Once you have opened a Maxima session, load package draw and then set global variable draw_renderer to vtk:
load("draw") $
draw_renderer: 'vtk $
We define here a short script for drawing molecules. The function has four arguments: the names of the atoms, together with their coordinates, the bonds to be plotted, the colors and radius of the atoms, and color and width of the bonds:
molecule(atoms, bonds, adesign, ldesign) :=
block([col, siz],
local(col, siz),
for k in adesign do (
col[first(k)]: second(k),
siz[first(k)]: third(k)),
[ /* bonds */
color = first(ldesign),
line_width = second(ldesign),
line_type = tube,
point_size = 0,
points_joined = true,
makelist(points(makelist(rest(atoms[k[m]]),
m,1,length(k))),
k, bonds),
points_joined = false,
/* atoms */
points_joined = false,
point_type = sphere,
makelist([color = col[first(k)],
point_size = siz[first(k)],
points([rest(k)])], k, atoms)] ) $
And now let's play with it. This first example is the methane. See the syntax for the atoms, bonds, and atoms and bonds plotting styles. Coordinates are in Angstrom:
methane_atoms: [
[O,0.000000,0.000000,0.000000],
[H,0.000000,0.000000,1.089000],
[H,1.026719,0.000000,-0.363000],
[H,-0.513360,-0.889165,-0.363000],
[H,-0.513360,0.889165,-0.363000]] $
methane_bonds: [[1,2], [1,3], [1,4], [1,5]] $
atoms_style: [[O,green,1], [H,white,1/2]] $
bonds_style: [red, 1/10] $
draw3d(molecule(methane_atoms, methane_bonds, atoms_style, bonds_style)) $
A molecule of water. We don't use bonds here (empty list), but atoms radii are now larger:
water_atoms: [
[O,0.000000, 0.000000, 0.114079],
[H,0.000000, 0.780362, -0.456316],
[H,0.000000, -0.780362, -0.456316] ] $
water_bonds: [] $
atoms_style: [[O,navy,2.4], [H,white,1.5]] $
bonds_style: [red, 0.1] $
draw3d(molecule(water_atoms, water_bonds, atoms_style, bonds_style) )$
Two atoms of methanol in a multiplot, with and without bonds:
methanol_atoms: [
[C,0.7333,0.0115,0.0000],
[O,-0.6955,-0.0656,0.0000],
[H,1.0934,0.5490,0.9107],
[H,1.0934,0.5490,-0.9107],
[H,1.1599,-1.0124,0.0000],
[H,-1.0408,0.8175,0.0000] ] $
methanol_bonds: [[1,2], [1,3], [1,4], [1,5], [2,6]] $
atoms_style: [[C,green,1], [O,red,3/4], [H,white,1/2]] $
bonds_style: [blue, 0.18] $
draw(
dimensions = [300, 600],
gr3d(background_color = gray50,
molecule(methanol_atoms, methanol_bonds, atoms_style, bonds_style)),
gr3d(background_color = orange,
molecule(methanol_atoms, [], atoms_style, bonds_style)))$
Boron trifluoride and benzene in one plot:
/* Boron trifluoride */
boron_trifluoride_atoms: [
[B,3.0,3.0,3.0],
[F,4.33,3.0,3.0],
[F,2.335,4.152,3.0],
[F,2.335,1.848,3.0] ] $
boron_trifluoride_links: [] $
boron_trifluoride_atoms_style: [[B,green,1], [F,cyan,1/2]] $
boron_trifluoride_links_style: [red, 0.2] $
/* Benzene */
benzene_atoms: [
[C,0.00000,1.40272,0.00000],
[H,0.00000,2.49029,0.00000],
[C,-1.21479,0.70136,0.00000],
[H,-2.15666,1.24515,0.00000],
[C,-1.21479,-0.70136,0.00000],
[H,-2.15666,-1.24515,0.00000],
[C,0.00000,-1.40272,0.00000],
[H,0.00000,-2.49029,0.00000],
[C,1.21479,-0.70136,0.00000],
[H,2.15666,-1.24515,0.00000],
[C,1.21479,0.70136,0.00000],
[H,2.15666,1.24515,0.00000] ] $
benzene_links: [[1,3,5,7,9,11,1], [1,2], [3,4],
[5,6], [7,8], [9,10], [11,12]] $
benzene_atoms_style: [[C,orange,1], [H,white,1/2]] $
benzene_links_style: [red, 0.15] $
draw3d(
molecule(benzene_atoms,
benzene_links,
benzene_atoms_style,
benzene_links_style),
molecule(boron_trifluoride_atoms,
boron_trifluoride_links,
boron_trifluoride_atoms_style,
boron_trifluoride_links_style) )$
Caffeine. Here we plot a partial number of bonds:
caffeine_atoms:
[[C, -1.799, 0.022, 0.602],
[N, -1.586, -0.945, -0.363],
[C, -2.731, -1.654, -0.954],
[C, -0.301, -1.248, -0.776],
[C, 0.789, -0.574, -0.214],
[C, 0.563, 0.404, 0.763],
[N, -0.728, 0.694, 1.163],
[C, -0.964, 1.720, 2.189],
[N, 1.752, 0.896, 1.139],
[C, 2.729, 0.287, 0.454],
[N, 2.158, -0.638, -0.400],
[C, 2.871, -1.524, -1.331],
[O, -0.101, -2.186, -1.712],
[O, -3.048, 0.309, 0.996],
[H, 3.786, 0.485, 0.553],
[H, -2.947, -2.544, -0.368],
[H, -2.491, -1.941, -1.976],
[H, -3.601, -1.000, -0.955],
[H, -1.088, 2.689, 1.711],
[H, -0.114, 1.756, 2.868],
[H, -1.864, 1.473, 2.748],
[H, 2.981, -1.026, -2.293],
[H, 2.305, -2.444, -1.462],
[H, 3.855, -1.757, -0.929]] $
caffeine_bonds: [
[1,2], [1,7], [1,14],
[2,3], [2,4],
/* [3,16], [3,17], [3,18],
[4,5], [4,13],
[5,6], [5,11],
[6,7], [6,9],
[7,8],
[8,19], [8,20], [8,21], */
[9,10],
[10,11], [10,15],
[11,12],
[12,22], [12,23], [12,24] ] $
atoms_style: [[C,green,1], [N,brown,1/2], [O,yellow,3/4], [H,black,1/3]] $
bonds_style: [cyan, 0.01] $
draw3d(
axis_3d = false,
molecule(caffeine_atoms, caffeine_bonds, atoms_style,bonds_style) )$
Nanotube. Screenshots from different positions:
nt_atoms: [[H, 3.7887837463, 1.2310504983, -6.8241051525], [H, 2.3415971110, 3.2229319842, -6.8241051525], [H, -0.0000000327, 3.9837629956, -6.8241051525], [H, -2.3415971639, 3.2229319458, -6.8241051525], [H, -3.7887837665, 1.2310504361, -6.8241051525], [H, -3.7887837463, -1.2310504983, -6.8241051525], [H, -2.3415971110, -3.2229319842, -6.8241051525], [H, 0.0000000327, -3.9837629956, -6.8241051525], [H, 2.3415971639, -3.2229319458, -6.8241051525], [H, 3.7887837665, -1.2310504361, -6.8241051525], [C, 3.8076800766, 1.2371902884, -5.7281027302], [C, 2.3532756853, 3.2390061631, -5.7281027302], [C, -0.0000000329, 4.0036317732, -5.7281027302], [C, -2.3532757385, 3.2390061244, -5.7281027302], [C, -3.8076800969, 1.2371902259, -5.7281027302], [C, -3.8076800766, -1.2371902884, -5.7281027302], [C, -2.3532756853, -3.2390061631, -5.7281027302], [C, 0.0000000329, -4.0036317732, -5.7281027302], [C, 2.3532757385, -3.2390061244, -5.7281027302], [C, 3.8076800969, -1.2371902259, -5.7281027302], [C, 3.9865457289, 0.0000000327, -5.0377225142], [C, 3.2251832243, 2.3432328135, -5.0377225142], [C, 1.2319103479, 3.7914303031, -5.0377225142], [C, -1.2319104102, 3.7914302828, -5.0377225142], [C, -3.2251832627, 2.3432327605, -5.0377225142], [C, -3.9865457289, -0.0000000327, -5.0377225142], [C, -3.2251832243, -2.3432328135, -5.0377225142], [C, -1.2319103479, -3.7914303031, -5.0377225142], [C, 1.2319104102, -3.7914302828, -5.0377225142], [C, 3.2251832627, -2.3432327605, -5.0377225142], [C, 3.9845747152, 0.0000000327, -3.5890478179], [C, 3.2235886408, 2.3420742807, -3.5890478179], [C, 1.2313012713, 3.7895557577, -3.5890478179], [C, -1.2313013335, 3.7895557375, -3.5890478179], [C, -3.2235886792, 2.3420742278, -3.5890478179], [C, -3.9845747152, -0.0000000327, -3.5890478179], [C, -3.2235886408, -2.3420742807, -3.5890478179], [C, -1.2313012713, -3.7895557577, -3.5890478179], [C, 1.2313013335, -3.7895557375, -3.5890478179], [C, 3.2235886792, -2.3420742278, -3.5890478179], [C, 3.7886931714, 1.2310210688, -2.8732875320], [C, 2.3415411327, 3.2228549367, -2.8732875320], [C, -0.0000000327, 3.9836677596, -2.8732875320], [C, -2.3415411856, 3.2228548982, -2.8732875320], [C, -3.7886931916, 1.2310210066, -2.8732875320], [C, -3.7886931714, -1.2310210688, -2.8732875320], [C, -2.3415411327, -3.2228549367, -2.8732875320], [C, 0.0000000327, -3.9836677596, -2.8732875320], [C, 2.3415411856, -3.2228548982, -2.8732875320], [C, 3.7886931916, -1.2310210066, -2.8732875320], [C, 3.7912985860, 1.2318676193, -1.4355100990], [C, 2.3431513674, 3.2250712347, -1.4355100990], [C, -0.0000000327, 3.9864072546, -1.4355100990], [C, -2.3431514204, 3.2250711962, -1.4355100990], [C, -3.7912986062, 1.2318675571, -1.4355100990], [C, -3.7912985860, -1.2318676193, -1.4355100990], [C, -2.3431513674, -3.2250712347, -1.4355100990], [C, 0.0000000327, -3.9864072546, -1.4355100990], [C, 2.3431514204, -3.2250711962, -1.4355100990], [C, 3.7912986062, -1.2318675571, -1.4355100990], [C, 3.9873938658, 0.0000000327, -0.7180431612], [C, 3.2258693815, 2.3437313359, -0.7180431612], [C, 1.2321724367, 3.7922369292, -0.7180431612], [C, -1.2321724989, 3.7922369090, -0.7180431612], [C, -3.2258694200, 2.3437312829, -0.7180431612], [C, -3.9873938658, -0.0000000327, -0.7180431612], [C, -3.2258693815, -2.3437313359, -0.7180431612], [C, -1.2321724367, -3.7922369292, -0.7180431612], [C, 1.2321724989, -3.7922369090, -0.7180431612], [C, 3.2258694200, -2.3437312829, -0.7180431612], [C, 3.9873938658, 0.0000000327, 0.7180431612], [C, 3.2258693815, 2.3437313359, 0.7180431612], [C, 1.2321724367, 3.7922369292, 0.7180431612], [C, -1.2321724989, 3.7922369090, 0.7180431612], [C, -3.2258694200, 2.3437312829, 0.7180431612], [C, -3.9873938658, -0.0000000327, 0.7180431612], [C, -3.2258693815, -2.3437313359, 0.7180431612], [C, -1.2321724367, -3.7922369292, 0.7180431612], [C, 1.2321724989, -3.7922369090, 0.7180431612], [C, 3.2258694200, -2.3437312829, 0.7180431612], [C, 3.7912985860, 1.2318676193, 1.4355100990], [C, 2.3431513674, 3.2250712347, 1.4355100990], [C, -0.0000000327, 3.9864072546, 1.4355100990], [C, -2.3431514204, 3.2250711962, 1.4355100990], [C, -3.7912986062, 1.2318675571, 1.4355100990], [C, -3.7912985860, -1.2318676193, 1.4355100990], [C, -2.3431513674, -3.2250712347, 1.4355100990], [C, 0.0000000327, -3.9864072546, 1.4355100990], [C, 2.3431514204, -3.2250711962, 1.4355100990], [C, 3.7912986062, -1.2318675571, 1.4355100990], [C, 3.7886931714, 1.2310210688, 2.8732875320], [C, 2.3415411327, 3.2228549367, 2.8732875320], [C, -0.0000000327, 3.9836677596, 2.8732875320], [C, -2.3415411856, 3.2228548982, 2.8732875320], [C, -3.7886931916, 1.2310210066, 2.8732875320], [C, -3.7886931714, -1.2310210688, 2.8732875320], [C, -2.3415411327, -3.2228549367, 2.8732875320], [C, 0.0000000327, -3.9836677596, 2.8732875320], [C, 2.3415411856, -3.2228548982, 2.8732875320], [C, 3.7886931916, -1.2310210066, 2.8732875320], [C, 3.9845747152, 0.0000000327, 3.5890478179], [C, 3.2235886408, 2.3420742807, 3.5890478179], [C, 1.2313012713, 3.7895557577, 3.5890478179], [C, -1.2313013335, 3.7895557375, 3.5890478179], [C, -3.2235886792, 2.3420742278, 3.5890478179], [C, -3.9845747152, -0.0000000327, 3.5890478179], [C, -3.2235886408, -2.3420742807, 3.5890478179], [C, -1.2313012713, -3.7895557577, 3.5890478179], [C, 1.2313013335, -3.7895557375, 3.5890478179], [C, 3.2235886792, -2.3420742278, 3.5890478179], [C, 3.9865457289, 0.0000000327, 5.0377225142], [C, 3.2251832243, 2.3432328135, 5.0377225142], [C, 1.2319103479, 3.7914303031, 5.0377225142], [C, -1.2319104102, 3.7914302828, 5.0377225142], [C, -3.2251832627, 2.3432327605, 5.0377225142], [C, -3.9865457289, -0.0000000327, 5.0377225142], [C, -3.2251832243, -2.3432328135, 5.0377225142], [C, -1.2319103479, -3.7914303031, 5.0377225142], [C, 1.2319104102, -3.7914302828, 5.0377225142], [C, 3.2251832627, -2.3432327605, 5.0377225142], [C, 3.8076800766, 1.2371902884, 5.7281027302], [C, 2.3532756853, 3.2390061631, 5.7281027302], [C, -0.0000000329, 4.0036317732, 5.7281027302], [C, -2.3532757385, 3.2390061244, 5.7281027302], [C, -3.8076800969, 1.2371902259, 5.7281027302], [C, -3.8076800766, -1.2371902884, 5.7281027302], [C, -2.3532756853, -3.2390061631, 5.7281027302], [C, 0.0000000329, -4.0036317732, 5.7281027302], [C, 2.3532757385, -3.2390061244, 5.7281027302], [C, 3.8076800969, -1.2371902259, 5.7281027302], [H, 3.7887837463, 1.2310504983, 6.8241051525], [H, 2.3415971110, 3.2229319842, 6.8241051525], [H, -0.0000000327, 3.9837629956, 6.8241051525], [H, -2.3415971639, 3.2229319458, 6.8241051525], [H, -3.7887837665, 1.2310504361, 6.8241051525], [H, -3.7887837463, -1.2310504983, 6.8241051525], [H, -2.3415971110, -3.2229319842, 6.8241051525], [H, 0.0000000327, -3.9837629956, 6.8241051525], [H, 2.3415971639, -3.2229319458, 6.8241051525], [H, 3.7887837665, -1.2310504361, 6.8241051525]] $ bonds: [[1,11],[2,12],[3,13],[4,14],[5,15],[6,16],[7,17],[8,18],[9,19],[10,20], [11,21],[11,22],[12,22],[12,23],[13,23],[13,24],[14,24],[14,25],[15,25], [15,26],[16,26],[16,27],[17,27],[17,28],[18,28],[18,29],[19,29],[19,30], [20,21],[20,30],[21,31],[22,32],[23,33],[24,34],[25,35],[26,36],[27,37], [28,38],[29,39],[30,40],[31,41],[31,50],[32,41],[32,42],[33,42],[33,43], [34,43],[34,44],[35,44],[35,45],[36,45],[36,46],[37,46],[37,47],[38,47], [38,48],[39,48],[39,49],[40,49],[40,50],[41,51],[42,52],[43,53],[44,54], [45,55],[46,56],[47,57],[48,58],[49,59],[50,60],[51,61],[51,62],[52,62], [52,63],[53,63],[53,64],[54,64],[54,65],[55,65],[55,66],[56,66],[56,67], [57,67],[57,68],[58,68],[58,69],[59,69],[59,70],[60,61],[60,70],[61,71], [62,72],[63,73],[64,74],[65,75],[66,76],[67,77],[68,78],[69,79],[70,80], [71,81],[71,90],[72,81],[72,82],[73,82],[73,83],[74,83],[74,84],[75,84], [75,85],[76,85],[76,86],[77,86],[77,87],[78,87],[78,88],[79,88],[79,89], [80,89],[80,90],[81,91],[82,92],[83,93],[84,94],[85,95],[86,96],[87,97], [88,98],[89,99],[90,100],[91,101],[91,102],[92,102],[92,103],[93,103], [93,104],[94,104],[94,105],[95,105],[95,106],[96,106],[96,107],[97,107], [97,108],[98,108],[98,109],[99,109],[99,110],[100,101],[100,110],[101,111], [102,112],[103,113],[104,114],[105,115],[106,116],[107,117],[108,118], [109,119],[110,120],[111,121],[111,130],[112,121],[112,122],[113,122], [113,123],[114,123],[114,124],[115,124],[115,125],[116,125],[116,126], [117,126],[117,127],[118,127],[118,128],[119,128],[119,129],[120,129], [120,130],[121,131],[122,132],[123,133],[124,134],[125,135],[126,136], [127,137],[128,138],[129,139],[130,140]] $ atoms_style: [[C,green,1], [H,white,1/2]] $ bonds_style: [blue, 0.1] $ draw3d(molecule(nt_atoms, bonds, atoms_style, bonds_style) )$
© 2016, TecnoStats.