PoreMS
0.2
API
Molecule
Pore
Workflow
Site
Page
Index
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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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J
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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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X
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Y
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Z
_
__repr__() (porems.atom.Atom method)
(porems.molecule.Molecule method)
__str__() (porems.molecule.Molecule method)
_back() (porems.dice.Dice method)
_block() (porems.pattern.Pattern method)
_bot() (porems.dice.Dice method)
_box_size() (porems.molecule.Molecule method)
_concat() (porems.molecule.Molecule method)
_fill() (porems.dice.Dice method)
_front() (porems.dice.Dice method)
_hexagonal() (porems.pattern.BetaCristobalit method)
_left() (porems.dice.Dice method)
_normal_ex() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
_normal_in() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
_orientation() (porems.pattern.Pattern method)
_pos_to_index() (porems.dice.Dice method)
_read() (porems.molecule.Molecule method)
_right() (porems.dice.Dice method)
_siloxane() (porems.system.PoreSystem method)
_split() (porems.dice.Dice method)
_step() (porems.dice.Dice method)
_table_base() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
_temp() (porems.molecule.Molecule method)
_top() (porems.dice.Dice method)
_vector() (porems.molecule.Molecule method)
A
add() (porems.matrix.Matrix method)
(porems.molecule.Molecule method)
alcohol() (in module porems.generic)
alkane() (in module porems.generic)
allocation() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
amorph() (porems.pore.Pore method)
angle() (in module porems.geometry)
angle_azi() (in module porems.geometry)
angle_polar() (in module porems.geometry)
append() (porems.molecule.Molecule method)
Atom (class in porems.atom)
attach() (porems.pore.Pore method)
(porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
attach_special() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
B
BetaCristobalit (class in porems.pattern)
bond() (porems.molecule.Molecule method)
bound() (porems.matrix.Matrix method)
box() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
C
centroid() (porems.molecule.Molecule method)
(porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
column() (in module porems.utils)
column_pos() (porems.molecule.Molecule method)
com() (porems.molecule.Molecule method)
convert() (porems.shape.Shape method)
copy() (in module porems.utils)
cross_product() (in module porems.geometry)
Cuboid (class in porems.shape)
Cylinder (class in porems.shape)
D
d_Phi_phi() (porems.shape.Cylinder method)
(porems.shape.Sphere method)
d_Phi_theta() (porems.shape.Sphere method)
d_Phi_z() (porems.shape.Cylinder method)
delete() (porems.molecule.Molecule method)
diameter() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
Dice (class in porems.dice)
dot_product() (in module porems.geometry)
E
exterior() (porems.pore.Pore method)
F
fill_sites() (porems.pore.Pore method)
finalize() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
find_bond() (porems.dice.Dice method)
find_parallel() (porems.dice.Dice method)
G
generate() (porems.pattern.Pattern method)
get_atom_list() (porems.molecule.Molecule method)
get_atom_type() (porems.atom.Atom method)
(porems.molecule.Molecule method)
get_block() (porems.pattern.Pattern method)
(porems.pore.Pore method)
get_box() (porems.molecule.Molecule method)
(porems.pore.Pore method)
get_charge() (porems.molecule.Molecule method)
get_count() (porems.dice.Dice method)
get_gap() (porems.pattern.Pattern method)
get_mass() (in module porems.database)
(porems.molecule.Molecule method)
get_masses() (porems.molecule.Molecule method)
get_matrix() (porems.matrix.Matrix method)
get_mol() (porems.dice.Dice method)
get_mol_dict() (porems.pore.Pore method)
get_name() (porems.atom.Atom method)
(porems.molecule.Molecule method)
(porems.pore.Pore method)
get_num() (porems.molecule.Molecule method)
get_num_in_ex() (porems.pore.Pore method)
get_orient() (porems.pattern.Pattern method)
get_origin() (porems.dice.Dice method)
get_pointer() (porems.dice.Dice method)
get_pos() (porems.atom.Atom method)
get_repeat() (porems.pattern.Pattern method)
get_residue() (porems.atom.Atom method)
get_short() (porems.molecule.Molecule method)
get_site_dict() (porems.pore.Pore method)
get_sites() (porems.pore.Pore method)
get_size() (porems.dice.Dice method)
(porems.pattern.Pattern method)
grid() (porems.store.Store method)
gro() (porems.store.Store method)
H
height() (porems.system.PoreSlit method)
I
is_in() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
J
job() (porems.store.Store method)
K
ketone() (in module porems.generic)
L
length() (in module porems.geometry)
lmp() (porems.store.Store method)
load() (in module porems.utils)
M
main_axis() (in module porems.geometry)
Matrix (class in porems.matrix)
mkdirp() (in module porems.utils)
mmol_g_to_mumol_m2() (in module porems.utils)
mmol_l_to_mols() (in module porems.utils)
Molecule (class in porems.molecule)
mols_to_mmol_l() (in module porems.utils)
mols_to_mumol_m2() (in module porems.utils)
move() (porems.molecule.Molecule method)
mumol_m2_to_mols() (in module porems.utils)
N
neighbor() (porems.dice.Dice method)
normal() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
O
obj() (porems.store.Store method)
objectify() (porems.pore.Pore method)
overlap() (porems.molecule.Molecule method)
P
part_angle() (porems.molecule.Molecule method)
part_move() (porems.molecule.Molecule method)
part_rotate() (porems.molecule.Molecule method)
Pattern (class in porems.pattern)
pattern() (porems.pattern.BetaCristobalit method)
pdb() (porems.store.Store method)
Phi() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
plot() (porems.shape.Shape method)
Pore (class in porems.pore)
PoreAmorphCylinder (class in porems.system)
PoreCapsule (class in porems.system)
PoreCylinder (class in porems.system)
porems.database (module)
porems.generic (module)
porems.geometry (module)
porems.utils (module)
PoreSlit (class in porems.system)
PoreSystem (class in porems.system)
pos() (porems.molecule.Molecule method)
prepare() (porems.pore.Pore method)
put() (porems.molecule.Molecule method)
R
replace() (in module porems.utils)
reservoir() (porems.pore.Pore method)
(porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
rim() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
rotate() (in module porems.geometry)
(porems.molecule.Molecule method)
roughness() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
S
save() (in module porems.utils)
set_atom_name() (porems.molecule.Molecule method)
set_atom_residue() (porems.molecule.Molecule method)
set_atom_type() (porems.atom.Atom method)
(porems.molecule.Molecule method)
set_box() (porems.molecule.Molecule method)
(porems.pore.Pore method)
set_charge() (porems.molecule.Molecule method)
set_mass() (porems.molecule.Molecule method)
set_masses() (porems.molecule.Molecule method)
set_name() (porems.atom.Atom method)
(porems.molecule.Molecule method)
(porems.pore.Pore method)
set_pbc() (porems.dice.Dice method)
set_pos() (porems.atom.Atom method)
set_residue() (porems.atom.Atom method)
set_short() (porems.molecule.Molecule method)
Shape (class in porems.shape)
shape() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
silanol() (in module porems.generic)
siloxane() (porems.pore.Pore method)
sites() (porems.pore.Pore method)
Sphere (class in porems.shape)
split() (porems.matrix.Matrix method)
Store (class in porems.store)
store() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
strip() (porems.matrix.Matrix method)
surf() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
surface() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
(porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
switch_atom_order() (porems.molecule.Molecule method)
T
table() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
tic() (in module porems.utils)
tms() (in module porems.generic)
toc() (in module porems.utils)
top() (porems.store.Store method)
translate() (porems.molecule.Molecule method)
U
unit() (in module porems.geometry)
V
vector() (in module porems.geometry)
volume() (porems.shape.Cuboid method)
(porems.shape.Cylinder method)
(porems.shape.Sphere method)
(porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
X
xyz() (porems.store.Store method)
Y
yml() (porems.system.PoreAmorphCylinder method)
(porems.system.PoreCapsule method)
(porems.system.PoreCylinder method)
(porems.system.PoreSlit method)
(porems.system.PoreSystem method)
Z
zero() (porems.molecule.Molecule method)