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Index
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Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
a_priori_refinement (apbs.input_file.calculate.finite_element.FiniteElement attribute)
adjust_counts() (apbs.input_file.calculate.finite_difference.GridDimensions method)
alias (apbs.input_file.calculate.Calculate attribute)
(apbs.input_file.process.Element attribute)
(apbs.input_file.process.Operation attribute)
(apbs.input_file.read.DielectricMapGroup attribute)
(apbs.input_file.read.Map attribute)
(apbs.input_file.read.Molecule attribute)
(apbs.input_file.read.Parameter attribute)
apbs (module)
apbs.input_file (module)
apbs.input_file.calculate (module)
apbs.input_file.calculate.boundary_element (module)
apbs.input_file.calculate.finite_difference (module)
apbs.input_file.calculate.finite_element (module)
apbs.input_file.calculate.generic (module)
apbs.input_file.calculate.nonpolar.Nonpolar (module)
apbs.input_file.process (module)
apbs.input_file.read (module)
asynchronous_rank (apbs.input_file.calculate.finite_difference.ParallelFocus attribute)
B
boundary_condition (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
BoundaryElement (class in apbs.input_file.calculate.boundary_element)
C
Calculate (class in apbs.input_file.calculate)
calculate_energy (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
(in module apbs.input_file.calculate.nonpolar.Nonpolar)
calculate_forces (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
(in module apbs.input_file.calculate.nonpolar.Nonpolar)
calculation_parameters (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
calculation_type (apbs.input_file.calculate.Calculate attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
charge (apbs.input_file.calculate.generic.Ion attribute)
charge_density_maps (apbs.input_file.read.Read attribute)
charge_discretization (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
coarse_grid_center (apbs.input_file.calculate.finite_difference.Focus attribute)
coarse_grid_dimensions (apbs.input_file.calculate.finite_difference.Focus attribute)
coefficient (apbs.input_file.process.Element attribute)
concentration (apbs.input_file.calculate.generic.Ion attribute)
counts (apbs.input_file.calculate.finite_difference.GridDimensions attribute)
D
dielectric_maps (apbs.input_file.read.Read attribute)
DielectricMapGroup (class in apbs.input_file.read)
displacement (in module apbs.input_file.calculate.nonpolar.Nonpolar)
domain_length (apbs.input_file.calculate.finite_element.FiniteElement attribute)
E
Element (class in apbs.input_file.process)
elements (apbs.input_file.process.Operation attribute)
equation (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
error_based_refinement (apbs.input_file.calculate.finite_element.FiniteElement attribute)
error_tolerance (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
ERROR_TOLERANCE (in module apbs.input_file.calculate.finite_difference)
exps (apbs.input_file.process.Process attribute)
F
find_count() (apbs.input_file.calculate.finite_difference.GridDimensions static method)
fine_grid_center (apbs.input_file.calculate.finite_difference.Focus attribute)
fine_grid_dimensions (apbs.input_file.calculate.finite_difference.Focus attribute)
FiniteDifference (class in apbs.input_file.calculate.finite_difference)
FiniteElement (class in apbs.input_file.calculate.finite_element)
Focus (class in apbs.input_file.calculate.finite_difference)
format (apbs.input_file.calculate.generic.WriteMap attribute)
(apbs.input_file.read.DielectricMapGroup attribute)
(apbs.input_file.read.Map attribute)
(apbs.input_file.read.Molecule attribute)
(apbs.input_file.read.Parameter attribute)
from_dict() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
from_json() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
from_yaml() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
G
grid_center (apbs.input_file.calculate.finite_difference.Manual attribute)
grid_dimensions (apbs.input_file.calculate.finite_difference.Manual attribute)
grid_spacings (in module apbs.input_file.calculate.nonpolar.Nonpolar)
GridCenter (class in apbs.input_file.calculate.finite_difference)
GridDimensions (class in apbs.input_file.calculate.finite_difference)
I
initial_mesh_resolution (apbs.input_file.calculate.finite_element.FiniteElement attribute)
initial_mesh_vertices (apbs.input_file.calculate.finite_element.FiniteElement attribute)
InputFile (class in apbs.input_file)
Ion (class in apbs.input_file.calculate.generic)
ion_accessibility_maps (apbs.input_file.read.Read attribute)
ions (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
L
lengths (apbs.input_file.calculate.finite_difference.GridDimensions attribute)
levels (apbs.input_file.calculate.finite_difference.GridDimensions attribute)
M
Manual (class in apbs.input_file.calculate.finite_difference)
Map (class in apbs.input_file.read)
maximum_particles (apbs.input_file.calculate.boundary_element.TABIParameters attribute)
maximum_refinement_iterations (apbs.input_file.calculate.finite_element.FiniteElement attribute)
maximum_vertices (apbs.input_file.calculate.finite_element.FiniteElement attribute)
mesh (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
Mesh (class in apbs.input_file.calculate.boundary_element)
MIN_LEVEL (in module apbs.input_file.calculate.finite_difference)
MobileIons (class in apbs.input_file.calculate.generic)
molecule (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_difference.GridCenter attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
Molecule (class in apbs.input_file.read)
molecule (in module apbs.input_file.calculate.nonpolar.Nonpolar)
molecules (apbs.input_file.read.Read attribute)
multipole_acceptance_criterion (apbs.input_file.calculate.boundary_element.TABIParameters attribute)
N
noop (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
O
Operation (class in apbs.input_file.process)
overlap_fraction (apbs.input_file.calculate.finite_difference.ParallelFocus attribute)
P
parallel (apbs.input_file.calculate.finite_difference.Focus attribute)
parallel_parameters (apbs.input_file.calculate.finite_difference.Focus attribute)
ParallelFocus (class in apbs.input_file.calculate.finite_difference)
Parameter (class in apbs.input_file.read)
parameters (apbs.input_file.calculate.Calculate attribute)
path (apbs.input_file.calculate.generic.WriteMap attribute)
(apbs.input_file.read.Map attribute)
(apbs.input_file.read.Molecule attribute)
(apbs.input_file.read.Parameter attribute)
paths (apbs.input_file.read.DielectricMapGroup attribute)
position (apbs.input_file.calculate.finite_difference.GridCenter attribute)
potential_maps (apbs.input_file.read.Read attribute)
pressure (in module apbs.input_file.calculate.nonpolar.Nonpolar)
Process (class in apbs.input_file.process)
processor_array (apbs.input_file.calculate.finite_difference.ParallelFocus attribute)
products (apbs.input_file.process.Process attribute)
property (apbs.input_file.calculate.generic.UseMap attribute)
(apbs.input_file.calculate.generic.WriteMap attribute)
R
radius (apbs.input_file.calculate.generic.Ion attribute)
Read (class in apbs.input_file.read)
S
software (apbs.input_file.calculate.boundary_element.Mesh attribute)
solute_dielectric (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
solvent_density (in module apbs.input_file.calculate.nonpolar.Nonpolar)
solvent_dielectric (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
solvent_radius (apbs.input_file.calculate.boundary_element.Mesh attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
(in module apbs.input_file.calculate.nonpolar.Nonpolar)
solver (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
solver_parameters (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
spacings (apbs.input_file.calculate.finite_difference.GridDimensions attribute)
species (apbs.input_file.calculate.generic.MobileIons attribute)
sums (apbs.input_file.process.Process attribute)
surface_density (apbs.input_file.calculate.boundary_element.Mesh attribute)
(in module apbs.input_file.calculate.nonpolar.Nonpolar)
surface_method (apbs.input_file.calculate.boundary_element.Mesh attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
(in module apbs.input_file.calculate.nonpolar.Nonpolar)
surface_spline_window (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
surface_tension (in module apbs.input_file.calculate.nonpolar.Nonpolar)
T
TABIParameters (class in apbs.input_file.calculate.boundary_element)
temperature (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
(in module apbs.input_file.calculate.nonpolar.Nonpolar)
to_dict() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
to_json() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
to_yaml() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
tree_order (apbs.input_file.calculate.boundary_element.TABIParameters attribute)
U
use_maps (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
UseMap (class in apbs.input_file.calculate.generic)
V
validate() (apbs.input_file.calculate.boundary_element.BoundaryElement method)
(apbs.input_file.InputFile method)
(apbs.input_file.calculate.Calculate method)
(apbs.input_file.calculate.boundary_element.Mesh method)
(apbs.input_file.calculate.boundary_element.TABIParameters method)
(apbs.input_file.calculate.finite_difference.FiniteDifference method)
(apbs.input_file.calculate.finite_difference.Focus method)
(apbs.input_file.calculate.finite_difference.GridCenter method)
(apbs.input_file.calculate.finite_difference.GridDimensions method)
(apbs.input_file.calculate.finite_difference.Manual method)
(apbs.input_file.calculate.finite_difference.ParallelFocus method)
(apbs.input_file.calculate.finite_element.FiniteElement method)
(apbs.input_file.calculate.generic.Ion method)
(apbs.input_file.calculate.generic.MobileIons method)
(apbs.input_file.calculate.generic.UseMap method)
(apbs.input_file.calculate.generic.WriteMap method)
(apbs.input_file.process.Element method)
(apbs.input_file.process.Operation method)
(apbs.input_file.process.Process method)
(apbs.input_file.read.DielectricMapGroup method)
(apbs.input_file.read.Map method)
(apbs.input_file.read.Molecule method)
(apbs.input_file.read.Parameter method)
(apbs.input_file.read.Read method)
W
write_atom_potentials (apbs.input_file.calculate.boundary_element.BoundaryElement attribute)
(apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
write_maps (apbs.input_file.calculate.finite_difference.FiniteDifference attribute)
(apbs.input_file.calculate.finite_element.FiniteElement attribute)
WriteMap (class in apbs.input_file.calculate.generic)
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