\documentclass[a4paper]{book}
\usepackage{a4wide}
\usepackage{makeidx}
\usepackage{fancyhdr}
\usepackage{graphicx}
\usepackage{float}
\usepackage{alltt}
\usepackage{doxygen}
\makeindex
\setcounter{tocdepth}{1}
\setlength{\footrulewidth}{0.4pt}
\begin{document}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large GRAPE:  Generalizable Replaceable Atomic Position Engine Reference Manual}\\
\vspace*{1cm}
{\large Generated by Doxygen 1.2.5}\\
\vspace*{0.5cm}
{\small Fri Aug 24 17:08:33 2001}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\pagenumbering{roman}
\tableofcontents
\clearemptydoublepage
\pagenumbering{arabic}
\chapter{GRAPE:  Generalizable Replaceable Atomic Position Engine Hierarchical Index}
\input{hierarchy}
\chapter{GRAPE:  Generalizable Replaceable Atomic Position Engine Compound Index}
\input{annotated}
\chapter{GRAPE:  Generalizable Replaceable Atomic Position Engine File Index}
\input{files}
\chapter{GRAPE:  Generalizable Replaceable Atomic Position Engine Class Documentation}
\input{class_ABitSet}
\include{class_AMatrix}
\include{class_AMatrix__AMatrixRep}
\include{class_AnimFrame}
\include{class_Atom}
\include{class_AtomBuildup}
\include{class_AtomConstraint}
\include{class_AtomRegistry}
\include{class_base_iterator}
\include{class_bf_iterator}
\include{class_BinEnvelopeConstraint}
\include{class_ConstIterator}
\include{class_Constraint}
\include{class_ConstraintManager}
\include{class_ConstraintRegistry}
\include{class_CycleAll}
\include{class_ddEdge}
\include{class_ddGraph}
\include{class_ddVertex}
\include{class_df_iterator}
\include{class_DistanceConstraint}
\include{class_DLList}
\include{class_DLListNode}
\include{class_DLListRep}
\include{class_DSIterator}
\include{class_DynString}
\include{class_Envelope}
\include{class_EnvelopeConstraint}
\include{class_Grid}
\include{class_gwNumerics}
\include{class_gwRelaxAtom}
\include{class_IdGen}
\include{class_IntPriorityQueue}
\include{class_IntVec}
\include{class_Iterator}
\include{class_ABitSet__Iterator}
\include{class_jdErr_Eval}
\include{class_jdIterator}
\include{class_jdOcc_Count}
\include{class_jdRand_Eval}
\include{class_jVector}
\include{class_KAdjMat}
\include{class_Matrix}
\include{class_Molecule}
\include{class_neighbor_iterator}
\include{class_path_iterator}
\include{class_PositionConstraint}
\include{class_Process}
\include{class_Queue}
\include{class_RanBaseClass}
\include{class_RanChar}
\include{class_RanDbl}
\include{class_RanInt}
\include{class_RanLetter}
\include{class_RanWord}
\include{class_RefRep}
\include{class_RelaxSubset}
\include{class_Residue}
\include{class_ResidueRegistry}
\include{class_SatisfyMolecule}
\include{class_sdEdge}
\include{class_sdGraph}
\include{class_sdVertex}
\include{class_Segment}
\include{class_Segments}
\include{class_Stack}
\include{class_StopEval}
\include{class_UnitWeight}
\include{class_z}
\chapter{GRAPE:  Generalizable Replaceable Atomic Position Engine File Documentation}
\input{abbrev_h}
\include{abitset_C}
\include{abitset_h}
\include{ajiobin_h}
\include{amatrix_h}
\include{amatrix_inc}
\include{atom_h}
\include{atom_buildup_C}
\include{atom_buildup_h}
\include{atom_constraint_C}
\include{atom_constraint_h}
\include{atom_registry_C}
\include{atom_registry_h}
\include{bin_envelope_constraint_C}
\include{bin_envelope_constraint_h}
\include{bits_h}
\include{compoper_h}
\include{constraint_C}
\include{constraint_h}
\include{constraint_manager_C}
\include{constraint_manager_h}
\include{constraint_registry_C}
\include{constraint_registry_h}
\include{cycle_all_C}
\include{cycle_all_h}
\include{ddgraph_h}
\include{ddgraph_inc}
\include{ddvertex_h}
\include{ddvertex_inc}
\include{dens-trans_C}
\include{dist_C}
\include{distance_constraint_C}
\include{distance_constraint_h}
\include{dllist_h}
\include{dllist_inc}
\include{dlliter_inc}
\include{dsiter_inc}
\include{dynstring_C}
\include{dynstring_h}
\include{env_diff_C}
\include{envelope_C}
\include{envelope_h}
\include{envelope_constraint_C}
\include{envelope_constraint_h}
\include{err_eval_C}
\include{error_handler_h}
\include{globals_C}
\include{globals_h}
\include{grape_C}
\include{graph_weights_h}
\include{grid_C}
\include{grid_h}
\include{gw_numerics_C}
\include{gw_numerics_h}
\include{gw_relax_atom_C}
\include{gw_relax_atom_h}
\include{idgen_h}
\include{intvec_C}
\include{intvec_h}
\include{intvec_inc}
\include{ipqueue_h}
\include{ipqueue_inc}
\include{jd_anim_frame_C}
\include{jd_anim_frame_h}
\include{jd_err_eval_C}
\include{jd_err_eval_h}
\include{jd_iterator_C}
\include{jd_iterator_h}
\include{jd_occ_count_C}
\include{jd_occ_count_h}
\include{jd_rand_eval_C}
\include{jd_rand_eval_h}
\include{jd_relax_subset_C}
\include{jd_relax_subset_h}
\include{jd_stop_eval_C}
\include{jd_stop_eval_h}
\include{jsmisc_h}
\include{jvector_C}
\include{jvector_h}
\include{kadjmat_h}
\include{LeakTracer_Makefile}
\include{lib_Makefile}
\include{Makefile}
\include{src_aux_Makefile}
\include{src_Makefile}
\include{matrix_C}
\include{matrix_h}
\include{molecule_C}
\include{molecule_h}
\include{molio_C}
\include{ocount_C}
\include{position_constraint_C}
\include{position_constraint_h}
\include{process_C}
\include{process_h}
\include{queue_h}
\include{rand_eval_C}
\include{randomgenerator_C}
\include{randomgenerator_h}
\include{refrep_h}
\include{residue_C}
\include{residue_h}
\include{residue_registry_h}
\include{satisfy_molecule_h}
\include{sdgalg_inc}
\include{sdgiter_inc}
\include{sdgraph_h}
\include{sdgraph_inc}
\include{sdvertex_h}
\include{sdvertex_inc}
\include{search-sort_h}
\include{segments_inc}
\include{stack_h}
\include{streamoper_h}
\include{top_process_h}
\include{utils_C}
\include{utils_h}
\printindex
\end{document}
