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Automated Forcefield Optimization Extension
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A
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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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K
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L
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M
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N
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O
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P
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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
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X
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Y
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Z
_
_net_charge (FOX.armc.ParamMapping attribute)
(FOX.armc.ParamMappingABC attribute)
A
a_target (FOX.armc.PhiUpdater attribute)
(FOX.armc.PhiUpdaterABC attribute)
(phi attribute)
acceptance() (FOX.armc.ARMC method)
(FOX.armc.ARMCPT method)
add_atoms() (FOX.MultiMolecule method)
add_param() (FOX.armc.ParamMappingABC method)
add_pes_evaluator() (FOX.armc.MonteCarloABC method)
ALIGNED (FOX.MultiMolecule attribute)
all() (FOX.MultiMolecule method)
allclose() (FOX.TOPContainer method)
allow_non_existent (param.validation attribute)
any() (FOX.MultiMolecule method)
apply_constraints() (FOX.armc.ParamMapping method)
(FOX.armc.ParamMappingABC method)
apply_phi (FOX.armc.ARMC property)
argmax() (FOX.MultiMolecule method)
argmin() (FOX.MultiMolecule method)
argpartition() (FOX.MultiMolecule method)
argsort() (FOX.MultiMolecule method)
ARMC (class in FOX.armc)
ARMCPT (class in FOX.armc)
as_ase() (FOX.MultiMolecule method)
as_gro() (FOX.MultiMolecule method)
as_mass_weighted() (FOX.MultiMolecule method)
as_mol() (FOX.MultiMolecule method)
as_mol2() (FOX.MultiMolecule method)
as_Molecule() (FOX.MultiMolecule method)
as_pdb() (FOX.MultiMolecule method)
as_xyz() (FOX.MultiMolecule method)
assemble_job() (FOX.armc.PackageManager static method)
(FOX.armc.PackageManagerABC static method)
astype() (FOX.MultiMolecule method)
atnum (FOX.MultiMolecule property)
atom1 (FOX.MultiMolecule property)
atom12 (FOX.MultiMolecule property)
atom2 (FOX.MultiMolecule property)
atoms (FOX.MultiMolecule attribute)
atoms() (in module FOX.io._top_concat._TOPConcat)
atoms_view (FOX.MultiMolecule attribute)
auto_to_explicit() (FOX.RTFContainer method)
B
base (FOX.MultiMolecule attribute)
BEHAVED (FOX.MultiMolecule attribute)
bonds (FOX.MultiMolecule attribute)
byteswap() (FOX.MultiMolecule method)
C
C_CONTIGUOUS (FOX.MultiMolecule attribute)
call_method() (in module FOX.properties)
CARRAY (FOX.MultiMolecule attribute)
CHARGE_LIKE (FOX.armc.ParamMapping attribute)
charge_tolerance (param.validation attribute)
choose() (FOX.MultiMolecule method)
clear_jobs (FOX.armc.MonteCarloABC property)
clear_jobs() (FOX.armc.PackageManager static method)
(FOX.armc.PackageManagerABC method)
clip() (FOX.MultiMolecule method)
clip_move() (FOX.armc.ParamMapping method)
(FOX.armc.ParamMappingABC method)
collapse_charges() (FOX.RTFContainer method)
columns (FOX.io.cp2k_to_prm.PRMMapping attribute)
compare_trajectories() (in module FOX.recipes)
compress() (FOX.MultiMolecule method)
concatenate (FOX.TOPContainer attribute)
concatenate() (FOX.MultiMolecule method)
(FOX.PRMContainer method)
(FOX.RTFContainer method)
conj() (FOX.MultiMolecule method)
conjugate() (FOX.MultiMolecule method)
connectors (FOX.MultiMolecule property)
constraints (param.block attribute)
constraints_to_str() (FOX.armc.ParamMappingABC method)
copy() (FOX.MultiMolecule method)
(FOX.TOPContainer method)
CP2K_TO_PRM (in module FOX.io.cp2k_to_prm)
create_top() (in module FOX.recipes)
ctypes (FOX.MultiMolecule attribute)
cumprod() (FOX.MultiMolecule method)
cumsum() (FOX.MultiMolecule method)
D
data (FOX.armc.PackageManagerABC property)
(FOX.MultiMolecule attribute)
default_error_func (in module FOX.armc)
default_unit (FOX.io.cp2k_to_prm.PRMMapping attribute)
delete_atoms() (FOX.MultiMolecule method)
diagonal() (FOX.MultiMolecule method)
do_inner() (FOX.armc.ARMC method)
(FOX.armc.ARMCPT method)
dtype (FOX.MultiMolecule attribute)
dump() (FOX.MultiMolecule method)
dumps() (FOX.MultiMolecule method)
E
enforce_constraints (param.validation attribute)
err_func (pes.block attribute)
err_normalized() (in module FOX.armc)
err_normalized_weighted() (in module FOX.armc)
estimate_lj() (in module FOX.ff.lj_param)
example_xyz (in module FOX)
extract_ligand() (in module FOX.recipes)
F
F_CONTIGUOUS (FOX.MultiMolecule attribute)
FARRAY (FOX.MultiMolecule attribute)
fill() (FOX.MultiMolecule method)
FILL_VALUE (FOX.armc.ParamMappingABC attribute)
flags (FOX.MultiMolecule attribute)
flat (FOX.MultiMolecule attribute)
flatten() (FOX.MultiMolecule method)
FNC (FOX.MultiMolecule attribute)
folder (monte_carlo attribute)
FORC (FOX.MultiMolecule attribute)
FOX.armc.err_funcs
module
FOX.ff.lj_param
module
FOX.io._read_rtf
module
FOX.io._read_top
module
FOX.io.cp2k_to_prm
module
FOX.io.read_prm
module
FOX.io.read_psf
module
FOX.properties
module
FOX.recipes._xyz_to_gro
module
FOX.recipes.ligands
module
FOX.recipes.param
module
FOX.recipes.psf
module
FOX.recipes.similarity
module
FOX.recipes.time_resolution
module
FOX.recipes.top
module
fps_reduce() (in module FOX.recipes)
from_ase() (FOX.MultiMolecule class method)
from_file() (FOX.RTFContainer class method)
(FOX.TOPContainer class method)
from_kf() (FOX.MultiMolecule class method)
from_mass_weighted() (FOX.MultiMolecule method)
from_Molecule() (FOX.MultiMolecule class method)
from_result() (FOX.properties.get_bulk_modulus method)
(FOX.properties.get_pressure method)
from_xyz() (FOX.MultiMolecule class method)
FromResult (class in FOX.properties)
FromResult.REDUCTION_NAMES (in module FOX.properties)
frozen (param.block attribute)
func (FOX.armc.ParamMapping attribute)
(FOX.armc.ParamMappingABC attribute)
(FOX.armc.PhiUpdater attribute)
(FOX.armc.PhiUpdaterABC attribute)
(param attribute)
(pes.block attribute)
(pes_validation.block attribute)
(phi attribute)
G
gamma (FOX.armc.PhiUpdater attribute)
(FOX.armc.PhiUpdaterABC attribute)
(phi attribute)
generate_pairs() (FOX.TOPContainer method)
generate_pairs_nb() (FOX.TOPContainer method)
generate_psf() (in module FOX.recipes)
generate_psf2() (in module FOX.recipes)
get() (FOX.armc.MonteCarloABC method)
(FOX.armc.PackageManagerABC method)
get_at_idx() (FOX.MultiMolecule static method)
get_attr() (in module FOX.properties)
get_aux_error() (FOX.armc.ARMC method)
get_average_velocity() (FOX.MultiMolecule method)
get_best() (in module FOX.recipes)
get_bonds_per_atom() (FOX.MultiMolecule method)
get_bulk_modulus() (in module FOX.properties)
get_center_of_mass() (FOX.MultiMolecule method)
get_cp2k_dicts() (FOX.armc.ParamMappingABC method)
get_dist_mat() (FOX.MultiMolecule method)
get_free_energy() (in module FOX.ff.lj_param)
get_lig_center() (in module FOX.recipes)
get_multi_lig_center() (in module FOX.recipes)
get_pair_dict() (FOX.MultiMolecule method)
get_pes_descriptors() (FOX.armc.MonteCarloABC method)
get_pressure() (in module FOX.properties)
get_rmsd() (FOX.MultiMolecule method)
get_rmsf() (FOX.MultiMolecule method)
get_supercell() (FOX.MultiMolecule method)
get_time_averaged_velocity() (FOX.MultiMolecule method)
get_vacf() (FOX.MultiMolecule method)
get_velocity() (FOX.MultiMolecule method)
getfield() (FOX.MultiMolecule method)
gro_to_xyz() (in module FOX.recipes)
guess (param.block attribute)
guess_bonds() (FOX.MultiMolecule method)
H
hdf5_file (monte_carlo attribute)
hook (FOX.armc.PackageManagerABC property)
I
identify_move() (FOX.armc.ParamMapping method)
(FOX.armc.ParamMappingABC method)
imag (FOX.MultiMolecule attribute)
init_adf() (FOX.MultiMolecule method)
init_average_velocity() (FOX.MultiMolecule method)
init_debye_scattering() (FOX.MultiMolecule method)
init_power_spectrum() (FOX.MultiMolecule method)
init_rdf() (FOX.MultiMolecule method)
init_rmsd() (FOX.MultiMolecule method)
init_rmsf() (FOX.MultiMolecule method)
init_shell_search() (FOX.MultiMolecule method)
init_time_averaged_velocity() (FOX.MultiMolecule method)
item() (FOX.MultiMolecule method)
items() (FOX.armc.MonteCarloABC method)
(FOX.armc.PackageManagerABC method)
itemset() (FOX.MultiMolecule method)
itemsize (FOX.MultiMolecule attribute)
iter_len (FOX.armc.ARMC attribute)
(monte_carlo attribute)
K
keep_files (monte_carlo attribute)
key (FOX.io.cp2k_to_prm.PRMMapping attribute)
key_path (FOX.io.cp2k_to_prm.PRMMapping attribute)
keys() (FOX.armc.MonteCarloABC method)
(FOX.armc.PackageManagerABC method)
kwargs (param attribute)
(pes.block attribute)
(pes_validation.block attribute)
(phi attribute)
L
lattice (FOX.MultiMolecule attribute)
(job attribute)
ligand_atoms (psf attribute)
loc (FOX.MultiMolecule property)
logfile (monte_carlo attribute)
logger (FOX.armc.MonteCarloABC property)
M
mass (FOX.MultiMolecule property)
max() (FOX.MultiMolecule method)
mean() (FOX.MultiMolecule method)
min() (FOX.MultiMolecule method)
module
FOX.armc.err_funcs
FOX.ff.lj_param
FOX.io._read_rtf
FOX.io._read_top
FOX.io.cp2k_to_prm
FOX.io.read_prm
FOX.io.read_psf
FOX.properties
FOX.recipes._xyz_to_gro
FOX.recipes.ligands
FOX.recipes.param
FOX.recipes.psf
FOX.recipes.similarity
FOX.recipes.time_resolution
FOX.recipes.top
mol (FOX.MultiMolecule attribute)
molecule (FOX.armc.MonteCarloABC property)
(job attribute)
MonteCarloABC (class in FOX.armc)
move() (FOX.armc.MonteCarloABC method)
move_range (FOX.armc.ParamMapping attribute)
(FOX.armc.ParamMappingABC attribute)
(param attribute)
mse_normalized() (in module FOX.armc)
mse_normalized_max() (in module FOX.armc)
mse_normalized_v2() (in module FOX.armc)
mse_normalized_weighted() (in module FOX.armc)
mse_normalized_weighted_v2() (in module FOX.armc)
MultiMolecule (class in FOX)
N
name (FOX.io.cp2k_to_prm.PRMMapping attribute)
nbytes (FOX.MultiMolecule attribute)
ndim (FOX.MultiMolecule attribute)
newbyteorder() (FOX.MultiMolecule method)
nonbond_params() (in module FOX.io._top_concat._TOPConcat)
nonzero() (FOX.MultiMolecule method)
O
order (FOX.MultiMolecule property)
overlay_cp2k_settings() (FOX.PRMContainer method)
overlay_descriptor() (in module FOX.recipes)
overlay_mapping() (FOX.PRMContainer method)
OWNDATA (FOX.MultiMolecule attribute)
P
PackageManager (class in FOX.armc)
PackageManagerABC (class in FOX.armc)
pairs() (in module FOX.io._top_concat._TOPConcat)
pairs_nb() (in module FOX.io._top_concat._TOPConcat)
param (param.block attribute)
ParamMapping (class in FOX.armc)
ParamMappingABC (class in FOX.armc)
partition() (FOX.MultiMolecule method)
path (monte_carlo attribute)
pes_post_process (FOX.armc.MonteCarloABC property)
phi (FOX.armc.ARMC attribute)
(FOX.armc.PhiUpdater attribute)
(FOX.armc.PhiUpdaterABC attribute)
(phi attribute)
PhiUpdater (class in FOX.armc)
PhiUpdaterABC (class in FOX.armc)
plot_descriptor() (in module FOX.recipes)
post_process (FOX.io.cp2k_to_prm.PRMMapping attribute)
PRMMapping (class in FOX.io.cp2k_to_prm)
prod() (FOX.MultiMolecule method)
properties (FOX.MultiMolecule attribute)
psf_file (psf attribute)
ptp() (FOX.MultiMolecule method)
put() (FOX.MultiMolecule method)
R
radius (FOX.MultiMolecule property)
random_slice() (FOX.MultiMolecule method)
ravel() (FOX.MultiMolecule method)
read() (FOX.PRMContainer class method)
read_multi_xyz() (in module FOX.io.read_xyz)
real (FOX.MultiMolecule attribute)
ref (pes.block attribute)
(pes_validation.block attribute)
repeat() (FOX.MultiMolecule method)
reset_origin() (FOX.MultiMolecule method)
reshape() (FOX.MultiMolecule method)
residue_argsort() (FOX.MultiMolecule method)
resize() (FOX.MultiMolecule method)
restart() (FOX.armc.ARMC method)
round() (FOX.MultiMolecule method)
rtf_file (psf attribute)
run_jobs() (FOX.armc.MonteCarloABC method)
S
searchsorted() (FOX.MultiMolecule method)
setfield() (FOX.MultiMolecule method)
setflags() (FOX.MultiMolecule method)
settings (job.block attribute)
shape (FOX.armc.PhiUpdaterABC property)
(FOX.MultiMolecule attribute)
size (FOX.MultiMolecule attribute)
sort() (FOX.MultiMolecule method)
squeeze() (FOX.MultiMolecule method)
std() (FOX.MultiMolecule method)
str_file (psf attribute)
strides (FOX.MultiMolecule attribute)
sub_iter_len (FOX.armc.ARMC attribute)
(monte_carlo attribute)
sum() (FOX.MultiMolecule method)
super_iter_len (FOX.armc.ARMC attribute)
swapaxes() (FOX.MultiMolecule method)
symbol (FOX.MultiMolecule property)
T
T (FOX.MultiMolecule attribute)
take() (FOX.MultiMolecule method)
template (job.block attribute)
time_resolved_adf() (in module FOX.recipes)
time_resolved_rdf() (in module FOX.recipes)
to_file() (FOX.TOPContainer method)
to_hdf5() (FOX.armc.ARMC method)
to_struct_array() (FOX.armc.ParamMappingABC method)
to_yaml_dict() (FOX.armc.ARMC method)
(FOX.armc.ARMCPT method)
(FOX.armc.PhiUpdaterABC method)
tobytes() (FOX.MultiMolecule method)
tofile() (FOX.MultiMolecule method)
tolist() (FOX.MultiMolecule method)
TOPContainer.atomtypes() (in module FOX.io._top_concat._TOPConcat)
tostring() (FOX.MultiMolecule method)
trace() (FOX.MultiMolecule method)
transpose() (FOX.MultiMolecule method)
type (job attribute)
(job.block attribute)
(monte_carlo attribute)
(param attribute)
(phi attribute)
U
unit (FOX.io.cp2k_to_prm.PRMMapping attribute)
(param.block attribute)
update() (FOX.armc.PhiUpdater method)
(FOX.armc.PhiUpdaterABC method)
update_settings() (FOX.armc.PackageManager method)
(FOX.armc.PackageManagerABC method)
V
values() (FOX.armc.MonteCarloABC method)
(FOX.armc.PackageManagerABC method)
var() (FOX.MultiMolecule method)
view() (FOX.MultiMolecule method)
W
weight (pes.block attribute)
write() (FOX.PRMContainer method)
WRITEABLE (FOX.MultiMolecule attribute)
WRITEBACKIFCOPY (FOX.MultiMolecule attribute)
X
x (FOX.MultiMolecule property)
xyz_to_gro() (in module FOX.recipes)
Y
y (FOX.MultiMolecule property)
Z
z (FOX.MultiMolecule property)
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