- a -

ASP1 : hczndimer.cc
ASP2 : hczndimer.cc
ASP3 : hczndimer.cc

- b -

BLUE : capri15_scoring.hh

- c -

C : unique_atoms.h , gpu_homog_atom_coords.h
C_SVC : Svm.hh
CA : gpu_homog_atom_coords.h , unique_atoms.h
CB : gpu_homog_atom_coords.h , unique_atoms.h
CB_P : gpu_homog_atom_coords.h , unique_atoms.h
CD : gpu_homog_atom_coords.h , unique_atoms.h
CD1 : gpu_homog_atom_coords.h , unique_atoms.h
CD1_W : gpu_homog_atom_coords.h , unique_atoms.h
CD2 : gpu_homog_atom_coords.h , unique_atoms.h
CD2_H : unique_atoms.h , gpu_homog_atom_coords.h
CD2_L : gpu_homog_atom_coords.h , unique_atoms.h
CD2_W : gpu_homog_atom_coords.h , unique_atoms.h
CD_P : gpu_homog_atom_coords.h , unique_atoms.h
CE1 : gpu_homog_atom_coords.h , unique_atoms.h
CE1_H : gpu_homog_atom_coords.h , unique_atoms.h
CE2 : gpu_homog_atom_coords.h , unique_atoms.h
CE2_W : gpu_homog_atom_coords.h , unique_atoms.h
CE3_W : unique_atoms.h , gpu_homog_atom_coords.h
CE_K : gpu_homog_atom_coords.h , unique_atoms.h
CE_M : gpu_homog_atom_coords.h , unique_atoms.h
CEN : FunGroupTK.cc
CEN_ANG : FunGroupTK.cc
CEN_AXS : FunGroupTK.cc
CEN_AXS_ORI : FunGroupTK.cc
CG : gpu_homog_atom_coords.h , unique_atoms.h
CG2 : gpu_homog_atom_coords.h , unique_atoms.h
CG_P : gpu_homog_atom_coords.h , unique_atoms.h
CH2_W : gpu_homog_atom_coords.h , unique_atoms.h
chain_index : InterfaceMutMaker.cc , exposed_strand_finder.cc
CHI1 : plot_scoreterm.cc
CHI2 : plot_scoreterm.cc
CHI3 : plot_scoreterm.cc
CHI4 : plot_scoreterm.cc
CUBIC : spacegroup.hh
CYAN : capri15_scoring.hh
CYS : hczndimer.cc
CZ : gpu_homog_atom_coords.h , unique_atoms.h
CZ2_W : gpu_homog_atom_coords.h , unique_atoms.h
CZ3_W : gpu_homog_atom_coords.h , unique_atoms.h
CZ_R : gpu_homog_atom_coords.h , unique_atoms.h

- e -

E1_V0 : T01.enum.hpp , T60.custom_shared.hpp , T61.smart_holder.hpp
E1_V1 : T01.enum.hpp , T60.custom_shared.hpp , T61.smart_holder.hpp
E4_V0 : T01.enum.hpp
E4_V1 : T01.enum.hpp
end_index : exposed_strand_finder.cc
EPSILON_SVR : Svm.hh

- f -

fast_relax_perfbench_mmstd : FastRelax.bench.hh
fast_relax_perfbench_sc12he : FastRelax.bench.hh
fast_relax_perfbench_sc12sp2 : FastRelax.bench.hh
fast_relax_perfbench_score12 : FastRelax.bench.hh
fast_relax_perfbench_sp2hecart : FastRelax.bench.hh

- h -

HEXAGONAL : spacegroup.hh
High : Docking.bench.hh
HIS1 : hczndimer.cc
HIS2 : hczndimer.cc

- i -

inline_buffer_size : format.h
interaction_graph_perfbench_denseig_current_default_sfxn : InteractionGraph.bench.hh
interaction_graph_perfbench_denseig_score12 : InteractionGraph.bench.hh
interaction_graph_perfbench_linmemig_current_default_sfxn : InteractionGraph.bench.hh
interaction_graph_perfbench_linmemig_mmstd : InteractionGraph.bench.hh
interaction_graph_perfbench_linmemig_sc12he : InteractionGraph.bench.hh
interaction_graph_perfbench_linmemig_sc12sp2 : InteractionGraph.bench.hh
interaction_graph_perfbench_linmemig_score12 : InteractionGraph.bench.hh
interaction_graph_perfbench_pdig_current_default_sfxn : InteractionGraph.bench.hh
interaction_graph_perfbench_pdig_score12 : InteractionGraph.bench.hh

- l -

LINEAR : Svm.hh
Low : Docking.bench.hh

- m -

max_neighbors : exposed_strand_finder.cc
metal : MetalInterface.hh , zinc_heterodimer_design.cc
MONOCLINIC : spacegroup.hh
MU : plot_scoreterm.cc
mut_index : InterfaceMutMaker.cc

- n -

N : unique_atoms.h , gpu_homog_atom_coords.h
n_experimental_constraint_scores : capri15_scoring.hh
ND1_H : gpu_homog_atom_coords.h , unique_atoms.h
ND2_N : gpu_homog_atom_coords.h , unique_atoms.h
NE1_W : gpu_homog_atom_coords.h , unique_atoms.h
NE2_H : gpu_homog_atom_coords.h , unique_atoms.h
NE2_Q : gpu_homog_atom_coords.h , unique_atoms.h
NE_R : gpu_homog_atom_coords.h , unique_atoms.h
NH1_R : gpu_homog_atom_coords.h , unique_atoms.h
NH2_R : gpu_homog_atom_coords.h , unique_atoms.h
NOSETTING : spacegroup.hh
NRTYPES : hczndimer.cc
NU_SVC : Svm.hh
NU_SVR : Svm.hh
NV_P : gpu_homog_atom_coords.h , unique_atoms.h
NZ_K : gpu_homog_atom_coords.h , unique_atoms.h

- o -

O : unique_atoms.h , gpu_homog_atom_coords.h
OD1 : gpu_homog_atom_coords.h , unique_atoms.h
OD2_D : gpu_homog_atom_coords.h , unique_atoms.h
OE1 : gpu_homog_atom_coords.h , unique_atoms.h
OE2_E : unique_atoms.h , gpu_homog_atom_coords.h
OG : gpu_homog_atom_coords.h , unique_atoms.h
OH_Y : gpu_homog_atom_coords.h , unique_atoms.h
OMEGA : plot_scoreterm.cc
OMEGA_MINUSONE : plot_scoreterm.cc
ONE_CLASS : Svm.hh
ORTHORHOMBIC : spacegroup.hh

- p -

p1_1 : MetalInterface.hh , zinc_heterodimer_design.cc
p1_2 : MetalInterface.hh , zinc_heterodimer_design.cc
p1_3 : MetalInterface.hh , zinc_heterodimer_design.cc
p2 : MetalInterface.hh , zinc_heterodimer_design.cc
PHI : plot_scoreterm.cc
PINK : capri15_scoring.hh
POLY : Svm.hh
PRECOMPUTED : Svm.hh
PSI : plot_scoreterm.cc

- r -

- s -

SD_M : gpu_homog_atom_coords.h , unique_atoms.h
SFT_dfpmin : Minimizer.bench.hh
SFT_dfpmin_armijo : Minimizer.bench.hh
SFT_dfpmin_armijo_nonmonotone : Minimizer.bench.hh
SG_C : gpu_homog_atom_coords.h , unique_atoms.h
SIGMOID : Svm.hh
start_index : exposed_strand_finder.cc

- t -

TETRAGONAL : spacegroup.hh
THETA : plot_scoreterm.cc
trans : homodimer_design.cc
TRICLINIC : spacegroup.hh

- w -

wt_index : InterfaceMutMaker.cc