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

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

⨍ Functions 753◇ Types & classes 130

↓ 1 callersMethodinitialize_from_rigid

src/lib/parse_pdbqt.cpp:574

↓ 1 callersMethodinsert_immobile

insertion into non_rigid_parsed

src/lib/parse_pdbqt.cpp:213

↓ 1 callersMethodinsert_immobile_inflex

inflex insertion

src/lib/parse_pdbqt.cpp:203

↓ 1 callersMethodinsert_immobiles

src/lib/parse_pdbqt.cpp:181

↓ 1 callersMethodinsert_immobiles_inflex

src/lib/parse_pdbqt.cpp:168

↓ 1 callersMethodis_heteroatom

src/lib/atom_type.h:45

↓ 1 callersFunctionis_non_ad_metal_name

src/lib/atom_constants.h:351

↓ 1 callersMethodisbound

Depends on atomic number

example/autodock_scripts/zinc_pseudo.py:133

↓ 1 callersMethodligand_length

src/lib/model.cpp:77

↓ 1 callersFunctionline_search

src/lib/bfgs.h:66

↓ 1 callersFunctionload_pdbqt

Creates a list of PDBQT atom objects

example/autodock_scripts/zinc_pseudo.py:158

↓ 1 callersFunctionload_receptor

(filename, filter = True)

example/autodock_scripts/dry.py:277

↓ 1 callersMethodlocal_to_lab

src/lib/tree.h:31

↓ 1 callersMethodlocal_to_lab_direction

src/lib/tree.h:36

↓ 1 callersFunctionmain

example/autodock_scripts/zinc_pseudo.py:498

↓ 1 callersFunctionmax_covalent_radius

src/lib/atom_constants.h:406

↓ 1 callersFunctionmerge_output_containers

src/lib/parallel_mc.cpp:51

↓ 1 callersFunctionmetropolis_accept

src/lib/monte_carlo.cpp:35

↓ 1 callersFunctionminmax

Return max/min coordinates of the box including the given atoms list

example/autodock_scripts/dry.py:248

↓ 1 callersFunctionmutate_conf

does not set model

src/lib/mutate.cpp:35

↓ 1 callersFunctionnorm

Return vector norm

example/autodock_scripts/wet.py:233

↓ 1 callersMethodnum_atoms

src/lib/model.h:92

↓ 1 callersMethodnum_degrees_of_freedom

src/lib/conf.h:41

↓ 1 callersMethodnum_ligands

src/lib/model.h:96

↓ 1 callersFunctionomit_whitespace

src/lib/parse_pdbqt.cpp:56

↓ 1 callersFunctionpairwise_clash_penalty

src/lib/model.cpp:1106

↓ 1 callersFunctionparse_dlg

(filename, raw_output = False)

example/autodock_scripts/dry.py:121

↓ 1 callersFunctionparse_models

example/autodock_scripts/dry.py:225

↓ 1 callersFunctionparse_multimodel_pdbqt

src/split/split.cpp:61

↓ 1 callersFunctionparse_one_unsigned

src/lib/parse_pdbqt.cpp:234

↓ 1 callersFunctionparse_pdbqt

example/autodock_scripts/dry.py:155

↓ 1 callersFunctionparse_pdbqt_branch

src/lib/parse_pdbqt.cpp:533

↓ 1 callersFunctionparse_pdbqt_flex

src/lib/parse_pdbqt.cpp:508

↓ 1 callersFunctionparse_pdbqt_residue

src/lib/parse_pdbqt.cpp:503

↓ 1 callersFunctionparse_pdbqt_rigid

src/lib/parse_pdbqt.cpp:258

↓ 1 callersFunctionparse_pdbqt_root

src/lib/parse_pdbqt.cpp:299

↓ 1 callersFunctionparse_pdbqt_root_aux

src/lib/parse_pdbqt.cpp:278

↓ 1 callersFunctionparse_receptor_pdbqt

src/lib/parse_pdbqt.cpp:648

↓ 1 callersFunctionpdbatom

(coords, kw = "ATOM ", atype = "X", pcharge = 0.)

example/autodock_scripts/dry.py:505

↓ 1 callersMethodpopulate

src/lib/cache.cpp:435

↓ 1 callersFunctionpostprocess_residue

src/lib/parse_pdbqt.cpp:447

↓ 1 callersMethodproc_rec

(self, nearAtoms)

example/autodock_scripts/zinc_pseudo.py:256

↓ 1 callersFunctionquaternion_difference

src/lib/quaternion.cpp:136

↓ 1 callersFunctionrandom_in_box

src/lib/random.cpp:77

↓ 1 callersFunctionrandom_orientation

src/lib/quaternion.cpp:114

↓ 1 callersMethodrandomize

src/lib/conf.h:337

↓ 1 callersFunctionread_vina_map

src/lib/cache.cpp:233

↓ 1 callersMethodrmsd_lower_bound

src/lib/model.cpp:907

↓ 1 callersFunctionrmsd_upper_bound

src/lib/coords.cpp:25

↓ 1 callersMethodrmsd_upper_bound

src/lib/model.cpp:911

↓ 1 callersMethodsame_element

src/lib/atom_type.h:56

↓ 1 callersFunctionsave_pdb

(list, filename)

example/autodock_scripts/dry.py:558

↓ 1 callersFunctionscoreCorrection

ugly function, just temporary for helping Yang. To be rewritten in a more clean way... it works only with PDBQT+ structures!

example/autodock_scripts/dry.py:744

↓ 1 callersFunctionselfoverlap

(model, cutoff = CLASH)

example/autodock_scripts/dry.py:346

↓ 1 callersMethodset_ad4_weights

src/lib/vina.cpp:261

↓ 1 callersMethodset_range

src/lib/model.cpp:81

↓ 1 callersFunctionset_rotor

src/lib/parse_pdbqt.cpp:377

↓ 1 callersMethodset_vina_weights

src/lib/vina.cpp:218

↓ 1 callersMethodset_vinardo_weights

src/lib/vina.cpp:240

↓ 1 callersFunctionstring_to_ad_type

src/lib/atom_constants.h:396

↓ 1 callersFunctionsubstring_is_blank

src/lib/convert_substring.h:50

↓ 1 callersFunctionsubtract_change

src/lib/bfgs.h:91

↓ 1 callersFunctiontargetoverlap

(model, target, cutoff = CLASH)

example/autodock_scripts/dry.py:401

↓ 1 callersMethodtoo_close

src/lib/conf.h:315

↓ 1 callersFunctionvector_append

src/lib/common.h:252

↓ 1 callersMethodwiden

src/lib/precalculate.h:171

↓ 1 callersMethodwithin

src/lib/non_cache.cpp:91

↓ 1 callersMethodwrite_model

src/lib/model.cpp:733

↓ 1 callersFunctionwrite_multimodel_pdbqt

src/split/split.cpp:119

↓ 1 callersMethodwrite_structure

src/lib/model.h:111

(oxygen, hydrogen)

example/autodock_scripts/mapwater.py:257

src/lib/scoring_function.h:100

FunctionOsp2_NEW

(oxygen, atom1, atom2)

example/autodock_scripts/wet.py:431

MethodScoringFunction

src/lib/scoring_function.h:41

FunctionVINA_FOR

src/lib/conf_independent.cpp:84

src/lib/scoring_function.h:121

src/lib/precalculate.h:63

FunctionVINA_FOR_IN

src/lib/conf_independent.cpp:43

FunctionVINA_FOR_IN

src/lib/cache.cpp:174

FunctionVINA_FOR_IN

src/lib/ad4cache.cpp:185

MethodVINA_FOR_IN

no sub-branches besides immobile atom, including sub-sub-branches, etc

src/lib/parse_pdbqt.cpp:223

MethodVINA_FOR_IN

returns by value

src/lib/conf.h:224

MethodVINA_FOR_IN

torsions are not normalized after this

src/lib/conf.h:320

MethodVINA_FOR_IN

returned if smooth.empty()

src/lib/precalculate.h:81

MethodVINA_FOR_IN

src/lib/model.cpp:315

MethodVINA_RANGE

src/lib/tree.h:75

FunctionVINA_U_FOR

src/lib/monte_carlo.cpp:52

FunctionVINA_U_FOR

src/lib/bfgs.h:74

src/lib/vina.h:73

example/autodock_scripts/zinc_pseudo.py:50

(self, ZnAtom, cutOffDist = 2.5, carboxyExp = 0.5)

example/autodock_scripts/zinc_pseudo.py:210

Method_filter_NOS

example/autodock_scripts/zinc_pseudo.py:265

src/lib/model.cpp:981

Methodad4_electrostatic

src/lib/potentials.h:358

src/lib/potentials.h:462

Methodad4_solvation

src/lib/potentials.h:382

Methodad4_tors_add

src/lib/conf_independent.h:121

src/lib/potentials.h:429

src/lib/ad4cache.h:45

src/lib/matrix.h:60

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