Functions — github.com/ccsb-scripps/AutoDock-Vina

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Functions753 in github.com/ccsb-scripps/AutoDock-Vina

⨍ Functions 753◇ Types & classes 130

Methodgenerate_external

src/lib/conf.h:327

Methodgenerate_internal

src/lib/conf.h:319

Methodgenerate_seed

src/lib/vina.cpp:51

Methodget_cutoff

src/lib/scoring_function.h:147

Methodget_cutoff

src/lib/potentials.h:130

Methodget_cutoff

src/lib/potentials.h:150

Methodget_cutoff

src/lib/potentials.h:183

Methodget_cutoff

src/lib/potentials.h:210

Methodget_cutoff

src/lib/potentials.h:237

Methodget_cutoff

src/lib/potentials.h:261

Methodget_cutoff

src/lib/potentials.h:294

Methodget_cutoff

src/lib/potentials.h:321

Methodget_cutoff

src/lib/potentials.h:348

Methodget_cutoff

src/lib/potentials.h:374

Methodget_cutoff

src/lib/potentials.h:402

Methodget_cutoff

src/lib/potentials.h:453

Methodget_cutoff

src/lib/potentials.h:514

Methodget_factor

src/lib/precalculate.h:242

Methodget_glue_pairs

src/lib/model.h:83

Methodget_inter_pairs

src/lib/model.h:82

Methodget_names

src/lib/conf_independent.cpp:110

any modification or reading of mutables should lock this first

src/lib/parallel.h:147

Methodget_num_atom_types

src/lib/scoring_function.h:158

Functionget_occurrence

src/main/main.cpp:51

Methodget_other_pairs

src/lib/model.h:81

Methodget_poses

src/lib/vina.cpp:557

Methodget_poses_coordinates

src/lib/vina.cpp:453

Methodget_poses_energies

src/lib/vina.cpp:495

any modification or reading of mutables should lock this first

src/lib/parallel.h:89

Methodget_weights

src/lib/scoring_function.h:159

FIXME? - make cache a friend, and convert this back to private?

src/lib/grid.h:38

number of intervals == number of sample points - 1

src/lib/grid_dim.h:34

Functiongrid_dims_begin

src/lib/grid_dim.h:62

Functiongrid_dims_end

src/lib/grid_dim.h:69

Methodheterotree

src/lib/tree.h:190

(atom1, atom2, atom3)

example/autodock_scripts/wet.py:189

never use ifstream pointer to destroy ifile - no virtual destructors, possibly

src/lib/file.h:36

Methodincrement

src/lib/conf.h:98

Methodincrement

src/lib/conf.h:164

Methodincrement

src/lib/conf.h:197

src/lib/matrix.h:78

src/lib/matrix.h:91

Methodindex_permissive

src/lib/matrix.h:97

Methodindex_permissive

src/lib/precalculate.h:239

Methodindex_to_coord

src/lib/szv_grid.cpp:76

src/lib/parallel_progress.h:42

Methodinitialize

src/lib/model.cpp:571

Methodinitialize_pairs

src/lib/model.cpp:532

Functioninput_ligand_pdbqt

example/autodock_scripts/dry.py:332

Functionint_pow

src/lib/int_pow.h:29

Functionint_pow<0>

src/lib/int_pow.h:34

Methodinteracting_pair

src/lib/model.h:39

Methodinternal_error

src/lib/common.h:192

Methodinternal_too_close

src/lib/conf.h:297

Methodis_atom_type_grid_initialized

src/lib/cache.h:56

Methodis_atom_type_grid_initialized

src/lib/ad4cache.h:53

Methodis_closure_clash

remove 1-2, 1-3 and 1-4 interactions around CG-CG bond

src/lib/model.cpp:474

Methodis_glue_pair

src/lib/model.cpp:506

Methodis_in_grid

src/lib/ad4cache.cpp:180

Methodis_movable_atom

src/lib/model.cpp:665

Methodis_unmatched_closure_dummy

exclude pair if one atom is G0 but the other atom is not CG0

src/lib/model.cpp:520

MethodligTZrmsd

example/autodock_scripts/zinc_pseudo.py:471

src/lib/model.h:51

Methodligand_degrees_of_freedom

src/lib/model.h:98

Methodligand_length

src/lib/conf_independent.h:85

Methodligand_longest_branch

src/lib/model.cpp:73

Methodlinearattraction

src/lib/potentials.h:497

src/lib/quaternion.h:50

Functionlonewaters

(model, target, cutoff = CUTOFF)

example/autodock_scripts/dry.py:446

src/lib/parallel.h:123

src/main/main.cpp:69

src/split/split.cpp:131

src/lib/common.h:150

src/lib/matrix.h:46

Methodmax_cutoff_sqr

src/lib/precalculate.h:241

Methodmin_smooth_fst

src/lib/precalculate.h:79

Had to move it from private to public to make it work. So we might have to fix that later

src/lib/model.h:74

Methodmonte_carlo

T = 600K, R = 2cal/(K*mol) -> temperature = RT = 1.2; global_steps = 50*lig_atoms = 2500

src/lib/monte_carlo.h:39

Methodmovable_atom

src/lib/parse_pdbqt.cpp:124

Methodmutate_orientation

src/lib/conf.h:115

Methodmutate_position

src/lib/conf.h:112

Methodnew_grid_index

src/lib/model.cpp:102

src/lib/parse_pdbqt.cpp:160

Methodnon_cache

src/lib/non_cache.h:31

Methodnon_cache

src/lib/non_cache.cpp:26

src/lib/common.h:71

Methodnum_bonded_heavy_atoms

src/lib/conf_independent.cpp:39

src/lib/model.h:97

Methodnum_heavy_atoms

src/lib/conf_independent.h:106

Methodnum_heavy_atoms_div

src/lib/conf_independent.h:99

Methodnum_hydrophobic_atoms

src/lib/conf_independent.h:113

Methodnum_internal_pairs

src/lib/model.cpp:582

Methodnum_ligands

src/lib/conf_independent.h:92

Methodnum_other_pairs

src/lib/model.h:95

Methodnum_tors_div

src/lib/conf_independent.h:78

Methodnum_tors_sqr

src/lib/conf_independent.h:64

Methodnum_tors_sqrt

src/lib/conf_independent.h:71

never use ofstream pointer to destroy ofile - no virtual destructors, possibly

src/lib/file.h:47

Methodoperator()

src/lib/conf.h:223

Methodoperator()

src/lib/monte_carlo.cpp:28

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