Auto-FOX
Auto-FOX-0.7
Automated Forcefield Optimization Extension 0.7.4
Auto-FOX Documentation
Auto-FOX
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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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J
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L
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M
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N
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Z
_
__bool__() (FOX.typed_mapping.TypedMapping method)
__contains__() (FOX.io.file_container.AbstractFileContainer method)
(FOX.typed_mapping.TypedMapping method)
__copy__() (FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
__delattr__() (FOX.typed_mapping.TypedMapping method)
__eq__() (FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
__getitem__() (FOX.typed_mapping.TypedMapping method)
__hash__() (FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
__init__() (FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
__iter__() (FOX.typed_mapping.TypedMapping method)
__len__() (FOX.typed_mapping.TypedMapping method)
__repr__() (FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
__setattr__() (FOX.typed_mapping.TypedMapping method)
__setitem__() (FOX.typed_mapping.TypedMapping method)
__weakref__ (FOX.io.file_container.AbstractFileContainer attribute)
(FOX.io.read_prm.PRMContainer attribute)
(FOX.io.read_psf.PSFContainer attribute)
_ATTR (FOX.typed_mapping.TypedMapping attribute)
_construct_segment_name() (FOX.io.read_psf.PSFContainer method)
_get_writer() (FOX.io.file_container.AbstractFileContainer static method)
_HEADER_DICT (FOX.io.read_psf.PSFContainer attribute)
_is_dict() (FOX.io.read_psf.PSFContainer static method)
_is_mapping() (FOX.io.read_prm.PRMContainer static method)
_MultiMolecule (class in FOX.classes.multi_mol_magic)
_overlay_cp2k_settings() (FOX.io.read_prm.PRMContainer method)
_post_process_psf() (FOX.io.read_psf.PSFContainer class method)
_PRIVATE_ATTR (FOX.io.read_prm.PRMContainer attribute)
(FOX.io.read_psf.PSFContainer attribute)
(FOX.typed_mapping.TypedMapping attribute)
_read_iterate() (FOX.io.file_container.AbstractFileContainer class method)
(FOX.io.read_prm.PRMContainer class method)
(FOX.io.read_psf.PSFContainer class method)
_read_post_iterate() (FOX.io.read_prm.PRMContainer class method)
_read_postprocess() (FOX.io.file_container.AbstractFileContainer method)
(FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
_serialize_array() (FOX.io.read_psf.PSFContainer static method)
_set_nd_array() (FOX.io.read_psf.PSFContainer method)
_SHAPE_DICT (FOX.io.read_psf.PSFContainer attribute)
_str_iterator() (FOX.io.read_psf.PSFContainer method)
_write_bottom() (FOX.io.read_psf.PSFContainer method)
_write_iterate() (FOX.io.file_container.AbstractFileContainer method)
(FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
_write_top() (FOX.io.read_psf.PSFContainer method)
A
AbstractFileContainer (class in FOX.io.file_container)
acceptors (FOX.io.read_psf.PSFContainer attribute)
acceptors() (FOX.io.read_psf.PSFContainer property)
add_atoms() (FOX.classes.multi_mol.MultiMolecule method)
add_pes_evaluator() (FOX.classes.monte_carlo.MonteCarlo method)
angles (FOX.io.read_psf.PSFContainer attribute)
angles() (FOX.io.read_psf.PSFContainer property)
ARMC (class in FOX.classes.armc)
as_dict() (FOX.io.read_psf.PSFContainer method)
as_mass_weighted() (FOX.classes.multi_mol.MultiMolecule method)
as_mol() (FOX.classes.multi_mol.MultiMolecule method)
as_mol2() (FOX.classes.multi_mol.MultiMolecule method)
as_Molecule() (FOX.classes.multi_mol.MultiMolecule method)
as_pdb() (FOX.classes.multi_mol.MultiMolecule method)
as_xyz() (FOX.classes.multi_mol.MultiMolecule method)
atnum() (FOX.classes.multi_mol_magic._MultiMolecule property)
atom1() (FOX.classes.multi_mol_magic._MultiMolecule property)
atom12() (FOX.classes.multi_mol_magic._MultiMolecule property)
atom2() (FOX.classes.multi_mol_magic._MultiMolecule property)
atom_name() (FOX.io.read_psf.PSFContainer property)
atom_type() (FOX.io.read_psf.PSFContainer property)
atoms (FOX.classes.multi_mol.MultiMolecule attribute)
(FOX.io.read_psf.PSFContainer attribute)
atoms() (FOX.io.read_psf.PSFContainer property)
B
bonds (FOX.classes.multi_mol.MultiMolecule attribute)
(FOX.io.read_psf.PSFContainer attribute)
bonds() (FOX.io.read_psf.PSFContainer property)
C
charge() (FOX.io.read_psf.PSFContainer property)
clear_job_cache() (FOX.classes.monte_carlo.MonteCarlo method)
clip_move() (FOX.classes.monte_carlo.MonteCarlo method)
columns (FOX.io.cp2k_to_prm.PRMMapping attribute)
COLUMNS (FOX.io.read_prm.PRMContainer attribute)
connectors() (FOX.classes.multi_mol_magic._MultiMolecule property)
copy() (FOX.classes.multi_mol_magic._MultiMolecule method)
(FOX.io.read_prm.PRMContainer method)
(FOX.io.read_psf.PSFContainer method)
CP2K_TO_PRM (FOX.io.read_prm.PRMContainer attribute)
,
[1]
(in module FOX.io.cp2k_to_prm)
D
default_unit (FOX.io.cp2k_to_prm.PRMMapping attribute)
delete_atoms() (FOX.classes.multi_mol.MultiMolecule method)
dihedrals (FOX.io.read_psf.PSFContainer attribute)
dihedrals() (FOX.io.read_psf.PSFContainer property)
do_inner() (FOX.classes.armc.ARMC method)
donors (FOX.io.read_psf.PSFContainer attribute)
donors() (FOX.io.read_psf.PSFContainer property)
E
estimate_lj() (in module FOX.ff.lj_param)
example_xyz (in module FOX)
extract_ligand() (in module FOX.recipes.psf)
F
filename (FOX.io.read_psf.PSFContainer attribute)
filename() (FOX.io.read_psf.PSFContainer property)
FOX.ff.lj_param
module
FOX.io.cp2k_to_prm
module
FOX.io.file_container
module
FOX.io.read_prm
module
FOX.io.read_psf
module
FOX.recipes.ligands
module
FOX.recipes.param
module
FOX.recipes.psf
module
FOX.typed_mapping
module
from_kf() (FOX.classes.multi_mol.MultiMolecule class method)
from_mass_weighted() (FOX.classes.multi_mol.MultiMolecule method)
from_Molecule() (FOX.classes.multi_mol.MultiMolecule class method)
from_xyz() (FOX.classes.multi_mol.MultiMolecule class method)
from_yaml() (FOX.classes.armc.ARMC class method)
G
generate_angles() (FOX.io.read_psf.PSFContainer method)
generate_atoms() (FOX.io.read_psf.PSFContainer method)
generate_bonds() (FOX.io.read_psf.PSFContainer method)
generate_dihedrals() (FOX.io.read_psf.PSFContainer method)
generate_impropers() (FOX.io.read_psf.PSFContainer method)
generate_psf() (in module FOX.recipes.psf)
generate_psf2() (in module FOX.recipes.psf)
get() (FOX.typed_mapping.TypedMapping method)
get_angle_mat() (FOX.classes.multi_mol.MultiMolecule method)
get_at_idx() (FOX.classes.multi_mol.MultiMolecule static method)
get_aux_error() (FOX.classes.armc.ARMC method)
get_average_velocity() (FOX.classes.multi_mol.MultiMolecule method)
get_best() (in module FOX.recipes.param)
get_bonds_per_atom() (FOX.classes.multi_mol.MultiMolecule method)
get_center_of_mass() (FOX.classes.multi_mol.MultiMolecule method)
get_dist_mat() (FOX.classes.multi_mol.MultiMolecule method)
get_free_energy() (in module FOX.ff.lj_param)
get_lig_center() (in module FOX.recipes.ligands)
get_multi_lig_center() (in module FOX.recipes.ligands)
get_pair_dict() (FOX.classes.multi_mol.MultiMolecule method)
get_pes_descriptors() (FOX.classes.monte_carlo.MonteCarlo method)
get_rmsd() (FOX.classes.multi_mol.MultiMolecule method)
get_rmsf() (FOX.classes.multi_mol.MultiMolecule method)
get_time_averaged_velocity() (FOX.classes.multi_mol.MultiMolecule method)
get_vacf() (FOX.classes.multi_mol.MultiMolecule method)
get_velocity() (FOX.classes.multi_mol.MultiMolecule method)
guess_bonds() (FOX.classes.multi_mol.MultiMolecule method)
H
HEADERS (FOX.io.read_prm.PRMContainer attribute)
I
improper() (FOX.io.read_prm.PRMContainer property)
impropers (FOX.io.read_psf.PSFContainer attribute)
impropers() (FOX.io.read_psf.PSFContainer property)
INDEX (FOX.io.read_prm.PRMContainer attribute)
inherit_annotations() (FOX.io.file_container.AbstractFileContainer class method)
init_adf() (FOX.classes.multi_mol.MultiMolecule method)
init_average_velocity() (FOX.classes.multi_mol.MultiMolecule method)
init_power_spectrum() (FOX.classes.multi_mol.MultiMolecule method)
init_rdf() (FOX.classes.multi_mol.MultiMolecule method)
init_rmsd() (FOX.classes.multi_mol.MultiMolecule method)
init_rmsf() (FOX.classes.multi_mol.MultiMolecule method)
init_shell_search() (FOX.classes.multi_mol.MultiMolecule method)
init_time_averaged_velocity() (FOX.classes.multi_mol.MultiMolecule method)
items() (FOX.classes.monte_carlo.MonteCarlo method)
(FOX.typed_mapping.TypedMapping method)
J
job_name() (FOX.classes.monte_carlo.MonteCarlo property)
K
key (FOX.io.cp2k_to_prm.PRMMapping attribute)
key_path (FOX.io.cp2k_to_prm.PRMMapping attribute)
keys() (FOX.classes.monte_carlo.MonteCarlo method)
(FOX.typed_mapping.TypedMapping method)
L
loc() (FOX.classes.multi_mol_magic._MultiMolecule property)
logger() (FOX.classes.monte_carlo.MonteCarlo property)
M
mass() (FOX.classes.multi_mol_magic._MultiMolecule property)
(FOX.io.read_psf.PSFContainer property)
md_settings() (FOX.classes.monte_carlo.MonteCarlo property)
module
FOX.ff.lj_param
FOX.io.cp2k_to_prm
FOX.io.file_container
FOX.io.read_prm
FOX.io.read_psf
FOX.recipes.ligands
FOX.recipes.param
FOX.recipes.psf
FOX.typed_mapping
mol (FOX.classes.multi_mol_magic._MultiMolecule attribute)
molecule() (FOX.classes.monte_carlo.MonteCarlo property)
MonteCarlo (class in FOX.classes.monte_carlo)
move() (FOX.classes.monte_carlo.MonteCarlo method)
move_range() (FOX.classes.monte_carlo.MonteCarlo property)
MultiMolecule (class in FOX.classes.multi_mol)
N
name (FOX.io.cp2k_to_prm.PRMMapping attribute)
no_nonbonded (FOX.io.read_psf.PSFContainer attribute)
no_nonbonded() (FOX.io.read_psf.PSFContainer property)
np_printoptions (FOX.io.read_psf.PSFContainer attribute)
O
order() (FOX.classes.multi_mol_magic._MultiMolecule property)
overlay_cp2k_settings() (FOX.io.read_prm.PRMContainer method)
,
[1]
overlay_descriptor() (in module FOX.recipes.param)
overlay_mapping() (FOX.io.read_prm.PRMContainer method)
,
[1]
P
pd_printoptions (FOX.io.read_prm.PRMContainer attribute)
,
[1]
(FOX.io.read_psf.PSFContainer attribute)
plot_descriptor() (in module FOX.recipes.param)
post_process (FOX.io.cp2k_to_prm.PRMMapping attribute)
preopt_settings() (FOX.classes.monte_carlo.MonteCarlo property)
PRMContainer (class in FOX.io.read_prm)
,
[1]
PRMMapping (class in FOX.io.cp2k_to_prm)
properties (FOX.classes.multi_mol.MultiMolecule attribute)
PSFContainer (class in FOX.io.read_psf)
R
radius() (FOX.classes.multi_mol_magic._MultiMolecule property)
random_slice() (FOX.classes.multi_mol.MultiMolecule method)
read() (FOX.io.file_container.AbstractFileContainer class method)
(FOX.io.read_prm.PRMContainer class method)
,
[1]
(FOX.io.read_psf.PSFContainer class method)
read_multi_xyz() (in module FOX.io.read_xyz)
reset_origin() (FOX.classes.multi_mol.MultiMolecule method)
residue_argsort() (FOX.classes.multi_mol.MultiMolecule method)
residue_id() (FOX.io.read_psf.PSFContainer property)
residue_name() (FOX.io.read_psf.PSFContainer property)
restart() (FOX.classes.armc.ARMC method)
round() (FOX.classes.multi_mol.MultiMolecule method)
run_md() (FOX.classes.monte_carlo.MonteCarlo method)
S
segment_name() (FOX.io.read_psf.PSFContainer property)
sort() (FOX.classes.multi_mol.MultiMolecule method)
super_iter_len() (FOX.classes.armc.ARMC property)
symbol() (FOX.classes.multi_mol_magic._MultiMolecule property)
T
title (FOX.io.read_psf.PSFContainer attribute)
title() (FOX.io.read_psf.PSFContainer property)
to_atom_dict() (FOX.io.read_psf.PSFContainer method)
to_yaml() (FOX.classes.armc.ARMC method)
TypedMapping (class in FOX.typed_mapping)
U
unit (FOX.io.cp2k_to_prm.PRMMapping attribute)
update_atom_charge() (FOX.io.read_psf.PSFContainer method)
update_atom_type() (FOX.io.read_psf.PSFContainer method)
update_phi() (FOX.classes.armc.ARMC method)
V
values() (FOX.classes.monte_carlo.MonteCarlo method)
(FOX.typed_mapping.TypedMapping method)
view (FOX.typed_mapping.TypedMapping attribute)
W
write() (FOX.io.file_container.AbstractFileContainer method)
(FOX.io.read_prm.PRMContainer method)
,
[1]
(FOX.io.read_psf.PSFContainer method)
write_pdb() (FOX.io.read_psf.PSFContainer method)
X
x() (FOX.classes.multi_mol_magic._MultiMolecule property)
Y
y() (FOX.classes.multi_mol_magic._MultiMolecule property)
Z
z() (FOX.classes.multi_mol_magic._MultiMolecule property)
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