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

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

⨍ Functions 753◇ Types & classes 130

↓ 4 callersFunctionrotatePoint

example/autodock_scripts/wet.py:96

↓ 4 callersMethodrun

src/lib/parallel.h:42

↓ 4 callersMethodset_receptor

src/lib/vina.cpp:62

↓ 4 callersFunctionxs_h_bond_possible

src/lib/atom_constants.h:386

↓ 3 callersFunctionVINA_FOR

src/lib/vina.cpp:653

↓ 3 callersFunctionVINA_FOR_IN

src/lib/common.h:329

↓ 3 callersMethod_avgCarboxy

example/autodock_scripts/zinc_pseudo.py:315

↓ 3 callersMethod_rm_too_far

example/autodock_scripts/zinc_pseudo.py:390

↓ 3 callersFunctionadd_to_output_container

src/lib/coords.cpp:43

↓ 3 callersFunctionangle_to_quaternion

src/lib/quaternion.cpp:36

↓ 3 callersMethodatom_typing_used

src/lib/model.h:86

↓ 3 callersFunctionbranches_derivative

src/lib/tree.h:155

↓ 3 callersFunctionbranches_set_conf

src/lib/tree.h:149

↓ 3 callersFunctionconvert_XS_to_string

src/lib/cache.cpp:30

↓ 3 callersMethodcoords_append

src/lib/model.cpp:173

↓ 3 callersMethodcorner1

src/lib/cache.h:53

↓ 3 callersMethodcorner2

src/lib/cache.h:54

↓ 3 callersMethodcount_torsions

src/lib/tree.h:128

↓ 3 callersMethodcovalent_radius

src/lib/atom_type.h:59

↓ 3 callersFunctiondefault_output

src/lib/utils.cpp:56

↓ 3 callersMethodeval

src/lib/scoring_function.h:119

↓ 3 callersMethodeval_inter

src/lib/model.cpp:820

↓ 3 callersMethodeval_intramolecular

src/lib/model.cpp:856

↓ 3 callersMethodevali

src/lib/model.cpp:825

↓ 3 callersMethodevalo

src/lib/model.cpp:815

↓ 3 callersFunctionget_adtype_str

src/lib/ad4cache.cpp:28

↓ 3 callersFunctionget_type_pair_index

src/lib/atom_type.h:88

↓ 3 callersFunctionhas

src/lib/common.h:359

↓ 3 callersMethodinitialize_from_nrp

src/lib/parse_pdbqt.cpp:578

↓ 3 callersMethodload_maps

src/lib/vina.cpp:389

↓ 3 callersFunctionmean_pdb

(firstline, secondline)

example/autodock_scripts/wet.py:59

↓ 3 callersMethodmobility_matrix

src/lib/parse_pdbqt.cpp:146

↓ 3 callersMethodnorm

src/lib/common.h:74

↓ 3 callersFunctionnormalize_angle

src/lib/common.h:267

↓ 3 callersFunctionnr_update_matrixes

src/lib/parse_pdbqt.cpp:396

↓ 3 callersMethodoptimize

src/lib/vina.cpp:782

↓ 3 callersFunctionparse_pdbqt_atom_string

src/lib/parse_pdbqt.cpp:96

↓ 3 callersFunctionparse_pdbqt_aux

src/lib/parse_pdbqt.cpp:338

↓ 3 callersFunctionpdb_atom_type

example/autodock_scripts/dry.py:319

↓ 3 callersFunctionquaternion_increment

src/lib/quaternion.cpp:129

↓ 3 callersFunctionquaternion_norm_sqr

src/lib/quaternion.h:70

↓ 3 callersFunctionquaternion_to_r3

src/lib/quaternion.cpp:75

↓ 3 callersFunctionrandom_int

src/lib/random.cpp:44

↓ 3 callersFunctionrawVec

example/autodock_scripts/zinc_pseudo.py:45

↓ 3 callersMethodread

src/lib/cache.cpp:296

↓ 3 callersFunctionread_ad4_map

src/lib/ad4cache.cpp:243

↓ 3 callersFunctionseparator

src/lib/utils.cpp:26

↓ 3 callersMethodset_derivative

src/lib/tree.h:91

↓ 3 callersMethodset_ligand_from_file

src/lib/vina.cpp:183

↓ 3 callersMethodspan

src/lib/grid_dim.h:35

↓ 3 callersFunctionsplit

src/lib/ad4cache.cpp:232

↓ 3 callersFunctionstring_write_coord

src/lib/model.cpp:688

↓ 3 callersMethodsum_force_and_torque

src/lib/tree.h:71

↓ 3 callersFunctiontriangular_matrix_index_permissive

src/lib/triangular_matrix_index.h:35

↓ 3 callersFunctionusage

example/autodock_scripts/wet.py:516

↓ 3 callersFunctionusage

example/autodock_scripts/mapwater.py:58

↓ 3 callersFunctionusage

example/autodock_scripts/prepare_gpf4zn.py:17

↓ 3 callersFunctionusage

example/autodock_scripts/prepare_gpf.py:17

↓ 3 callersFunctionusage

example/autodock_scripts/zinc_pseudo.py:489

↓ 3 callersFunctionvec_sum

example/autodock_scripts/wet.py:371

↓ 3 callersFunctionvina_split

src/lib/cache.cpp:222

↓ 3 callersMethodwrite_maps

src/lib/vina.cpp:425

↓ 3 callersMethodwrite_poses

src/lib/vina.cpp:604

↓ 3 callersFunctionxs_radius

src/lib/atom_constants.h:333

↓ 2 callersFunctionOsp2

(oxygen, atom1, atom2)

example/autodock_scripts/wet.py:413

↓ 2 callersFunctionVINA_FOR_IN

src/lib/szv_grid.cpp:28

↓ 2 callersMethod_getBonds

example/autodock_scripts/zinc_pseudo.py:273

↓ 2 callersFunctionabout

example/autodock_scripts/zinc_pseudo.py:478

↓ 2 callersFunctionad4_hb_radius

src/lib/potentials.h:84

↓ 2 callersFunctionad4_vdw_eps

src/lib/potentials.h:90

↓ 2 callersMethodadd

src/lib/parse_pdbqt.cpp:193

↓ 2 callersFunctionadd_bonds

src/lib/parse_pdbqt.cpp:366

↓ 2 callersMethodatomnr_vdw

example/autodock_scripts/zinc_pseudo.py:141

↓ 2 callersFunctionbound

identify all the atoms in "structure" that are @bond_dist from "atom" NOTE: this should be made with a lookup table!

example/autodock_scripts/wet.py:243

↓ 2 callersFunctionbrick_distance_sqr

src/lib/brick.h:42

↓ 2 callersMethodbuildShell

start the analysis process

example/autodock_scripts/zinc_pseudo.py:217

↓ 2 callersFunctionchecked_multiply

src/lib/array3d.h:29

↓ 2 callersMethodconf_independent

src/lib/scoring_function.h:135

↓ 2 callersFunctionconf_smooth_div

src/lib/conf_independent.cpp:129

↓ 2 callersFunctioncoords_to_pdbqt_string

src/lib/model.cpp:701

↓ 2 callersFunctioncross_product

src/lib/common.h:136

↓ 2 callersFunctiondefault_prefix

src/split/split.cpp:41

↓ 2 callersFunctiondotProd

example/autodock_scripts/zinc_pseudo.py:33

↓ 2 callersMethodessentially_empty

src/lib/parse_pdbqt.cpp:222

↓ 2 callersFunctiongetLines

(file, mode = "r")

example/autodock_scripts/mapwater.py:52

↓ 2 callersMethodget_atom_types

src/lib/scoring_function.h:150

↓ 2 callersFunctionget_branch_metrics

src/lib/model.cpp:48

↓ 2 callersMethodget_cutoff

src/lib/potentials.h:487

↓ 2 callersFunctionget_file_contents

src/lib/utils.cpp:105

↓ 2 callersFunctionget_filename

src/lib/utils.cpp:95

↓ 2 callersMethodget_heavy_atom_movable_coords

src/lib/model.cpp:639

↓ 2 callersMethodget_initial_conf

src/lib/model.cpp:608

↓ 2 callersFunctionget_lelc

(filename, cluster_number = None)

example/autodock_scripts/dry.py:189

↓ 2 callersMethodget_max_cutoff

src/lib/scoring_function.h:148

↓ 2 callersFunctionget_waters

(pdbqt_poses, type = "W")

example/autodock_scripts/dry.py:390

↓ 2 callersMethodglobal_search

src/lib/vina.cpp:865

↓ 2 callersMethodincrement

src/lib/conf.h:291

↓ 2 callersMethodinit_from_smooth_fst

src/lib/precalculate.h:59

↓ 2 callersMethodinsert_inflex

inflex atom insertion

src/lib/parse_pdbqt.cpp:163

↓ 2 callersFunctionis_directory

src/lib/utils.cpp:82

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