/
__init__.py
250 lines (220 loc) · 10.4 KB
/
__init__.py
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
import time
import json
try:
import IPython.display
_has_IPython = True
except ImportError:
_has_IPython = False
#surface type constants
VDW =1
MS=2
SAS=3
SES=4
def using_ipython(func):
def inner(*args, **kwargs):
if not _has_IPython:
raise ImportError("This function requires an active IPython notebook.")
return func(*args, **kwargs)
return inner
class view(object):
'''A class for constructing embedded 3Dmol.js views in ipython notebooks.
The results are completely static which means there is no need for there
to be an active kernel but also that there is no communication between
the javascript viewer and ipython.
Optionally, a viewergrid tuple (rows,columns) can be passed to create
a grid of viewers in a single canvas object. Successive commands than need to
specify which viewer they apply to (with viewer=(r,c)) or will apply to all
viewers in the grid.
The API for the created object is exactly that for $3Dmol.GLViewer, with
the exception that the functions all return None.
http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html
'''
def __init__(self,width=640,height=480,query='',viewergrid=None,linked=True,options=dict(),js='https://3dmol.csb.pitt.edu/build/3Dmol.js'):
'''Create a 3Dmol.js view.
width -- width in pixels of container
height -- height in pixels of container
query -- optional argument to provide to $3Dmol.download
options -- optional options to provide to $3Dmol.download
js -- url for 3Dmol.js'''
divid = "3dmolviewer_UNIQUEID"
warnid = "3dmolwarning_UNIQUEID"
self.uniqueid = None
self.startjs = '''<div id="%s" style="position: relative; width: %dpx; height: %dpx">
<p id="%s" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>
<tt>jupyter labextension install jupyterlab_3dmol</tt></p>
</div>\n''' % (divid,width,height,warnid)
self.startjs += '<script>\n'
self.endjs = '</script>'
self.updatejs = '' # code added since last show
#load 3dmol, but only once, can't use jquery :-(
#https://medium.com/@vschroeder/javascript-how-to-execute-code-from-an-asynchronously-loaded-script-although-when-it-is-not-bebcbd6da5ea
self.startjs += """
var loadScriptAsync = function(uri){
return new Promise((resolve, reject) => {
var tag = document.createElement('script');
tag.src = uri;
tag.async = true;
tag.onload = () => {
resolve();
};
var firstScriptTag = document.getElementsByTagName('script')[0];
firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);
});
};
if(typeof $3Dmolpromise === 'undefined') {
$3Dmolpromise = null;
$3Dmolpromise = loadScriptAsync('%s');
}
var viewer_UNIQUEID = null;
var warn = document.getElementById("%s");
if(warn) {
warn.parentNode.removeChild(warn);
}
""" % (js,warnid)
self.startjs += "$3Dmolpromise.then(function() {\n";
self.endjs = "});\n" + self.endjs
self.viewergrid = None
if viewergrid: #create split view
if len(viewergrid) != 2:
raise ValueError("Incorrectly formated viewergrid arguments. Must specify rows x columns",viewergrid)
self.startjs += "var viewergrid_UNIQUEID = null;\n";
self.startjs += 'viewergrid_UNIQUEID = $3Dmol.createViewerGrid($("#%s"),{rows: %d, cols: %d, control_all: %s},{backgroundColor:"white"});\n' % (divid, viewergrid[0],viewergrid[1],'true' if linked else 'false')
self.startjs += "viewer_UNIQUEID = viewergrid_UNIQUEID[0][0];\n"
self.viewergrid = viewergrid
else:
self.startjs += 'viewer_UNIQUEID = $3Dmol.createViewer($("#%s"),{backgroundColor:"white"});\n' % divid
if query:
if viewergrid:
for r in range(viewergrid[0]):
for c in range(viewergrid[1]):
self.startjs += '$3Dmol.download("%s", viewergrid_UNIQUEID[%d][%d], %s, function() {\n' % (query,r,c,json.dumps(options))
self.endjs = "})\n" + self.endjs
else:
self.startjs += '$3Dmol.download("%s", viewer_UNIQUEID, %s, function() {\n' % (query,json.dumps(options))
self.endjs = "})\n" + self.endjs
if viewergrid:
for r in range(viewergrid[0]):
for c in range(viewergrid[1]):
self.endjs = "viewergrid_UNIQUEID[%d][%d].render();\n"%(r,c) + self.endjs;
else:
self.endjs = "viewer_UNIQUEID.render();\n" + self.endjs;
@using_ipython
def show(self):
'''Instantiate a new viewer window. Calling this will orphan any previously instantiated viewer windows.'''
self.updatejs = ''
html = self._make_html()
return IPython.display.publish_display_data({'application/3dmoljs_load.v0':html, 'text/html': html})
@using_ipython
def insert(self, containerid):
'''Instead of inserting into notebook here, insert html
into existing container'''
html = self._make_html()
html += '''<script>$("#%s").append($("#3dmolviewer_%s")); </script>'''%(containerid,self.uniqueid)
return IPython.display.publish_display_data({'application/3dmoljs_load.v0':html, 'text/html': html})
def _make_html(self):
self.uniqueid = str(time.time()).replace('.','')
self.updatejs = ''
html = (self.startjs+self.endjs).replace('UNIQUEID',self.uniqueid)
return html
@using_ipython
def _repr_html_(self):
html = self._make_html()
return IPython.display.publish_display_data({'application/3dmoljs_load.v0':html, 'text/html': html})
@using_ipython
def update(self):
'''Apply commands to existing viewer (will auto-instantiate if necessary).'''
script = ''
if self.uniqueid == None:
script = self._make_html()
script += '''<script>
$3Dmolpromise.then(function() { //wrap in promise for non-interactive functionality
%s
viewer_%s.render();
});
</script>''' % (self.updatejs.replace('UNIQUEID',self.uniqueid),self.uniqueid)
self.updatejs = ''
return IPython.display.publish_display_data({'application/3dmoljs_load.v0':script, 'text/html': script})
@using_ipython
def png(self):
'''output png image of viewer, which must already be instantiated'''
if not self.uniqueid:
raise AssertionError('Must instantiate viewer before generating image.')
script = '''<img id="img_{0}">
<script>
var png = viewer_{0}.pngURI()
$('#img_{0}').attr('src', png)
</script>'''.format(self.uniqueid)
return IPython.display.publish_display_data({'application/3dmoljs_load.v0':script, 'text/html': script})
class model(object):
'''Wrapper for referencing a model within a viewer'''
def __init__(self, viewer, accesscmd):
self.accesscmd = accesscmd
self.viewer = viewer
def __getattr__(self,name):
'''auto-instantiate javascript calls through model'''
if name.startswith('_'): #object to ipython canary functions
raise AttributeError("%r object has no attribute %r" % (self.__class__, name))
def makejs(*args,**kwargs):
cmd = '\t%s.%s(' % (self.accesscmd,name);
for arg in args:
cmd += '%s,' % json.dumps(arg)
cmd = cmd.rstrip(',')
cmd += ');\n';
self.viewer.startjs += cmd
self.viewer.updatejs += cmd
return self.viewer
return makejs #return from getattr
def getModel(self,*args,**kwargs):
if self.viewergrid:
if kwargs and 'viewer' in kwargs:
coords = kwargs['viewer']
if len(coords) != 2 or coords[0] >= self.viewergrid[0] or coords[1] >= self.viewergrid[1] or coords[0] < 0 or coords[1] < 0:
raise ValueError("Incorrectly formated viewer argument. Must specify row and column",self.viewergrid)
cmd = '\tviewergrid_UNIQUEID[%d][%d].getModel(' % (coords[0],coords[1]);
for arg in args:
cmd += '%s,' % json.dumps(arg)
cmd = cmd.rstrip(',')
cmd += ')';
else:
raise ValueError('Must specify specific viewer with getModel and viewergrid enabled')
else:
cmd = '\tviewer_UNIQUEID.getModel(';
for arg in args:
cmd += '%s,' % json.dumps(arg)
cmd = cmd.rstrip(',')
cmd += ')';
return self.model(self,cmd)
def __getattr__(self,name):
'''auto-instantiate javascript calls based on whatever the user provided'''
if name.startswith('_'): #object to ipython canary functions
raise AttributeError("%r object has no attribute %r" % (self.__class__, name))
def makejs(*args,**kwargs):
if self.viewergrid:
if kwargs and 'viewer' in kwargs:
coords = kwargs['viewer']
if len(coords) != 2 or coords[0] >= self.viewergrid[0] or coords[1] >= self.viewergrid[1] or coords[0] < 0 or coords[1] < 0:
raise ValueError("Incorrectly formated viewer argument. Must specify row and column",self.viewergrid)
cmd = '\tviewergrid_UNIQUEID[%d][%d].%s(' % (coords[0],coords[1],name);
for arg in args:
cmd += '%s,' % json.dumps(arg)
cmd = cmd.rstrip(',')
cmd += ');\n';
else: #apply to every viewer
cmd = ''
for r in range(self.viewergrid[0]):
for c in range(self.viewergrid[1]):
cmd += '\tviewergrid_UNIQUEID[%d][%d].%s(' % (r,c,name);
for arg in args:
cmd += '%s,' % json.dumps(arg)
cmd = cmd.rstrip(',')
cmd += ');\n';
else:
cmd = '\tviewer_UNIQUEID.%s(' % name;
for arg in args:
cmd += '%s,' % json.dumps(arg)
cmd = cmd.rstrip(',')
cmd += ');\n';
self.startjs += cmd
self.updatejs += cmd
return self
return makejs