (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [protected]</code><li><b>~DescribedClass</b>() (defined in <a class="el" href="class_sc__DescribedClass.html">sc::DescribedClass</a>)<code> [virtual]</code><li><b>~Identity</b>() (defined in <a class="el" href="class_sc__Identity.html">sc::Identity</a>)<code> [virtual]</code><li><b>~Molecule</b>() (defined in <a class="el" href="class_sc__Molecule.html">sc::Molecule</a>)<code> [virtual]</code><li><b>~RefCount</b>() (defined in <a class="el" href="class_sc__RefCount.html">sc::RefCount</a>)<code> [virtual]</code><li><b>~SavableState</b>() (defined in <a class="el" href="class_sc__SavableState.html">sc::SavableState</a>)<code> [virtual]</code></ul> <hr> <address> <small> Generated at Mon Oct 14 14:17:11 2002 for <a href="http://aros.ca.sandia.gov/~cljanss/mpqc">MPQC</a> 2.1.2 using the documentation package <a href="http://www.stack.nl/~dimitri/doxygen/index.html">Doxygen</a> 1.2.5. </small> </address> </body> </html>
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