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Wolfram Language
MoleculeComplex
Guides
MoleculeComplex
Symbols
Packmol
FindCoordinationBonds
FindHydrogenBonds
MakeMolecule3D
MoleculeComplexAngle
MoleculeComplexAppend
MoleculeComplexDelete
MoleculeComplexDistance
MoleculeComplexEnergy
MoleculeComplexJoin
MoleculeComplex
MoleculeComplexOptimizeGeometry
MoleculeComplexPart
MoleculeComplexPlot3D
MoleculeComplexPosition
MoleculeComplexQ
MoleculeComplexToMolecule
Packmol
RandomRotationTransform
$MoleculeComplexVersion
MoleculeComplex
The
M
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is a symbolic representation of an ensemble of molecules in a common three-dimensional coordinate space.
MoleculeComplex Construction
M
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c
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C
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x
— a molecule complex specified by a list of molecules
P
a
c
k
m
o
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— use PACKMOL program to construct a molecule complex
M
o
l
e
c
u
l
e
C
o
m
p
l
e
x
T
o
M
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c
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e
— combine all the molecules in a molecule complex into a single molecule
M
a
k
e
M
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c
u
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e
3
D
▪
M
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C
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x
Q
MoleculeComplex Editing
M
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c
u
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C
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m
p
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x
A
p
p
e
n
d
— append a molecule to a molecule complex
M
o
l
e
c
u
l
e
C
o
m
p
l
e
x
D
e
l
e
t
e
— delete one or more molecules from a molecule complex
M
o
l
e
c
u
l
e
C
o
m
p
l
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x
J
o
i
n
— join a list of molecules to a molecule complex
M
o
l
e
c
u
l
e
C
o
m
p
l
e
x
P
a
r
t
— get one or more molecules from a molecule complex
M
o
l
e
c
u
l
e
C
o
m
p
l
e
x
P
o
s
i
t
i
o
n
— find index positions of molecules in a molecule complex
F
r
a
m
e
B
o
x
[
"
\
"
X
X
X
X
\
"
"
]
O
p
e
n
MoleculeComplex Visualization
M
o
l
e
c
u
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e
C
o
m
p
l
e
x
P
l
o
t
3
D
— 3D molecule complex rendering including hydrogen bonds
F
r
a
m
e
B
o
x
[
"
\
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X
X
X
X
\
"
"
]
O
p
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MoleculeComplex Energetics
M
o
l
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c
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e
C
o
m
p
l
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x
E
n
e
r
g
y
— compute the MMFF energy of a molecule complex including intermolecular interactions
M
o
l
e
c
u
l
e
C
o
m
p
l
e
x
O
p
t
i
m
i
z
e
G
e
o
m
e
t
r
y
— minimize the MMFF enegy of a molecule complex
F
r
a
m
e
B
o
x
[
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\
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X
X
X
X
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]
O
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n