e3fp
v1.2.2
Overview of E3FP
Setup and Installation
Usage and Examples
Developer Notes
e3fp API
e3fp
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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P
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Q
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R
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S
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T
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U
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V
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W
A
add() (in module e3fp.fingerprint.fprint)
add_conformer_energies_to_mol() (in module e3fp.conformer.util)
add_fingerprints() (FingerprintDatabase method)
as_type() (FingerprintDatabase method)
as_unit() (in module e3fp.fingerprint.array_ops)
atom_tuples_from_shell() (in module e3fp.fingerprint.fprinter)
atoms() (Shell property)
(Substruct property)
B
back() (ShellsGenerator method)
bit_count() (Fingerprint property)
bits() (Fingerprint property)
(FingerprintDatabase property)
bound_atoms_from_mol() (in module e3fp.fingerprint.fprinter)
built-in function
deprecated_method()
C
calculate_angles() (in module e3fp.fingerprint.array_ops)
center_atom() (Shell property)
(Substruct property)
clear() (Fingerprint method)
coerce_to_valid_dtype() (in module e3fp.fingerprint.fprint)
concat() (in module e3fp.fingerprint.db)
conf_name() (MolItemName property)
conf_num (MolItemTuple attribute)
ConformerGenerator (class in e3fp.conformer.generator)
confs_from_smiles() (in module e3fp.pipeline)
coords_from_atoms() (in module e3fp.fingerprint.fprinter)
copy() (MolItemName method)
cosine() (in module e3fp.fingerprint.metrics)
(in module e3fp.fingerprint.metrics.array_metrics)
(in module e3fp.fingerprint.metrics.fprint_metrics)
CountFingerprint (class in e3fp.fingerprint.fprint)
counts() (CountFingerprint property)
(Fingerprint property)
(FloatFingerprint property)
current_level() (Fingerprinter property)
D
density() (Fingerprint property)
deprecate_function() (deprecated method)
deprecated (class in e3fp.util)
deprecated_method()
built-in function
dice() (in module e3fp.fingerprint.metrics)
(in module e3fp.fingerprint.metrics.array_metrics)
(in module e3fp.fingerprint.metrics.fprint_metrics)
dict_to_smiles() (in module e3fp.conformer.util)
diff_counts_dict() (in module e3fp.fingerprint.fprint)
distance() (in module e3fp.fingerprint.metrics.fprint_metrics)
dtype_from_fptype() (in module e3fp.fingerprint.fprint)
E
e3fp
module
e3fp.config
module
e3fp.config.params
module
e3fp.conformer
module
e3fp.conformer.generate
module
e3fp.conformer.generator
module
e3fp.conformer.protonation
module
e3fp.conformer.util
module
e3fp.fingerprint
module
e3fp.fingerprint.array_ops
module
e3fp.fingerprint.db
module
e3fp.fingerprint.fprint
module
e3fp.fingerprint.fprinter
module
e3fp.fingerprint.generate
module
e3fp.fingerprint.metrics
module
e3fp.fingerprint.metrics.array_metrics
module
e3fp.fingerprint.metrics.fprint_metrics
module
e3fp.fingerprint.structs
module
e3fp.fingerprint.util
module
e3fp.pipeline
module
e3fp.util
module
E3FPBitsValueError
E3FPCountsError
E3FPDeprecationWarning
E3FPEfficiencyWarning
E3FPError
E3FPInvalidFingerprintError
E3FPMolError
E3FPOptionError
E3FPWarning
embed_molecule() (ConformerGenerator method)
F
filter_conformers() (ConformerGenerator method)
Fingerprint (class in e3fp.fingerprint.fprint)
FingerprintDatabase (class in e3fp.fingerprint.db)
Fingerprinter (class in e3fp.fingerprint.fprinter)
FloatFingerprint (class in e3fp.fingerprint.fprint)
fold() (CountFingerprint method)
(Fingerprint method)
(FingerprintDatabase method)
FormatError
fp_num() (FingerprintDatabase property)
fprints_dict_from_mol() (in module e3fp.fingerprint.generate)
fprints_dict_from_sdf() (in module e3fp.fingerprint.generate)
fprints_from_fprints_dict() (in module e3fp.pipeline)
fprints_from_mol() (in module e3fp.pipeline)
fprints_from_sdf() (in module e3fp.pipeline)
fprints_from_smiles() (in module e3fp.pipeline)
fptype_from_dtype() (in module e3fp.fingerprint.fprint)
from_array() (FingerprintDatabase class method)
from_bitstring() (Fingerprint class method)
from_counts() (CountFingerprint class method)
from_fingerprint() (CountFingerprint class method)
(Fingerprint class method)
from_indices() (CountFingerprint class method)
(Fingerprint class method)
from_rdkit() (Fingerprint class method)
from_shell() (Substruct class method)
from_str() (MolItemName class method)
from_substruct() (Shell class method)
from_tuple() (MolItemName class method)
from_vector() (Fingerprint class method)
G
generate_conformers() (ConformerGenerator method)
(in module e3fp.conformer.generate)
get_conformer_energies() (ConformerGenerator method)
get_conformer_energies_from_mol() (in module e3fp.conformer.util)
get_count() (CountFingerprint method)
(Fingerprint method)
get_default_value() (in module e3fp.config.params)
get_density() (FingerprintDatabase method)
get_fingerprint_at_level() (Fingerprinter method)
get_first_unique_tuple_inds() (in module e3fp.fingerprint.fprinter)
get_folding_index_map() (Fingerprint method)
get_match_atoms() (ShellsGenerator method)
get_molecule_force_field() (ConformerGenerator method)
get_num_conformers() (ConformerGenerator static method)
get_prop() (Fingerprint method)
(FingerprintDatabase method)
get_shells_at_level() (Fingerprinter method)
(ShellsGenerator method)
get_subset() (FingerprintDatabase method)
get_unfolding_index_map() (Fingerprint method)
get_value() (in module e3fp.config.params)
H
hamming() (in module e3fp.fingerprint.metrics.fprint_metrics)
hash_int64_array() (in module e3fp.fingerprint.fprinter)
I
identifier_from_shell() (in module e3fp.fingerprint.fprinter)
identifiers_from_invariants() (in module e3fp.fingerprint.fprinter)
index_id_map() (Fingerprint property)
indices() (Fingerprint property)
initialize_conformer() (Fingerprinter method)
initialize_identifiers() (Fingerprinter method)
initialize_mol() (Fingerprinter method)
invariants_from_atom() (in module e3fp.fingerprint.fprinter)
iter_to_smiles() (in module e3fp.conformer.util)
L
level() (Fingerprint property)
load() (FingerprintDatabase class method)
(in module e3fp.fingerprint.fprint)
loadz() (in module e3fp.fingerprint.fprint)
M
make_distance_matrix() (in module e3fp.fingerprint.array_ops)
make_rotation_matrix() (in module e3fp.fingerprint.array_ops)
make_transform_matrix() (in module e3fp.fingerprint.array_ops)
mean() (CountFingerprint method)
(Fingerprint method)
(in module e3fp.fingerprint.fprint)
minimize_conformers() (ConformerGenerator method)
module
e3fp
e3fp.config
e3fp.config.params
e3fp.conformer
e3fp.conformer.generate
e3fp.conformer.generator
e3fp.conformer.protonation
e3fp.conformer.util
e3fp.fingerprint
e3fp.fingerprint.array_ops
e3fp.fingerprint.db
e3fp.fingerprint.fprint
e3fp.fingerprint.fprinter
e3fp.fingerprint.generate
e3fp.fingerprint.metrics
e3fp.fingerprint.metrics.array_metrics
e3fp.fingerprint.metrics.fprint_metrics
e3fp.fingerprint.structs
e3fp.fingerprint.util
e3fp.pipeline
e3fp.util
mol() (Fingerprint property)
mol2_generator() (in module e3fp.conformer.util)
mol_from_mol2() (in module e3fp.conformer.util)
mol_from_sdf() (in module e3fp.conformer.util)
mol_from_smiles() (in module e3fp.conformer.util)
mol_item_name() (MolItemName property)
mol_item_name_to_dict() (MolItemName static method)
mol_name (MolItemTuple attribute)
mol_name() (MolItemName property)
mol_to_sdf() (in module e3fp.conformer.util)
mol_to_standardised_mol() (in module e3fp.conformer.util)
MolItemName (class in e3fp.conformer.util)
MolItemTuple (class in e3fp.conformer.util)
N
name() (Fingerprint property)
next() (Fingerprinter method)
(ShellsGenerator method)
P
pad_array() (in module e3fp.fingerprint.array_ops)
params_to_dicts() (in module e3fp.pipeline)
params_to_sections_dict() (in module e3fp.config.params)
pearson() (in module e3fp.fingerprint.metrics)
(in module e3fp.fingerprint.metrics.array_metrics)
(in module e3fp.fingerprint.metrics.fprint_metrics)
pick_y() (in module e3fp.fingerprint.fprinter)
pick_z() (in module e3fp.fingerprint.fprinter)
project_to_plane() (in module e3fp.fingerprint.array_ops)
props() (Fingerprint property)
proto_name() (MolItemName property)
proto_state_num (MolItemTuple attribute)
Q
quad_indicators_from_coords() (in module e3fp.fingerprint.fprinter)
quaternion_to_transform_matrix() (in module e3fp.fingerprint.array_ops)
R
rdkit_invariants_from_atom() (in module e3fp.fingerprint.fprinter)
read_params() (in module e3fp.config.params)
reset() (CountFingerprint method)
(Fingerprint method)
(Fingerprinter method)
reset_conf() (Fingerprinter method)
reset_mol() (Fingerprinter method)
reverse_enumerate() (ConformerGenerator static method)
rotate_angles() (in module e3fp.fingerprint.array_ops)
run() (Fingerprinter method)
(in module e3fp.conformer.generate)
(in module e3fp.fingerprint.generate)
S
save() (FingerprintDatabase method)
(in module e3fp.fingerprint.fprint)
savetxt() (FingerprintDatabase method)
savez() (FingerprintDatabase method)
(in module e3fp.fingerprint.fprint)
sdf_from_smiles() (in module e3fp.pipeline)
set_prop() (Fingerprint method)
(FingerprintDatabase method)
Shell (class in e3fp.fingerprint.structs)
shell_to_pdb() (in module e3fp.fingerprint.structs)
shells() (Shell property)
ShellsGenerator (class in e3fp.fingerprint.fprinter)
signed_to_unsigned_int() (in module e3fp.fingerprint.fprinter)
smiles_dict_to_proto_smiles_dict() (in module e3fp.conformer.protonation)
smiles_generator() (in module e3fp.conformer.util)
smiles_list_to_proto_smiles_list() (in module e3fp.conformer.protonation)
smiles_to_dict() (in module e3fp.conformer.util)
smiles_to_proto_smiles() (in module e3fp.conformer.protonation)
soergel() (in module e3fp.fingerprint.metrics)
(in module e3fp.fingerprint.metrics.array_metrics)
(in module e3fp.fingerprint.metrics.fprint_metrics)
std() (CountFingerprint method)
(Fingerprint method)
stereo_indicators_from_shell() (in module e3fp.fingerprint.fprinter)
Substruct (class in e3fp.fingerprint.structs)
substruct() (Shell property)
substructs_to_pdb() (Fingerprinter method)
sum_counts_dict() (in module e3fp.fingerprint.fprint)
T
tanimoto() (in module e3fp.fingerprint.metrics)
(in module e3fp.fingerprint.metrics.array_metrics)
(in module e3fp.fingerprint.metrics.fprint_metrics)
to_bitstring() (Fingerprint method)
to_bitvector() (Fingerprint method)
to_conf_name() (MolItemName method)
to_mol_name() (MolItemName method)
to_proto_name() (MolItemName method)
to_rdkit() (Fingerprint method)
to_str() (MolItemName method)
to_tuple() (MolItemName method)
to_vector() (Fingerprint method)
transform_array() (in module e3fp.fingerprint.array_ops)
transform_matrix_to_quaternion() (in module e3fp.fingerprint.array_ops)
U
unfold() (Fingerprint method)
unpad_array() (in module e3fp.fingerprint.array_ops)
update_docstring() (deprecated method)
update_names_map() (FingerprintDatabase method)
update_params() (in module e3fp.config.params)
update_props() (Fingerprint method)
(FingerprintDatabase method)
V
values_to_hdf5() (in module e3fp.conformer.generate)
vector_dtype (CountFingerprint attribute)
(Fingerprint attribute)
(FloatFingerprint attribute)
W
write_params() (in module e3fp.config.params)
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