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

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

⨍ Functions 753◇ Types & classes 130

↓ 308 callersFunctionprint

src/lib/common.h:319

↓ 177 callersMethodsize

src/lib/common.h:123

↓ 146 callersMethodappend

src/lib/model.cpp:195

↓ 54 callersFunctionVINA_FOR_IN

new torsions are normalized

src/lib/conf.h:52

↓ 50 callersMethodget

src/lib/atom_type.h:33

↓ 38 callersFunctionVINA_FOR

src/lib/bfgs.h:33

↓ 38 callersFunctionstarts_with

src/lib/common.h:354

↓ 34 callersFunctionsqr

src/lib/common.h:48

↓ 23 callersMethoddim

src/lib/array3d.h:59

↓ 22 callersFunctionVINA_FOR_IN

src/lib/model.cpp:295

↓ 22 callersMethodadd

src/lib/model.cpp:314

↓ 20 callersFunctionnum_atom_types

src/lib/atom_type.h:78

↓ 17 callersMethodnum_movable_atoms

src/lib/model.h:93

↓ 17 callersMethodwrite

src/lib/cache.cpp:352

↓ 15 callersFunctionatom_coord

example/autodock_scripts/wet.py:121

↓ 15 callersFunctionvector

(p1 , p2 = None)

example/autodock_scripts/wet.py:203

↓ 14 callersMethodset

src/lib/model.cpp:749

↓ 14 callersFunctionvec_distance_sqr

src/lib/common.h:241

↓ 13 callersMethodresize

src/lib/matrix.h:48

↓ 12 callersFunctionVINA_FOR

src/lib/cache.cpp:305

↓ 12 callersMethoddim0

src/lib/array3d.h:56

↓ 12 callersMethoddim1

src/lib/array3d.h:57

↓ 12 callersMethoddim2

src/lib/array3d.h:58

↓ 12 callersMethodevaluate

src/lib/grid.h:49

↓ 12 callersMethodgetcoords

example/autodock_scripts/zinc_pseudo.py:65

↓ 12 callersFunctionrandom_fl

src/lib/random.cpp:27

↓ 12 callersMethodwhat

src/lib/vina.h:62

↓ 10 callersMethodinsert

insertion into non_rigid_parsed

src/lib/parse_pdbqt.cpp:174

↓ 10 callersFunctionnormalize

Normalize the Vector

example/autodock_scripts/wet.py:237

↓ 10 callersFunctionto_string

src/lib/common.h:294

↓ 9 callersFunctionVINA_FOR

src/lib/ad4cache.cpp:306

↓ 9 callersFunctiondist

example/autodock_scripts/wet.py:55

↓ 9 callersFunctiondist

example/autodock_scripts/zinc_pseudo.py:7

↓ 9 callersFunctiondoing

src/lib/utils.cpp:42

↓ 9 callersFunctionnot_max

src/lib/common.h:237

↓ 9 callersFunctionread_iterator

src/lib/conf_independent.cpp:123

↓ 9 callersFunctionxs_is_hydrophobic

src/lib/atom_constants.h:359

↓ 8 callersFunctionconfirm_predictions

(calc_list, exp_list, cutoff = MATCH_DISTANCE)

example/autodock_scripts/dry.py:640

↓ 8 callersFunctioncurl

src/lib/curl.h:30

↓ 8 callersMethodcutoff_sqr

src/lib/precalculate.h:169

↓ 8 callersFunctiondone

src/lib/utils.cpp:49

↓ 8 callersMethodindex

src/lib/matrix.h:41

↓ 8 callersFunctionoptimal_distance

src/lib/potentials.h:46

↓ 8 callersFunctionoptimal_distance_vinardo

Vinardo common functions

src/lib/potentials.h:58

↓ 8 callersFunctionquaternion_is_normalized

src/lib/quaternion.cpp:25

↓ 8 callersFunctionslope_step

Vina common functions

src/lib/potentials.h:30

↓ 8 callersFunctionsum

src/lib/common.h:304

↓ 7 callersMethodassign

src/lib/common.h:120

↓ 7 callersMethoddim_1

src/lib/matrix.h:68

↓ 7 callersMethoddim_2

src/lib/matrix.h:70

↓ 7 callersFunctiondist

(firstline, secondline)

example/autodock_scripts/dry.py:63

↓ 7 callersMethodget_atom_typing

src/lib/scoring_function.h:149

↓ 7 callersFunctionhydro

(atom1, atom2, atom3 = None, spacing = 3)

example/autodock_scripts/wet.py:148

↓ 7 callersFunctionmake_path

src/lib/utils.cpp:36

↓ 7 callersFunctionprintnl

src/lib/common.h:349

↓ 7 callersFunctionwrite_this

(filename, list)

example/autodock_scripts/dry.py:1171

↓ 6 callersFunctionVINA_FOR_IN

src/lib/tree.h:156

↓ 6 callersMethodare_atom_types_grid_initialized

src/lib/cache.cpp:186

↓ 6 callersFunctionatom_type

example/autodock_scripts/dry.py:307

↓ 6 callersFunctioncoord

example/autodock_scripts/dry.py:117

↓ 6 callersMethoddist

example/autodock_scripts/zinc_pseudo.py:59

↓ 6 callersMethodeval

src/lib/cache.cpp:56

↓ 6 callersMethodeval_fast

src/lib/precalculate.h:160

↓ 6 callersMethodis_hydrogen

src/lib/atom_type.h:42

↓ 6 callersFunctionpc

example/autodock_scripts/dry.py:82

↓ 6 callersFunctionpdbqt_atom_type

example/autodock_scripts/dry.py:327

↓ 6 callersFunctionscalar_product

src/lib/bfgs.h:42

↓ 6 callersMethodset_conf

src/lib/tree.h:169

↓ 5 callersFunctionadd_context

src/lib/parse_pdbqt.cpp:52

↓ 5 callersMethodget_atom

for precalculate_byatom

src/lib/model.h:78

↓ 5 callersFunctionget_lines

example/autodock_scripts/dry.py:85

↓ 5 callersMethodget_movable_atom_types

src/lib/model.cpp:589

↓ 5 callersMethodinitialized

src/lib/grid.h:46

↓ 5 callersMethodscore

src/lib/vina.cpp:690

↓ 5 callersFunctiontriangular_matrix_index

src/lib/triangular_matrix_index.h:28

↓ 5 callersFunctionusage

Print helpful, accurate usage statement to stdout.

example/autodock_scripts/prepare_flexreceptor.py:23

↓ 5 callersFunctionusage

example/autodock_scripts/dry.py:842

↓ 5 callersMethodwrite_pose

src/lib/vina.cpp:617

↓ 4 callersFunctionVINA_FOR

Add interaction pairs between previously added atoms and (very likely) ligand atoms Interactions: - flex - ligand : YES (inter_pairs) - flex_i

src/lib/model.cpp:224

↓ 4 callersFunctionad4_hb_eps

src/lib/potentials.h:78

↓ 4 callersFunctionad4_vdw_radius

src/lib/potentials.h:96

↓ 4 callersMethodcompute_vina_maps

src/lib/vina.cpp:318

↓ 4 callersFunctioncrossProd

Pretty self-explanatory, this function bakes cookies

example/autodock_scripts/zinc_pseudo.py:37

↓ 4 callersMethodderivative

src/lib/tree.h:173

↓ 4 callersMethoddim

src/lib/matrix.h:82

↓ 4 callersFunctioneq

src/lib/quaternion.cpp:29

↓ 4 callersFunctioneq

src/lib/common.h:212

↓ 4 callersFunctioneval_interacting_pairs

src/lib/model.cpp:769

↓ 4 callersFunctioneval_interacting_pairs_deriv

src/lib/model.cpp:789

↓ 4 callersMethodeval_intra

src/lib/cache.cpp:92

↓ 4 callersMethodget_size

src/lib/model.cpp:601

↓ 4 callersMethodinit

src/lib/grid.cpp:25

↓ 4 callersMethodinitialize

src/lib/parse_pdbqt.cpp:618

↓ 4 callersMethodis_atom_in_ligand

src/lib/model.cpp:657

↓ 4 callersFunctionis_glue_type

src/lib/potentials.h:42

↓ 4 callersMethodis_in_grid

src/lib/cache.cpp:168

↓ 4 callersMethodprint

src/lib/conf.h:343

↓ 4 callersFunctionrandom_inside_sphere

src/lib/random.cpp:65

↓ 4 callersFunctionrandom_normal

src/lib/random.cpp:37

↓ 4 callersMethodrandomize

src/lib/vina.cpp:631

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