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<h1>sc::Molecule Member List</h1>This is the complete list of members for <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>, including all inherited members.<p><table>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#00bc438d80337c95c0ec330fafd6b25f">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)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#71a8a7cca4f0908f482005b5f583c96a">atom_at_position</a>(double *, double tol=0.05) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#dbb8e57bdcb6f09ffcbb2cfaf8447982">atom_label_to_index</a>(const char *label) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#8f5a07e9742358c96010b339410406bc">atom_name</a>(int iatom) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#a218035531686af7a333046f1d2fb97d">atom_symbol</a>(int iatom) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>atom_to_uniq_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#ad1e770152d7cf10e9a63e7be9abab56">atom_to_unique</a>(int iatom) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#2c1d3d586b023f29ca0e78a7ac5278bd">atom_to_unique_offset</a>(int iatom) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#35970f4dcdd80a8a3172e0e700fc4389">atominfo</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>atominfo_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#dcf28de935547bbe20527a4d2d5cc95e">center_of_mass</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#a3e0484650800d1d7fddc305c32f5e27">charge</a>(int iatom) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#7900ee64fc2eb867014ecc908c84ca01">charges</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>charges_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1DescribedClass.html#543db7ca087135f8bd28776c2801f930">class_desc</a>() const </td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1DescribedClass.html#4c3305b01115fbfd560a4dc397d4842c">class_name</a>() const </td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1DescribedClass.html#05088e3cd127293ac1c5f61e507c34f9">class_version</a>() const </td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#ba372e38e4c63e15976894144b4588bb">cleanup_molecule</a>(double tol=0.1)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>clear</b>() (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>clear_symmetry_info</b>() (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#e391eb4734abf89fde3475bc9b013243">dereference</a>()</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>DescribedClass</b>() (defined in <a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a>)</td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>DescribedClass</b>(const DescribedClass &) (defined in <a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a>)</td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>dir_restore_state</b>(StateIn &si, const char *objectname, const char *keyword=0) (defined in <a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a>)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [static]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>equiv_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#9501f36f54a462eafac50264fe23c34d">equivalent</a>(int iuniq, int j) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>geometry_units_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#251784416ed5928210704e56aa4a7840">has_inversion</a>(SCVector3 &origin, double tol=1.0e-8) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#1c72c3747bf634cf5075297e3ff7ab3f">highest_point_group</a>(double tol=1.0e-8) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Identity.html#077335fa5900cf01495cb3fe485382a7">identifier</a>()</td><td><a class="el" href="classsc_1_1Identity.html">sc::Identity</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#034618f0b2872eb86b3f72def469bece">include_q</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>include_q_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#a67e7b521026e9af831912d1be8211cb">include_qq</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>include_qq_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>init_symmetry_info</b>(double tol=0.5) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#6bea2cd2b87891c9988e997104e1672a">is_axis</a>(SCVector3 &origin, SCVector3 &udirection, int order, double tol=1.0e-8) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#775221d24eb232418af12964186efeda">is_linear</a>(double tolerance=1.0e-5) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#4ef5c31897b1b545c3f85758728cb210">is_linear_planar</a>(int &linear, int &planar, double tol=1.0e-5) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#46e33d810285526ab4cde25f053b56e2">is_planar</a>(double tolerance=1.0e-5) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#18564f473b198df4f14f105941cd434e">is_plane</a>(SCVector3 &origin, SCVector3 &uperp, double tol=1.0e-8) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1SavableState.html#6ef0380c1ff52586e335a15dc37c519e">key_restore_state</a>(StateIn &si, const char *keyword)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [static]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#d2a87e6d05cf5fd421b9da301bfa5185">label</a>(int atom) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>labels_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#1c8e9c58bf57dc265d9e842823494cb7">lock_ptr</a>() const </td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>managed</b>() const (defined in <a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a>)</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#25faf9649131022f7f67052aef3d3361">managed</a>() const </td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>mass</b>(int atom) const (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>mass_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#1c999a16909475e32a447b04fe4eaf3e">max_z</a>()</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>Molecule</b>() (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>Molecule</b>(const Molecule &) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>Molecule</b>(StateIn &) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#8e04ebdcbc07d8ca4c69f7e42511b081">Molecule</a>(const Ref< KeyVal > &input)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>move_to_com</b>() (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#9e7e7122d8fc559831eaaf8e39ca4dc4">n_core_electrons</a>()</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#91cbf250883243e87fdddc2825edc9b8">n_non_q_atom</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#09fd65cc67b6490322de5f9880428b47">n_q_atom</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#2d12d117494be731bf10e0901a623b82">natom</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>natoms_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>nequiv_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#ef5de4bf620e6ad2513484c3186138a6">nequivalent</a>(int iuniq) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#86231d441dcac105318001c93e92fb66">non_q_atom</a>(int i) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>non_q_atoms_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#e94a2d6c0083fc7ffd4c3e6e107ce839">nreference</a>() const </td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#7423f54a90deee592c01e95ecf4ff121">nuclear_charge</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#8dbca87503d084af87c02fb7d197561c">nuclear_charge_efield</a>(const double *charges, const double *position, double *efield)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#58e9e0c2497caf0a03ca599d035f87fc">nuclear_efield</a>(const double *position, double *efield)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#cf9914731937c41c37f707e9c71ca449">nuclear_repulsion_1der</a>(int center, double xyz[3])</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#54ffd95060e628f06019b3364ad48ad0">nuclear_repulsion_energy</a>()</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>nuniq_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#64ef3eb01d52d6bb0527d0005db78d95">nunique</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>operator=</b>(const Molecule &) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>operator=</b>(const SavableState &) (defined in <a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a>)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>operator=</b>(const DescribedClass &) (defined in <a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a>)</td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>operator=</b>(const RefCount &) (defined in <a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a>)</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline, protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>pg_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#d40b425a01e1bc20e524a50b317042bd">point_group</a>() const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#eb520ea35c820fcf5aeb0bd564616294">principal_moments_of_inertia</a>(double *evals, double **evecs=0) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#fe59cd6cd33d5a7f2b73fa906c0faa35">print</a>(std::ostream &=ExEnv::out0()) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [virtual]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><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="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [virtual]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>print_pdb</b>(std::ostream &=ExEnv::out0(), char *title=0) const (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#6c1b4b7aa47f4f06877a2e2d4ebce44c">q_atom</a>(int i) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>q_atoms_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>q_Z_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>r</b>(int atom, int xyz) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>r</b>(int atom, int xyz) const (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>r</b>(int atom) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>r</b>(int atom) const (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>r_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>read_pdb</b>(const char *filename) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>RefCount</b>() (defined in <a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a>)</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline, protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>RefCount</b>(const RefCount &) (defined in <a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a>)</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline, protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#10326b12fc26912be4a78f1e709d16da">reference</a>()</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1SavableState.html#01c14e9cff8a3a586e9cb36bcd049799">restore_state</a>(StateIn &si)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [static]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>SavableState</b>() (defined in <a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a>)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>SavableState</b>(const SavableState &) (defined in <a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a>)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1SavableState.html#565c4a3a2de82340b0266e7303f933d1">SavableState</a>(StateIn &)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [protected]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#d32cb69bf428ad40d2bd448d6788d27e">save_data_state</a>(StateOut &)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [virtual]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1SavableState.html#70472a338ac579eeef503aaec97c7776">save_object_state</a>(StateOut &)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1SavableState.html#fe8ddc4e284265dcb3174d321471a1b0">save_state</a>(StateOut &)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>save_state</b>(SavableState *s, StateOut &) (defined in <a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a>)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [static]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1SavableState.html#4fb1224545c2db5358f3e095792dcffe">save_vbase_state</a>(StateOut &)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [virtual]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#4363095f8ed8d8d581f4df7e6630caa2">set_include_q</a>(bool iq)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#e20845074f66ef9a2aca7925bbd526a1">set_include_qq</a>(bool iqq)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#47d838d4ce264d10c47b8701db2fb212">set_point_group</a>(const Ref< PointGroup > &, double tol=1.0e-7)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#9ccc779036e0750b56f9c7632e0a50c5">symmetrize</a>(double tol=0.5)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#1940ef63772b351dc7a4536f36592729">symmetrize</a>(const Ref< PointGroup > &pg, double tol=0.5)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>throw_if_atom_duplicated</b>(int begin=0, double tol=1e-3) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>transform_to_principal_axes</b>(int trans_frame=1) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>transform_to_symmetry_frame</b>() (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>translate</b>(const double *r) (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1Molecule.html#3ae99990f2cc620bfc6d7b28cd7f7f57">unique</a>(int iuniq) const </td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#65b50a51d8cb99d806323ffc934fa2c4">unlock_ptr</a>() const </td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#e1ae4f1d5308822563eeafd0bdec0713">unmanage</a>()</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [inline]</code></td></tr>
<tr class="memlist"><td><a class="el" href="classsc_1_1RefCount.html#f05189b4c9aff106cef46f1b4c00211a">use_locks</a>(bool inVal)</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td></td></tr>
<tr bgcolor="#f0f0f0"><td><b>Z</b>(int atom) const (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [inline]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>Z_</b> (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [protected]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>~DescribedClass</b>() (defined in <a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a>)</td><td><a class="el" href="classsc_1_1DescribedClass.html">sc::DescribedClass</a></td><td><code> [virtual]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>~Identity</b>() (defined in <a class="el" href="classsc_1_1Identity.html">sc::Identity</a>)</td><td><a class="el" href="classsc_1_1Identity.html">sc::Identity</a></td><td><code> [virtual]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>~Molecule</b>() (defined in <a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a>)</td><td><a class="el" href="classsc_1_1Molecule.html">sc::Molecule</a></td><td><code> [virtual]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>~RefCount</b>() (defined in <a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a>)</td><td><a class="el" href="classsc_1_1RefCount.html">sc::RefCount</a></td><td><code> [virtual]</code></td></tr>
<tr bgcolor="#f0f0f0"><td><b>~SavableState</b>() (defined in <a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a>)</td><td><a class="el" href="classsc_1_1SavableState.html">sc::SavableState</a></td><td><code> [virtual]</code></td></tr>
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