Index

A

acceptor_metal() (in module oddt.interactions) activities (oddt.datasets.pdbbind attribute) addh() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method) 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 attribute) (oddt.toolkits.rdk.Molecule attribute)

atomicmass (oddt.toolkits.ob.Atom attribute) atomicnum (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.rdk.Atom attribute) atoms (oddt.toolkits.ob.Bond attribute) (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.ob.Residue attribute) (oddt.toolkits.rdk.Molecule attribute) atoms_by_type() (in module oddt.scoring.descriptors) 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) binana_descriptor (class in oddt.scoring.descriptors.binana) bits (oddt.toolkits.ob.Fingerprint attribute) Bond (class in oddt.toolkits.ob)

bonds (oddt.toolkits.ob.Molecule attribute) BondStack (class in oddt.toolkits.ob) build() (oddt.scoring.descriptors.autodock_vina_descriptor method) (oddt.scoring.descriptors.binana.binana_descriptor method) (oddt.scoring.descriptors.close_contacts method) (oddt.scoring.descriptors.fingerprints method) (oddt.scoring.ensemble_descriptor method)

C

calccharges() (oddt.toolkits.ob.Molecule method) calcdesc() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method) calcfp() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method) canonic_order (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) charge (oddt.toolkits.ob.Molecule attribute) charges (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) cidx (oddt.toolkits.ob.Atom attribute) clean() (oddt.docking.autodock_vina method) (oddt.docking.AutodockVina.autodock_vina method) clear() (oddt.toolkits.rdk.MoleculeData method) clone (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute)

clone_coords() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method) close() (oddt.toolkits.rdk.Outputfile method) close_contacts (class in oddt.scoring.descriptors) close_contacts() (in module oddt.interactions) conformers (oddt.toolkits.ob.Molecule attribute) convertdbonds() (oddt.toolkits.ob.Molecule method) coordidx (oddt.toolkits.ob.Atom attribute) coords (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Atom attribute) (oddt.toolkits.rdk.Molecule attribute) cross_validate() (in module oddt.scoring)

D

data (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) descs (in module oddt.toolkits.rdk) dihedral() (in module oddt.spatial) dim (oddt.toolkits.ob.Molecule attribute)

distance() (in module oddt.spatial) dock() (oddt.docking.autodock_vina method) (oddt.docking.AutodockVina.autodock_vina method) (oddt.virtualscreening.virtualscreening method) draw() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method)

E

energy (oddt.toolkits.ob.Molecule attribute) enrichment_factor() (in module oddt.metrics) ensemble_descriptor (class in oddt.scoring)

ensemble_model (class in oddt.scoring) exactmass (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.ob.Molecule attribute)

F

fetch() (oddt.virtualscreening.virtualscreening method) findall() (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.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.models.neuralnetwork.neuralnetwork method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.scorer method)

forcefields (in module oddt.toolkits.rdk) formalcharge (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.rdk.Atom attribute) formula (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) fps (in module oddt.toolkits.rdk)

G

gen_training_data() (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.rfscore method) generate_descriptor() (in module oddt.scoring.functions.NNScore)

get_params() (oddt.scoring.models.neuralnetwork.neuralnetwork method) (oddt.scoring.models.regressors.neuralnetwork method)

H

halogenbond() (in module oddt.interactions) halogenbond_acceptor_halogen() (in module oddt.interactions) has_key() (oddt.toolkits.rdk.MoleculeData method) hbond() (in module oddt.interactions) hbond_acceptor_donor() (in module oddt.interactions)

heavyvalence (oddt.toolkits.ob.Atom attribute) heterovalence (oddt.toolkits.ob.Atom attribute) hyb (oddt.toolkits.ob.Atom attribute) hydrophobic_contacts() (in module oddt.interactions)

I

ids (oddt.datasets.pdbbind attribute) idx (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.ob.Residue attribute) (oddt.toolkits.rdk.Atom attribute) implicitvalence (oddt.toolkits.ob.Atom attribute) informats (in module oddt.toolkits.rdk)

isotope (oddt.toolkits.ob.Atom attribute) isrotor (oddt.toolkits.ob.Bond attribute) 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.RFScore.rfscore class method) (oddt.scoring.functions.rfscore class method) (oddt.scoring.scorer class method) load_ligands() (oddt.virtualscreening.virtualscreening method)

localopt() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method)

M

make3D() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method) mlr (in module oddt.scoring.models.regressors) Mol (oddt.toolkits.rdk.Molecule attribute)

Molecule (class in oddt.toolkits.ob) (class in oddt.toolkits.rdk) MoleculeData (class in oddt.toolkits.rdk) molwt (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute)

N

name (oddt.toolkits.ob.Residue attribute) neighbors (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.rdk.Atom attribute) neuralnetwork (class in oddt.scoring.models.neuralnetwork) (class in oddt.scoring.models.regressors)

nnscore (class in oddt.scoring.functions) (class in oddt.scoring.functions.NNScore) num_rotors (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute)

O

OBMol (oddt.toolkits.ob.Molecule attribute) oddt (module) oddt.datasets (module) oddt.docking (module) oddt.docking.AutodockVina (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.RFScore (module)

oddt.scoring.models (module) oddt.scoring.models.classifiers (module) oddt.scoring.models.neuralnetwork (module) oddt.scoring.models.regressors (module) oddt.spatial (module) oddt.toolkits (module) oddt.toolkits.ob (module) oddt.toolkits.rdk (module) oddt.virtualscreening (module) order (oddt.toolkits.ob.Bond attribute) outformats (in module oddt.toolkits.rdk) Outputfile (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.ob.Atom attribute) (oddt.toolkits.rdk.Atom attribute) pdbbind (class in oddt.datasets) pi_cation() (in module oddt.interactions) pi_metal() (in module oddt.interactions)

pi_stacking() (in module oddt.interactions) pickle_mol() (in module oddt.toolkits.ob) pls (in module oddt.scoring.models.regressors) predict() (oddt.scoring.ensemble_model method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.models.neuralnetwork.neuralnetwork method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.scorer method) predict_ligand() (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.scorer method) predict_ligands() (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.scorer method)

R

random() (in module oddt.docking.AutodockVina) 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 attribute) (oddt.toolkits.rdk.Fingerprint attribute) readfile() (in module oddt.toolkits.ob) (in module oddt.toolkits.rdk) readstring() (in module oddt.toolkits.rdk) removeh() (oddt.toolkits.ob.Molecule method) (oddt.toolkits.rdk.Molecule method) res_dict (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) Residue (class in oddt.toolkits.ob)

residue (oddt.toolkits.ob.Atom attribute) residues (oddt.toolkits.ob.Molecule attribute) rfscore (class in oddt.scoring.functions) (class in oddt.scoring.functions.RFScore) ring_dict (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) rmse() (in module oddt.metrics) roc() (in module oddt.metrics) roc_auc() (in module oddt.metrics) roc_log_auc() (in module oddt.metrics)

S

salt_bridge_plus_minus() (in module oddt.interactions) salt_bridges() (in module oddt.interactions) save() (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.scorer method) score() (oddt.docking.autodock_vina method) (oddt.docking.AutodockVina.autodock_vina method) (oddt.scoring.ensemble_model method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.models.neuralnetwork.neuralnetwork method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.scorer method) (oddt.virtualscreening.virtualscreening method) scorer (class in oddt.scoring) set_params() (oddt.scoring.models.neuralnetwork.neuralnetwork method) (oddt.scoring.models.regressors.neuralnetwork method)

set_protein() (oddt.docking.autodock_vina method) (oddt.docking.AutodockVina.autodock_vina method) (oddt.scoring.descriptors.autodock_vina_descriptor method) (oddt.scoring.descriptors.binana.binana_descriptor method) (oddt.scoring.ensemble_descriptor method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.rfscore method) (oddt.scoring.scorer method) Smarts (class in oddt.toolkits.rdk) spin (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.ob.Molecule attribute) sssr (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) svm (in module oddt.scoring.models.classifiers) (in module oddt.scoring.models.regressors)

T

title (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Molecule attribute) tmp_dir (oddt.docking.autodock_vina attribute) (oddt.docking.AutodockVina.autodock_vina attribute)

train() (oddt.scoring.functions.nnscore method) (oddt.scoring.functions.NNScore.nnscore method) (oddt.scoring.functions.RFScore.rfscore method) (oddt.scoring.functions.rfscore method) type (oddt.toolkits.ob.Atom attribute)

U

unitcell (oddt.toolkits.ob.Molecule attribute) unpickle_mol() (in module oddt.toolkits.ob)

update() (oddt.toolkits.rdk.MoleculeData method)

V

valence (oddt.toolkits.ob.Atom attribute) values() (oddt.toolkits.rdk.MoleculeData method)

vector (oddt.toolkits.ob.Atom attribute) virtualscreening (class in oddt.virtualscreening)

W

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)