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ChemistryFunctions

Guides

  • Wolfram Chemistry Functions

Symbols

  • AtomSelector3D
  • AtomSelector
  • BohrModelPlot
  • ChemicalFormulaQ
  • ChemicalReactionQ
  • ConstitutionalIsomersQ
  • DiastereomersQ
  • EmbeddedMoleculeQ
  • EmpiricalFormula
  • EmptyMoleculeQ
  • EnantiomersQ
  • EpimersQ
  • FormatMoleculesAsGraphics
  • HydrocarbonQ
  • ImportComputationalChemistryData
  • IonCounts
  • MoleculeDelete
  • MoleculeGridPlot3D
  • MoleculeGridPlot
  • MoleculeJoin
  • MoleculeManipulate3D
  • MoleculeManipulate
  • MoleculeMirrorPlot3D
  • MoleculePatternQ
  • MoleculePlotOptions
  • MoleculeScaffold
  • MoleculeSubstructureMatches
  • PatternReactionQ
  • PeriodicTablePlot
  • RandomMolecule
  • RingMoleculeQ
  • RingPattern
  • SmilesPlot
  • StereoisomersQ
WolframChemistry`ChemistryFunctions`
EmbeddedMoleculeQ
​
EmbeddedMoleculeQ
[m]
returns
True
if
m
is a
Molecule
with specified three-dimensional coordinates.
​
​
EmbeddedMoleculeQ
[m,n]
returns
True
if
m
has specified n-dimensional coordinates.
​
Details and Options

Examples  
(2)
Basic Examples  
(2)
Most molecules from the Wolfram Knowledgebase have 3D coordinates:
In[1]:=
EmbeddedMoleculeQ
Molecule
water
CHEMICAL

Out[1]=
True
A molecule created from a string will not be automatically embedded:
In[2]:=
EmbeddedMoleculeQ
[Molecule["water"]]
Out[2]=
False
​
A molecule that was imported from a file may contain 3D coordinates:
In[1]:=
Import["ExampleData/caffeine.xyz"]
Out[1]=
Molecule
Formula:
C
8
H
10
N
4
O
2
Atoms: 24 Bonds: 25

In[2]:=
EmbeddedMoleculeQ
[%]
Out[2]=
True
Other files contain 2D instead of 3D coordinates:
In[3]:=
mol=Import["ExampleData/fluoxetine.mol"]
Out[3]=
Molecule
Formula:
C
17
H
18
F
3
NO
Atoms:
40
Bonds:
41

In[4]:=
EmbeddedMoleculeQ
[mol]
Out[4]=
False
In[5]:=
EmbeddedMoleculeQ
[mol,2]
Out[5]=
True
SeeAlso
MoleculeQ
 
▪
AtomCoordinates
 
▪
AtomDiagramCoordinates
RelatedGuides
▪
Wolfram Chemistry Functions
""

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