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.Bond attribute) (oddt.toolkits.rdk.Molecule attribute) (oddt.toolkits.rdk.Residue attribute) 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) (class in oddt.toolkits.rdk)

bonds (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.Atom attribute) (oddt.toolkits.rdk.Molecule attribute) 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.fingerprints method) (oddt.scoring.descriptors.oddt_vina_descriptor 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) change_dihedral() (in module oddt.docking.internal) 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() (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) correct_radius() (oddt.docking.internal.vina_docking method) 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.classifiers.neuralnetwork method) (oddt.scoring.models.classifiers.svm method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.models.regressors.svm 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) get_children() (in module oddt.docking.internal)

get_close_neighbors() (in module oddt.docking.internal) get_params() (oddt.scoring.models.classifiers.neuralnetwork method) (oddt.scoring.models.classifiers.svm method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.models.regressors.svm 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) (oddt.toolkits.rdk.Residue 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) (oddt.toolkits.rdk.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) mutate() (oddt.docking.internal.vina_ligand method)

N

name (oddt.toolkits.ob.Residue attribute) (oddt.toolkits.rdk.Residue attribute) neighbors (oddt.toolkits.ob.Atom attribute) (oddt.toolkits.rdk.Atom attribute) 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 attribute) (oddt.toolkits.rdk.Molecule attribute) num_rotors_pdbqt() (in module oddt.docking.internal)

O

OBMol (oddt.toolkits.ob.Molecule attribute) oddt (module) oddt.datasets (module) oddt.docking (module) oddt.docking.AutodockVina (module) oddt.docking.internal (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) oddt_vina_descriptor (class in oddt.scoring.descriptors) order (oddt.toolkits.ob.Bond attribute) (oddt.toolkits.rdk.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) 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.classifiers.neuralnetwork method) (oddt.scoring.models.classifiers.svm method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.models.regressors.svm method) (oddt.scoring.scorer method) predict_ligand() (oddt.docking.autodock_vina method) (oddt.docking.AutodockVina.autodock_vina 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) predict_ligands() (oddt.docking.autodock_vina method) (oddt.docking.AutodockVina.autodock_vina 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)

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) (class in oddt.toolkits.rdk) residue (oddt.toolkits.ob.Atom attribute)

residues (oddt.toolkits.ob.Molecule attribute) (oddt.toolkits.rdk.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) 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) 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.docking.internal.vina_docking 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.classifiers.neuralnetwork method) (oddt.scoring.models.classifiers.svm method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.models.regressors.svm 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_params() (oddt.scoring.models.classifiers.neuralnetwork method) (oddt.scoring.models.classifiers.svm method) (oddt.scoring.models.regressors.neuralnetwork method) (oddt.scoring.models.regressors.svm 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.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 (class in oddt.scoring.models.classifiers) (class in 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)

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)

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)