| 1 | # $Id: import_cif.tcl 280 2009-12-04 23:03:25Z toby $ |
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| 2 | |
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| 3 | #------------------------------------------------- |
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| 4 | # define info used in addcmds.tcl |
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| 5 | set description "Crystallographic Information File (CIF)" |
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| 6 | set extensions .cif |
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| 7 | set procname ReadCIFFile |
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| 8 | #------------------------------------------------- |
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| 9 | |
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| 10 | proc ReadCIFFile {filename} { |
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| 11 | global expgui |
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| 12 | set fp [open $filename r] |
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| 13 | pleasewait "Reading CIF file" |
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| 14 | set blocks [ParseCIF $filename] |
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| 15 | if {$blocks == ""} { |
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| 16 | donewait |
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| 17 | MyMessageBox -parent . -type ok -icon warning \ |
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| 18 | -message "Note: no valid CIF blocks were read from file $filename" |
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| 19 | return |
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| 20 | } |
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| 21 | set allblocks {} |
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| 22 | set coordblocks {} |
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| 23 | # search each block for coordinate |
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| 24 | for {set i 1} {$i <= $blocks} {incr i} { |
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| 25 | lappend allblocks $i |
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| 26 | global block$i |
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| 27 | set flag 1 |
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| 28 | foreach id {_atom_site_fract_x _atom_site_fract_y _atom_site_fract_z} { |
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| 29 | if {[array name block$i $id] == ""} {set flag 0} |
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| 30 | } |
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| 31 | if $flag {lappend coordblocks $i} |
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| 32 | } |
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| 33 | donewait |
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| 34 | if {$coordblocks == ""} { |
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| 35 | MyMessageBox -parent . -type ok -icon warning \ |
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| 36 | -message "Note: CIF $filename contains no coordinates" |
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| 37 | return |
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| 38 | } |
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| 39 | set expgui(choose) [lindex $coordblocks 0] |
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| 40 | # there is more than one appropriate block |
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| 41 | if {[llength $coordblocks] > 1} { |
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| 42 | catch {destroy .choose} |
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| 43 | toplevel .choose |
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| 44 | wm title .choose "Choose CIF Block" |
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| 45 | grid [label .choose.0 -text \ |
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| 46 | "More than one block in CIF $filename\ncontains coordinates.\nSelect the block to use" \ |
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| 47 | ] -row 0 -column 0 -columnspan 2 |
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| 48 | set row 0 |
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| 49 | foreach i $coordblocks { |
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| 50 | incr row |
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| 51 | set name "" |
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| 52 | catch {set name [set block${i}(data_)]} |
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| 53 | grid [radiobutton .choose.$row -value $i \ |
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| 54 | -text "block $i ($name)" -variable expgui(choose)] \ |
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| 55 | -row $row -column 0 -sticky w |
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| 56 | } |
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| 57 | grid [button .choose.browse -text CIF\nBrowser -command \ |
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| 58 | "BrowseCIF [list $allblocks] [list $coordblocks] .choose.cif" \ |
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| 59 | ] -row 1 -rowspan $row -column 1 |
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| 60 | grid [button .choose.ok -text OK -command "destroy .choose"] \ |
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| 61 | -row [incr row] -column 0 -columnspan 2 |
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| 62 | tkwait window .choose |
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| 63 | } |
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| 64 | |
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| 65 | set i $expgui(choose) |
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| 66 | # get the space group |
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| 67 | set spg {} |
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| 68 | set msg {} |
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| 69 | catch { |
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| 70 | set spg [set block${i}(_symmetry_space_group_name_H-M)] |
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| 71 | regsub -all {'} $spg {} spg |
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| 72 | # see if this space group exists in the table |
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| 73 | set fp [open [file join $expgui(scriptdir) spacegrp.ref] r] |
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| 74 | while {[gets $fp line] >= 0} { |
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| 75 | if {[string trim $spg] == [lindex $line 8]} { |
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| 76 | close $fp |
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| 77 | break |
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| 78 | set fp {} |
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| 79 | } |
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| 80 | } |
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| 81 | if {$fp != ""} { |
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| 82 | close $fp |
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| 83 | set msg "Warning: the Space Group ($spg) may not be correctly specified for GSAS" |
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| 84 | } |
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| 85 | } |
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| 86 | set cell {} |
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| 87 | foreach var {_cell_length_a _cell_length_b _cell_length_c \ |
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| 88 | _cell_angle_alpha _cell_angle_beta _cell_angle_gamma} { |
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| 89 | # leave blank any unspecified values |
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| 90 | set val {} |
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| 91 | catch {set val [set block${i}($var)]} |
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| 92 | lappend cell [lindex [ParseSU $val] 0] |
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| 93 | } |
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| 94 | |
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| 95 | set atomlist {} |
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| 96 | set lbllist {} |
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| 97 | catch { |
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| 98 | set lbllist [set block${i}(_atom_site_label)] |
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| 99 | } |
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| 100 | set uisolist {} |
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| 101 | catch { |
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| 102 | set uisolist [set block${i}(_atom_site_U_iso_or_equiv)] |
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| 103 | set Uconv 1 |
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| 104 | } |
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| 105 | if {$uisolist == ""} { |
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| 106 | set uisolist [set block${i}(_atom_site_B_iso_or_equiv)] |
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| 107 | set Uconv [expr 1/(8*3.14159*3.14159)] |
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| 108 | } |
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| 109 | set occlist {} |
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| 110 | catch { |
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| 111 | set occlist [set block${i}(_atom_site_occupancy)] |
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| 112 | } |
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| 113 | set typelist {} |
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| 114 | catch { |
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| 115 | set typelist [set block${i}(_atom_site_type_symbol)] |
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| 116 | } |
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| 117 | foreach x [set block${i}(_atom_site_fract_x)] \ |
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| 118 | y [set block${i}(_atom_site_fract_y)] \ |
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| 119 | z [set block${i}(_atom_site_fract_z)] \ |
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| 120 | lbl $lbllist uiso $uisolist occ $occlist type $typelist { |
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| 121 | # should not be any quotes, but remove them, if there are |
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| 122 | regsub -all {'} $lbl {} lbl |
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| 123 | regsub -all {'} $type {} type |
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| 124 | # CIF specifies types as Cu2+; GSAS uses Cu+2 |
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| 125 | if {[regexp {([A-Za-z]+)([1-9])([+-])} $type junk elem sign val]} { |
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| 126 | set type ${elem}${val}$sign |
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| 127 | } |
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| 128 | # if type is missing, attempt to parse an element in the label |
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| 129 | if {$type == "" && $lbl != ""} { |
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| 130 | regexp {[A-Za-z][A-Za-z]?} $lbl type |
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| 131 | } |
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| 132 | # get rid of standard uncertainies |
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| 133 | foreach var {x y z occ uiso} { |
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| 134 | catch { |
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| 135 | set $var [lindex [ParseSU [set $var]] 0] |
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| 136 | } |
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| 137 | } |
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| 138 | # convert Biso to Uiso (if needed) |
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| 139 | if {$Uconv != 1} { |
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| 140 | catch {set $uiso [expr $Uconv*$uiso]} |
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| 141 | } |
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| 142 | lappend atomlist [list $lbl $x $y $z $type $occ $uiso] |
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| 143 | } |
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| 144 | |
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| 145 | # clean up -- get rid of the CIF arrays |
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| 146 | for {set i 1} {$i <= $blocks} {incr i} { |
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| 147 | unset block$i |
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| 148 | } |
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| 149 | return "[list $spg] [list $cell] [list $atomlist] [list $msg]" |
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| 150 | } |
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| 151 | |
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| 152 | # ParseCIF reads and parses a CIF file putting the contents of |
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| 153 | # each block into arrays block1, block2,... in the caller's level |
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| 154 | # the name of the block is saved as blockN(data_) |
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| 155 | # data items are saved as blockN(_cif_name) = value |
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| 156 | # values are not reformatted, thus quotes, semicolons & newlines |
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| 157 | # are included in the value string |
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| 158 | # for looped data items, the values are included in a list: |
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| 159 | # blockN(_cif_name) = {value list ...} |
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| 160 | # the contents of each loop are saved as blockN(loop_M) |
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| 161 | # |
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| 162 | # the proc returns the number of blocks that have been read or a |
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| 163 | # null string if the file cannot be opened |
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| 164 | proc ParseCIF {filename} { |
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| 165 | if [catch { |
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| 166 | set fp [open $filename r] |
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| 167 | }] {return ""} |
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| 168 | |
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| 169 | set blocks 0 |
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| 170 | set EOF 1 |
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| 171 | set line {} |
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| 172 | set loopflag -1 |
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| 173 | # loop over tokens |
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| 174 | while {$EOF} { |
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| 175 | if {[string length [string trim $line]] <= 0} { |
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| 176 | if {[gets $fp line] < 0} {set EOF 0} |
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| 177 | } |
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| 178 | set hidden 0 |
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| 179 | set trimline [string trim $line] |
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| 180 | set firstchar [string index $trimline 0] |
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| 181 | |
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| 182 | if {[string length $trimline] <= 0} { |
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| 183 | # the line is blank |
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| 184 | set line {} |
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| 185 | continue |
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| 186 | } |
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| 187 | |
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| 188 | if {$firstchar == "#"} { |
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| 189 | # this is a comment |
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| 190 | set line {} |
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| 191 | continue |
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| 192 | } |
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| 193 | |
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| 194 | if {[string tolower [string range $trimline 0 4]] == "data_"} { |
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| 195 | # this is the beginning of a data block |
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| 196 | incr blocks |
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| 197 | # are there other tokens on this line? |
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| 198 | if {[set pos [string first { } $trimline]] == -1} { |
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| 199 | set blockname [string range $trimline 5 end] |
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| 200 | set line {} |
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| 201 | } else { |
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| 202 | set blockname [string range $trimline 5 [expr $pos-1]] |
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| 203 | set line [string range $trimline $pos end] |
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| 204 | } |
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| 205 | global block$blocks |
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| 206 | catch {unset block$blocks} |
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| 207 | set block${blocks}(data_) $blockname |
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| 208 | set loopnum -1 |
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| 209 | |
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| 210 | if {$line == ""} continue |
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| 211 | set dataname {} |
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| 212 | } |
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| 213 | |
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| 214 | if {$firstchar == "_"} { |
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| 215 | # this is a data item |
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| 216 | # are there other tokens on this line? |
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| 217 | if {[set pos [string first { } $trimline]] == -1} { |
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| 218 | set dataname $trimline |
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| 219 | set line {} |
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| 220 | } else { |
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| 221 | set dataname [string range $trimline 0 [expr $pos-1]] |
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| 222 | set line [string range $trimline $pos end] |
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| 223 | } |
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| 224 | |
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| 225 | if {$loopflag == 0} { |
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| 226 | # in a loop header, save the names in the loop |
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| 227 | lappend looplist $dataname |
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| 228 | set block${blocks}(loop_${loopnum}) $looplist |
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| 229 | # clear the data item -- should not be needed, but... |
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| 230 | set block${blocks}($dataname) {} |
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| 231 | set dataname {} |
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| 232 | } elseif {$loopflag > 0} { |
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| 233 | # in a loop body, so the loop is over |
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| 234 | set loopflag -1 |
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| 235 | } |
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| 236 | continue |
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| 237 | } |
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| 238 | |
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| 239 | if {[string tolower [string range $trimline 0 4]] == "loop_"} { |
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| 240 | set loopflag 0 |
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| 241 | incr loopnum |
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| 242 | set looplist {} |
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| 243 | set block${blocks}(loop_${loopnum}) {} |
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| 244 | # save any other tokens on this line |
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| 245 | set line [string range $trimline 5 end] |
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| 246 | continue |
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| 247 | } |
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| 248 | |
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| 249 | # keywords not matched, must be some type of value item |
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| 250 | set item {} |
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| 251 | |
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| 252 | # multiline entry with semicolon termination |
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| 253 | if {[string index $line 0] == ";"} { |
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| 254 | set item $line |
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| 255 | # read lines until we get a naked semicolon |
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| 256 | while {$EOF} { |
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| 257 | if {[gets $fp line] < 0} {set EOF 0} |
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| 258 | append item \n $line |
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| 259 | if {[string index $line 0] == ";" && \ |
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| 260 | [string trim [string range $line 1 end]] == ""} break |
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| 261 | } |
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| 262 | set line {} |
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| 263 | } elseif {$firstchar == {'}} { |
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| 264 | # hide any \' sequences in a non-ASCII character |
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| 265 | set hidden [regsub -all {\\'} $trimline \200 trimline] |
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| 266 | regexp {('[^']*')(.*)} $trimline junk item line |
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| 267 | } else { |
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| 268 | set pos [string first { } $trimline] |
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| 269 | if {$pos < 0} { |
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| 270 | set item $trimline |
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| 271 | set line {} |
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| 272 | } else { |
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| 273 | set line [string range $trimline $pos end] |
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| 274 | incr pos -1 |
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| 275 | set item [string range $trimline 0 $pos] |
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| 276 | } |
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| 277 | } |
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| 278 | |
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| 279 | # a data value has been read |
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| 280 | if $hidden { |
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| 281 | regsub -all \200 $item {\\'} item |
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| 282 | } |
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| 283 | |
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| 284 | # if in a loop, increment the loop element counter |
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| 285 | if {$loopflag >= 0} { |
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| 286 | incr loopflag |
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| 287 | set i [expr ($loopflag - 1) % [llength $looplist]] |
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| 288 | lappend block${blocks}([lindex $looplist $i]) $item |
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| 289 | } else { |
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| 290 | set block${blocks}($dataname) $item |
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| 291 | } |
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| 292 | } |
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| 293 | close $fp |
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| 294 | return $blocks |
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| 295 | } |
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| 296 | |
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| 297 | # this proc creates a hierarchical CIF browser |
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| 298 | # note that the BWidget package is required |
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| 299 | proc BrowseCIF {blocklist "selected {}" "frame .cif"} { |
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| 300 | |
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| 301 | if [catch {package require BWidget}] { |
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| 302 | tk_dialog $frame {No BWidget} \ |
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| 303 | "Sorry, the CIF Browser requires the BWidget package" \ |
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| 304 | warning 0 Continue |
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| 305 | return |
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| 306 | } |
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| 307 | if {$selected == ""} {set selected $blocklist} |
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| 308 | catch {destroy $frame} |
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| 309 | toplevel $frame |
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| 310 | wm title $frame "CIF Browser" |
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| 311 | |
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| 312 | set pw [PanedWindow $frame.pw -side top] |
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| 313 | grid $pw -sticky news -column 0 -row 0 |
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| 314 | grid columnconfigure $frame 0 -weight 1 |
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| 315 | grid rowconfigure $frame 0 -minsize 250 -weight 1 |
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| 316 | |
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| 317 | # create a left hand side pane for the hierarchical tree |
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| 318 | set pane [$pw add -weight 1] |
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| 319 | set sw [ScrolledWindow $pane.lf \ |
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| 320 | -relief sunken -borderwidth 2] |
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| 321 | set tree [Tree $sw.tree \ |
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| 322 | -relief flat -borderwidth 0 -width 15 -highlightthickness 0 \ |
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| 323 | -redraw 1] |
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| 324 | grid $sw |
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| 325 | grid $sw -sticky news -column 0 -row 0 |
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| 326 | grid columnconfigure $pane 0 -minsize 275 -weight 1 |
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| 327 | grid rowconfigure $pane 0 -weight 1 |
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| 328 | $sw setwidget $tree |
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| 329 | |
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| 330 | # create a right hand side pane to show the value |
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| 331 | set pane [$pw add -weight 1] |
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| 332 | set sw [ScrolledWindow $pane.sw \ |
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| 333 | -relief sunken -borderwidth 2] |
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| 334 | pack $sw -fill both -expand yes -side bottom |
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| 335 | set lb [ScrollableFrame::create $sw.lb -width 250] |
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| 336 | $sw setwidget $lb |
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| 337 | |
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| 338 | set num 0 |
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| 339 | foreach n $blocklist { |
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| 340 | global block$n |
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| 341 | # make a list of data items in loops |
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| 342 | set looplist {} |
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| 343 | foreach loop [array names block$n loop_*] { |
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| 344 | eval lappend looplist [set block${n}($loop)] |
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| 345 | } |
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| 346 | # put the block name |
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| 347 | set blockname [set block${n}(data_)] |
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| 348 | set open 0 |
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| 349 | if {[lsearch $selected $n] != -1} {set open 1} |
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| 350 | $tree insert end root block$n -text "_data_$blockname" \ |
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| 351 | -open $open -image [Bitmap::get copy] |
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| 352 | # loop over the items in each block |
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| 353 | foreach item [array names block$n _*] { |
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| 354 | # don't include looped items |
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| 355 | if {[lsearch $looplist $item] == -1} { |
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| 356 | $tree insert end block$n [incr num] -text $item \ |
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| 357 | -image [Bitmap::get folder] -data block$n |
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| 358 | } |
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| 359 | } |
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| 360 | foreach loop [array names block$n loop_*] { |
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| 361 | $tree insert end block$n block${n}$loop -text $loop \ |
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| 362 | -image [Bitmap::get file] -data "block$n loop" |
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| 363 | foreach item [set block${n}($loop)] { |
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| 364 | $tree insert end block${n}$loop [incr num] -text $item \ |
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| 365 | -image [Bitmap::get folder] -data "block$n $loop" |
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| 366 | } |
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| 367 | } |
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| 368 | } |
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| 369 | $tree bindImage <1> "showCIFvalue $tree $sw" |
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| 370 | $tree bindText <1> "showCIFvalue $tree $sw" |
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| 371 | grid [button $frame.c -text Close -command "destroy $frame"] -column 0 -row 1 |
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| 372 | } |
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| 373 | |
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| 374 | # used in BrowseCIF in response to the spinbox |
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| 375 | # show the contents of a loop |
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| 376 | proc ShowLoopVar {array loop frame sb} { |
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| 377 | global $array |
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| 378 | set looplist [set ${array}($loop)] |
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| 379 | set index [$sb getvalue] |
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| 380 | set i 0 |
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| 381 | foreach var $looplist { |
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| 382 | incr i |
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| 383 | [$frame.$i getframe].l config \ |
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| 384 | -text [lindex [set ${array}($var)] $index] |
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| 385 | } |
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| 386 | } |
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| 387 | |
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| 388 | # used in BrowseCIF in response to the clicking on a CIF dataname |
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| 389 | # shows the contents data item or a loop |
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| 390 | proc showCIFvalue {tree sw item} { |
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| 391 | set data [$tree itemcget $item -data] |
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| 392 | set text [$tree itemcget $item -text] |
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| 393 | |
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| 394 | # delete old contents of frame |
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| 395 | set frame [$sw.lb getframe] |
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| 396 | eval destroy [grid slaves $frame] |
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| 397 | # reset the scrollbars |
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| 398 | $sw.lb xview moveto 0 |
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| 399 | $sw.lb yview moveto 0 |
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| 400 | # leave room for a scrollbar |
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| 401 | grid columnconfig $frame 0 -minsize [expr \ |
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| 402 | [winfo width [winfo parent $frame]] - 20] |
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| 403 | if {$data == ""} { |
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| 404 | return |
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| 405 | } |
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| 406 | |
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| 407 | # |
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| 408 | if {[llength $data] == 2} { |
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| 409 | global [lindex $data 0] |
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| 410 | if {[lindex $data 1] == "loop"} { |
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| 411 | set looplist [set [lindex $data 0]($text)] |
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| 412 | # get number of elements for first item |
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| 413 | set items [llength [set [lindex $data 0]([lindex $looplist 0])]] |
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| 414 | set sb $frame.spin |
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| 415 | grid [SpinBox $sb -range "1 $items 1" \ |
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| 416 | -label "Loop\nelement #" -labelwidth 10 -width 10 \ |
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| 417 | -command "ShowLoopVar [lindex $data 0] $text $frame $sb" \ |
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| 418 | -modifycmd "ShowLoopVar [lindex $data 0] $text $frame $sb"] \ |
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| 419 | -column 0 -row 0 -sticky w |
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| 420 | set i 0 |
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| 421 | # grid columnconfig $frame 0 -minsize 250 |
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| 422 | foreach var $looplist { |
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| 423 | incr i |
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| 424 | grid [TitleFrame $frame.$i -text $var -side left] \ |
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| 425 | -column 0 -row $i -sticky ew |
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| 426 | pack [label [$frame.$i getframe].l -anchor w -justify left] -side left |
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| 427 | } |
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| 428 | ShowLoopVar [lindex $data 0] $text $frame $sb |
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| 429 | } else { |
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| 430 | grid [TitleFrame $frame.0 -text $text -side left] \ |
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| 431 | -column 0 -row 0 -sticky ew |
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| 432 | set row 0 |
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| 433 | set frame0 [$frame.0 getframe] |
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| 434 | grid columnconfig $frame0 2 -weight 1 |
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| 435 | foreach item [set [lindex $data 0]($text)] { |
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| 436 | incr row |
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| 437 | grid [label $frame0.a$row -justify left -text $row]\ |
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| 438 | -sticky w -column 0 -row $row |
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| 439 | grid [label $frame0.b$row -bd 2 -relief groove \ |
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| 440 | -justify left -anchor w -text $item]\ |
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| 441 | -sticky new -column 1 -row $row |
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| 442 | } |
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| 443 | } |
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| 444 | } else { |
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| 445 | # unlooped data item |
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| 446 | global [lindex $data 0] |
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| 447 | grid [TitleFrame $frame.0 -text $text -side left] \ |
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| 448 | -column 0 -row 0 -sticky ew |
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| 449 | pack [label [$frame.0 getframe].l -anchor w -justify left\ |
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| 450 | -text [set ${data}($text)]] -side left |
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| 451 | } |
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| 452 | # $lf configure -text $text |
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| 453 | } |
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| 454 | |
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| 455 | # Parse a number in CIF, that may include a SU (ESD) value |
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| 456 | # note that this routine will ignore spaces, quotes & semicolons |
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| 457 | proc ParseSU {value} { |
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| 458 | # if there is no SU just return the value |
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| 459 | if {[string first "(" $value] == -1} { |
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| 460 | return $value |
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| 461 | } |
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| 462 | # is there a decimal point? |
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| 463 | if [regexp {([-+]?[0-9]*\.)([0-9]*)\(([0-9]+)\)} $value junk a b err] { |
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| 464 | set ex [string length $b] |
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| 465 | return [list ${a}${b} [expr {pow(10.,-$ex)*$err}]] |
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| 466 | } |
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| 467 | if [regexp {([-+]?[0-9]*)\(([0-9]+)\)} $value junk a err] { |
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| 468 | return [list ${a} $err] |
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| 469 | } |
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| 470 | tk_dialog .err {ParseSU Error} \ |
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| 471 | "ParseSU: Error processing value $value" \ |
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| 472 | warning 0 Continue |
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| 473 | } |
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