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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`
MoleculeComplex
​
MoleculeComplex
[{
mol
1
,
mol
2
,…}]
returns a
MoleculeComplex
given a list of molecules. The molecules must have three-dimensional coordinates.
​
​
MoleculeComplex
[
key
1

mol
1
,
key
2

mol
2
,…]
returns a
MoleculeComplex
given an association of molecules.
​
​
MoleculeComplex
[…][prop]
returns the property
prop
of the molecule complex.
​
Details and Options

Examples  
(4)
Basic Examples  
(2)
Build a molecule complex from a list of a water molecule and an ammonia molecule:
In[1]:=
waterAmmoniaDimer=
MoleculeComplex
Molecule
water
CHEMICAL
,MoleculeModifyMolecule
ammonia
CHEMICAL
,{"TransformAtomCoordinates",TranslationTransform[{3,0,0}]}
Out[1]=
MoleculeComplex
Molecules: 2
Atoms: 7

Visualize the molecule complex:
In[2]:=
MoleculeComplexPlot3D
[waterAmmoniaDimer,"IncludeHydrogenBonds"All,"MoleculeLabels"Automatic]
Out[2]=
​
Build a molecule complex from an association of a water molecule and an ammonia molecule:
In[1]:=
waterAmmoniaDimer=
MoleculeComplex
"water"Molecule
water
CHEMICAL
,"ammonia"MoleculeModifyMolecule
ammonia
CHEMICAL
,{"TransformAtomCoordinates",TranslationTransform[{3,0,0}]}
Out[1]=
MoleculeComplex
Molecules: 2
Atoms: 7

Visualize the molecule complex:
In[2]:=
MoleculeComplexPlot3D
[waterAmmoniaDimer,"IncludeHydrogenBonds"All,"MoleculeLabels"Automatic]
Out[2]=
Scope  
(1)

Generalizations & Extensions  
(1)

SeeAlso
Molecule
 
▪
MoleculeValue
RelatedGuides
▪
MoleculeComplex
""

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