PlotMolecule(molecule, options) returns a 3D Maple plot of the molecules.  The molecule can be fully rotated.

The options available are model, units, bonds, addbonds, removebonds, numberatoms, and viewpoint.  

The value of model is either the string "ballandstick" (default) or "spacefilling".   

The value of units is either the string "Angstrom" (default) or "Bohr".   

The value of bonds can be a set of sets where each set contains two integers denoting the atoms to be connected by a chemical bond.  The integers correspond to the positions of the atoms in molecule.  If the optional keyword bonds is not set, the bonds to be shown are determined automatically.  

Automatic bonds can also be modified with addbonds  and/or removebonds.  The keywords addbonds and removebonds can be a set of sets where each set contains two integers denoting atoms between which a chemical bond should be added or removed, respectively.  

 The keyword viewpoint generates a molecular fly-through animation.  It can be set to one of the following strings "flythrough", "flythrough2", "flythrough3", "flythrough4", "circleleft", and "circleright".  It can also be set to a custom fly-through animation as described on the help page for viewpoint.

$\mathrm{with}\left(\mathrm{QuantumChemistry}\right)\:$

$\mathrm{molecule} ≔ \left[ \left[''H''\, 0\, 0\, -0.55\right]\, \left[''F''\, 0\, 0\, \+0.55\right] \right]\;$

$\mathrm{molecule}≔\left[\left[''H''\,0\,0\,\mathrm{-0.55000000}\right]\,\left[''F''\,0\,0\,0.55000000\right]\right]$

$\mathrm{PlotMolecule}\left(\mathrm{molecule}\right)\;$

$\mathrm{tnt}≔ \mathrm{MolecularData}\left(''TNT''\,''geometry3d''\right)\;$

$\mathrm{tnt}≔\left[\left[''O''\,0.54540000\,\mathrm{-3.51400000}\,0.00120000\right]\,\left[''O''\,0.54950000\,3.51370000\,0.00080000\right]\,\left[''O''\,2.46770000\,\mathrm{-2.45390000}\,\mathrm{-0.00050000}\right]\,\left[''O''\,2.47050000\,2.45130000\,0.00030000\right]\,\left[''O''\,\mathrm{-3.59310000}\,\mathrm{-1.09590000}\,0.00040000\right]\,\left[''O''\,\mathrm{-3.59220000}\,1.09930000\,0.00060000\right]\,\left[''N''\,1.21420000\,\mathrm{-2.45400000}\,0.00020000\right]\,\left[''N''\,1.21700000\,2.45270000\,0\right]\,\left[''N''\,\mathrm{-2.98460000}\,0.00150000\,0.00010000\right]\,\left[''C''\,1.22530000\,\mathrm{-0.00060000}\,\mathrm{-0.00090000}\right]\,\left[''C''\,0.52710000\,\mathrm{-1.20820000}\,\mathrm{-0.00080000}\right]\,\left[''C''\,0.52840000\,1.20780000\,\mathrm{-0.00080000}\right]\,\left[''C''\,\mathrm{-1.56460000}\,0.00080000\,\mathrm{-0.00040000}\right]\,\left[''C''\,\mathrm{-0.86780000}\,\mathrm{-1.20740000}\,\mathrm{-0.00060000}\right]\,\left[''C''\,\mathrm{-0.86660000}\,1.20840000\,\mathrm{-0.00060000}\right]\,\left[''C''\,2.72390000\,\mathrm{-0.00160000}\,0.00110000\right]\,\left[''H''\,\mathrm{-1.41590000}\,\mathrm{-2.14680000}\,\mathrm{-0.00030000}\right]\,\left[''H''\,\mathrm{-1.41370000}\,2.14830000\,\mathrm{-0.00030000}\right]\,\left[''H''\,3.12260000\,0.24180000\,\mathrm{-0.98910000}\right]\,\left[''H''\,3.08630000\,0.69340000\,0.76620000\right]\,\left[''H''\,3.31540000\,\mathrm{-0.81110000}\,0.41090000\right]\right]$

$\mathrm{PlotMolecule}\left(\mathrm{tnt}\right)\;$

$\mathrm{molecule}\,\mathrm{bonding} ≔ \mathrm{MolecularData}\left(''tylenol''\,''geometry3d''\, \mathrm{returnbonds}\=\mathrm{true}\right)\;$

$\mathrm{molecule},\mathrm{bonding}≔\left[\left[''O''\,3.85090000\,0.45160000\,0.00120000\right]\,\left[''O''\,\mathrm{-2.59990000}\,1.40410000\,\mathrm{-0.00180000}\right]\,\left[''N''\,\mathrm{-1.57050000}\,\mathrm{-0.71710000}\,0.00010000\right]\,\left[''C''\,\mathrm{-0.20660000}\,\mathrm{-0.42310000}\,\mathrm{-0.00020000}\right]\,\left[''C''\,0.22050000\,0.90470000\,0.00040000\right]\,\left[''C''\,0.72980000\,\mathrm{-1.45700000}\,\mathrm{-0.00070000}\right]\,\left[''C''\,1.58410000\,1.19860000\,0.00020000\right]\,\left[''C''\,2.09330000\,\mathrm{-1.16290000}\,\mathrm{-0.00070000}\right]\,\left[''C''\,2.52040000\,0.16480000\,\mathrm{-0.00030000}\right]\,\left[''C''\,\mathrm{-2.64850000}\,0.17820000\,0.00090000\right]\,\left[''C''\,\mathrm{-3.97350000}\,\mathrm{-0.54200000}\,0.00100000\right]\,\left[''H''\,\mathrm{-0.44360000}\,1.75770000\,0.00120000\right]\,\left[''H''\,0.41130000\,\mathrm{-2.49630000}\,\mathrm{-0.00100000}\right]\,\left[''H''\,\mathrm{-1.80100000}\,\mathrm{-1.70860000}\,0.00010000\right]\,\left[''H''\,1.90530000\,2.23700000\,0.00090000\right]\,\left[''H''\,2.81800000\,\mathrm{-1.97260000}\,\mathrm{-0.00080000}\right]\,\left[''H''\,\mathrm{-4.06550000}\,\mathrm{-1.14630000}\,\mathrm{-0.90580000}\right]\,\left[''H''\,\mathrm{-4.79040000}\,0.18440000\,0.02880000\right]\,\left[''H''\,\mathrm{-4.04450000}\,\mathrm{-1.18860000}\,0.88020000\right]\,\left[''H''\,3.96500000\,1.41760000\,0.00170000\right]\right],\left\{\left\{1\,9\right\}\,\left\{1\,20\right\}\,\left\{2\,10\right\}\,\left\{3\,4\right\}\,\left\{3\,10\right\}\,\left\{3\,14\right\}\,\left\{4\,5\right\}\,\left\{4\,6\right\}\,\left\{5\,7\right\}\,\left\{5\,12\right\}\,\left\{6\,8\right\}\,\left\{6\,13\right\}\,\left\{7\,9\right\}\,\left\{7\,15\right\}\,\left\{8\,9\right\}\,\left\{8\,16\right\}\,\left\{10\,11\right\}\,\left\{11\,17\right\}\,\left\{11\,18\right\}\,\left\{11\,19\right\}\right\}$

$\mathrm{PlotMolecule}\left(\mathrm{molecule}\, \'\mathrm{bonds}\'\=\mathrm{bonding}\right)\;$

$\mathrm{PlotMolecule}\left(\mathrm{molecule}\,\mathrm{numberatoms}\=\mathrm{true}\right)\;$

$\mathrm{PlotMolecule}\left(\mathrm{molecule}\,\mathrm{removebonds}\=\left\{\left\{3\,10\right\}\right\}\right)\;$

$\mathrm{PlotMolecule}\left(\mathrm{tnt}\, \mathrm{viewpoint}\=''flythrough3''\right)\;$