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mbuild
Index
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Index
A
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B
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C
|
D
|
E
|
F
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G
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I
|
L
|
M
|
N
|
P
|
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
A
access_labels (mbuild.Port property)
add() (mbuild.Compound method)
add_bond() (mbuild.Compound method)
add_end_groups() (mbuild.lib.recipes.polymer.Polymer method)
add_monomer() (mbuild.lib.recipes.polymer.Polymer method)
all_ports() (mbuild.Compound method)
ancestors() (mbuild.Compound method)
angles (mbuild.Box property)
apply() (mbuild.pattern.Pattern method)
apply_to_compound() (mbuild.pattern.Pattern method)
available_ports() (mbuild.Compound method)
B
bonds() (mbuild.Compound method)
Box (class in mbuild)
box (mbuild.Compound property)
box_parameters (mbuild.Box property)
bravais_parameters (mbuild.Box property)
build() (mbuild.lib.recipes.polymer.Polymer method)
C
center (mbuild.Compound property)
(mbuild.Port property)
charge (mbuild.Compound property)
Compound (class in mbuild)
condense() (mbuild.Compound method)
contains_rigid (mbuild.Compound property)
create_hoomd_forcefield() (in module mbuild.formats.hoomd_forcefield)
create_hoomd_simulation() (in module mbuild.formats.hoomd_simulation)
create_periodic_bond() (mbuild.lib.recipes.polymer.Polymer method)
D
direct_bonds() (mbuild.Compound method)
direction (mbuild.Port property)
DiskPattern (class in mbuild.pattern)
E
element (mbuild.Compound property)
end_groups (mbuild.lib.recipes.polymer.Polymer property)
energy_minimize() (mbuild.Compound method)
F
fill_box() (in module mbuild.packing)
fill_region() (in module mbuild.packing)
fill_sphere() (in module mbuild.packing)
flatten() (mbuild.Compound method)
force_overlap() (in module mbuild.coordinate_transform)
freud_generate_bonds() (mbuild.Compound method)
from_gmso() (mbuild.Compound method)
from_lengths_angles() (mbuild.Box class method)
from_lengths_tilt_factors() (mbuild.Box class method)
from_lo_hi_tilt_factors() (mbuild.Box class method)
from_mins_maxs_angles() (mbuild.Box class method)
from_parmed() (mbuild.Compound method)
from_pybel() (mbuild.Compound method)
from_snapshot() (in module mbuild.formats.hoomd_snapshot)
from_trajectory() (mbuild.Compound method)
from_uvec_lengths() (mbuild.Box class method)
from_vectors() (mbuild.Box class method)
G
generate_bonds() (mbuild.Compound method)
get_boundingbox() (mbuild.Compound method)
get_smiles() (mbuild.Compound method)
Grid2DPattern (class in mbuild.pattern)
Grid3DPattern (class in mbuild.pattern)
I
is_independent() (mbuild.Compound method)
L
label_rigid_bodies() (mbuild.Compound method)
Lattice (class in mbuild)
lengths (mbuild.Box property)
Lx (mbuild.Box property)
Ly (mbuild.Box property)
Lz (mbuild.Box property)
M
mass (mbuild.Compound property)
max_rigid_id (mbuild.Compound property)
maxs (mbuild.Compound property)
mbuild.conversion.load
module
mbuild.formats.cassandramcf
module
mbuild.formats.gsdwriter
module
mbuild.formats.hoomd_forcefield
module
mbuild.formats.hoomd_simulation
module
mbuild.formats.hoomd_snapshot
module
mbuild.formats.lammpsdata
module
mbuild.lattice.load_cif
module
mbuild.packing
module
mbuild.pattern
module
min_periodic_distance() (mbuild.Compound method)
mins (mbuild.Compound property)
module
mbuild.conversion.load
mbuild.formats.cassandramcf
mbuild.formats.gsdwriter
mbuild.formats.hoomd_forcefield
mbuild.formats.hoomd_simulation
mbuild.formats.hoomd_snapshot
mbuild.formats.lammpsdata
mbuild.lattice.load_cif
mbuild.packing
mbuild.pattern
Monolayer (class in mbuild.lib.recipes.monolayer)
monomers (mbuild.lib.recipes.polymer.Polymer property)
N
n_bonds (mbuild.Compound property)
n_direct_bonds (mbuild.Compound property)
n_particles (mbuild.Compound property)
P
particles() (mbuild.Compound method)
particles_by_element() (mbuild.Compound method)
particles_by_name() (mbuild.Compound method)
particles_in_range() (mbuild.Compound method)
Pattern (class in mbuild.pattern)
periodicity (mbuild.Compound property)
Polymer (class in mbuild.lib.recipes.polymer)
populate() (mbuild.Lattice method)
Port (class in mbuild)
pos (mbuild.Compound property)
precision (mbuild.Box property)
print_hierarchy() (mbuild.Compound method)
R
Random2DPattern (class in mbuild.pattern)
Random3DPattern (class in mbuild.pattern)
referenced_ports() (mbuild.Compound method)
remove() (mbuild.Compound method)
remove_bond() (mbuild.Compound method)
rigid_id (mbuild.Compound property)
rigid_particles() (mbuild.Compound method)
root (mbuild.Compound property)
rotate() (in module mbuild.compound.Compound)
(mbuild.Compound method)
rotate_dihedral() (mbuild.Compound method)
S
save() (mbuild.Compound method)
scale() (mbuild.pattern.Pattern method)
separation (mbuild.Port property)
SilicaInterface (class in mbuild.lib.recipes.silica_interface)
solvate() (in module mbuild.packing)
SpherePattern (class in mbuild.pattern)
spin() (in module mbuild.compound.Compound)
(mbuild.Compound method)
successors() (mbuild.Compound method)
T
TiledCompound (class in mbuild.lib.recipes.tiled_compound)
tilt_factors (mbuild.Box property)
to_gmso() (mbuild.Compound method)
to_hoomdsnapshot() (in module mbuild.formats.hoomd_snapshot)
to_intermol() (mbuild.Compound method)
to_networkx() (mbuild.Compound method)
to_parmed() (mbuild.Compound method)
to_pybel() (mbuild.Compound method)
to_rdkit() (mbuild.Compound method)
to_smiles() (mbuild.Compound method)
to_trajectory() (mbuild.Compound method)
translate() (in module mbuild.compound.Compound)
(mbuild.Compound method)
translate_to() (in module mbuild.compound.Compound)
(mbuild.Compound method)
Triangle2DPattern (class in mbuild.pattern)
U
unlabel_rigid_bodies() (mbuild.Compound method)
update_coordinates() (mbuild.Compound method)
update_orientation() (mbuild.Port method)
update_separation() (mbuild.Port method)
V
vectors (mbuild.Box property)
visualize() (mbuild.Compound method)
W
write_gsd() (in module mbuild.formats.gsdwriter)
write_lammpsdata() (in module mbuild.formats.lammpsdata)
write_mcf() (in module mbuild.formats.cassandramcf)
X
x_axis_transform() (in module mbuild.coordinate_transform)
xy (mbuild.Box property)
xyz (mbuild.Compound property)
xyz_with_ports (mbuild.Compound property)
xz (mbuild.Box property)
Y
y_axis_transform() (in module mbuild.coordinate_transform)
yz (mbuild.Box property)
Z
z_axis_transform() (in module mbuild.coordinate_transform)
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