class Molecule
-def export_ortep(fp)
+# Export ortep to File fp
+# If attr is a hash, it represents options for drawing.
+# "atoms"=>[[group, type, color], [group, type, color], ...]
+# group is an IntGroup, representing a group of atoms.
+# type is an atom type: 0 = boundary, 1 = boundary + principal, 2 = 1 + axes, 3 = 2 + shades
+# color is 0..7 (0,1=black, 2=red, 3=green, 4=blue, 5=cyan, 6=magenta, 7=yellow)
+# If an atom appears in multiple entries, the later entry is valid.
+# "bonds"=>[[group1, group2, type, color], [group1, group2, type, color], ...]
+# group1 and group2 are IntGroups, reprensenting the atoms constituting the bonds.
+# type is a bond type: 0 to 4 for bonds with no shades to 4 shades.
+# color is 0..7 as in atoms.
+# If a bond appears in multiple entries, the later entry is valid.
+def export_ortep(fp, attr = nil)
# Create atom list
hidden = atom_group { |ap| !is_atom_visible(ap.index) }
fp.print " 604 1.538\n"
# Explicit bonds
- bond_inst = Array.new(6) { [] } # Bonds for types 1 to 5
+ bond_inst = Array.new(35) { [] } # Bonds for types 0 to 4 and colors 1 to 7
+ battr = (attr ? attr["bonds"] : nil)
bonds.each { |b|
next if !atomlist.include?(b[0]) || !atomlist.include?(b[1])
- # TODO: determination of bond types should be refined
- an1 = atoms[b[0]].atomic_number
- an2 = atoms[b[1]].atomic_number
- if an1 == 1 || an2 == 1
- btype = 1
- elsif an1 <= 8 && an2 <= 8
- btype = 3
- else
- btype = 5
- end
- bond_inst[btype].push(b[0], b[1])
+ btype = bcol = nil
+ if battr
+ battr.reverse_each { |at|
+ if (at[0].include?(b[0]) && at[1].include?(b[1])) || (at[0].include?(b[1]) && at[1].include?(b[0]))
+ btype = at[2] % 5
+ bcol = (at[3] != 0 ? at[3] - 1 : at[3]) % 7
+ break
+ end
+ }
+ end
+ if btype == nil
+ bcol = 0
+ an1 = atoms[b[0]].atomic_number
+ an2 = atoms[b[1]].atomic_number
+ if an1 == 1 || an2 == 1
+ btype = 0
+ elsif an1 <= 8 && an2 <= 8
+ btype = 2
+ else
+ btype = 4
+ end
+ end
+ bond_inst[btype * 7 + bcol].push(b[0], b[1])
}
# Output bond specifications
output_bonds = lambda { |icode|
bond_inst.each_with_index { |inst, ii|
next if inst.length == 0
+ btype = ii / 7 + 1
+ if icode / 10 == 81 # 811 instructions
+ fp.printf " 204%9d\n", ii % 7 + 1 # Pen color
+ end
inst.each_with_index { |b, i|
if i % 6 == 0
fp.printf " %d %3s", (i >= inst.length - 6 || i % 36 == 30 ? 2 : 1), (i % 36 == 0 ? icode.to_s : "")
if i % 6 == 5 || i == inst.length - 1
fp.print "\n"
if i == inst.length - 1 || i % 36 == 35
- fp.printf "%21s%3d%12s%6.3f\n", "", ii, "", 0.05
+ fp.printf "%21s%3d%12s%6.3f\n", "", btype, "", 0.05
end
end
}
output_bonds.call(821)
# Atom types
- atom_inst = Array.new(5) { IntGroup.new } # Atoms for 714 (sphere), 712 (with axes), 711 (shade and axes)
+ # Atom type 0=714 (boundary), 1=712 (+principal), 2=716 (+axes), 3=711 (+shades)
+ atom_inst = Array.new(28) { IntGroup.new }
+ aattr = (attr ? attr["atoms"] : nil)
atomlist.each { |i|
- # TODO: determination of atom types should be refined
- an1 = atoms[i].atomic_number
- if an1 == 1
- atype = 4
- elsif an1 <= 6
- atype = 2
- else
- atype = 1
- end
+ atype = acol = nil
+ if aattr
+ aattr.reverse_each { |at|
+ if at[0].include?(i)
+ atype = at[1] % 4
+ acol = (at[2] != 0 ? at[2] - 1 : at[2]) % 7
+ break
+ end
+ }
+ end
+ if atype == nil
+ acol = 0
+ an1 = atoms[i].atomic_number
+ if an1 == 1
+ atype = 0
+ elsif an1 <= 6
+ atype = 1
+ else
+ atype = 3
+ end
+ end
idx, scode = atoms[i].to_adc
- atom_inst[atype].add(idx)
+ atom_inst[atype * 7 + acol].add(idx)
}
- [4,2,1].each { |ii|
+ (atom_inst.count - 1).downto(0) { |ii|
inst = atom_inst[ii]
+ next if inst.count == 0
+ fp.printf " 204%9d\n", ii % 7 + 1 # Pen color
i = 0
+ atype = [714, 712, 716, 711][ii / 7]
while (r = inst.range_at(i)) != nil
- fp.printf " 1 %3d\n", 710 + ii
+ fp.printf " 1 %3d\n", atype
fp.printf "%27s%9d%9d\n", "", r.first, r.last
i += 1
end
end
tepdata = []
tepbounds = [0, 0, 400, 400]
+ descs = {
+ "atoms"=>[],
+ "bonds"=>[]
+ }
Dialog.new("Show ORTEP:" + mol.name, nil, nil, :resizable=>true, :has_close_box=>true) {
tepview = nil # Forward declaration
on_update_ortep = lambda { |it|
+ # ORTEP attributes
+ attr = Hash.new
+ at = []
+ atom_type = lambda { |an|
+ if an <= 1
+ 0
+ elsif an == 6
+ 1
+ elsif an <= 9
+ 2
+ else
+ 3
+ end
+ }
+ mol.each_atom { |ap|
+ a = (at[ap.atomic_number] ||= [IntGroup[], atom_type.call(ap.atomic_number), ap.atomic_number % 6 + 2])
+ a[0].add(ap.index)
+ }
+ attr["atoms"] = at.compact
+ attr["bonds"] = []
+ ans = (0...at.count).select { |i| at[i] != nil } # Array of valid atomic numbers
+ ans.each_with_index { |ai, i|
+ next if ai <= 6
+ i.times { |j|
+ aj = ans[j]
+ next if aj <= 6
+ attr["bonds"].push([at[ai][0], at[aj][0], 4, (i + j) % 6 + 2])
+ }
+ }
+ puts attr.inspect
# Create ORTEP input in the temporary directory
- open(tmp + "/TEP.IN", "w") { |fp| mol.export_ortep(fp) }
+ open(tmp + "/TEP.IN", "w") { |fp| mol.export_ortep(fp, attr) }
# Run ORTEP
cwd = Dir.pwd
Dir.chdir(tmp)
on_draw_ortep = lambda { |it|
clear
frame = it[:frame]
+ brush(:color=>[1, 1, 1, 1])
+ pen(:color=>[1, 1, 1, 1])
+ draw_rectangle(frame)
+ pen(:color=>[0, 0, 0, 1])
rx = (frame[2] - 10.0) / (tepbounds[2] - tepbounds[0])
ry = (frame[3] - 10.0) / (tepbounds[3] - tepbounds[1])
rx = ry if rx > ry
}
}
}
+ # Close handler (called when the close box is pressed or the document is closed)
@on_close = lambda { |*d|
- puts "#{self}: on_close invoked"
cleanup_temp_dir(tmp)
tmp = nil
true
}
- layout(1,
- item(:view, :width=>400, :height=>400, :tag=>"ortep", :on_paint=>on_draw_ortep, :flex=>[0,0,0,0,1,1]),
- layout(2,
- item(:button, :title=>"Refresh", :action=>on_update_ortep, :align=>:left),
- -1,
- :flex=>[0,1,0,0,1,0]),
- :flex=>[0,0,0,0,1,1])
+ # Internal info (dependent on the molecule contents)
+ elements = []
+ update_internal = lambda { |m|
+ elements.clear
+ mol.each_atom { |ap|
+ e = ap.element
+ if !elements.include?(e)
+ elements.push(e)
+ end
+ }
+ elements.push((mol.selection.count == 0 ? "-" : "") + "Current Selection")
+ }
+ tab = "atoms"
+ columns = {
+ "atoms"=>[["atom list", 70], ["type", 90], ["color", 40]],
+ "bonds"=>[["list1", 70], ["list2", 70], ["type", 90], ["color", 40]]
+ }
+ atom_types = ["Boundary", "Principals", "Axes", "Shaded"]
+ bond_types = ["Open", "1 Shade", "2 Shades", "3 Shades", "4 Shades", "5 Shades"]
+ get_count = lambda { |it| descs[tab].count }
+ get_value = lambda { |it, row, col| descs[tab][row][col] }
+ is_item_editable = lambda { |it, row, col| false }
+ has_popup_menu = lambda { |it, row, col|
+ if tab == "atoms"
+ if col == 0
+ return elements
+ elsif col == 1
+ return atom_types
+ end
+ elsif tab == "bonds"
+ if col == 0 || col == 1
+ return elements
+ elsif col == 2
+ return bond_types
+ end
+ end
+ return nil
+ }
+ popup_menu_selected = lambda { |it, row, col, sel|
+ titles = has_popup_menu.call(it, row, col)
+ return nil if titles == nil
+ t = titles[sel]
+ if t == "Current Selection"
+ t = mol.selection.inspect[9..-2].gsub(" ", "")
+ end
+ descs[tab][row][col] = t
+ item_with_tag("table")[:refresh] = true
+ }
+ set_value = lambda { |it, row, col, val|
+ }
+ add_to_table = lambda { |it|
+ if tab == "atoms"
+ n = [elements[0], atom_types[0], ""]
+ elsif tab == "bonds"
+ n = [elements[0], elements[0], bond_types[0], ""]
+ else
+ return nil
+ end
+ descs[tab].push(n)
+ item_with_tag("table")[:refresh] = true
+ }
+ remove_from_table = lambda { |it|
+ }
+ layout(2,
+ layout(1,
+ item(:popup, :subitems=>["Atoms", "Bonds"]),
+ item(:table, :width=>240, :height=>380, :flex=>[0,0,0,0,1,1], :tag=>"table",
+ :columns=>columns["atoms"],
+ :on_count=>get_count,
+ :on_get_value=>get_value,
+ :on_set_value=>set_value,
+ :is_item_editable=>is_item_editable,
+ :has_popup_menu=>has_popup_menu,
+ :on_popup_menu_selected=>popup_menu_selected),
+ layout(2,
+ item(:button, :title=>"Add", :action=>add_to_table),
+ item(:button, :title=>"Remove", :action=>remove_from_table),
+ :flex=>[0,1,0,0,0,0]),
+ :flex=>[0,0,0,0,0,1]),
+ layout(1,
+ item(:view, :width=>400, :height=>400, :tag=>"ortep", :on_paint=>on_draw_ortep, :flex=>[0,0,0,0,1,1]),
+ layout(2,
+ item(:button, :title=>"Refresh", :action=>on_update_ortep, :align=>:left),
+ -1,
+ :flex=>[0,1,0,0,0,0]),
+ :flex=>[0,0,0,0,1,1]),
+ :flex=>[0,0,0,0,1,1]
+ )
+ set_min_size(480, 200)
tepview = item_with_tag("ortep")
- listen(mol, "documentWillClose", :close )
+ listen(mol, "documentModified", update_internal)
+ listen(mol, "documentWillClose", lambda { |m| close } )
+ update_internal.call(nil)
on_update_ortep.call(nil)
show
}
register_menu("Bonds and Angles with Sigma...", :cmd_bond_angle_with_sigma)
register_menu("Complete by Symmetry", :complete_by_symmetry)
register_menu("Create Packing Diagram...", :create_packing_diagram)
+ register_menu("Show ORTEP", :cmd_show_ortep)
end
end
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