PlotMolecule - Maple Help

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, and bonds.  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.

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

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

 >
 >