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MoleculeComplex

Guides

  • MoleculeComplex

Symbols

  • Packmol
  • FindCoordinationBonds
  • FindHydrogenBonds
  • MakeMolecule3D
  • MoleculeComplexAngle
  • MoleculeComplexAppend
  • MoleculeComplexDelete
  • MoleculeComplexDistance
  • MoleculeComplexEnergy
  • MoleculeComplexJoin
  • MoleculeComplex
  • MoleculeComplexOptimizeGeometry
  • MoleculeComplexPart
  • MoleculeComplexPlot3D
  • MoleculeComplexPosition
  • MoleculeComplexQ
  • MoleculeComplexToMolecule
  • Packmol
  • RandomRotationTransform
  • $MoleculeComplexVersion
RobertNachbar`MoleculeComplex`
MoleculeComplexToMolecule
​
MoleculeComplexToMolecule
[mc]
returns a single molecule containing all the atoms, bonds, and atom coordinates of the molecules in the molecule complex.
​
​
MoleculeComplexToMolecule
[mc,
All
]
returns an association with keys
"Molecule"
,
"ToMoleculeMapping"
, and
"ToMoleculeComplexMapping"
.
​
Details and Options

Examples  
(4)
Basic Examples  
(1)
Define a molecule complex with three molecules:
In[1]:=
trimer=MoleculeComplex
Molecules: 3
Atoms: 12
;
In[2]:=
MoleculeComplexPlot3D
[%]
Out[2]=
Combine the molecules of the molecule complex into a single molecule:
In[3]:=
mol=
MoleculeComplexToMolecule
[trimer]
Out[3]=
Molecule
Formula: C
H
4
N
H
3
·
H
2
O
Atoms: 12 Bonds: 9

Count the number of connected molecule components:
In[4]:=
ConnectedMoleculeComponents[mol]//Length
Out[4]=
3
Visualize the molecule:
In[5]:=
MoleculePlot3D[mol]
Out[5]=
Scope  
(1)

Options  
(2)

SeeAlso
MoleculeComplex
 
▪
Molecule
RelatedGuides
▪
MoleculeComplex
""

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