Index

A | B | C | D | E | F | H | I | K | L | M | N | O | P | R | S | T | U | V | W

A

acceptor_metal() (in module oddt.interactions)
addh() (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.rdk)
atom_dict (oddt.toolkits.rdk.Molecule attribute)
atomicnum (oddt.toolkits.rdk.Atom attribute)
atoms (oddt.toolkits.ob.Residue attribute)
(oddt.toolkits.rdk.Molecule attribute)
atoms_by_type() (in module oddt.scoring.descriptors)
auc() (in module oddt.metrics)
autodock_vina (class in oddt.docking.autodock_vina)

B

binana_descriptor (class in oddt.scoring.descriptors.binana)
build() (oddt.scoring.descriptors.binana.binana_descriptor method)
(oddt.scoring.descriptors.close_contacts method)
(oddt.scoring.descriptors.fingerprints method)

C

calcdesc() (oddt.toolkits.rdk.Molecule method)
calcfp() (oddt.toolkits.rdk.Molecule method)
canonic_order (oddt.toolkits.rdk.Molecule attribute)
charges (oddt.toolkits.rdk.Molecule attribute)
clean() (oddt.docking.autodock_vina.autodock_vina method)
clear() (oddt.toolkits.rdk.MoleculeData method)
clone (oddt.toolkits.rdk.Molecule attribute)
clone_coords() (oddt.toolkits.rdk.Molecule method)
close() (oddt.toolkits.rdk.Outputfile method)
close_contacts (class in oddt.scoring.descriptors)
close_contacts() (in module oddt.interactions)
coords (oddt.toolkits.rdk.Atom attribute)
(oddt.toolkits.rdk.Molecule attribute)
cross_validate() (in module oddt.scoring)

D

data (oddt.toolkits.rdk.Molecule attribute)
descs (in module oddt.toolkits.rdk)
dihedral() (in module oddt.spatial)
distance() (in module oddt.spatial)
dock() (oddt.docking.autodock_vina.autodock_vina method)
(oddt.virtualscreening.virtualscreening method)
draw() (oddt.toolkits.rdk.Molecule method)

E

enrichment_factor() (in module oddt.metrics)
ensemble_model (class in oddt.scoring)

F

fetch() (oddt.virtualscreening.virtualscreening method)
findall() (oddt.toolkits.rdk.Smarts method)
Fingerprint (class in oddt.toolkits.rdk)
fingerprints (class in oddt.scoring.descriptors)
fit() (oddt.scoring.ensemble_model method)
(oddt.scoring.scorer method)
forcefields (in module oddt.toolkits.rdk)
formalcharge (oddt.toolkits.rdk.Atom attribute)
formula (oddt.toolkits.rdk.Molecule attribute)
fps (in module oddt.toolkits.rdk)

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)
hydrophobic_contacts() (in module oddt.interactions)

I

idx (oddt.toolkits.ob.Residue attribute)
(oddt.toolkits.rdk.Atom attribute)
informats (in module oddt.toolkits.rdk)
items() (oddt.toolkits.rdk.MoleculeData method)
iteritems() (oddt.toolkits.rdk.MoleculeData method)

K

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

L

load() (oddt.scoring.scorer class method)
load_ligands() (oddt.virtualscreening.virtualscreening method)
localopt() (oddt.toolkits.rdk.Molecule method)

M

make3D() (oddt.toolkits.rdk.Molecule method)
Mol (oddt.toolkits.rdk.Molecule attribute)
Molecule (class in oddt.toolkits.rdk)
MoleculeData (class in oddt.toolkits.rdk)
molwt (oddt.toolkits.rdk.Molecule attribute)

N

name (oddt.toolkits.ob.Residue attribute)
neighbors (oddt.toolkits.rdk.Atom attribute)
num_rotors (oddt.toolkits.rdk.Molecule attribute)

O

oddt (module), [1]
oddt.docking (module)
oddt.docking.autodock_vina (module)
oddt.interactions (module)
oddt.metrics (module)
oddt.scoring (module)
oddt.scoring.descriptors (module)
oddt.scoring.descriptors.binana (module)
oddt.scoring.models (module)
oddt.scoring.models.classifiers (module)
oddt.spatial (module)
oddt.toolkits (module)
oddt.toolkits.ob (module)
oddt.toolkits.rdk (module)
oddt.virtualscreening (module)
outformats (in module oddt.toolkits.rdk)
Outputfile (class in oddt.toolkits.rdk)

P

parse_vina_docking_output() (in module oddt.docking.autodock_vina)
parse_vina_scoring_output() (in module oddt.docking.autodock_vina)
partialcharge (oddt.toolkits.rdk.Atom attribute)
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)
predict() (oddt.scoring.ensemble_model method)
(oddt.scoring.scorer method)
predict_ligand() (oddt.scoring.scorer method)
predict_ligands() (oddt.scoring.scorer method)

R

random() (in module oddt.docking.autodock_vina)
random_roc_log_auc() (in module oddt.metrics)
randomforest (in module oddt.scoring.models.classifiers)
raw (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.rdk.Molecule method)
res_dict (oddt.toolkits.rdk.Molecule attribute)
Residue (class in oddt.toolkits.ob)
ring_dict (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.scorer method)
score() (oddt.docking.autodock_vina.autodock_vina method)
(oddt.scoring.ensemble_model method)
(oddt.scoring.scorer method)
(oddt.virtualscreening.virtualscreening method)
scorer (class in oddt.scoring)
set_protein() (oddt.docking.autodock_vina.autodock_vina method)
(oddt.scoring.descriptors.binana.binana_descriptor method)
(oddt.scoring.scorer method)
Smarts (class in oddt.toolkits.rdk)
sssr (oddt.toolkits.rdk.Molecule attribute)
svm (in module oddt.scoring.models.classifiers)

T

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

U

unpickle_mol() (in module oddt.toolkits.ob)
update() (oddt.toolkits.rdk.MoleculeData method)

V

values() (oddt.toolkits.rdk.MoleculeData method)
virtualscreening (class in oddt.virtualscreening)

W

write() (oddt.toolkits.rdk.Molecule method)
(oddt.toolkits.rdk.Outputfile method)
(oddt.virtualscreening.virtualscreening method)
write_csv() (oddt.virtualscreening.virtualscreening method)