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

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

⨍ Functions 753◇ Types & classes 130

↓ 2 callersFunctionis_glued

Macrocycle - Vina and AD42

src/lib/potentials.h:103

↓ 2 callersMethodloop

src/lib/parallel.h:61

↓ 2 callersFunctionmake_path

src/split/split.cpp:36

↓ 2 callersMethodmax_cutoff_sqr

src/lib/precalculate.h:170

↓ 2 callersFunctionmean3

(firstline, secondline, thirdline)

example/autodock_scripts/wet.py:128

↓ 2 callersFunctionminus_mat_vec_product

src/lib/bfgs.h:31

↓ 2 callersFunctionnormalized_angle

src/lib/common.h:288

↓ 2 callersMethodnum_floats

src/lib/conf.h:259

↓ 2 callersMethodoptimal_covalent_bond_length

src/lib/atom_type.h:64

↓ 2 callersFunctionparse_ligand_pdbqt_from_string

src/lib/parse_pdbqt.cpp:635

↓ 2 callersFunctionparse_pdbqt_branch_aux

src/lib/parse_pdbqt.cpp:322

↓ 2 callersFunctionparse_pdbqt_ligand

dkoes, stream version

src/lib/parse_pdbqt.cpp:470

↓ 2 callersFunctionparse_two_unsigneds

src/lib/parse_pdbqt.cpp:245

↓ 2 callersFunctionpostprocess_branch

B == branch or main_branch or flexible_body

src/lib/parse_pdbqt.cpp:405

↓ 2 callersFunctionpostprocess_ligand

src/lib/parse_pdbqt.cpp:440

↓ 2 callersFunctionquaternion_normalize_approx

src/lib/quaternion.h:83

↓ 2 callersFunctionquaternion_to_angle

src/lib/quaternion.cpp:57

↓ 2 callersFunctionsave_output_pdbqt

(dictionary, output_filename, count = 0, nowaters = False, index = False, printrms = False)

example/autodock_scripts/dry.py:565

↓ 2 callersFunctionset_diagonal

src/lib/bfgs.h:85

↓ 2 callersMethodset_to_null

src/lib/conf.h:285

↓ 2 callersMethodshow_score

src/lib/vina.cpp:673

↓ 2 callersFunctionsmoothen

AD42 common functions

src/lib/potentials.h:64

↓ 2 callersFunctionszv_grid_dims

src/lib/szv_grid.cpp:84

↓ 2 callersMethodtetrahedral_pseudo

(self, d = 2.0)

example/autodock_scripts/zinc_pseudo.py:426

↓ 2 callersFunctiontorsions_generate

src/lib/conf.h:71

↓ 2 callersFunctiontorsions_increment

src/lib/conf.h:51

↓ 2 callersFunctiontorsions_randomize

src/lib/conf.h:58

↓ 2 callersFunctiontorsions_set_to_null

src/lib/conf.h:46

↓ 2 callersFunctiontorsions_too_close

src/lib/conf.h:63

↓ 2 callersMethodtransform

src/lib/tree.h:58

↓ 2 callersFunctiontransform_ranges

tree or heterotree - like structure

src/lib/tree.h:253

↓ 2 callersFunctionwrite_pdbqt

src/split/split.cpp:111

↓ 2 callersFunctionxs_donor_acceptor

src/lib/atom_constants.h:382

↓ 2 callersFunctionxs_is_acceptor

src/lib/atom_constants.h:367

↓ 2 callersFunctionxs_is_donor

src/lib/atom_constants.h:374

↓ 2 callersFunctionxs_vinardo_radius

src/lib/atom_constants.h:340

↓ 1 callersFunctionVINA_FOR_IN

src/lib/vina.cpp:299

↓ 1 callersFunctionVINA_FOR_IN

src/lib/coords.cpp:35

↓ 1 callersFunctionVINA_FOR_IN

src/lib/non_cache.cpp:63

↓ 1 callersMethod_build13

(self, connect)

example/autodock_scripts/zinc_pseudo.py:347

↓ 1 callersMethod_getCarboxyOxyIndx

(self,atoms,connect,n_conn)

example/autodock_scripts/zinc_pseudo.py:285

↓ 1 callersMethod_parse_common

Common to PDB and PDBQT formats

example/autodock_scripts/zinc_pseudo.py:72

↓ 1 callersMethod_parse_specific

PDBQT characters [68:79]

example/autodock_scripts/zinc_pseudo.py:91

↓ 1 callersMethod_print_common

Characters [0:68]

example/autodock_scripts/zinc_pseudo.py:98

↓ 1 callersMethod_print_specific

PDBQT characters [68:79]

example/autodock_scripts/zinc_pseudo.py:119

↓ 1 callersMethod_rmCarboxy

(self, nearAtoms, indxPairs)

example/autodock_scripts/zinc_pseudo.py:305

↓ 1 callersMethod_selectBinders

This function here is pretty cool. It goes up atom-index by atom-index, starting with the closest atoms to Zn, (they are sorte

example/autodock_scripts/zinc_pseudo.py:401

↓ 1 callersMethodacceptable_type

src/lib/atom_type.h:48

↓ 1 callersFunctionad_is_heteroatom

src/lib/atom_constants.h:218

↓ 1 callersFunctionad_is_hydrogen

src/lib/atom_constants.h:214

↓ 1 callersFunctionad_type_to_el_type

src/lib/atom_constants.h:224

↓ 1 callersFunctionangle

Calculate the angle between three points. First point in the middle

example/autodock_scripts/zinc_pseudo.py:10

↓ 1 callersMethodangle

example/autodock_scripts/zinc_pseudo.py:62

↓ 1 callersFunctionangled

example/autodock_scripts/zinc_pseudo.py:19

↓ 1 callersMethodassign_el

src/lib/atom_type.h:51

↓ 1 callersMethodatype_to_atomnr

example/autodock_scripts/zinc_pseudo.py:146

↓ 1 callersFunctionauto_seed

src/lib/random.cpp:84

↓ 1 callersFunctionaverage

example/autodock_scripts/dry.py:490

↓ 1 callersMethodavgCarboxyInner

Find a pseudo point that is representative of the two Oxygen atoms with a dist based approach. This will be used to calculate the

example/autodock_scripts/zinc_pseudo.py:334

↓ 1 callersFunctionbfgs

src/lib/bfgs.h:97

↓ 1 callersFunctionbfgs_update

src/lib/bfgs.h:50

↓ 1 callersFunctionbrick_closest

src/lib/brick.h:35

↓ 1 callersFunctionbruteNearbyAtoms

Find atoms close to given atype in pdb/pdbqt

example/autodock_scripts/zinc_pseudo.py:187

↓ 1 callersFunctioncalc_plane

(atom1, atom2, atom3)

example/autodock_scripts/wet.py:348

↓ 1 callersMethodcenter

src/lib/model.cpp:672

↓ 1 callersMethodclash_penalty

src/lib/model.cpp:1128

↓ 1 callersFunctionclosest_between

src/lib/brick.h:28

↓ 1 callersFunctioncluster_waters

(model, cutoff = OVERLAP_DISTANCE)

example/autodock_scripts/dry.py:515

↓ 1 callersFunctioncoplanar

(plane, structure, reference, tolerance = .2)

example/autodock_scripts/wet.py:374

↓ 1 callersFunctioncountWatoms

(madels,excludeH = True)

example/autodock_scripts/dry.py:828

↓ 1 callersFunctioncount_mutable_entities

src/lib/mutate.cpp:25

↓ 1 callersFunctioncount_torsions

T = main_branch, branch, flexible_body

src/lib/tree.h:223

↓ 1 callersFunctiondihedral

Calculate dihedral considering a in the beggining

example/autodock_scripts/zinc_pseudo.py:22

↓ 1 callersFunctiondot

(vector1, vector2)

example/autodock_scripts/wet.py:386

↓ 1 callersFunctionelementwise_product

src/lib/common.h:142

↓ 1 callersMethodeval_deriv

src/lib/non_cache.cpp:103

↓ 1 callersMethodeval_deriv

src/lib/cache.cpp:129

↓ 1 callersMethodeval_deriv

src/lib/precalculate.h:164

↓ 1 callersMethodeval_deriv

src/lib/model.cpp:832

↓ 1 callersFunctionfind_closest

src/lib/coords.cpp:33

↓ 1 callersFunctionfl_to_sz

src/lib/common.h:203

↓ 1 callersFunctionfuranbolic

(atom, structure, max = 2.35)

example/autodock_scripts/wet.py:393

↓ 1 callersMethodgenerate

src/lib/conf.h:119

↓ 1 callersMethodgetAngles

example/autodock_scripts/zinc_pseudo.py:450

↓ 1 callersFunctionget_atom_range

src/lib/model.cpp:31

↓ 1 callersMethodget_atoms

src/lib/model.h:77

↓ 1 callersMethodget_coords

src/lib/model.h:80

↓ 1 callersMethodget_ligand

src/lib/model.h:79

↓ 1 callersMethodget_ligand_coords

src/lib/model.cpp:617

↓ 1 callersMethodgetline

example/autodock_scripts/zinc_pseudo.py:54

↓ 1 callersFunctiongetmap

example/autodock_scripts/dry.py:659

↓ 1 callersFunctiongetpoints

(mapdata, coords=None, distance=None)

example/autodock_scripts/dry.py:697

↓ 1 callersFunctiongpfminmax

Return max/min coordinates of the box described in the GPF

example/autodock_scripts/wet.py:453

↓ 1 callersMethodgrid_dimensions_from_ligand

src/lib/vina.cpp:287

↓ 1 callersMethodgyration_radius

src/lib/model.cpp:754

↓ 1 callersFunctionin_the_box

(atom_list, MIN, MAX)

example/autodock_scripts/wet.py:496

↓ 1 callersFunctionin_the_box

(atom_list, MIN, MAX)

example/autodock_scripts/dry.py:290

↓ 1 callersMethodindex_permissive

src/lib/matrix.h:79

↓ 1 callersMethodindex_permissive

src/lib/precalculate.h:168

↓ 1 callersMethodindex_to_argument

src/lib/grid.h:41

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