1: #!/usr/bin/perl
2:
3: # Coded by Guy Ashkenazi, guy@fh.huji.ac.il
4: # Based on the work of Peter Ertl, peter.ertl@pharma.novartis.com
5:
6: use strict;
7: use lib '/home/httpd/lib/perl';
8: use GD;
9: use PostScript::Simple;
10: use LONCAPA::loncgi();
11:
12: if (! &LONCAPA::loncgi::check_cookie_and_load_env()) {
13: print <<END;
14: Content-type: text/html
15:
16: <html>
17: <head><title>Bad Cookie</title></head>
18: <body>
19: Your cookie information is incorrect.
20: </body>
21: </html>
22: END
23: exit;
24: }
25:
26: sub unescape {
27: my $str=shift;
28: $str =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C",hex($1))/eg;
29: return $str;
30: }
31:
32: # read the width and the JME string from the cgi query
33: my $id=$ENV{'QUERY_STRING'};
34: my @JMEstring = split(/ /,&unescape($ENV{'cgi.'.$id.'.JME'}));
35: my $width = $ENV{'cgi.'.$id.'.WIDTH'};
36: my $png = $ENV{'cgi.'.$id.'.PNG'};
37: my $ps = $ENV{'cgi.'.$id.'.PS'};
38: if (!$width) { $width = 200; }
39:
40: # parse JME string
41:
42: my $natoms= shift @JMEstring;
43: my $nbonds= shift @JMEstring;
44: my (@name,@x,@y);
45: for (my $i = 0; $i < $natoms; $i++) {
46: @name[$i] = shift @JMEstring;
47: @x[$i] = shift @JMEstring;
48: @y[$i] = shift @JMEstring;
49: }
50:
51: my (@atomA,@atomB,@bondType);
52: for (my $i = 0; $i < $nbonds; $i++) {
53: @atomA[$i] = (shift @JMEstring)-1;
54: @atomB[$i] = (shift @JMEstring)-1;
55: @bondType[$i] = shift @JMEstring;
56: }
57:
58: # Find border and move lower left corner to (1.5,1.0)
59:
60: my $xmin = my $xmax = @x[0];
61: my $ymin = my $ymax = $y[0];
62: my $maxName = 0;
63:
64: for (my $i = 1; $i < $natoms; $i++) {
65: $xmax = @x[$i] if (@x[$i] > $xmax);
66: $xmin = @x[$i] if (@x[$i] < $xmin);
67: $ymax = @y[$i] if (@y[$i] > $ymax);
68: $ymin = @y[$i] if (@y[$i] < $ymin);
69: @name[$i] =~ /(\@{1,2})?(\w+)([\+|\-])?(\d)?/;
70: $maxName = length $2 if (length $2 > $maxName);
71: }
72: $maxName = ($maxName-3 < 0) ? 0 : $maxName-3;
73: my $scale = $width / ($xmax-$xmin+3+$maxName);
74: my $height = $scale * ($ymax-$ymin+2);
75:
76: for (my $i = 0; $i < $natoms; $i++) {
77: @x[$i] += (1.5+$maxName/2-$xmin);
78: if ($png) { @x[$i] *= $scale; }
79: @y[$i] += (1.0-$ymin);
80: if ($png) { @y[$i] *= $scale; }
81: }
82:
83: # Count bonds
84:
85: my @bonds = map {0} 0..$natoms-1;
86: my @adjacent = map {0} 0..$natoms-1;
87: my @bondsx = map {0} 0..$natoms-1;
88: my @bondsy = map {0} 0..$natoms-1;
89: for (my $i = 0; $i < $nbonds; $i++) {
90: @bonds[@atomA[$i]] += (@bondType[$i]>0) ? @bondType[$i] : 1;
91: @bonds[@atomB[$i]] += (@bondType[$i]>0) ? @bondType[$i] : 1;
92:
93: @adjacent[@atomA[$i]]++;
94: @adjacent[@atomB[$i]]++;
95:
96: @bondsx[@atomA[$i]] += @x[@atomB[$i]] - @x[@atomA[$i]];
97: @bondsy[@atomA[$i]] += @y[@atomB[$i]] - @y[@atomA[$i]];
98: @bondsx[@atomB[$i]] += @x[@atomA[$i]] - @x[@atomB[$i]];
99: @bondsy[@atomB[$i]] += @y[@atomA[$i]] - @y[@atomB[$i]];
100: }
101:
102: # Create a new PostScript object
103: my ($im,$white,$black,$gray);
104: if ($png) {
105: $im = new GD::Image($width,$height);
106: $white = $im->colorAllocate(255,255,255);
107: $black = $im->colorAllocate(0,0,0);
108: $gray = $im->colorAllocate(200,200,200);
109: #$gdAntiAliased = $im->colorAllocate(1,1,1);
110: $im->setAntiAliased($black);
111: } elsif ($ps) {
112: $im = new PostScript::Simple(xsize => $xmax-$xmin+3+$maxName,
113: ysize => $ymax-$ymin+2,
114: clip => 1,
115: eps => 1,
116: color => 0,
117: units => "cm");
118: }
119:
120: # Draw bonds
121: my $doubleWidth;
122: my $tripleWidth;
123: if ($png) {
124: $doubleWidth = 0.10*$scale;
125: $tripleWidth = 0.15*$scale;
126: } elsif ($ps) {
127: $doubleWidth = 0.10;
128: $tripleWidth = 0.15;
129: }
130:
131: for (my $i = 0; $i < $nbonds; $i++) {
132: my $xa = @x[@atomA[$i]];
133: my $ya = @y[@atomA[$i]];
134: my $xb = @x[@atomB[$i]];
135: my $yb = @y[@atomB[$i]];
136:
137: my ($sina,$cosa,$dx,$dy);
138: if (@bondType[$i] != 1) {
139: $dx = $xb-$xa;
140: $dy = $yb-$ya;
141: my $dd = sqrt($dx*$dx + $dy*$dy);
142: $sina=$dy/$dd;
143: $cosa=$dx/$dd;
144: }
145: if (@bondType[$i] == -2) {
146: for (my $t = 0; $t <= 1; $t += 0.1) {
147: my $xab = $xa + $t*$dx;
148: my $yab = $ya + $t*$dy;
149: my $xperp = $tripleWidth*$sina*$t;
150: my $yperp = $tripleWidth*$cosa*$t;
151: if ($png) {
152: $im->line($xab+$xperp,$height-($yab-$yperp),
153: $xab-$xperp,$height-($yab+$yperp),
154: gdAntiAliased);
155: } elsif ($ps) {
156: $im->line($xab+$xperp,$yab-$yperp,$xab-$xperp,$yab+$yperp);
157: }
158: }
159: }
160: elsif (@bondType[$i] == -1) {
161: my $xperp = $tripleWidth*$sina;
162: my $yperp = $tripleWidth*$cosa;
163: if ($png) {
164: my $poly = new GD::Polygon;
165: $poly->addPt($xa,$height-$ya);
166: $poly->addPt($xb+$xperp,$height-($yb-$yperp));
167: $poly->addPt($xb-$xperp,$height-($yb+$yperp));
168: $im->filledPolygon($poly,$black);
169: } elsif ($ps) {
170: $im->polygon({filled=>1},
171: $xa,$ya,
172: $xb+$xperp,$yb-$yperp,
173: $xb-$xperp,$yb+$yperp);
174: }
175: }
176: elsif (@bondType[$i] == 1) {
177: if ($png) {
178: $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased);
179: } elsif ($ps) {
180: $im->line($xa,$ya,$xb,$yb);
181: }
182: }
183: elsif (@bondType[$i] == 2 &&
184: ((@adjacent[@atomA[$i]] == 1 && @adjacent[@atomB[$i]] > 2)||
185: (@adjacent[@atomB[$i]] == 1 && @adjacent[@atomA[$i]] > 2))) {
186: # centered bond
187: my $xperp = $doubleWidth*$sina;
188: my $yperp = $doubleWidth*$cosa;
189: if ($png) {
190: $im->line($xa+$xperp,$height-($ya-$yperp),
191: $xb+$xperp,$height-($yb-$yperp),
192: gdAntiAliased);
193: $im->line($xa-$xperp,$height-($ya+$yperp),
194: $xb-$xperp,$height-($yb+$yperp),
195: gdAntiAliased);
196: } elsif ($ps) {
197: $im->line($xa+$xperp,$ya-$yperp,$xb+$xperp,$yb-$yperp);
198: $im->line($xa-$xperp,$ya+$yperp,$xb-$xperp,$yb+$yperp);
199: }
200: }
201: elsif (@bondType[$i] == 2) {
202: my $xperp = 2*$doubleWidth*$sina;
203: my $yperp = 2*$doubleWidth*$cosa;
204: if ($png) {
205: $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased);
206: $im->line($xa+0.1*$dx-$xperp,$height-($ya+0.1*$dy+$yperp),
207: $xb-0.1*$dx-$xperp,$height-($yb-0.1*$dy+$yperp),
208: gdAntiAliased);
209: } elsif ($ps) {
210: $im->line($xa,$ya,$xb,$yb);
211: $im->line($xa+0.1*$dx-$xperp,$ya+0.1*$dy+$yperp,
212: $xb-0.1*$dx-$xperp,$yb-0.1*$dy+$yperp);
213:
214: }
215: }
216: elsif (@bondType[$i] == 3) {
217: my $xperp = $tripleWidth*$sina;
218: my $yperp = $tripleWidth*$cosa;
219: if ($png) {
220: $im->line($xa,$height-$ya,$xb,$height-$yb,gdAntiAliased);
221: $im->line($xa+$xperp,$height-($ya-$yperp),
222: $xb+$xperp,$height-($yb-$yperp),
223: gdAntiAliased);
224: $im->line($xa-$xperp,$height-($ya+$yperp),
225: $xb-$xperp,$height-($yb+$yperp),
226: gdAntiAliased);
227: } elsif ($ps) {
228: $im->line($xa,$ya,$xb,$yb);
229: $im->line($xa+$xperp,$ya-$yperp,$xb+$xperp,$yb-$yperp);
230: $im->line($xa-$xperp,$ya+$yperp,$xb-$xperp,$yb+$yperp);
231: }
232: }
233: }
234:
235: # Write labels
236:
237: my %valence = ("C",4,"N",3,"P",3,"O",2,"S",2);
238: my %font_width = (" ",250,"+",564,"-",500,"0",500,"1",500,"2",500,"3",500,"4",500,"5",500,"6",500,"7",500,"8",500,"9",500,"A",722,"B",667,"C",667,"D",722,"E",611,"F",556,"G",722,"H",722,"I",333,"J",389,"K",722,"L",611,"M",889,"N",722,"O",722,"P",556,"Q",722,"R",667,"S",556,"T",611,"U",722,"V",722,"W",944,"X",722,"Y",722,"Z",611,"a",444,"b",500,"c",444,"d",500,"e",444,"f",333,"g",500,"h",500,"i",278,"j",278,"k",500,"l",278,"m",778,"n",500,"o",500,"p",500,"q",500,"r",333,"s",389,"t",278,"u",500,"v",500,"w",722,"x",500,"y",500,"z",444);
239: my $font = '/usr/share/fonts/default/Type1/n021003l.pfb';
240: my $pointsize = 20;
241: my ($ptsize,@bounds);
242: if ($png) {
243: @bounds = GD::Image->stringTTF($black,$font,100,0,0,0,"H");
244: $ptsize = 100*0.662*$pointsize*(2.54/72)*$scale/(@bounds[3]-@bounds[5]);
245: }
246:
247: for (my $i = 0; $i < $natoms; $i++) {
248: my ($formula,$sign,$charge) =
249: (@name[$i] =~ /(\w+)([\+|\-])?(\d)?/);
250: if ($png) {
251: $sign = "–" if ($sign eq "-"); # replace by n-dash
252: }
253: if ($formula ne "C" || $sign ne ""||
254: @adjacent[$i] < 2 || (@adjacent[$i] == 2 && @bonds[$i] == 4)) {
255: # don't show C, unless charged, terminal, or linear
256: my $nH = 0;
257: if (exists $valence{$formula}) {
258: $nH = $valence{$formula} - @bonds[$i];
259: $nH += (($charge eq "")? 1 : $charge) if ($sign eq "+");
260: $nH -= (($charge eq "")? 1 : $charge) if ($sign eq "-");
261: }
262: $formula .= "H" if ($nH > 0);
263: $formula .= $nH if ($nH > 1);
264: my @formula = $formula=~ /[A-Z][a-z]?\d*/g;
265:
266: my $PI = 3.1415;
267: my $bondAngle;
268: if (abs(@bondsy[$i]) < 0.01 && abs(@bondsx[$i]) < 0.01) {
269: $bondAngle = -$PI;
270: }
271: else {
272: $bondAngle = atan2(@bondsy[$i],@bondsx[$i]);
273: }
274:
275: my $direction;
276: if (@adjacent[$i] < 2) {
277: $direction = (@bondsx[$i] < 0.01) ? "r" : "l";
278: }
279: else {
280: if ($bondAngle >= -$PI/4 && $bondAngle <= $PI/4) {
281: $direction = "l";
282: }
283: elsif ($bondAngle > $PI/4 && $bondAngle < 3*$PI/4) {
284: $direction = "d";
285: }
286: elsif ($bondAngle < -$PI/4 && $bondAngle > -3*$PI/4) {
287: $direction = "u";
288: }
289: else {
290: $direction = "r";
291: }
292: }
293:
294: if ($direction eq "r") { # direction = right
295: @formula[0] =~ /([A-Z][a-z]?)(\d*)/;
296: my $carrige = @x[$i]-stringWidth($1)/2;
297: foreach (@formula) {
298: $_ =~ /([A-Z][a-z]?)(\d*)/;
299: $carrige = printElement ($1,$2,$carrige,@y[$i]);
300: }
301: printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne "");
302: }
303: elsif ($direction eq "l") { # direction = left, reverse hydrogens
304: @formula[0] =~ /([A-Z][a-z]?)(\d*)/;
305: my $carrige = @x[$i]+
306: stringWidth($1)/2+stringWidth($2)-stringWidth($formula);
307: foreach (reverse @formula) {
308: $_ =~ /([A-Z][a-z]?)(\d*)/;
309: $carrige = printElement ($1,$2,$carrige,@y[$i]);
310: }
311: printCharge ($sign,$charge,$carrige,@y[$i]) if ($sign ne "");
312: }
313: elsif ($direction eq "u") { # direction = up
314: (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;
315: my $carrige = @x[$i]-stringWidth($1)/2;
316: $carrige = printElement ($1,$2,$carrige,@y[$i]);
317: my $y = (@formula > 0) ? @y[$i] + fm2cm(800) : @y[$i];
318: $carrige =
319: (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige;
320: foreach (@formula) {
321: $_ =~ /([A-Z][a-z]?)(\d*)/;
322: $carrige = printElement ($1,$2,$carrige,$y);
323: }
324: printCharge ($sign,$charge,$carrige,$y) if ($sign ne "");
325: }
326: else { # direction = down
327: (shift @formula) =~ /([A-Z][a-z]?)(\d*)/;
328: my $carrige = @x[$i]-stringWidth($1)/2;
329: $carrige = printElement ($1,$2,$carrige,@y[$i]);
330: my $y = (@formula > 0) ? @y[$i] + fm2cm(-800) : @y[$i];
331: $carrige =
332: (@formula > 0) ? @x[$i]-stringWidth($1)/2 : $carrige;
333: foreach (@formula) {
334: $_ =~ /([A-Z][a-z]?)(\d*)/;
335: $carrige = printElement ($1,$2,$carrige,$y);
336: }
337: printCharge ($sign,$charge,$carrige,$y) if ($sign ne "");
338: }
339: }
340: }
341:
342: if ($png) {
343: # make sure we are writing to a binary stream
344: binmode STDOUT;
345:
346: # Convert the image to PNG and print it on standard output
347: print "Content-type: image/png\n\n";
348: print $im->png;
349: } elsif ($ps) {
350: my $psfile = "/home/httpd/perl/tmp/".$id.'.eps';
351: $im->output($psfile);
352: print "Content-type: text/html\n\n";
353: print (<<HTML)
354: <html>
355: <body>
356: Wrote eps file $psfile
357: </body>
358: </html>
359: HTML
360: }
361:
362: sub stringWidth {
363: my ($string) = @_;
364: my $width = 0;
365: while ($string =~ /[A-Za-z]/g) {
366: if ($png) {
367: my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,0,0,$&);
368: $width += @bounds[2]-@bounds[0]+2;
369: } elsif ($ps) {
370: $width += $font_width{$&};
371: }
372: }
373: while ($string =~ /[\d+-]/g) {
374: if ($png) {
375: my @bounds=GD::Image->stringTTF($black,$font,0.6*$ptsize,0,0,0,$&);
376: $width += @bounds[2]-@bounds[0]+2;
377: } elsif ($ps) {
378: $width += 0.6*$font_width{$&};
379: }
380: }
381:
382: return $width;
383: }
384:
385: sub fm2cm { #font metrics to cm
386: my ($fm) = @_;
387: if ($png) {
388: return $scale*(2.54/72)*$pointsize*$fm/1000;
389: } elsif ($ps) {
390: return (2.54/72)*$pointsize*$fm/1000;
391: }
392: }
393:
394: sub printElement {
395: if ($png) {
396: return &printElement_png(@_);
397: } elsif ($ps) {
398: return &printElement_ps(@_);
399: }
400: }
401:
402: sub printElement_png { #element symbol + optional subscript
403: my ($element,$subscript,$x,$y) = @_;
404: my $yy = 662;
405:
406: my @bounds = GD::Image->stringTTF($black,$font,$ptsize,0,
407: $x,$height-($y+fm2cm(-$yy/2)),$element);
408: $im->filledRectangle(
409: @bounds[6]-1,@bounds[7]-fm2cm(135),
410: @bounds[2]+1,@bounds[3]+fm2cm(135),$white);
411:
412: $im->stringTTF($black,$font,$ptsize,0,
413: $x,$height-($y+fm2cm(-$yy/2)),$element);
414: $x = @bounds[2] + 1;
415:
416: if ($subscript ne "") {
417: @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,
418: $x,$height-($y+fm2cm(-0.8*$yy)),$subscript);
419: $im->filledRectangle(
420: @bounds[6]-1,@bounds[7]-fm2cm(45),
421: @bounds[2]+1,@bounds[3]+fm2cm(45),$white);
422: $im->stringTTF($black,$font,0.6*$ptsize,0,
423: $x,$height-($y+fm2cm(-0.8*$yy)),$subscript);
424: }
425: $x = @bounds[2] + 1;
426: }
427:
428: sub printElement_ps { #element symbol + optional subscript
429: my ($element,$subscript,$x,$y) = @_;
430: $height = 662;
431:
432: $im->setcolour("white");
433: $im->box({filled=>1},
434: $x+fm2cm(-30),$y+fm2cm(-$height/2-150),
435: $x+fm2cm(stringWidth($element)+50),$y+fm2cm(+$height/2+150));
436: $im->setcolour("black");
437: $im->setfont("Times-Roman",$pointsize);
438: $im->text($x,$y+fm2cm(-$height/2),$element);
439: $x += fm2cm(stringWidth($element));
440:
441: if ($subscript ne "") {
442: $im->setcolour("white");
443: $im->box({filled=>1},
444: $x,$y+fm2cm(-0.8*$height-45),
445: $x+fm2cm(stringWidth($subscript)+50),$y+fm2cm(-0.2*$height+45));
446: $im->setcolour("black");
447: $im->setfont("Times-Roman",0.6*$pointsize);
448: $im->text($x,$y+fm2cm(-0.8*$height),$subscript);
449: }
450: $x += fm2cm(stringWidth($subscript));
451: }
452:
453: sub printCharge {
454: if ($png) {
455: return &printCharge_png(@_);
456: } elsif ($ps) {
457: return &printCharge_ps(@_);
458: }
459: }
460:
461: sub printCharge_png {
462: my ($sign,$charge,$x,$y) = @_;
463: my $yy = 662;
464:
465: $charge = "" if ($charge == 1);
466: $charge .= $sign;
467:
468: my @bounds = GD::Image->stringTTF($black,$font,0.6*$ptsize,0,
469: $x,$height-($y+fm2cm(0.2*$yy)),$charge);
470: $im->filledRectangle(
471: @bounds[6]-1,@bounds[7]-fm2cm(45),
472: @bounds[2]+1,@bounds[3]+fm2cm(45),$white);
473:
474: $im->stringTTF($black,$font,0.6*$ptsize,0,$x,$height-($y+fm2cm(0.2*$yy)),$charge);
475: $x = @bounds[2] + 1;
476: }
477:
478: sub printCharge_ps {
479: my ($sign,$charge,$x,$y) = @_;
480: $height = 662;
481:
482: $charge = "" if ($charge == 1);
483: $charge .= $sign;
484:
485: $im->setcolour("white");
486: $im->box({filled=>1},
487: $x,$y+fm2cm(0.2*$height-45),
488: $x+fm2cm(stringWidth($charge)+50),$y+fm2cm(0.8*$height+45));
489:
490: if ($sign eq "-") { # replace by n-dash
491: chop $charge;
492: $charge .= "\xb1";
493: }
494: $im->setcolour("black");
495: $im->setfont("Times-Roman",0.6*$pointsize);
496: $im->text($x,$y+fm2cm(0.2*$height),$charge);
497: $x += fm2cm(stringWidth($charge));
498: }
499:
500:
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