Open Drug Discovery Toolkit
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oddt package
Open Drug Discovery Toolkit
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P
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T
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U
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V
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W
A
acceptor_metal() (in module oddt.interactions)
activities() (oddt.datasets.pdbbind property)
AddAtomsError
addh() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
AddMissingAtoms() (in module oddt.toolkits.extras.rdkit.fixer)
angle() (in module oddt.spatial)
angle_2v() (in module oddt.spatial)
apply_filter() (oddt.virtualscreening.virtualscreening method)
Atom (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
atom_dict() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
atomicnum() (oddt.toolkits.rdk.Atom property)
AtomListToSubMol() (in module oddt.toolkits.extras.rdkit)
atoms() (oddt.toolkits.ob.Bond property)
(oddt.toolkits.ob.Molecule property)
(oddt.toolkits.ob.Residue property)
(oddt.toolkits.rdk.Bond property)
(oddt.toolkits.rdk.Molecule property)
(oddt.toolkits.rdk.Residue property)
AtomStack (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
auc() (in module oddt.metrics)
autodock_vina (class in oddt.docking)
(class in oddt.docking.AutodockVina)
autodock_vina_descriptor (class in oddt.scoring.descriptors)
B
base_feature_factory (in module oddt.toolkits.rdk)
bedroc() (in module oddt.metrics)
binana_descriptor (class in oddt.scoring.descriptors.binana)
Bond (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
bonds() (oddt.toolkits.ob.Atom property)
(oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Atom property)
(oddt.toolkits.rdk.Molecule property)
BondStack (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
build() (oddt.scoring.descriptors.autodock_vina_descriptor method)
(oddt.scoring.descriptors.binana.binana_descriptor method)
(oddt.scoring.descriptors.close_contacts_descriptor method)
(oddt.scoring.descriptors.fingerprints method)
(oddt.scoring.descriptors.oddt_vina_descriptor method)
(oddt.scoring.ensemble_descriptor method)
C
calccharges() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
calcdesc() (oddt.toolkits.rdk.Molecule method)
calcfp() (oddt.toolkits.rdk.Molecule method)
canonic_order() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
canonize_ring_path() (in module oddt.toolkits.common)
CASF (class in oddt.datasets)
chain() (oddt.toolkits.ob.Residue property)
(oddt.toolkits.rdk.Residue property)
change_dihedral() (in module oddt.docking.internal)
charges() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
check_molecule() (in module oddt.utils)
chunker() (in module oddt.utils)
clean() (oddt.docking.autodock_vina method)
(oddt.docking.AutodockVina.autodock_vina method)
clear() (oddt.toolkits.rdk.MoleculeData method)
clone() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
clone_coords() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
close() (oddt.toolkits.rdk.Outputfile method)
close_contacts() (in module oddt.interactions)
close_contacts_descriptor (class in oddt.scoring.descriptors)
common_usr() (in module oddt.shape)
compose_iter() (in module oddt.utils)
coords() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Atom property)
(oddt.toolkits.rdk.Molecule property)
correct_radius() (oddt.docking.internal.vina_docking method)
cross_validate() (in module oddt.scoring)
D
data() (oddt.toolkits.rdk.Molecule property)
descs (in module oddt.toolkits.rdk)
detect_secondary_structure() (in module oddt.toolkits.common)
dice() (in module oddt.fingerprints)
dihedral() (in module oddt.spatial)
distance() (in module oddt.spatial)
diverse_conformers_generator() (in module oddt.toolkits.ob)
(in module oddt.toolkits.rdk)
dock() (oddt.docking.autodock_vina method)
(oddt.docking.AutodockVina.autodock_vina method)
(oddt.virtualscreening.virtualscreening method)
dude (class in oddt.datasets)
E
ECFP() (in module oddt.fingerprints)
electroshape() (in module oddt.shape)
enrichment_factor() (in module oddt.metrics)
ensemble_descriptor (class in oddt.scoring)
ensemble_model (class in oddt.scoring)
ExtractPocketAndLigand() (in module oddt.toolkits.extras.rdkit.fixer)
F
fetch() (oddt.virtualscreening.virtualscreening method)
FetchAffinityTable() (in module oddt.toolkits.extras.rdkit.fixer)
FetchStructure() (in module oddt.toolkits.extras.rdkit.fixer)
find_surface_residues() (in module oddt.surface)
findall() (oddt.toolkits.ob.Smarts method)
(oddt.toolkits.rdk.Smarts method)
Fingerprint (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
fingerprints (class in oddt.scoring.descriptors)
fit() (oddt.scoring.ensemble_model method)
(oddt.scoring.scorer method)
FixerError
forcefields (in module oddt.toolkits.rdk)
formalcharge() (oddt.toolkits.rdk.Atom property)
formula() (oddt.toolkits.rdk.Molecule property)
fps (in module oddt.toolkits.rdk)
G
gen_json() (oddt.scoring.functions.PLECscore method)
(oddt.scoring.functions.PLECscore.PLECscore method)
gen_training_data() (oddt.scoring.functions.nnscore method)
(oddt.scoring.functions.NNScore.nnscore method)
(oddt.scoring.functions.PLECscore method)
(oddt.scoring.functions.PLECscore.PLECscore method)
(oddt.scoring.functions.rfscore method)
(oddt.scoring.functions.RFScore.rfscore method)
generate_surface_marching_cubes() (in module oddt.surface)
get_children() (in module oddt.docking.internal)
get_close_neighbors() (in module oddt.docking.internal)
GetAtomResidueId() (in module oddt.toolkits.extras.rdkit.fixer)
GetResidues() (in module oddt.toolkits.extras.rdkit.fixer)
H
halogenbond_acceptor_halogen() (in module oddt.interactions)
halogenbonds() (in module oddt.interactions)
has_key() (oddt.toolkits.rdk.MoleculeData method)
hbond_acceptor_donor() (in module oddt.interactions)
hbonds() (in module oddt.interactions)
hydrophobic_contacts() (in module oddt.interactions)
I
ids() (oddt.datasets.pdbbind property)
idx() (oddt.toolkits.ob.Atom property)
(oddt.toolkits.ob.Residue property)
(oddt.toolkits.rdk.Atom property)
(oddt.toolkits.rdk.Residue property)
idx0() (oddt.toolkits.ob.Atom property)
(oddt.toolkits.ob.Residue property)
(oddt.toolkits.rdk.Atom property)
(oddt.toolkits.rdk.Residue property)
idx1() (oddt.toolkits.ob.Atom property)
(oddt.toolkits.rdk.Atom property)
informats (in module oddt.toolkits.rdk)
InteractionFingerprint() (in module oddt.fingerprints)
is_molecule() (in module oddt.utils)
is_openbabel_molecule() (in module oddt.utils)
is_rdkit_molecule() (in module oddt.utils)
IsResidueConnected() (in module oddt.toolkits.extras.rdkit.fixer)
isrotor() (oddt.toolkits.ob.Bond property)
(oddt.toolkits.rdk.Bond property)
items() (oddt.toolkits.rdk.MoleculeData method)
iteritems() (oddt.toolkits.rdk.MoleculeData method)
K
keys() (oddt.toolkits.rdk.MoleculeData method)
L
load() (oddt.scoring.functions.nnscore class method)
(oddt.scoring.functions.NNScore.nnscore class method)
(oddt.scoring.functions.PLECscore class method)
(oddt.scoring.functions.PLECscore.PLECscore class method)
(oddt.scoring.functions.rfscore class method)
(oddt.scoring.functions.RFScore.rfscore class method)
(oddt.scoring.scorer class method)
load_ligands() (oddt.virtualscreening.virtualscreening method)
localopt() (oddt.toolkits.rdk.Molecule method)
M
make2D() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
make3D() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
match() (oddt.toolkits.ob.Smarts method)
(oddt.toolkits.rdk.Smarts method)
method_caller() (in module oddt.utils)
mlr (in module oddt.scoring.models.regressors)
module
oddt
oddt.datasets
oddt.docking
oddt.docking.AutodockVina
oddt.docking.internal
oddt.fingerprints
oddt.interactions
oddt.metrics
oddt.scoring
oddt.scoring.descriptors
oddt.scoring.descriptors.binana
oddt.scoring.functions
oddt.scoring.functions.NNScore
oddt.scoring.functions.PLECscore
oddt.scoring.functions.RFScore
oddt.scoring.models
oddt.scoring.models.classifiers
oddt.scoring.models.regressors
oddt.shape
oddt.spatial
oddt.surface
oddt.toolkits
oddt.toolkits.common
oddt.toolkits.extras
oddt.toolkits.extras.rdkit
oddt.toolkits.extras.rdkit.fixer
oddt.toolkits.ob
oddt.toolkits.rdk
oddt.utils
oddt.virtualscreening
Mol() (oddt.toolkits.rdk.Molecule property)
Molecule (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
MoleculeData (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
MolFromPDBBlock() (in module oddt.toolkits.extras.rdkit)
MolFromPDBQTBlock() (in module oddt.toolkits.extras.rdkit)
MolToPDBQTBlock() (in module oddt.toolkits.extras.rdkit)
MolToTemplates() (in module oddt.toolkits.extras.rdkit.fixer)
molwt() (oddt.toolkits.rdk.Molecule property)
mutate() (oddt.docking.internal.vina_ligand method)
N
name() (oddt.toolkits.ob.Residue property)
(oddt.toolkits.rdk.Residue property)
neighbors() (oddt.toolkits.ob.Atom property)
(oddt.toolkits.rdk.Atom property)
neuralnetwork (class in oddt.scoring.models.classifiers)
(class in oddt.scoring.models.regressors)
nnscore (class in oddt.scoring.functions)
(class in oddt.scoring.functions.NNScore)
num_rotors() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
num_rotors_pdbqt() (in module oddt.docking.internal)
number() (oddt.toolkits.ob.Residue property)
(oddt.toolkits.rdk.Residue property)
O
OBMol() (oddt.toolkits.ob.Molecule property)
oddt
module
oddt.datasets
module
oddt.docking
module
oddt.docking.AutodockVina
module
oddt.docking.internal
module
oddt.fingerprints
module
oddt.interactions
module
oddt.metrics
module
oddt.scoring
module
oddt.scoring.descriptors
module
oddt.scoring.descriptors.binana
module
oddt.scoring.functions
module
oddt.scoring.functions.NNScore
module
oddt.scoring.functions.PLECscore
module
oddt.scoring.functions.RFScore
module
oddt.scoring.models
module
oddt.scoring.models.classifiers
module
oddt.scoring.models.regressors
module
oddt.shape
module
oddt.spatial
module
oddt.surface
module
oddt.toolkits
module
oddt.toolkits.common
module
oddt.toolkits.extras
module
oddt.toolkits.extras.rdkit
module
oddt.toolkits.extras.rdkit.fixer
module
oddt.toolkits.ob
module
oddt.toolkits.rdk
module
oddt.utils
module
oddt.virtualscreening
module
oddt_vina_descriptor (class in oddt.scoring.descriptors)
order() (oddt.toolkits.ob.Bond property)
(oddt.toolkits.rdk.Bond property)
outformats (in module oddt.toolkits.rdk)
Outputfile (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
P
parse_vina_docking_output() (in module oddt.docking.AutodockVina)
parse_vina_scoring_output() (in module oddt.docking.AutodockVina)
partialcharge() (oddt.toolkits.rdk.Atom property)
PathFromAtomList() (in module oddt.toolkits.extras.rdkit)
pdbbind (class in oddt.datasets)
PDBQTAtomLines() (in module oddt.toolkits.extras.rdkit)
pi_cation() (in module oddt.interactions)
pi_metal() (in module oddt.interactions)
pi_stacking() (in module oddt.interactions)
PLEC() (in module oddt.fingerprints)
PLECscore (class in oddt.scoring.functions)
(class in oddt.scoring.functions.PLECscore)
pls (in module oddt.scoring.models.regressors)
precomputed_score() (oddt.datasets.CASF method)
precomputed_screening() (oddt.datasets.CASF method)
predict() (oddt.scoring.ensemble_model method)
(oddt.scoring.scorer method)
predict_ligand() (oddt.docking.autodock_vina method)
(oddt.docking.AutodockVina.autodock_vina method)
(oddt.scoring.scorer method)
predict_ligands() (oddt.docking.autodock_vina method)
(oddt.docking.AutodockVina.autodock_vina method)
(oddt.scoring.scorer method)
PrepareComplexes() (in module oddt.toolkits.extras.rdkit.fixer)
PreparePDBMol() (in module oddt.toolkits.extras.rdkit.fixer)
PreparePDBResidue() (in module oddt.toolkits.extras.rdkit.fixer)
protein() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
R
random_roc_log_auc() (in module oddt.metrics)
randomforest (in module oddt.scoring.models.classifiers)
(in module oddt.scoring.models.regressors)
raw() (oddt.toolkits.ob.Fingerprint property)
(oddt.toolkits.rdk.Fingerprint property)
readfile() (in module oddt.toolkits.ob)
(in module oddt.toolkits.rdk)
readstring() (in module oddt.toolkits.rdk)
ReadTemplates() (in module oddt.toolkits.extras.rdkit.fixer)
removeh() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
res_dict() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
Residue (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
residue() (oddt.toolkits.ob.Atom property)
residues() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
ResidueStack (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
rfscore (class in oddt.scoring.functions)
(class in oddt.scoring.functions.RFScore)
rie() (in module oddt.metrics)
ring_dict() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
rmsd() (in module oddt.spatial)
rmse() (in module oddt.metrics)
roc() (in module oddt.metrics)
roc_auc() (in module oddt.metrics)
roc_log_auc() (in module oddt.metrics)
rotate() (in module oddt.spatial)
S
salt_bridge_plus_minus() (in module oddt.interactions)
salt_bridges() (in module oddt.interactions)
SanitizeError
save() (oddt.scoring.scorer method)
score() (oddt.docking.autodock_vina method)
(oddt.docking.AutodockVina.autodock_vina method)
(oddt.docking.internal.vina_docking method)
(oddt.scoring.ensemble_model method)
(oddt.scoring.scorer method)
(oddt.virtualscreening.virtualscreening method)
score_inter() (oddt.docking.internal.vina_docking method)
score_intra() (oddt.docking.internal.vina_docking method)
score_total() (oddt.docking.internal.vina_docking method)
scorer (class in oddt.scoring)
set_box() (oddt.docking.internal.vina_docking method)
set_coords() (oddt.docking.internal.vina_docking method)
set_ligand() (oddt.docking.internal.vina_docking method)
set_protein() (oddt.docking.autodock_vina method)
(oddt.docking.AutodockVina.autodock_vina method)
(oddt.docking.internal.vina_docking method)
(oddt.scoring.descriptors.autodock_vina_descriptor method)
(oddt.scoring.descriptors.binana.binana_descriptor method)
(oddt.scoring.descriptors.oddt_vina_descriptor method)
(oddt.scoring.ensemble_descriptor method)
(oddt.scoring.scorer method)
similarity() (oddt.virtualscreening.virtualscreening method)
similarity_SPLIF() (in module oddt.fingerprints)
SimpleInteractionFingerprint() (in module oddt.fingerprints)
SimplifyMol() (in module oddt.toolkits.extras.rdkit.fixer)
Smarts (class in oddt.toolkits.ob)
(class in oddt.toolkits.rdk)
smiles() (oddt.toolkits.ob.Molecule property)
(oddt.toolkits.rdk.Molecule property)
SPLIF() (in module oddt.fingerprints)
sssr() (oddt.toolkits.rdk.Molecule property)
SubstructureMatchError
svm (class in oddt.scoring.models.classifiers)
(class in oddt.scoring.models.regressors)
T
tanimoto() (in module oddt.fingerprints)
title() (oddt.toolkits.rdk.Molecule property)
tmp_dir() (oddt.docking.autodock_vina property)
(oddt.docking.AutodockVina.autodock_vina property)
to_dict() (oddt.toolkits.ob.MoleculeData method)
(oddt.toolkits.rdk.MoleculeData method)
train() (oddt.scoring.functions.nnscore method)
(oddt.scoring.functions.NNScore.nnscore method)
(oddt.scoring.functions.PLECscore method)
(oddt.scoring.functions.PLECscore.PLECscore method)
(oddt.scoring.functions.rfscore method)
(oddt.scoring.functions.RFScore.rfscore method)
U
UFFConstrainedOptimize() (in module oddt.toolkits.extras.rdkit.fixer)
update() (oddt.toolkits.rdk.MoleculeData method)
usr() (in module oddt.shape)
usr_cat() (in module oddt.shape)
usr_similarity() (in module oddt.shape)
V
values() (oddt.toolkits.rdk.MoleculeData method)
vina_docking (class in oddt.docking.internal)
vina_ligand (class in oddt.docking.internal)
virtualscreening (class in oddt.virtualscreening)
W
weighted_inter() (oddt.docking.internal.vina_docking method)
weighted_intra() (oddt.docking.internal.vina_docking method)
weighted_total() (oddt.docking.internal.vina_docking method)
write() (oddt.toolkits.ob.Molecule method)
(oddt.toolkits.rdk.Molecule method)
(oddt.toolkits.rdk.Outputfile method)
(oddt.virtualscreening.virtualscreening method)
write_csv() (oddt.virtualscreening.virtualscreening method)
write_vina_pdbqt() (in module oddt.docking.AutodockVina)
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