1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
|
# Another simple example of how PyMOL can be controlled using a web browser
# using Python's built-in web server capabilities
try:
import BaseHTTPServer
except ImportError:
import http.server as BaseHTTPServer
import time
import cgi
import string
import threading
import traceback
import os, sys, re
from pymol import cmd
from chempy.sdf import SDF
# example 3D sd file
input_sdf = os.environ['PYMOL_PATH']+"/test/dat/ligs3d.sdf"
if not os.path.exists(input_sdf):
from inspect import getsourcefile
current_file_dir = os.path.dirname(os.path.abspath(getsourcefile(lambda:0)))
input_sdf = os.path.join(current_file_dir, "../../test/dat/ligs3d.sdf")
class SafeDict(dict):
'''
we will need to synchronize access if we later adopt a
multi-threaded approach
'''
pass
# global singleton class for holding server state
ServerState = SafeDict()
# we're not maintaining session tokens yet...
default_token = 0
def write_table(out, table):
out.write('<html>\n')
out.write('<header>\n')
out.write('<link rel="stylesheet" type="text/css" href="/pymol.css"></link>')
out.write('<script type="text/javascript" src="pymol.js"></script>\n')
out.write('</header>')
out.write('<body>\n')
out.write('<form action="./quit.pymol"><button type="submit">Quit</button></form>\n')
out.write('<table>\n')
header = table['header']
for heading in header:
out.write('<th>')
out.write(heading)
out.write('</th>')
body = table['body']
for row in body:
out.write('<tr>')
for col in row:
out.write('<td>')
out.write(col)
out.write('</td>')
out.write('</tr>\n')
out.write('</table>')
out.write('<iframe name="myStatus" width="500" height="60" frameborder=0>')
out.write('</iframe>\n')
out.write('<form name="hidden" target="myStatus"></form>')
out.write('</body></html>\n')
_server = None
def _shutdown(self_cmd=cmd):
global _server
if _server != None:
_server.socket.close()
self_cmd.quit()
class PymolHandler(BaseHTTPServer.BaseHTTPRequestHandler):
def log_message(self, format, *args):
# nuke logging for the time being since it slows down PyMOL
pass
def do_css(self):
self.send_response(200)
self.send_header('Content-type','text/css')
self.end_headers()
self.wfile.write('''
table {
border-width: 1px 1px 1px 1px;
border-spacing: 1px;
border-style: outset outset outset outset;
border-color: gray gray gray gray;
border-collapse: separate;
background-color: gray;
}
table th {
border-width: 1px 1px 1px 1px;
padding: 2px 5px 2px 5px;
border-style: inset inset inset inset;
border-color: gray gray gray gray;
background-color: lightblue;
-moz-border-radius: 0px 0px 0px 0px;
}
table td {
border-width: 1px 1px 1px 1px;
padding: 2px 5px 2px 5px;
border-style: inset inset inset inset;
border-color: gray gray gray gray;
background-color: white;
-moz-border-radius: 0px 0px 0px 0px;
}
a:link {text-decoration: none; color: blue; }
a:visited {text-decoration: none; color: blue; }
a:active {text-decoration: none; color: blue; }
''')
def do_js(self):
self.send_response(200)
self.send_header('Content-type','text/javascript')
self.end_headers()
self.wfile.write('''
function load(molid)
{
// unnecessary...but keeping it around for later...
// this doesnt actually work anyway!
document.forms['hidden'].method='get';
document.forms['hidden'].action='http://localhost:8080/load.pymol?test=1&molid=' + molid;
document.forms['hidden'].submit();
}
''')
def do_pymol(self):
if "table.pymol" in self.path: # send table
session = ServerState[default_token]
self.send_response(200)
self.send_header('Content-type', 'text/html')
self.send_header('Cache-control', 'no-cache')
self.send_header('Pragma', 'no-cache')
self.end_headers()
if 'table' not in session:
self.wfile.write("<p>No table defined.</p>\n")
else:
write_table(self.wfile, session['table'])
elif "quit.pymol" in self.path:
self.wfile.write('<html><body><p>Quitting...</p></body></html>')
self.wfile.flush()
_shutdown()
elif "load.pymol" in self.path:
self.send_response(200)
self.send_header('Content-type', 'text/html')
self.send_header('Cache-control', 'no-cache')
self.send_header('Pragma', 'no-cache')
self.end_headers()
mo = re.search("molid\=([A-Z0-9]+)",self.path)
if mo:
mol_id = mo.groups(1)[0]
session = ServerState[default_token]
mol_dict = session['data']['mol_dict']
self_cmd = session['cmd']
if mol_id in self_cmd.get_names('objects'):
if mol_id in self_cmd.get_names('objects',enabled_only=1):
self.wfile.write("<p>Disabling %s...</p>"%mol_id)
self_cmd.disable(mol_id)
else:
self.wfile.write("<p>Enabling %s...</p>"%mol_id)
self_cmd.enable(mol_id)
else:
self.wfile.write("<p>Loading %s...</p>"%mol_id)
self_cmd.read_molstr(mol_dict[mol_id], mol_id)
self_cmd.show_as("sticks",mol_id)
else:
self.wfile.write("<p>Error processing query: %s</p>"%self.path)
else: # start page
self.send_response(200)
self.send_header('Content-type', 'text/html')
self.send_header('Cache-control', 'no-cache')
self.send_header('Pragma', 'no-cache')
self.end_headers()
self.wfile.write("<p>Unhandled PyMOL request</p>")
self.wfile.flush()
def do_GET(self):
try:
doc = self.path.split('?')[0]
if doc.endswith('.pymol'): # PyMOL
try:
self.do_pymol()
except:
traceback.print_exc()
elif doc.endswith('.js'): # Javascript
self.do_js()
elif doc.endswith('.css'): # Javascript
self.do_css()
elif doc.endswith('.html'):
f = open('.'+self.path) # UNSAFE!!!
self.send_response(200)
self.send_header('Content-type', 'text/html')
self.end_headers()
self.wfile.write(f.read())
f.close()
except IOError:
self.send_error(404,'File Not Found: %s' % self.path)
def do_POST(self): # not currently used
global rootnode
try:
ctype, pdict = cgi.parse_header(self.headers.getheader('content-type'))
if ctype == 'multipart/form-data':
query=cgi.parse_multipart(self.rfile, pdict)
self.send_response(301)
self.end_headers()
upfilecontent = query.get('upfile')
print("filecontent", upfilecontent[0])
self.wfile.write('<HTML>POST OK.<BR><BR>');
self.wfile.write(upfilecontent[0]);
except :
pass
def table_from_data(data):
# pull MOLID to the far left
col_id_list = ['MOLID'] + [x for x in data['col_id_list'] if x!='MOLID']
content = data['content']
# create the header fields
header = []
for col_id in col_id_list:
header.append(col_id)
# create the body
body = []
for row_id in data['row_id_list']:
row = []
for col_id in col_id_list:
if col_id == 'MOLID':
text = content.get( (row_id,col_id),'')
row.append('<a target="myStatus" href="load.pymol?molid=%s">'%text +
text + '</a>')
else:
row.append( content.get( (row_id,col_id),'' ))
body.append(row)
return {
'header' : header,
'body' : body,
}
def data_from_sdf(sdf_file_path):
mol_dict = {}
row_id_list = []
row_id_dict = {}
col_id_list = []
col_id_dict = {}
# first pass, load the identifiers, MOL files, and tag names
col = 0
sdf = SDF(sdf_file_path)
while 1:
rec = sdf.read()
if not rec:
break
mol = rec.get('MOL')
# get the unique identifier
mol_id = mol[0].strip()
# store the MOL record
mol_dict[mol_id] = ''.join(mol)
# add row (assuming mol_id is unique)
row_id_list.append(mol_id)
row_id_dict[mol_id] = None
# add column (if new)
for key in rec.kees:
if key != 'MOL':
if key not in col_id_dict:
col_id_list.append(key)
col_id_dict[key] = None
# second pass, read the actual data into the table structure
content = {}
sdf = SDF(sdf_file_path)
while 1:
rec = sdf.read()
if not rec:
break
mol_id = rec.get('MOL')[0].strip()
for key in rec.kees:
if key != 'MOL':
content[ (mol_id,key) ] = rec.get(key)[0].strip()
return {
'content' : content,
'row_id_list' : row_id_list,
'col_id_list' : col_id_list,
'mol_dict' : mol_dict
}
def open_browser():
import webbrowser
time.sleep(1)
webbrowser.open('http://localhost:8080/table.pymol')
# import os
# os.system('open http://localhost:8080/start.pymol')
def main():
try:
global _server
_server = BaseHTTPServer.HTTPServer(('', 8080), PymolHandler)
print('started httpserver...')
_server.serve_forever()
except KeyboardInterrupt:
print('^C received, shutting down server')
_server.socket.close()
if __name__ == '__main__':
print("this script must be run from within PyMOL")
if __name__ == 'pymol':
session = SafeDict()
session['cmd'] = cmd # could replaced by instance instead of module
session['data'] = data_from_sdf(input_sdf)
session['table'] = table_from_data(session['data'])
ServerState[default_token] = session
t = threading.Thread(target=main)
t.setDaemon(1)
t.start()
t = threading.Thread(target=open_browser)
t.setDaemon(1)
t.start()
"""
"""
|
