/
cif_plots.py
164 lines (148 loc) · 6.91 KB
/
cif_plots.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
import os
from ipywidgets import Tab, SelectMultiple, Accordion, ToggleButton, VBox, HBox, HTML, Image, Button, Text, Dropdown
#from _plotly_future_ import v4_subplots
import plotly as py
import plotly.graph_objs as go
from ipywidgets import HBox, VBox, Image, Layout, HTML
import numpy as np
import pandas as pd
from IPython.display import display, Javascript, FileLink
#from notebook import notebookapp
import urllib.parse
class JsMolFigure:
def __init__(self, cif_paths, fig_names, doi_values, widget_side=400):
self.cif_paths = cif_paths
self.fig_names = fig_names
self.doi_values = doi_values
self.widget_side = widget_side
#base_url = list(notebookapp.list_running_servers())[0]['base_url']
self.data_url = ''
self.html = """
<!doctype html>
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="content-type">
<script
src="https://code.jquery.com/jquery-3.4.1.min.js"
integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="
crossorigin="anonymous"></script>
<script type="text/javascript" src="jsmol/JSmol.min.js"></script>
<style type="text/css">
.plot_div{{
display: inline;
margin: 15px;
float: left;
}}
</style>
""".format(self.data_url)
jmol_html = ''
jmol_script = ''
for i, cif_path in enumerate(cif_paths):
jmol_script += """
<!-- CSS Style Inline: -->
<style type="text/css">
/* Jmol Applet */
/* defines height, width and orientation of the Jmol div element */
#jmol_div_{1}{{
height: {5}px;
width: {5}px;
margin: 5px;
}}
</style>
<!-- calls to jQuery and Jmol (inline) -->
<script type="text/javascript">
// Jmol readyFunction
// is called when Jmol is ready
jmol_isReady_{1} = function(applet) {{
Jmol._getElement(applet, "appletdiv").style.border="1px solid blue";
}}
// initialize Jmol Applet
var myJmol_{1} = "myJmol_{1}";
var Info_{1} = {{
width: "100%",
height: "100%",
color: "#000000", //black
use: "HTML5",
j2sPath: "./jsmol/j2s",
jarPath: "./jsmol/java",
jarFile: "JmolAppletSigned.jar",
debug: false,
readyFunction: jmol_isReady_{1},
script: 'load "{0}" ; hide _H;',
//script: 'load ":tylenol";',
allowJavaScript: true,
disableJ2SLoadMonitor: true,
}}
// jQuery ready functions
// is called when page has been completely loaded
$(document).ready(function() {{
console.log('Document is ready');
}} )
function populate_jmol_{1}(){{
html_text = "<center><h3>{4}</h3></center>" + Jmol.getAppletHtml(myJmol_{1}, Info_{1});
html_text += Jmol.jmolButton(myJmol_{1},'load "{0}" SUPERCELL {{2 2 2}}; hide _H;', "Show 2x2x2 supercell");
html_text += Jmol.jmolButton(myJmol_{1},'load "{0}"; hide _H;', "Reset");
// html_text += '<a href="{2}" target="_blank"><button> Download {4} CIF</button></a>'
$("#jmol_div_{1}").html(html_text);
}}
var lastPrompt=0;
</script>
""".format(cif_path, i, self.link_generator(self.fig_names[i], i), self.data_url, self.fig_names[i], self.widget_side)
jmol_html += """
<div class='plot_div'>
<div id='jmol_div_{0}'>
<div style="text-align: center;">
<button type="button" onclick=populate_jmol_{0}()>Show Molecule</button>
</div>
</div>
</div>
""".format(i)
self.html += jmol_script + "</head> <body>" + jmol_html + "</body> </html>"
def link_generator(self, fig_name, i):
if 'HUTVAV' not in fig_name:
return self.data_url + '/' + self.cif_paths[i]
else:
# return 'https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid={}&DatabaseToSearch=Published'.format(fig_name)
return 'https://www.ccdc.cam.ac.uk/structures/Search?Doi={}&DatabaseToSearch=Published'.format(urllib.parse.quote(self.doi_values[fig_name]))
@property
def plot(self):
from IPython.display import HTML
# from ipywidgets import HTML
return HTML(self.html)
@property
def controls(self):
get_supercell = ToggleButton(
value=False,
description='Get supercell',
disabled=False,
button_style='',
tooltip='Click to show supercell'
)
get_supercell.observe(self.supercell_callback, 'value')
run_command = Button(
description='Run Command',
disabled=False
)
run_command.on_click(self.run_cmd_callback)
self.command_text = Text(
value='spin on',
placeholder='spin on',
description='Command:',
disabled=False
)
data_filter_vbox = VBox(
[HBox([get_supercell]), HBox([self.command_text, run_command])])
return data_filter_vbox
def run_cmd_callback(self, b):
if self.command_text.value:
js_string = """Jmol.script(myJmol_{}, '{}');""".format(
self.id, self.command_text.value)
display(Javascript(js_string))
def supercell_callback(self, state):
if state.new:
js_string = """Jmol.script(myJmol_{0}, 'load "{1}" supercell {{2 2 2}}');""".format(
self.id, self.cif_path)
else:
js_string = """Jmol.script(myJmol_{0}, 'load "{1}"');""".format(
self.id, self.cif_path)
display(Javascript(js_string))