digichem-core 6.0.0rc1__py3-none-any.whl

digichem/data/functionals.csv

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+Name,Aliases,Turbomole,Gaussian
+B2PLYP,,b2-plyp,
+B3LYP,,b3-lyp,
+B3LYP Gaussian,,b3-lyp_Gaussian,B3LYP
+B97-3c,B973c,b97-3c,
+B97D,,b97-d,
+BHLYP,,bh-lyp,
+BLYP,,b-lyp,
+BP,,b-p,
+BVWN,,b-vwn,
+M062X,,m06-2x,
+M06L,,m06-l,
+PBE0,,pbe0,PBE1PBE
+SVWN,,s-vwn,
+SVWN Gaussian,,s-vwn_Gaussian,SVWN

digichem/data/solvents.csv

@@ -0,0 +1,185 @@
+Name,Aliases,Gaussian,Epsilon,Refractive Index
+1-Bromo-2-MethylPropane,,,7.7792,
+1-BromoOctane,,,5.0244,
+1-BromoPentane,,,6.269,
+1-BromoPropane,,,8.0496,
+1-Butanol,,,17.332,
+1-ChloroHexane,,,5.9491,
+1-ChloroPentane,,,6.5022,
+1-ChloroPropane,,,8.3548,
+1-Decanol,,,7.5305,
+1-FluoroOctane,,,3.89,
+1-Heptanol,,,11.321,
+1-Hexanol,,,12.51,
+1-Hexene,,,2.0717,
+1-Hexyne,,,2.615,
+1-IodoButane,,,6.173,
+1-IodoHexaDecane,,,3.5338,
+1-IodoPentane,,,5.6973,
+1-IodoPropane,,,6.9626,
+1-NitroPropane,,,23.73,
+1-Nonanol,,,8.5991,
+1-Pentanol,,,15.13,
+1-Pentene,,,1.9905,
+1-Propanol,,,20.524,
+"1,1,1-TriChloroEthane",,,7.0826,
+"1,1,2-TriChloroEthane",,,7.1937,
+"1,2-DiBromoEthane",,,4.9313,
+"1,2-EthaneDiol",,,40.245,
+"1,2,4-TriMethylBenzene",,,2.3653,
+"1,4-Dioxane",Dioxane,,2.2099,
+2-BromoPropane,,,9.361,
+2-Butanol,,,15.944,
+2-ChloroButane,,,8.393,
+2-Heptanone,,,11.658,
+2-Hexanone,,,14.136,
+2-MethoxyEthanol,,,17.2,
+2-Methyl-1-Propanol,,,16.777,
+2-Methyl-2-Propanol,,,12.47,
+2-MethylPentane,,,1.89,
+2-MethylPyridine,,,9.9533,
+2-NitroPropane,,,25.654,
+2-Octanone,,,9.4678,
+2-Pentanone,,,15.2,
+2-Propanol,,,19.264,
+2-Propen-1-ol,,,19.011,
+"2,2,2-TriFluoroEthanol",,,26.726,
+"2,2,4-TriMethylPentane",,,1.9358,
+"2,4-DiMethylPentane",,,1.8939,
+"2,4-DiMethylPyridine",,,9.4176,
+"2,6-DiMethylPyridine",,,7.1735,
+3-MethylPyridine,,,11.645,
+3-Pentanone,,,16.78,
+4-Heptanone,,,12.257,
+4-Methyl-2-Pentanone,,,12.887,
+4-MethylPyridine,,,11.957,
+5-Nonanone,,,10.6,
+a-ChloroToluene,,,6.7175,
+AceticAcid,EthanoicAcid,,6.2528,
+Acetone,Propanone,,20.493,1.359
+Acetonitrile,,,35.688,1.344
+AcetoPhenone,,,17.44,
+Aniline,,,6.8882,
+Anisole,,,4.2247,
+Argon,,,1.43,
+Benzaldehyde,,,18.22,
+Benzene,,,2.2706,1.501
+BenzoNitrile,,,25.592,
+BenzylAlcohol,,,12.457,
+BromoBenzene,,,5.3954,
+BromoEthane,,,9.01,
+Bromoform,,,4.2488,
+Butanal,,,13.45,
+ButanoicAcid,,,2.9931,
+Butanone,,,18.246,
+ButanoNitrile,,,24.291,
+ButylAmine,,,4.6178,
+ButylEthanoate,,,4.9941,
+CarbonDiSulfide,,,2.6105,
+CarbonTetraChloride,,,2.228,1.466
+ChloroBenzene,,,5.6968,
+Chloroform,,,4.7113,1.45
+"Cis-1,2-DiMethylCycloHexane",,,2.06,
+Cis-Decalin,,,2.2139,
+CycloHexane,,,2.0165,1.425
+CycloHexanone,,,15.619,
+CycloPentane,,,1.9608,
+CycloPentanol,,,16.989,
+CycloPentanone,,,13.58,
+Decalin-mixture,,,2.196,
+DiBromomEthane,,,7.2273,
+DiButylEther,,,3.0473,
+DiChloroEthane,,,10.125,
+DiChloroMethane,DCM,,8.93,1.424
+DiEthylAmine,,,3.5766,
+DiethylEther,,,4.24,
+DiEthylSulfide,,,5.723,
+DiIodoMethane,,,5.32,
+DiIsoPropylEther,,,3.38,
+DiMethylDiSulfide,,,9.6,
+DiMethylSulfoxide,DMSO,,46.826,1.479
+DiPhenylEther,,,3.73,
+DiPropylAmine,,,2.9112,
+"e-1,2-DiChloroEthene",,,2.14,
+e-2-Pentene,,,2.051,
+EthaneThiol,,,6.667,
+Ethanol,,,24.852,1.361
+EthylBenzene,,,2.4339,
+EthylEthanoate,,,5.9867,
+EthylMethanoate,,,8.331,
+EthylPhenylEther,,,4.1797,
+FluoroBenzene,,,5.42,
+Formamide,,,108.94,
+FormicAcid,,,51.1,
+Heptane,,,1.9113,
+HexanoicAcid,,,2.6,
+IodoBenzene,,,4.547,
+IodoEthane,,,7.6177,
+IodoMethane,,,6.865,
+IsoPropylBenzene,,,2.3712,
+IsoQuinoline,,,11,
+Krypton,,,1.519,
+m-Cresol,,,12.44,
+m-Xylene,,,2.3478,
+Mesitylene,,,2.265,
+Methanol,,,32.613,1.329
+MethylBenzoate,,,6.7367,
+MethylButanoate,,,5.5607,
+MethylCycloHexane,,,2.024,
+MethylEthanoate,,,6.8615,
+MethylMethanoate,,,8.8377,
+MethylPropanoate,,,6.0777,
+n-ButylBenzene,ButylBenzene,,2.36,
+n-Decane,Decane,,1.9846,
+n-Dodecane,Dodecane,,2.006,
+n-Hexadecane,Hexadecane,,2.0402,
+n-Hexane,Hexane,,1.8819,1.375
+n-MethylAniline,MethylAniline,,5.96,
+n-MethylFormamide-mixture,MethylFormamide-mixture,,181.56,
+n-Nonane,Nonane,,1.9605,
+n-Octane,Octane,,1.9406,
+n-Octanol,Octanol,,9.8629,1.421
+n-Pentadecane,Pentadecane,,2.0333,
+n-Pentane,Pentane,,1.8371,
+n-Undecane,Undecane,,1.991,
+"n,n-DiMethylAcetamide",DMA,,37.781,
+"n,n-DiMethylFormamide",DMF,,37.219,1.43
+NitroBenzene,,,34.809,
+NitroEthane,,,28.29,
+NitroMethane,,,36.562,
+o-ChloroToluene,,,4.6331,
+o-Cresol,,,6.76,
+o-DiChloroBenzene,,,9.9949,
+o-NitroToluene,,,25.669,
+o-Xylene,,,2.5454,
+p-IsoPropylToluene,,,2.2322,
+p-Xylene,,,2.2705,
+Pentanal,,,10,
+PentanoicAcid,,,2.6924,
+PentylAmine,,,4.201,
+PentylEthanoate,,,4.7297,
+PerFluoroBenzene,,,2.029,
+Propanal,,,18.5,
+PropanoicAcid,,,3.44,
+PropanoNitrile,,,29.324,
+PropylAmine,,,4.9912,
+PropylEthanoate,,,5.5205,
+Pyridine,,,12.978,1.51
+Quinoline,,,9.16,
+sec-ButylBenzene,,,2.3446,
+tert-ButylBenzene,,,2.3447,
+TetraChloroEthene,,,2.268,
+TetraHydroFuran,THF,,7.4257,1.407
+"TetraHydroThiophene-s,s-dioxide",,,43.962,
+Tetralin,,,2.771,
+Thiophene,,,2.727,
+Thiophenol,,,4.2728,
+Toluene,,,2.3741,1.497
+trans-Decalin,,,2.1781,
+TriButylPhosphate,,,8.1781,
+TriChloroEthene,,,3.422,
+TriEthylAmine,,,2.3832,
+Water,,,78.3553,1.33
+Xenon,,,1.706,
+Xylene-mixture,,,2.3879,
+"z-1,2-DiChloroEthene",,,9.2,

digichem/data/tachyon/COPYING.md

@@ -0,0 +1,5 @@
+The Tachyon ray-tracer is Copyright (c) 1994-2013 John E. Stone.
+
+It is distributed under the BSD-3-Clause license, see [LICENSE](LICENSE)
+
+See https://github.com/thesketh/Tachyon for more information.

digichem/data/tachyon/LICENSE

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 1994-2013 John E. Stone
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions 
+are met:
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS 
+OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY 
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) 
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY 
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF 
+SUCH DAMAGE.
+
+$Id: Copyright,v 1.11 2013/04/21 19:16:57 johns Exp $

digichem/data/vmd/common.tcl

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+# ----------------------------------------------------------------
+# Common Functions.
+# ----------------------------------------------------------------
+
+# Reset the rotation of the camera to the aligned X, Y and Z axes.
+proc reset_rotation {rotations} {
+    # Reset all axes to 0.
+    rotate x to 0
+
+    # rotations is a string, we want a list to iterate through.
+    set rot_list [split "$rotations" " "]
+
+    # Iterate through.
+    foreach rotation_str $rot_list {
+        # Split again to get axes, angle.
+        set rotation [split "$rotation_str" ","]
+        set axis [lindex $rotation 0]
+        set angle [lindex $rotation 1]
+
+        # What we rotate depends on our axes.
+        if {$axis == 0} {
+            rotate x by [expr -$angle]
+        } elseif {$axis == 1} {
+            rotate y by $angle
+        } elseif {$axis == 2} {
+            rotate z by $angle
+        } else {
+            puts "Unknown axis $axis"
+        }
+    }
+}
+
+# Rotate a molecule by a list of rotations.
+proc rotate_molecule {molecule translations rotations} {
+    # Split our translations string into a list.
+    set trans_list [split $translations ","]
+
+    # Now we get an atom selection encompassing our molecule.
+    set sel [atomselect $molecule all]
+
+    # Now move our atoms.
+    $sel moveby $trans_list
+
+    # rotations is a string, we want a list to iterate through.
+    set rot_list [split $rotations ":"]
+
+    # Iterate through.
+    foreach rotation_str $rot_list {
+        # Split again to get axes, angle.
+        set rotation [split $rotation_str ","]
+        set axis [lindex $rotation 0]
+        set angle [lindex $rotation 1]
+
+        # What we rotate depends on our axes.
+        if {$axis == 0} {
+            $sel move [transaxis x [expr -$angle]]
+        } elseif {$axis == 1} {
+            $sel move [transaxis y $angle]
+        } elseif {$axis == 2} {
+            $sel move [transaxis z $angle]
+        } else {
+            puts "Unknown axis $axis"
+        }
+    }
+
+    # Now we move our molecule back so it's still centered in the scene.
+    $sel moveby "[expr -[lindex $trans_list 0]] [expr -[lindex $trans_list 1]] [expr -[lindex $trans_list 2]]"
+}
+
+# Taken from the VMD docs.
+proc vmd_draw_arrow {mol start end} {
+    # an arrow is made of a cylinder and a cone
+    #set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
+    set middle [vecadd $start [vecscale 0.85 [vecsub $end $start]]]
+    #graphics $mol cylinder $start $middle radius 0.15 filled yes
+    graphics $mol cylinder $start $middle radius 0.20 filled yes
+    #graphics $mol cone $middle $end radius 0.25
+    graphics $mol cone $middle $end radius 0.40 resolution 12
+}
+
+# Also taken from the VMD docs http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node181.html#14132
+# Find the geometric center of our atoms.
+proc geom_center {selection} {
+        # Init our total to 0 0 0.
+        set total_coords [veczero]
+
+        # Iterate through all our coordinates and add to our total.
+        foreach coord [$selection get {x y z}] {
+            set total_coords [vecadd $total_coords $coord]
+        }
+
+        # And now get our average (we do total_coords * (1 / num_coords) which is the same as total_coords / num_coords).
+        return [vecscale [expr 1.0 /[$selection num]] $total_coords]
+}
+
+# Move our atoms to be centerd around the geometric center.
+proc reset_center {selection} {
+    # First get our center.
+    set center_coords [geom_center $selection]
+
+    # Now move.
+    $selection moveby {-[lindex center_coords 0] -[lindex center_coords 1] -[lindex center_coords 2]}
+}
+
+# Render the current scene. Rotations is our alignemnt rotations string. The four arguments are filenames to render each of the 4 angles to.
+proc render_images {rotations x0y0z0 x90y0z0 x0y90z0 x45y45z45} {
+
+    reset_rotation $rotations
+    #rotate x to 0
+    render Tachyon $x0y0z0
+
+    reset_rotation $rotations
+    #rotate x to 0
+    rotate x by 90
+    render Tachyon $x90y0z0
+
+    reset_rotation $rotations
+    #rotate x to 0
+    rotate y by 90
+    render Tachyon $x0y90z0
+
+
+    reset_rotation $rotations
+    #rotate x to 0
+    rotate x by 45
+    rotate y by 45
+    rotate z by 45
+    render Tachyon $x45y45z45
+}
+
+
+
+# Global flags that control our molecule style.
+# The colors of orbitals.
+set ORBITAL_PRIMARY_COLOR 0
+set ORBITAL_SECONDARY_COLOR 1
+set ORBITAL_MATERIAL Translucent
+
+# The radius of atoms in CPK
+set SPHERE_SCALE 1.0
+# The thickness of bonds in CPK.
+set BOND_THICKNESS 0.3
+
+# Switch to a visual style based on a string.
+proc use_style {style} {
+    if {$style == "pastel"} {
+        use_pastel_style
+    } elseif {$style == "light-pastel"} {
+        use_light_pastel_style
+    } elseif {$style == "dark-pastel"} {
+        use_dark_pastel_style 
+    } elseif {$style == "sharp"} {
+        use_sharp_style
+    } elseif {$style == "gaussian"} {
+        use_gaussian_style
+    } elseif {$style == "vesta"} {
+        use_vesta_style
+    } else {
+        error "Unknown rendering style $style"
+    }
+}
+
+# Set default atom colourings, based on https://sciencenotes.org/molecule-atom-colors-cpk-colors/ (but some have been modified).
+proc use_default_atom_colours {} {
+    # Set carbon colour to grey.
+    color Element C 2
+        
+    # B to pink
+    color Element B 9
+    color change rgb 9 1.00 0.709803922 0.709803922
+    
+    # Mg to green-yellow
+    color Element Mg 18
+    color change rgb 18 0.5412 1.00 0.00
+    
+    # Al to metallic-pink
+    color Element Al 27
+    color change rgb 27 0.749 0.651 0.651
+    
+    # Si to light-yellow
+    color Element Si 17
+    color change rgb 17 0.941176471 0.784313725 0.62745098
+    
+    # P to orange
+    color Element P 31
+    color change rgb 31 1.00 0.501960784 0.00
+    
+    # S to yellow
+    color Element S 4
+    color change rgb 4 1.00 1.00 0.188235294
+    
+    # Various metals to silver.
+    # Color code 14 is the default.
+    #color Element Ti 14
+    color change rgb 14 0.749019608 0.760784314 0.780392157
+    
+    # O to red
+    color Element O 1
+    color change rgb 1 1.00 0.050980392 0.050980392
+    
+    # N to blue
+    color Element N 23
+    #color change rgb 23 0.04 0.21 1.00
+    color change rgb 23 0.188235294 0.31372549 0.97254902
+    
+    # F to green.
+    color Element F 12
+    color change rgb 12 0.564705882 0.878431373 0.31372549
+    
+    # Cl to green.
+    color Element Cl 7
+    color change rgb 7 0.121568627 0.941176471 0.121568627
+    
+    # Br to red.
+    color Element Br 29
+    color change rgb 29 0.650980392 0.160784314 0.160784314
+    
+    # I to purple.
+    color Element I 11
+    color change rgb 11 0.580392157 0.0 0.580392157
+}
+
+# Set styles used by all pastel styles.
+proc use_common_pastel_style {} {
+    # Orbitals are transparent
+    global ORBITAL_MATERIAL 
+    set ORBITAL_MATERIAL Translucent
+
+    # Set our custom 'Translucent' material.
+    material change Ambient Translucent 0.10
+    material change Diffuse Translucent 0.64
+    material change Specular Translucent 0.00
+    material change Shininess Translucent 0.00
+    material change Mirror Translucent 0.00
+    material change Opacity Translucent 0.62
+    material change Outline Translucent 0.00
+    material change OutlineWidth Translucent 0.00
+    material change TransMode Translucent 1
+
+    # Use default bond thicknes.
+    global BOND_THICKNESS SPHERE_SCALE
+    set BOND_THICKNESS 0.3
+    set SPHERE_SCALE 1.0
+}
+
+# Use the 'pastel' visual style.
+proc use_pastel_style {} {
+    # Set common styles.
+    use_default_atom_colours
+    use_common_pastel_style
+    
+    # Orbitals should use red and blue.
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set ORBITAL_PRIMARY_COLOR 24
+    set ORBITAL_SECONDARY_COLOR 30
+    
+    # Make red and blue lighter.
+    #color change rgb 24 0.00 0.72 1.00
+    color change rgb 24 0.29 0.29 1.00
+    color change rgb 30 1.00 0.30 0.30
+}
+
+# Use the light 'pastel' visual style.
+proc use_light_pastel_style {} {
+    # Set common styles.
+    use_default_atom_colours
+    use_common_pastel_style
+    
+    # Orbitals should use red and blue.
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set ORBITAL_PRIMARY_COLOR 24
+    set ORBITAL_SECONDARY_COLOR 30
+    
+    # Make red and blue lighter.
+    #color change rgb 24 0.29 0.29 1.00
+    color change rgb 24 0.00 0.72 1.00
+    color change rgb 30 1.00 0.30 0.30
+}
+
+# Use the dark 'pastel' visual style.
+proc use_dark_pastel_style {} {
+    # Set common styles.
+    use_default_atom_colours
+    use_common_pastel_style
+    
+    # Orbitals should use red and blue.
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set ORBITAL_PRIMARY_COLOR 24
+    set ORBITAL_SECONDARY_COLOR 30
+    
+    # Make red and blue lighter.
+    color change rgb 24 0.05 0.05 1.00
+    color change rgb 30 1.00 0.05 0.05
+}
+
+# Use the 'sharp' style
+proc use_sharp_style {} {
+    # Set common styles.
+    use_default_atom_colours
+
+    # Orbitals should use red and blue.
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set ORBITAL_PRIMARY_COLOR 0
+    set ORBITAL_SECONDARY_COLOR 1
+
+    # Orbitals are transparent
+    global ORBITAL_MATERIAL 
+    set ORBITAL_MATERIAL Translucent
+
+    # Set our custom 'Translucent' material.
+    material change Ambient Translucent 0.04
+    material change Diffuse Translucent 0.70
+    material change Specular Translucent 1.00
+    material change Shininess Translucent 1.00
+    material change Mirror Translucent 0.00
+    material change Opacity Translucent 0.30
+    material change Outline Translucent 0.00
+    material change OutlineWidth Translucent 0.00
+    material change TransMode Translucent 1
+
+    # Use default bond thicknes.
+    global BOND_THICKNESS SPHERE_SCALE
+    set BOND_THICKNESS 0.3
+    set SPHERE_SCALE 1.0
+}
+
+# Set the visual style to Gaussian-like.
+proc use_gaussian_style {} {
+    # Set common styles.
+    use_default_atom_colours
+
+    # Make grey lighter (for carbon).
+    color change rgb 2 0.630000 0.630000 0.630000
+
+    # Orbitals should use red and green.
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set ORBITAL_PRIMARY_COLOR 19
+    set ORBITAL_SECONDARY_COLOR 30
+
+    # Orbitals are opaque
+    global ORBITAL_MATERIAL
+    set ORBITAL_MATERIAL Opaque
+
+    # Make red and green darker.
+    color change rgb 19 0.000000 0.500000 0.000000
+    color change rgb 30 0.580000 0.000000 0.000000
+
+    # Use thinner bonds.
+    global BOND_THICKNESS SPHERE_SCALE
+    set BOND_THICKNESS 0.2
+    set SPHERE_SCALE 1.0
+}
+
+# Set the visual style to VESTA-like.
+proc use_vesta_style {} {
+    # Set carbon colour to ochre.
+    # We use red2 rather than ochre because ochre is VMD's default for most atoms. This way we only change C's colour rather than all other elements.
+    color Element C 29
+    color change rgb 29 0.490196 0.286275 0.160784
+
+    # Modify the real ochre so other atoms are more distinct from carbon.
+    color change rgb 14 0.35 0.35 0.35
+
+    # N to iceblue
+    color Element N 15
+    color change rgb 15 0.690196 0.725490 0.901961
+
+    # H to pink
+    color Element H 9
+    color change rgb 9 1.000000 0.800000 0.800000
+
+    # O to red
+    color Element O 30
+    color change rgb 30 0.99997 0.01328 0.00000
+
+    # P to lilac
+    color Element P 13
+    color change rgb 13 0.75557 0.61256 0.76425
+
+    # S to yellow
+    color Element S 4
+
+    # The reflectance is different for atoms in vesta and is difficult to approximate, but we give it a go.
+    material change Ambient Opaque 0.10
+    material change Diffuse Opaque 0.65
+    #material change Specular Opaque 0.26
+    material change Specular Opaque 0.52
+    material change Shininess Opaque 0.51
+    material change Mirror Opaque 0.00
+    material change Opacity Opaque 1.00
+    material change Outline Opaque 0.00
+    material change OutlineWidth Opaque 0.00
+    material change TransMode Opaque 0
+
+    # Set our orbital colours to yellow and blue (they are opposites of each other?).    
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set ORBITAL_PRIMARY_COLOR 21
+    set ORBITAL_SECONDARY_COLOR 4
+    color change rgb 21 0.000000 1.000000 1.000000
+
+    # Orbitals are transparent
+    global ORBITAL_MATERIAL 
+    set ORBITAL_MATERIAL Translucent
+
+    # Set our custom 'Translucent' material.
+    material change Ambient Translucent 0.10
+    #material change Diffuse Translucent 0.70
+    material change Diffuse Translucent 0.64
+    material change Specular Translucent 0.00
+    material change Shininess Translucent 0.00
+    material change Mirror Translucent 0.00
+    material change Opacity Translucent 0.62
+    material change Outline Translucent 0.00
+    material change OutlineWidth Translucent 0.00
+    material change TransMode Translucent 1
+
+    # Set the size of our atoms.
+    global BOND_THICKNESS SPHERE_SCALE
+    set BOND_THICKNESS 0.4
+    set SPHERE_SCALE 0.75
+
+}
+
+# Set the standard display options for the body of a molecule.
+proc standard_molecule_style {representation molecule} {
+    # Change how our molecule looks from sticks (the default) to ball and stick.
+    molecule modstyle $representation $molecule CPK
+
+    # Use the more detailed Element colouring method rather than default name.
+    mol modcolor $representation $molecule Element
+
+    # Set connecting line thickness
+    global BOND_THICKNESS SPHERE_SCALE
+    mol modstyle $representation $molecule CPK $SPHERE_SCALE $BOND_THICKNESS 30.000000 30.000000
+}
+
+proc standard_orbital_style {representation molecule primary_secondary isovalue} {
+    # First decide which colour we're going to use.
+    global ORBITAL_PRIMARY_COLOR ORBITAL_SECONDARY_COLOR
+    set orbital_color 0
+    if {$primary_secondary == 0} {
+        set orbital_color $ORBITAL_PRIMARY_COLOR
+    } else {
+        set orbital_color $ORBITAL_SECONDARY_COLOR
+    }
+
+    # Switch the representation to the isosurface mode (which shows orbitals).
+    molecule modstyle $representation $molecule isosurface $isovalue 0 0 0 1 1
+    
+    # Change to our given color.
+    molecule modcolor $representation $molecule ColorID $orbital_color
+
+    # Set to target material
+    global ORBITAL_MATERIAL
+    molecule modmaterial $representation $molecule $ORBITAL_MATERIAL
+}
+
+# ----------------------------------------------------------------
+# VMD Options.
+# ----------------------------------------------------------------
+# General options that control the look and feel of our images.
+
+# Set background colour to white.
+color Display Background 8
+
+#display projection orthographic
+axes location off
+