PlotMolecule - Maple Help
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QuantumChemistry

 PlotMolecule
 plot molecule in 3D

 Calling Sequence PlotMolecule(molecule, options)

Parameters

 molecule - list of lists; each list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates options - (optional) equation(s) of the form option = value

Description

 • 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.

Examples

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

Define the molecule hydrogen fluoride

 >

Plot the molecule hydrogen fluoride

 ${\mathrm{molecule}}{≔}\left[\left[{"H"}{,}{0}{,}{0}{,}{-0.55000000}\right]{,}\left[{"F"}{,}{0}{,}{0}{,}{0.55000000}\right]\right]$ (1)
 >

Define the molecule TNT from MolecularData which obtains the geometry from a web database

 >
 ${\mathrm{tnt}}{≔}\left[\left[{"O"}{,}{0.54540000}{,}{-3.51400000}{,}{0.00120000}\right]{,}\left[{"O"}{,}{0.54950000}{,}{3.51370000}{,}{0.00080000}\right]{,}\left[{"O"}{,}{2.46770000}{,}{-2.45390000}{,}{-0.00050000}\right]{,}\left[{"O"}{,}{2.47050000}{,}{2.45130000}{,}{0.00030000}\right]{,}\left[{"O"}{,}{-3.59310000}{,}{-1.09590000}{,}{0.00040000}\right]{,}\left[{"O"}{,}{-3.59220000}{,}{1.09930000}{,}{0.00060000}\right]{,}\left[{"N"}{,}{1.21420000}{,}{-2.45400000}{,}{0.00020000}\right]{,}\left[{"N"}{,}{1.21700000}{,}{2.45270000}{,}{0}\right]{,}\left[{"N"}{,}{-2.98460000}{,}{0.00150000}{,}{0.00010000}\right]{,}\left[{"C"}{,}{1.22530000}{,}{-0.00060000}{,}{-0.00090000}\right]{,}\left[{"C"}{,}{0.52710000}{,}{-1.20820000}{,}{-0.00080000}\right]{,}\left[{"C"}{,}{0.52840000}{,}{1.20780000}{,}{-0.00080000}\right]{,}\left[{"C"}{,}{-1.56460000}{,}{0.00080000}{,}{-0.00040000}\right]{,}\left[{"C"}{,}{-0.86780000}{,}{-1.20740000}{,}{-0.00060000}\right]{,}\left[{"C"}{,}{-0.86660000}{,}{1.20840000}{,}{-0.00060000}\right]{,}\left[{"C"}{,}{2.72390000}{,}{-0.00160000}{,}{0.00110000}\right]{,}\left[{"H"}{,}{-1.41590000}{,}{-2.14680000}{,}{-0.00030000}\right]{,}\left[{"H"}{,}{-1.41370000}{,}{2.14830000}{,}{-0.00030000}\right]{,}\left[{"H"}{,}{3.12260000}{,}{0.24180000}{,}{-0.98910000}\right]{,}\left[{"H"}{,}{3.08630000}{,}{0.69340000}{,}{0.76620000}\right]{,}\left[{"H"}{,}{3.31540000}{,}{-0.81110000}{,}{0.41090000}\right]\right]$ (2)

Plot the molecule

 >

Define the molecule tylenol from MolecularData which obtains the geometry from a web database

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

Plot the molecule

 >

Number the atoms in tylenol

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

Remove the bond between atoms 3 and 4

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

Use the viewpoint keyword to make a fly-though animation for TNT

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