Spaces:
Runtime error
Runtime error
Fanwang Meng
commited on
Commit
•
2497be4
1
Parent(s):
2caab15
Add the initial draft
Browse files- .gitignore +111 -0
- .streamlit/config.toml +332 -0
- README.md +5 -4
- app.py +361 -0
- packages.txt +1 -0
- requirements.txt +17 -0
- sample_input.sdf +387 -0
- sample_input_smiles.csv +6 -0
- utils.py +155 -0
.gitignore
ADDED
@@ -0,0 +1,111 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# Prerequisites
|
2 |
+
*.d
|
3 |
+
|
4 |
+
# Compiled object files
|
5 |
+
*.slo
|
6 |
+
*.lo
|
7 |
+
*.o
|
8 |
+
*.obj
|
9 |
+
|
10 |
+
# Precompiled headers
|
11 |
+
*.gch
|
12 |
+
*.pch
|
13 |
+
|
14 |
+
# Compiled dynamic libraries
|
15 |
+
*.so
|
16 |
+
*.so.[0-9]*
|
17 |
+
*.dylib
|
18 |
+
*.dll
|
19 |
+
|
20 |
+
# Fortran module files
|
21 |
+
*.mod
|
22 |
+
*.smod
|
23 |
+
|
24 |
+
# Compiled static libraries
|
25 |
+
*.lai
|
26 |
+
*.la
|
27 |
+
*.a
|
28 |
+
*.lib
|
29 |
+
|
30 |
+
# Executables
|
31 |
+
*.exe
|
32 |
+
*.out
|
33 |
+
*.app
|
34 |
+
|
35 |
+
# Byte-compiled / optimized / DLL files
|
36 |
+
__pycache__/
|
37 |
+
*.py[cod]
|
38 |
+
*$py.class
|
39 |
+
|
40 |
+
# Distribution / packaging
|
41 |
+
.Python
|
42 |
+
build/
|
43 |
+
develop-eggs/
|
44 |
+
dist/
|
45 |
+
downloads/
|
46 |
+
eggs/
|
47 |
+
.eggs/
|
48 |
+
lib/
|
49 |
+
lib64/
|
50 |
+
parts/
|
51 |
+
sdist/
|
52 |
+
var/
|
53 |
+
wheels/
|
54 |
+
.installed.cfg
|
55 |
+
MANIFEST
|
56 |
+
*.egg-info/
|
57 |
+
*.egg
|
58 |
+
*.manifest
|
59 |
+
*.spec
|
60 |
+
pip-log.txt
|
61 |
+
pip-delete-this-directory.txt
|
62 |
+
# Unit test / coverage reports
|
63 |
+
htmlcov/
|
64 |
+
.tox/
|
65 |
+
.coverage
|
66 |
+
.coverage.*
|
67 |
+
.cache
|
68 |
+
nosetests.xml
|
69 |
+
coverage.xml
|
70 |
+
*,cover
|
71 |
+
.pytest_cache/
|
72 |
+
|
73 |
+
# Documentation
|
74 |
+
doc/html/
|
75 |
+
doc/latex/
|
76 |
+
doc/man/
|
77 |
+
doc/xml/
|
78 |
+
doc/_build/
|
79 |
+
doc/source
|
80 |
+
doc/modules
|
81 |
+
|
82 |
+
# Environments
|
83 |
+
.env
|
84 |
+
.venv
|
85 |
+
env/
|
86 |
+
venv/
|
87 |
+
ENV/
|
88 |
+
|
89 |
+
# Editor junk
|
90 |
+
tags
|
91 |
+
[._]*.s[a-v][a-z]
|
92 |
+
[._]*.sw[a-p]
|
93 |
+
[._]s[a-v][a-z]
|
94 |
+
[._]sw[a-p]
|
95 |
+
*~
|
96 |
+
\#*\#
|
97 |
+
.\#*
|
98 |
+
.ropeproject
|
99 |
+
.idea/
|
100 |
+
.spyderproject
|
101 |
+
.spyproject
|
102 |
+
.vscode/
|
103 |
+
# Mac .DS_Store
|
104 |
+
.DS_Store
|
105 |
+
|
106 |
+
# jupyter notebook checkpoints
|
107 |
+
.ipynb_checkpoints
|
108 |
+
|
109 |
+
# version file generated by rob
|
110 |
+
B3clf/_version.py
|
111 |
+
|
.streamlit/config.toml
ADDED
@@ -0,0 +1,332 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
|
2 |
+
[global]
|
3 |
+
|
4 |
+
# By default, Streamlit checks if the Python watchdog module is available
|
5 |
+
# and, if not, prints a warning asking for you to install it. The watchdog
|
6 |
+
# module is not required, but highly recommended. It improves Streamlit's
|
7 |
+
# ability to detect changes to files in your filesystem.
|
8 |
+
|
9 |
+
# If you'd like to turn off this warning, set this to True.
|
10 |
+
|
11 |
+
# Default: false
|
12 |
+
# disableWatchdogWarning = false
|
13 |
+
|
14 |
+
# By default, Streamlit displays a warning when a user sets both a widget
|
15 |
+
# default value in the function defining the widget and a widget value via
|
16 |
+
# the widget's key in `st.session_state`.
|
17 |
+
|
18 |
+
# If you'd like to turn off this warning, set this to True.
|
19 |
+
|
20 |
+
# Default: false
|
21 |
+
# disableWidgetStateDuplicationWarning = false
|
22 |
+
|
23 |
+
# If True, will show a warning when you run a Streamlit-enabled script
|
24 |
+
# via "python my_script.py".
|
25 |
+
|
26 |
+
# Default: true
|
27 |
+
# showWarningOnDirectExecution = true
|
28 |
+
|
29 |
+
# DataFrame serialization.
|
30 |
+
|
31 |
+
# Acceptable values:
|
32 |
+
# - 'legacy': Serialize DataFrames using Streamlit's custom format. Slow
|
33 |
+
# but battle-tested.
|
34 |
+
# - 'arrow': Serialize DataFrames using Apache Arrow. Much faster and versatile.
|
35 |
+
|
36 |
+
# Default: "arrow"
|
37 |
+
dataFrameSerialization = "arrow"
|
38 |
+
|
39 |
+
|
40 |
+
[logger]
|
41 |
+
|
42 |
+
# Level of logging: 'error', 'warning', 'info', or 'debug'.
|
43 |
+
|
44 |
+
# Default: 'info'
|
45 |
+
# level = "info"
|
46 |
+
|
47 |
+
# String format for logging messages. If logger.datetimeFormat is set,
|
48 |
+
# logger messages will default to `%(asctime)s.%(msecs)03d %(message)s`. See
|
49 |
+
# [Python's documentation](https://docs.python.org/2.6/library/logging.html#formatter-objects)
|
50 |
+
# for available attributes.
|
51 |
+
|
52 |
+
# Default: "%(asctime)s %(message)s"
|
53 |
+
# messageFormat = "%(asctime)s %(message)s"
|
54 |
+
|
55 |
+
|
56 |
+
[client]
|
57 |
+
|
58 |
+
# Whether to enable st.cache. This does not affect st.cache_data or
|
59 |
+
# st.cache_resource.
|
60 |
+
|
61 |
+
# Default: true
|
62 |
+
caching = true
|
63 |
+
|
64 |
+
# If false, makes your Streamlit script not draw to a
|
65 |
+
# Streamlit app.
|
66 |
+
|
67 |
+
# Default: true
|
68 |
+
# displayEnabled = true
|
69 |
+
|
70 |
+
# Controls whether uncaught app exceptions and deprecation warnings
|
71 |
+
# are displayed in the browser. By default, this is set to True and
|
72 |
+
# Streamlit displays app exceptions and associated tracebacks, and
|
73 |
+
# deprecation warnings, in the browser.
|
74 |
+
|
75 |
+
# If set to False, deprecation warnings and full exception messages
|
76 |
+
# will print to the console only. Exceptions will still display in the
|
77 |
+
# browser with a generic error message. For now, the exception type and
|
78 |
+
# traceback show in the browser also, but they will be removed in the
|
79 |
+
# future.
|
80 |
+
|
81 |
+
# Default: true
|
82 |
+
# showErrorDetails = true
|
83 |
+
|
84 |
+
# Change the visibility of items in the toolbar, options menu,
|
85 |
+
# and settings dialog (top right of the app).
|
86 |
+
|
87 |
+
# Allowed values:
|
88 |
+
# * "auto" : Show the developer options if the app is accessed through
|
89 |
+
# localhost or through Streamlit Community Cloud as a developer.
|
90 |
+
# Hide them otherwise.
|
91 |
+
# * "developer" : Show the developer options.
|
92 |
+
# * "viewer" : Hide the developer options.
|
93 |
+
# * "minimal" : Show only options set externally (e.g. through
|
94 |
+
# Streamlit Community Cloud) or through st.set_page_config.
|
95 |
+
# If there are no options left, hide the menu.
|
96 |
+
|
97 |
+
# Default: "auto"
|
98 |
+
# toolbarMode = "auto"
|
99 |
+
|
100 |
+
|
101 |
+
[runner]
|
102 |
+
|
103 |
+
# Allows you to type a variable or string by itself in a single line of
|
104 |
+
# Python code to write it to the app.
|
105 |
+
|
106 |
+
# Default: true
|
107 |
+
# magicEnabled = true
|
108 |
+
|
109 |
+
# Install a Python tracer to allow you to stop or pause your script at
|
110 |
+
# any point and introspect it. As a side-effect, this slows down your
|
111 |
+
# script's execution.
|
112 |
+
|
113 |
+
# Default: false
|
114 |
+
# installTracer = false
|
115 |
+
|
116 |
+
# Sets the MPLBACKEND environment variable to Agg inside Streamlit to
|
117 |
+
# prevent Python crashing.
|
118 |
+
|
119 |
+
# Default: true
|
120 |
+
# fixMatplotlib = true
|
121 |
+
|
122 |
+
# Run the Python Garbage Collector after each script execution. This
|
123 |
+
# can help avoid excess memory use in Streamlit apps, but could
|
124 |
+
# introduce delay in rerunning the app script for high-memory-use
|
125 |
+
# applications.
|
126 |
+
|
127 |
+
# Default: true
|
128 |
+
# postScriptGC = true
|
129 |
+
|
130 |
+
# Handle script rerun requests immediately, rather than waiting for script
|
131 |
+
# execution to reach a yield point. This makes Streamlit much more
|
132 |
+
# responsive to user interaction, but it can lead to race conditions in
|
133 |
+
# apps that mutate session_state data outside of explicit session_state
|
134 |
+
# assignment statements.
|
135 |
+
|
136 |
+
# Default: true
|
137 |
+
# fastReruns = true
|
138 |
+
|
139 |
+
# Raise an exception after adding unserializable data to Session State.
|
140 |
+
# Some execution environments may require serializing all data in Session
|
141 |
+
# State, so it may be useful to detect incompatibility during development,
|
142 |
+
# or when the execution environment will stop supporting it in the future.
|
143 |
+
|
144 |
+
# Default: false
|
145 |
+
# enforceSerializableSessionState = false
|
146 |
+
|
147 |
+
|
148 |
+
[server]
|
149 |
+
|
150 |
+
# List of folders that should not be watched for changes. This
|
151 |
+
# impacts both "Run on Save" and @st.cache.
|
152 |
+
|
153 |
+
# Relative paths will be taken as relative to the current working directory.
|
154 |
+
|
155 |
+
# Example: ['/home/user1/env', 'relative/path/to/folder']
|
156 |
+
|
157 |
+
# Default: []
|
158 |
+
# folderWatchBlacklist = []
|
159 |
+
|
160 |
+
# Change the type of file watcher used by Streamlit, or turn it off
|
161 |
+
# completely.
|
162 |
+
|
163 |
+
# Allowed values:
|
164 |
+
# * "auto" : Streamlit will attempt to use the watchdog module, and
|
165 |
+
# falls back to polling if watchdog is not available.
|
166 |
+
# * "watchdog" : Force Streamlit to use the watchdog module.
|
167 |
+
# * "poll" : Force Streamlit to always use polling.
|
168 |
+
# * "none" : Streamlit will not watch files.
|
169 |
+
|
170 |
+
# Default: "auto"
|
171 |
+
# fileWatcherType = "auto"
|
172 |
+
|
173 |
+
# Symmetric key used to produce signed cookies. If deploying on multiple replicas, this should
|
174 |
+
# be set to the same value across all replicas to ensure they all share the same secret.
|
175 |
+
|
176 |
+
# Default: randomly generated secret key.
|
177 |
+
# cookieSecret = "59320264f737a53fb01de73458c8849b0b623a7ba8174de8612fd569c2c25035"
|
178 |
+
|
179 |
+
# If false, will attempt to open a browser window on start.
|
180 |
+
|
181 |
+
# Default: false unless (1) we are on a Linux box where DISPLAY is unset, or
|
182 |
+
# (2) we are running in the Streamlit Atom plugin.
|
183 |
+
# headless = false
|
184 |
+
|
185 |
+
# Automatically rerun script when the file is modified on disk.
|
186 |
+
|
187 |
+
# Default: false
|
188 |
+
# runOnSave = false
|
189 |
+
|
190 |
+
# The address where the server will listen for client and browser
|
191 |
+
# connections. Use this if you want to bind the server to a specific address.
|
192 |
+
# If set, the server will only be accessible from this address, and not from
|
193 |
+
# any aliases (like localhost).
|
194 |
+
|
195 |
+
# Default: (unset)
|
196 |
+
# address =
|
197 |
+
|
198 |
+
# The port where the server will listen for browser connections.
|
199 |
+
|
200 |
+
# Default: 8501
|
201 |
+
# port = 8501
|
202 |
+
|
203 |
+
# The base path for the URL where Streamlit should be served from.
|
204 |
+
|
205 |
+
# Default: ""
|
206 |
+
# baseUrlPath = ""
|
207 |
+
|
208 |
+
# Enables support for Cross-Origin Resource Sharing (CORS) protection, for added security.
|
209 |
+
|
210 |
+
# Due to conflicts between CORS and XSRF, if `server.enableXsrfProtection` is on and
|
211 |
+
# `server.enableCORS` is off at the same time, we will prioritize `server.enableXsrfProtection`.
|
212 |
+
|
213 |
+
# Default: true
|
214 |
+
# enableCORS = true
|
215 |
+
|
216 |
+
# Enables support for Cross-Site Request Forgery (XSRF) protection, for added security.
|
217 |
+
|
218 |
+
# Due to conflicts between CORS and XSRF, if `server.enableXsrfProtection` is on and
|
219 |
+
# `server.enableCORS` is off at the same time, we will prioritize `server.enableXsrfProtection`.
|
220 |
+
|
221 |
+
# Default: true
|
222 |
+
# enableXsrfProtection = true
|
223 |
+
|
224 |
+
# Max size, in megabytes, for files uploaded with the file_uploader.
|
225 |
+
|
226 |
+
# Default: 200
|
227 |
+
maxUploadSize = 2
|
228 |
+
|
229 |
+
# Max size, in megabytes, of messages that can be sent via the WebSocket connection.
|
230 |
+
|
231 |
+
# Default: 200
|
232 |
+
# maxMessageSize = 200
|
233 |
+
|
234 |
+
# Enables support for websocket compression.
|
235 |
+
|
236 |
+
# Default: false
|
237 |
+
# enableWebsocketCompression = false
|
238 |
+
|
239 |
+
# Enable serving files from a `static` directory in the running app's directory.
|
240 |
+
|
241 |
+
# Default: false
|
242 |
+
# enableStaticServing = false
|
243 |
+
|
244 |
+
# Server certificate file for connecting via HTTPS.
|
245 |
+
# Must be set at the same time as "server.sslKeyFile".
|
246 |
+
|
247 |
+
# ['DO NOT USE THIS OPTION IN A PRODUCTION ENVIRONMENT. It has not gone through security audits or performance tests. For the production environment, we recommend performing SSL termination by the load balancer or the reverse proxy.']
|
248 |
+
# sslCertFile =
|
249 |
+
|
250 |
+
# Cryptographic key file for connecting via HTTPS.
|
251 |
+
# Must be set at the same time as "server.sslCertFile".
|
252 |
+
|
253 |
+
# ['DO NOT USE THIS OPTION IN A PRODUCTION ENVIRONMENT. It has not gone through security audits or performance tests. For the production environment, we recommend performing SSL termination by the load balancer or the reverse proxy.']
|
254 |
+
# sslKeyFile =
|
255 |
+
|
256 |
+
|
257 |
+
[browser]
|
258 |
+
|
259 |
+
# Internet address where users should point their browsers in order to
|
260 |
+
# connect to the app. Can be IP address or DNS name and path.
|
261 |
+
|
262 |
+
# This is used to:
|
263 |
+
# - Set the correct URL for CORS and XSRF protection purposes.
|
264 |
+
# - Show the URL on the terminal
|
265 |
+
# - Open the browser
|
266 |
+
|
267 |
+
# Default: "localhost"
|
268 |
+
# serverAddress = "localhost"
|
269 |
+
|
270 |
+
# Whether to send usage statistics to Streamlit.
|
271 |
+
|
272 |
+
# Default: true
|
273 |
+
# gatherUsageStats = true
|
274 |
+
|
275 |
+
# Port where users should point their browsers in order to connect to the
|
276 |
+
# app.
|
277 |
+
|
278 |
+
# This is used to:
|
279 |
+
# - Set the correct URL for CORS and XSRF protection purposes.
|
280 |
+
# - Show the URL on the terminal
|
281 |
+
# - Open the browser
|
282 |
+
|
283 |
+
# Default: whatever value is set in server.port.
|
284 |
+
# serverPort = 8501
|
285 |
+
|
286 |
+
|
287 |
+
[mapbox]
|
288 |
+
|
289 |
+
# Configure Streamlit to use a custom Mapbox
|
290 |
+
# token for elements like st.pydeck_chart and st.map.
|
291 |
+
# To get a token for yourself, create an account at
|
292 |
+
# https://mapbox.com. It's free (for moderate usage levels)!
|
293 |
+
|
294 |
+
# Default: ""
|
295 |
+
# token = ""
|
296 |
+
|
297 |
+
|
298 |
+
[deprecation]
|
299 |
+
|
300 |
+
# Set to false to disable the deprecation warning for the file uploader encoding.
|
301 |
+
|
302 |
+
# Default: true
|
303 |
+
# showfileUploaderEncoding = true
|
304 |
+
|
305 |
+
# Set to false to disable the deprecation warning for using the global pyplot instance.
|
306 |
+
|
307 |
+
# Default: true
|
308 |
+
# showPyplotGlobalUse = true
|
309 |
+
|
310 |
+
|
311 |
+
[theme]
|
312 |
+
|
313 |
+
# The preset Streamlit theme that your custom theme inherits from.
|
314 |
+
# One of "light" or "dark".
|
315 |
+
# base = "light"
|
316 |
+
|
317 |
+
# Primary accent color for interactive elements.
|
318 |
+
# primaryColor =
|
319 |
+
|
320 |
+
# Background color for the main content area.
|
321 |
+
# backgroundColor =
|
322 |
+
|
323 |
+
# Background color used for the sidebar and most interactive widgets.
|
324 |
+
# secondaryBackgroundColor =
|
325 |
+
|
326 |
+
# Color used for almost all text.
|
327 |
+
# textColor =
|
328 |
+
|
329 |
+
# Font family for all text in the app, except code blocks. One of "sans serif",
|
330 |
+
# "serif", or "monospace".
|
331 |
+
font = "sans serif"
|
332 |
+
|
README.md
CHANGED
@@ -1,10 +1,11 @@
|
|
1 |
---
|
2 |
-
title:
|
3 |
-
emoji:
|
4 |
-
colorFrom:
|
5 |
-
colorTo:
|
6 |
sdk: streamlit
|
7 |
sdk_version: 1.27.2
|
|
|
8 |
app_file: app.py
|
9 |
pinned: false
|
10 |
license: gpl-3.0
|
|
|
1 |
---
|
2 |
+
title: B3clf
|
3 |
+
emoji: 🏢
|
4 |
+
colorFrom: green
|
5 |
+
colorTo: pink
|
6 |
sdk: streamlit
|
7 |
sdk_version: 1.27.2
|
8 |
+
python_version: 3.8
|
9 |
app_file: app.py
|
10 |
pinned: false
|
11 |
license: gpl-3.0
|
app.py
ADDED
@@ -0,0 +1,361 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
import itertools as it
|
2 |
+
import os
|
3 |
+
import tempfile
|
4 |
+
from io import StringIO
|
5 |
+
|
6 |
+
import joblib
|
7 |
+
import numpy as np
|
8 |
+
import pandas as pd
|
9 |
+
import pkg_resources
|
10 |
+
# page set up
|
11 |
+
import streamlit as st
|
12 |
+
from b3clf.descriptor_padel import compute_descriptors
|
13 |
+
from b3clf.geometry_opt import geometry_optimize
|
14 |
+
from b3clf.utils import get_descriptors, scale_descriptors, select_descriptors
|
15 |
+
# from PIL import Image
|
16 |
+
from streamlit_extras.let_it_rain import rain
|
17 |
+
from streamlit_ketcher import st_ketcher
|
18 |
+
|
19 |
+
from utils import generate_predictions, load_all_models
|
20 |
+
|
21 |
+
st.cache_data.clear()
|
22 |
+
|
23 |
+
st.set_page_config(
|
24 |
+
page_title="BBB Permeability Prediction with Imbalanced Learning",
|
25 |
+
# page_icon="🧊",
|
26 |
+
layout="wide",
|
27 |
+
# initial_sidebar_state="expanded",
|
28 |
+
# menu_items={
|
29 |
+
# "Get Help": "https://www.extremelycoolapp.com/help",
|
30 |
+
# "Report a bug": "https://www.extremelycoolapp.com/bug",
|
31 |
+
# "About": "# This is a header. This is an *extremely* cool app!"
|
32 |
+
# }
|
33 |
+
)
|
34 |
+
|
35 |
+
|
36 |
+
keep_features = "no"
|
37 |
+
keep_sdf = "no"
|
38 |
+
classifiers_dict = {
|
39 |
+
"decision tree": "dtree",
|
40 |
+
"kNN": "knn",
|
41 |
+
"logistic regression": "logreg",
|
42 |
+
"XGBoost": "xgb",
|
43 |
+
}
|
44 |
+
resample_methods_dict = {
|
45 |
+
"random undersampling": "classic_RandUndersampling",
|
46 |
+
"SMOTE": "classic_SMOTE",
|
47 |
+
"Borderline SMOTE": "borderline_SMOTE",
|
48 |
+
"k-means SMOTE": "kmeans_SMOTE",
|
49 |
+
"ADASYN": "classic_ADASYN",
|
50 |
+
"no resampling": "common",
|
51 |
+
}
|
52 |
+
|
53 |
+
pandas_display_options = {
|
54 |
+
"line_limit": 50,
|
55 |
+
}
|
56 |
+
mol_features = None
|
57 |
+
info_df = None
|
58 |
+
results = None
|
59 |
+
temp_file_path = None
|
60 |
+
all_models = load_all_models()
|
61 |
+
|
62 |
+
# Create the Streamlit app
|
63 |
+
st.title(":blue[BBB Permeability Prediction with Imbalanced Learning]")
|
64 |
+
info_column, upload_column = st.columns(2)
|
65 |
+
|
66 |
+
# inatialize the molecule features and info dataframe session state
|
67 |
+
if "mol_features" not in st.session_state:
|
68 |
+
st.session_state.mol_features = None
|
69 |
+
if "info_df" not in st.session_state:
|
70 |
+
st.session_state.info_df = None
|
71 |
+
|
72 |
+
|
73 |
+
# download sample files
|
74 |
+
with info_column:
|
75 |
+
st.subheader("About `B3clf`")
|
76 |
+
# fmt: off
|
77 |
+
st.markdown(
|
78 |
+
"""
|
79 |
+
`B3clf` is a Python package for predicting the blood-brain barrier (BBB) permeability of small molecules using imbalanced learning. It supports decision tree, XGBoost, kNN, logistical regression and 5 resampling strategies (SMOTE, Borderline SMOTE, k-means SMOTE and ADASYN). The workflow of `B3clf` is summarized as below. The Source code and more details are available at https://github.com/theochem/B3clf. This project is supported by Digital Research Alliance of Canada (originally known as Compute Canada) and NSERC. This project is maintained by QC-Dev comminity. For further information and inquiries please contact us at qcdevs@gmail.com."""
|
80 |
+
)
|
81 |
+
st.text(" \n")
|
82 |
+
# text_body = """
|
83 |
+
# `B3clf` is a Python package for predicting the blood-brain barrier (BBB) permeability of small molecules using imbalanced learning. It supports decision tree, XGBoost, kNN, logistical regression and 5 resampling strategies (SMOTE, Borderline SMOTE, k-means SMOTE and ADASYN). The workflow of `B3clf` is summarized as below. The Source code and more details are available at https://github.com/theochem/B3clf.
|
84 |
+
# """
|
85 |
+
# st.markdown(f"<p align="justify">{text_body}</p>",
|
86 |
+
# unsafe_allow_html=True)
|
87 |
+
|
88 |
+
# image = Image.open("images/b3clf_workflow.png")
|
89 |
+
# st.image(image=image, use_column_width=True)
|
90 |
+
|
91 |
+
# image_path = "images/b3clf_workflow.png"
|
92 |
+
# image_width_percent = 80
|
93 |
+
# info_column.markdown(
|
94 |
+
# f"<img src="{image_path}" style="max-width: {image_width_percent}%; height: auto;">",
|
95 |
+
# unsafe_allow_html=True
|
96 |
+
# )
|
97 |
+
|
98 |
+
# fmt: on
|
99 |
+
sdf_col, smi_col = st.columns(2)
|
100 |
+
with sdf_col:
|
101 |
+
# uneven columns
|
102 |
+
# st.columns((2, 1, 1, 1))
|
103 |
+
# two subcolumns for sample input files
|
104 |
+
# download sample sdf
|
105 |
+
# st.markdown(" \n \n")
|
106 |
+
with open("sample_input.sdf", "r") as file_sdf:
|
107 |
+
btn = st.download_button(
|
108 |
+
label="Download SDF sample file",
|
109 |
+
data=file_sdf,
|
110 |
+
file_name="sample_input.sdf",
|
111 |
+
)
|
112 |
+
with smi_col:
|
113 |
+
with open("sample_input_smiles.csv", "r") as file_smi:
|
114 |
+
btn = st.download_button(
|
115 |
+
label="Download SMILES sample file",
|
116 |
+
data=file_smi,
|
117 |
+
file_name="sample_input_smiles.csv",
|
118 |
+
)
|
119 |
+
|
120 |
+
# Create a file uploader
|
121 |
+
with upload_column:
|
122 |
+
st.subheader("Model Selection")
|
123 |
+
with st.container():
|
124 |
+
algorithm_col, resampler_col = st.columns(2)
|
125 |
+
# algorithm and resampling method selection column
|
126 |
+
with algorithm_col:
|
127 |
+
classifier = st.selectbox(
|
128 |
+
label="Classification Algorithm:",
|
129 |
+
options=("XGBoost", "kNN", "decision tree", "logistic regression"),
|
130 |
+
)
|
131 |
+
with resampler_col:
|
132 |
+
resampler = st.selectbox(
|
133 |
+
label="Resampling Method:",
|
134 |
+
options=(
|
135 |
+
"ADASYN",
|
136 |
+
"random undersampling",
|
137 |
+
"Borderline SMOTE",
|
138 |
+
"k-means SMOTE",
|
139 |
+
"SMOTE",
|
140 |
+
"no resampling",
|
141 |
+
),
|
142 |
+
)
|
143 |
+
|
144 |
+
# horizontal line
|
145 |
+
st.divider()
|
146 |
+
# upload_col, submit_job_col = st.columns((2, 1))
|
147 |
+
upload_col, _, submit_job_col, _ = st.columns((4, 0.05, 1, 0.05))
|
148 |
+
# upload file column
|
149 |
+
with upload_col:
|
150 |
+
# session state tracking of the file uploader
|
151 |
+
if "uploaded_file" not in st.session_state:
|
152 |
+
st.session_state.uploaded_file = None
|
153 |
+
if "uploaded_file_changed" not in st.session_state:
|
154 |
+
st.session_state.uploaded_file_changed = False
|
155 |
+
|
156 |
+
# def update_uploader_session_info():
|
157 |
+
# """Update the session state of the file uploader."""
|
158 |
+
# st.session_state.uploaded_file = uploaded_file
|
159 |
+
|
160 |
+
uploaded_file = st.file_uploader(
|
161 |
+
label="Upload a CSV, SDF, TXT or SMI file",
|
162 |
+
type=["csv", "sdf", "txt", "smi"],
|
163 |
+
help="Input molecule file only supports *.csv, *.sdf, *.txt and *.smi.",
|
164 |
+
accept_multiple_files=False,
|
165 |
+
# key="uploaded_file",
|
166 |
+
# on_change=update_uploader_session_info,
|
167 |
+
)
|
168 |
+
|
169 |
+
if uploaded_file:
|
170 |
+
# st.write(f"the uploaded file: {uploaded_file}")
|
171 |
+
# when new file is uploaded is different from the previous one
|
172 |
+
if st.session_state.uploaded_file != uploaded_file:
|
173 |
+
st.session_state.uploaded_file_changed = True
|
174 |
+
else:
|
175 |
+
st.session_state.uploaded_file_changed = False
|
176 |
+
st.session_state.uploaded_file = uploaded_file
|
177 |
+
# when new file is the same as the previous one
|
178 |
+
# else:
|
179 |
+
# st.session_state.uploaded_file_changed = False
|
180 |
+
# st.session_state.uploaded_file = uploaded_file
|
181 |
+
|
182 |
+
# set session state for the file uploader
|
183 |
+
# st.write(f"the state of uploaded file: {st.session_state.uploaded_file}")
|
184 |
+
# st.write(f"the state of uploaded file changed: {st.session_state.uploaded_file_changed}")
|
185 |
+
|
186 |
+
# submit job column
|
187 |
+
with submit_job_col:
|
188 |
+
st.text(" \n")
|
189 |
+
st.text(" \n")
|
190 |
+
st.markdown(
|
191 |
+
"<div style='display: flex; justify-content: center;'>",
|
192 |
+
unsafe_allow_html=True,
|
193 |
+
)
|
194 |
+
submit_job_button = st.button(
|
195 |
+
label="Submit Job", type="secondary", key="job_button"
|
196 |
+
)
|
197 |
+
# submit_job_col.markdown("<div style="display: flex; justify-content: center;">",
|
198 |
+
# unsafe_allow_html=True)
|
199 |
+
# submit_job_button = submit_job_col.button(
|
200 |
+
# label="Submit job", key="submit_job_button", type="secondary"
|
201 |
+
# )
|
202 |
+
# submit_job_col.markdown("</div>", unsafe_allow_html=True)
|
203 |
+
|
204 |
+
|
205 |
+
# st.write("The content of the file will be displayed below once uploaded.")
|
206 |
+
# if file:
|
207 |
+
# if "csv" in file.name or "txt" in file.name:
|
208 |
+
# st.write(file.read().decode("utf-8"))
|
209 |
+
# st.write(file)
|
210 |
+
|
211 |
+
|
212 |
+
feature_column, prediction_column = st.columns(2)
|
213 |
+
with feature_column:
|
214 |
+
st.subheader("Molecular Features")
|
215 |
+
|
216 |
+
placeholder_features = st.empty()
|
217 |
+
# placeholder_features = pd.DataFrame(index=[1, 2, 3, 4],
|
218 |
+
# columns=["ID", "nAcid", "ALogP", "Alogp2",
|
219 |
+
# "AMR", "naAromAtom", "nH", "nN"])
|
220 |
+
# st.dataframe(placeholder_features)
|
221 |
+
# placeholder_features.text("molecular features")
|
222 |
+
|
223 |
+
with prediction_column:
|
224 |
+
st.subheader("Predictions")
|
225 |
+
# placeholder_predictions = st.empty()
|
226 |
+
# placeholder_predictions.text("prediction")
|
227 |
+
|
228 |
+
|
229 |
+
st.write(
|
230 |
+
f"the state of uploaded file changed before checking: {st.session_state.uploaded_file_changed}"
|
231 |
+
)
|
232 |
+
# Generate predictions when the user uploads a file
|
233 |
+
# if submit_job_button:
|
234 |
+
|
235 |
+
# if "job_button" in st.session_state:
|
236 |
+
# when new file is uploaded
|
237 |
+
# update_uploader_session_info()
|
238 |
+
# st.write(
|
239 |
+
# f"the state of uploaded file changed after checking: {st.session_state.uploaded_file_changed}"
|
240 |
+
# )
|
241 |
+
# if st.session_state.uploaded_file_changed:
|
242 |
+
# temp_dir = tempfile.mkdtemp()
|
243 |
+
# # Create a temporary file path for the uploaded file
|
244 |
+
# temp_file_path = os.path.join(temp_dir, uploaded_file.name)
|
245 |
+
# # Save the uploaded file to the temporary file path
|
246 |
+
# with open(temp_file_path, "wb") as temp_file:
|
247 |
+
# temp_file.write(uploaded_file.read())
|
248 |
+
|
249 |
+
# mol_features, info_df, results = generate_predictions(
|
250 |
+
# input_fname=temp_file_path,
|
251 |
+
# sep="\s+|\t+",
|
252 |
+
# clf=classifiers_dict[classifier],
|
253 |
+
# _models_dict=all_models,
|
254 |
+
# sampling=resample_methods_dict[resampler],
|
255 |
+
# time_per_mol=120,
|
256 |
+
# mol_features=None,
|
257 |
+
# info_df=None,
|
258 |
+
# )
|
259 |
+
# st.session_state.mol_features = mol_features
|
260 |
+
# st.session_state.info_df = info_df
|
261 |
+
# else:
|
262 |
+
# mol_features, info_df, results = generate_predictions(
|
263 |
+
# input_fname=None,
|
264 |
+
# sep="\s+|\t+",
|
265 |
+
# clf=classifiers_dict[classifier],
|
266 |
+
# _models_dict=all_models,
|
267 |
+
# sampling=resample_methods_dict[resampler],
|
268 |
+
# time_per_mol=120,
|
269 |
+
# mol_features=st.session_state.mol_features,
|
270 |
+
# info_df=st.session_state.info_df,
|
271 |
+
# )
|
272 |
+
if submit_job_button and uploaded_file:
|
273 |
+
temp_dir = tempfile.mkdtemp()
|
274 |
+
# Create a temporary file path for the uploaded file
|
275 |
+
temp_file_path = os.path.join(temp_dir, uploaded_file.name)
|
276 |
+
# Save the uploaded file to the temporary file path
|
277 |
+
with open(temp_file_path, "wb") as temp_file:
|
278 |
+
temp_file.write(uploaded_file.read())
|
279 |
+
mol_features, info_df, results = generate_predictions(
|
280 |
+
input_fname=temp_file_path,
|
281 |
+
sep="\s+|\t+",
|
282 |
+
clf=classifiers_dict[classifier],
|
283 |
+
_models_dict=all_models,
|
284 |
+
sampling=resample_methods_dict[resampler],
|
285 |
+
time_per_mol=120,
|
286 |
+
mol_features=None,
|
287 |
+
info_df=None,
|
288 |
+
)
|
289 |
+
|
290 |
+
# feture table
|
291 |
+
with feature_column:
|
292 |
+
if mol_features is not None:
|
293 |
+
selected_feature_rows = np.min(
|
294 |
+
[mol_features.shape[0], pandas_display_options["line_limit"]]
|
295 |
+
)
|
296 |
+
st.dataframe(mol_features.iloc[:selected_feature_rows, :], hide_index=False)
|
297 |
+
# placeholder_features.dataframe(mol_features, hide_index=False)
|
298 |
+
feature_file_name = uploaded_file.name.split(".")[0] + "_b3clf_features.csv"
|
299 |
+
features_csv = mol_features.to_csv(index=True)
|
300 |
+
st.download_button(
|
301 |
+
"Download features as CSV",
|
302 |
+
data=features_csv,
|
303 |
+
file_name=feature_file_name,
|
304 |
+
)
|
305 |
+
# prediction table
|
306 |
+
with prediction_column:
|
307 |
+
# st.subheader("Predictions")
|
308 |
+
if results is not None:
|
309 |
+
# Display the predictions in a table
|
310 |
+
selected_result_rows = np.min(
|
311 |
+
[results.shape[0], pandas_display_options["line_limit"]]
|
312 |
+
)
|
313 |
+
results_df_display = results.iloc[:selected_result_rows, :].style.format(
|
314 |
+
{"B3clf_predicted_probability": "{:.6f}".format}
|
315 |
+
)
|
316 |
+
st.dataframe(results_df_display, hide_index=True)
|
317 |
+
# Add a button to download the predictions as a CSV file
|
318 |
+
predictions_csv = results.to_csv(index=True)
|
319 |
+
results_file_name = (
|
320 |
+
uploaded_file.name.split(".")[0] + "_b3clf_predictions.csv"
|
321 |
+
)
|
322 |
+
st.download_button(
|
323 |
+
"Download predictions as CSV",
|
324 |
+
data=predictions_csv,
|
325 |
+
file_name=results_file_name,
|
326 |
+
)
|
327 |
+
# indicate the success of the job
|
328 |
+
# rain(
|
329 |
+
# emoji="🎈",
|
330 |
+
# font_size=54,
|
331 |
+
# falling_speed=5,
|
332 |
+
# animation_length=10,
|
333 |
+
# )
|
334 |
+
st.balloons()
|
335 |
+
|
336 |
+
|
337 |
+
# hide footer
|
338 |
+
# https://github.com/streamlit/streamlit/issues/892
|
339 |
+
hide_streamlit_style = """
|
340 |
+
<style>
|
341 |
+
#MainMenu {visibility: hidden;}
|
342 |
+
footer {visibility: hidden;}
|
343 |
+
</style>
|
344 |
+
"""
|
345 |
+
st.markdown(hide_streamlit_style, unsafe_allow_html=True)
|
346 |
+
|
347 |
+
# add google analytics
|
348 |
+
st.markdown(
|
349 |
+
"""
|
350 |
+
<!-- Google tag (gtag.js) -->
|
351 |
+
<script async src="https://www.googletagmanager.com/gtag/js?id=G-WG8QYRELP9"></script>
|
352 |
+
<script>
|
353 |
+
window.dataLayer = window.dataLayer || [];
|
354 |
+
function gtag(){dataLayer.push(arguments);}
|
355 |
+
gtag("js", new Date());
|
356 |
+
|
357 |
+
gtag("config", "G-WG8QYRELP9");
|
358 |
+
</script>
|
359 |
+
""",
|
360 |
+
unsafe_allow_html=True,
|
361 |
+
)
|
packages.txt
ADDED
@@ -0,0 +1 @@
|
|
|
|
|
1 |
+
default-jre
|
requirements.txt
ADDED
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
numpy==1.24.4
|
2 |
+
scipy==1.10.1
|
3 |
+
scikit-learn==0.24.2
|
4 |
+
joblib==1.3.2
|
5 |
+
pandas==2.0.3
|
6 |
+
openpyxl==3.1.2
|
7 |
+
xgboost==1.4.2
|
8 |
+
padelpy>=0.1.11
|
9 |
+
rdkit==2023.03.3
|
10 |
+
# streamlit-extra==0.3.4
|
11 |
+
git+https://github.com/arnaudmiribel/streamlit-extras@v0.3.4
|
12 |
+
# for visualization
|
13 |
+
streamlit-ketcher
|
14 |
+
# for single molecule
|
15 |
+
# py3Dmol==2.0.0.post2
|
16 |
+
# stmol==0.0.9
|
17 |
+
git+https://github.com/theochem/B3clf.git
|
sample_input.sdf
ADDED
@@ -0,0 +1,387 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
H1_Bepotastine
|
2 |
+
RDKit 3D
|
3 |
+
|
4 |
+
52 54 0 0 1 0 0 0 0 0999 V2000
|
5 |
+
6.2601 3.8627 -0.7580 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
6 |
+
0.7350 0.2169 -0.1032 O 0 0 0 0 0 0 0 0 0 0 0 0
|
7 |
+
-7.2627 2.0029 -1.7812 O 0 0 0 0 0 0 0 0 0 0 0 0
|
8 |
+
-7.8739 -0.0429 -1.1421 O 0 0 0 0 0 0 0 0 0 0 0 0
|
9 |
+
-3.2826 0.1387 1.0997 N 0 0 0 0 0 0 0 0 0 0 0 0
|
10 |
+
2.0420 -2.0119 -1.2138 N 0 0 0 0 0 0 0 0 0 0 0 0
|
11 |
+
-0.4341 -0.2713 0.5552 C 0 0 0 0 0 0 0 0 0 0 0 0
|
12 |
+
-1.5088 -0.5144 -0.4974 C 0 0 0 0 0 0 0 0 0 0 0 0
|
13 |
+
-0.9255 0.7694 1.5572 C 0 0 0 0 0 0 0 0 0 0 0 0
|
14 |
+
-2.8345 -0.8975 0.1550 C 0 0 0 0 0 0 0 0 0 0 0 0
|
15 |
+
-2.2740 0.3674 2.1479 C 0 0 0 0 0 0 0 0 0 0 0 0
|
16 |
+
-4.5811 -0.1850 1.7144 C 0 0 0 0 0 0 0 0 0 0 0 0
|
17 |
+
-5.7574 -0.2607 0.7330 C 0 0 0 0 0 0 0 0 0 0 0 0
|
18 |
+
1.9672 -0.2099 0.5040 C 0 0 2 0 0 0 0 0 0 0 0 0
|
19 |
+
-5.9298 1.0111 -0.0974 C 0 0 0 0 0 0 0 0 0 0 0 0
|
20 |
+
3.0410 0.8232 0.1855 C 0 0 0 0 0 0 0 0 0 0 0 0
|
21 |
+
2.3687 -1.6155 0.0463 C 0 0 0 0 0 0 0 0 0 0 0 0
|
22 |
+
3.9935 1.1819 1.1545 C 0 0 0 0 0 0 0 0 0 0 0 0
|
23 |
+
3.1185 1.4155 -1.0867 C 0 0 0 0 0 0 0 0 0 0 0 0
|
24 |
+
-7.1061 0.8976 -1.0266 C 0 0 0 0 0 0 0 0 0 0 0 0
|
25 |
+
3.0746 -2.4482 0.9176 C 0 0 0 0 0 0 0 0 0 0 0 0
|
26 |
+
4.9873 2.1194 0.8610 C 0 0 0 0 0 0 0 0 0 0 0 0
|
27 |
+
4.1084 2.3564 -1.3784 C 0 0 0 0 0 0 0 0 0 0 0 0
|
28 |
+
3.4496 -3.7187 0.4871 C 0 0 0 0 0 0 0 0 0 0 0 0
|
29 |
+
5.0380 2.7045 -0.4026 C 0 0 0 0 0 0 0 0 0 0 0 0
|
30 |
+
2.4252 -3.2455 -1.6060 C 0 0 0 0 0 0 0 0 0 0 0 0
|
31 |
+
3.1214 -4.1271 -0.7990 C 0 0 0 0 0 0 0 0 0 0 0 0
|
32 |
+
-0.2263 -1.2199 1.0679 H 0 0 0 0 0 0 0 0 0 0 0 0
|
33 |
+
-1.6364 0.3807 -1.1209 H 0 0 0 0 0 0 0 0 0 0 0 0
|
34 |
+
-1.1831 -1.3082 -1.1808 H 0 0 0 0 0 0 0 0 0 0 0 0
|
35 |
+
-0.1894 0.8975 2.3595 H 0 0 0 0 0 0 0 0 0 0 0 0
|
36 |
+
-1.0042 1.7496 1.0680 H 0 0 0 0 0 0 0 0 0 0 0 0
|
37 |
+
-3.5642 -1.0250 -0.6514 H 0 0 0 0 0 0 0 0 0 0 0 0
|
38 |
+
-2.7343 -1.8665 0.6611 H 0 0 0 0 0 0 0 0 0 0 0 0
|
39 |
+
-2.1498 -0.5299 2.7684 H 0 0 0 0 0 0 0 0 0 0 0 0
|
40 |
+
-2.6054 1.1766 2.8103 H 0 0 0 0 0 0 0 0 0 0 0 0
|
41 |
+
-4.5185 -1.1314 2.2673 H 0 0 0 0 0 0 0 0 0 0 0 0
|
42 |
+
-4.8272 0.5917 2.4507 H 0 0 0 0 0 0 0 0 0 0 0 0
|
43 |
+
-5.6514 -1.1306 0.0739 H 0 0 0 0 0 0 0 0 0 0 0 0
|
44 |
+
-6.6737 -0.4399 1.3108 H 0 0 0 0 0 0 0 0 0 0 0 0
|
45 |
+
1.8204 -0.2159 1.5927 H 0 0 0 0 0 0 0 0 0 0 0 0
|
46 |
+
-6.0945 1.8686 0.5639 H 0 0 0 0 0 0 0 0 0 0 0 0
|
47 |
+
-5.0396 1.1941 -0.7083 H 0 0 0 0 0 0 0 0 0 0 0 0
|
48 |
+
3.9687 0.7355 2.1458 H 0 0 0 0 0 0 0 0 0 0 0 0
|
49 |
+
2.3964 1.1402 -1.8552 H 0 0 0 0 0 0 0 0 0 0 0 0
|
50 |
+
3.3355 -2.1177 1.9176 H 0 0 0 0 0 0 0 0 0 0 0 0
|
51 |
+
5.7167 2.3889 1.6199 H 0 0 0 0 0 0 0 0 0 0 0 0
|
52 |
+
4.1451 2.8085 -2.3655 H 0 0 0 0 0 0 0 0 0 0 0 0
|
53 |
+
3.9993 -4.3824 1.1485 H 0 0 0 0 0 0 0 0 0 0 0 0
|
54 |
+
2.1492 -3.5132 -2.6219 H 0 0 0 0 0 0 0 0 0 0 0 0
|
55 |
+
3.4047 -5.1069 -1.1664 H 0 0 0 0 0 0 0 0 0 0 0 0
|
56 |
+
-8.0410 1.8004 -2.3409 H 0 0 0 0 0 0 0 0 0 0 0 0
|
57 |
+
1 25 1 0
|
58 |
+
2 7 1 0
|
59 |
+
2 14 1 0
|
60 |
+
3 20 1 0
|
61 |
+
3 52 1 0
|
62 |
+
4 20 2 0
|
63 |
+
5 10 1 0
|
64 |
+
5 11 1 0
|
65 |
+
5 12 1 0
|
66 |
+
6 17 2 0
|
67 |
+
6 26 1 0
|
68 |
+
7 8 1 0
|
69 |
+
7 9 1 0
|
70 |
+
7 28 1 0
|
71 |
+
8 10 1 0
|
72 |
+
8 29 1 0
|
73 |
+
8 30 1 0
|
74 |
+
9 11 1 0
|
75 |
+
9 31 1 0
|
76 |
+
9 32 1 0
|
77 |
+
10 33 1 0
|
78 |
+
10 34 1 0
|
79 |
+
11 35 1 0
|
80 |
+
11 36 1 0
|
81 |
+
12 13 1 0
|
82 |
+
12 37 1 0
|
83 |
+
12 38 1 0
|
84 |
+
13 15 1 0
|
85 |
+
13 39 1 0
|
86 |
+
13 40 1 0
|
87 |
+
14 16 1 0
|
88 |
+
14 17 1 0
|
89 |
+
14 41 1 1
|
90 |
+
15 20 1 0
|
91 |
+
15 42 1 0
|
92 |
+
15 43 1 0
|
93 |
+
16 18 2 0
|
94 |
+
16 19 1 0
|
95 |
+
17 21 1 0
|
96 |
+
18 22 1 0
|
97 |
+
18 44 1 0
|
98 |
+
19 23 2 0
|
99 |
+
19 45 1 0
|
100 |
+
21 24 2 0
|
101 |
+
21 46 1 0
|
102 |
+
22 25 2 0
|
103 |
+
22 47 1 0
|
104 |
+
23 25 1 0
|
105 |
+
23 48 1 0
|
106 |
+
24 27 1 0
|
107 |
+
24 49 1 0
|
108 |
+
26 27 2 0
|
109 |
+
26 50 1 0
|
110 |
+
27 51 1 0
|
111 |
+
M END
|
112 |
+
> <compoud_name> (1)
|
113 |
+
H1_Bepotastine
|
114 |
+
|
115 |
+
> <SMILES> (1)
|
116 |
+
[H]OC(=O)C([H])([H])C([H])([H])C([H])([H])N1C([H])([H])C([H])([H])C([H])(OC([H])(c2nc([H])c([H])c([H])c2[H])c2c([H])c([H])c(Cl)c([H])c2[H])C([H])([H])C1([H])[H]
|
117 |
+
|
118 |
+
> <cid> (1)
|
119 |
+
2350
|
120 |
+
|
121 |
+
> <category> (1)
|
122 |
+
N
|
123 |
+
|
124 |
+
> <inchi> (1)
|
125 |
+
InChI=1S/C21H25ClN2O3/c22-17-8-6-16(7-9-17)21(19-4-1-2-12-23-19)27-18-10-14-24(15-11-18)13-3-5-20(25)26/h1-2,4,6-9,12,18,21H,3,5,10-11,13-15H2,(H,25,26)/t21-/m1/s1
|
126 |
+
|
127 |
+
> <Energy> (1)
|
128 |
+
49.1758
|
129 |
+
|
130 |
+
$$$$
|
131 |
+
H1_Quifenadine
|
132 |
+
RDKit 3D
|
133 |
+
|
134 |
+
45 48 0 0 1 0 0 0 0 0999 V2000
|
135 |
+
0.1106 0.2102 -1.7897 O 0 0 0 0 0 0 0 0 0 0 0 0
|
136 |
+
3.4646 1.0770 -0.0854 N 0 0 0 0 0 0 0 0 0 0 0 0
|
137 |
+
2.0931 -1.1209 0.1252 C 0 0 0 0 0 0 0 0 0 0 0 0
|
138 |
+
1.1729 0.1166 0.3820 C 0 0 1 0 0 0 0 0 0 0 0 0
|
139 |
+
2.0299 1.3864 0.1159 C 0 0 0 0 0 0 0 0 0 0 0 0
|
140 |
+
2.7971 -1.0339 -1.2379 C 0 0 0 0 0 0 0 0 0 0 0 0
|
141 |
+
3.2148 -1.0584 1.1848 C 0 0 0 0 0 0 0 0 0 0 0 0
|
142 |
+
3.5902 0.2772 -1.3240 C 0 0 0 0 0 0 0 0 0 0 0 0
|
143 |
+
3.9592 0.2796 1.0561 C 0 0 0 0 0 0 0 0 0 0 0 0
|
144 |
+
-0.2029 0.1255 -0.3860 C 0 0 0 0 0 0 0 0 0 0 0 0
|
145 |
+
-1.1272 1.3230 -0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0
|
146 |
+
-0.9736 -1.1857 -0.1269 C 0 0 0 0 0 0 0 0 0 0 0 0
|
147 |
+
-1.0387 2.0636 1.1310 C 0 0 0 0 0 0 0 0 0 0 0 0
|
148 |
+
-1.3454 -2.0428 -1.1782 C 0 0 0 0 0 0 0 0 0 0 0 0
|
149 |
+
-2.1533 1.6708 -0.9653 C 0 0 0 0 0 0 0 0 0 0 0 0
|
150 |
+
-1.3459 -1.5543 1.1811 C 0 0 0 0 0 0 0 0 0 0 0 0
|
151 |
+
-1.9065 3.1310 1.3840 C 0 0 0 0 0 0 0 0 0 0 0 0
|
152 |
+
-2.0526 -3.2227 -0.9327 C 0 0 0 0 0 0 0 0 0 0 0 0
|
153 |
+
-3.0179 2.7377 -0.7134 C 0 0 0 0 0 0 0 0 0 0 0 0
|
154 |
+
-2.0493 -2.7364 1.4259 C 0 0 0 0 0 0 0 0 0 0 0 0
|
155 |
+
-2.8897 3.4721 0.4604 C 0 0 0 0 0 0 0 0 0 0 0 0
|
156 |
+
-2.4022 -3.5700 0.3691 C 0 0 0 0 0 0 0 0 0 0 0 0
|
157 |
+
1.5541 -2.0675 0.2237 H 0 0 0 0 0 0 0 0 0 0 0 0
|
158 |
+
0.9532 0.0967 1.4588 H 0 0 0 0 0 0 0 0 0 0 0 0
|
159 |
+
1.6691 1.9630 -0.7430 H 0 0 0 0 0 0 0 0 0 0 0 0
|
160 |
+
1.9423 2.0685 0.9712 H 0 0 0 0 0 0 0 0 0 0 0 0
|
161 |
+
2.0851 -1.1104 -2.0638 H 0 0 0 0 0 0 0 0 0 0 0 0
|
162 |
+
3.4846 -1.8820 -1.3506 H 0 0 0 0 0 0 0 0 0 0 0 0
|
163 |
+
3.9137 -1.8918 1.0436 H 0 0 0 0 0 0 0 0 0 0 0 0
|
164 |
+
2.7942 -1.1596 2.1923 H 0 0 0 0 0 0 0 0 0 0 0 0
|
165 |
+
4.6485 0.0638 -1.5199 H 0 0 0 0 0 0 0 0 0 0 0 0
|
166 |
+
3.2467 0.8670 -2.1831 H 0 0 0 0 0 0 0 0 0 0 0 0
|
167 |
+
3.8541 0.8576 1.9828 H 0 0 0 0 0 0 0 0 0 0 0 0
|
168 |
+
5.0353 0.0986 0.9430 H 0 0 0 0 0 0 0 0 0 0 0 0
|
169 |
+
0.1304 1.1516 -2.0295 H 0 0 0 0 0 0 0 0 0 0 0 0
|
170 |
+
-0.3059 1.8245 1.8958 H 0 0 0 0 0 0 0 0 0 0 0 0
|
171 |
+
-1.0856 -1.7976 -2.2061 H 0 0 0 0 0 0 0 0 0 0 0 0
|
172 |
+
-2.2926 1.0941 -1.8795 H 0 0 0 0 0 0 0 0 0 0 0 0
|
173 |
+
-1.0974 -0.9178 2.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
|
174 |
+
-1.8179 3.6927 2.3110 H 0 0 0 0 0 0 0 0 0 0 0 0
|
175 |
+
-2.3308 -3.8683 -1.7614 H 0 0 0 0 0 0 0 0 0 0 0 0
|
176 |
+
-3.7962 2.9864 -1.4300 H 0 0 0 0 0 0 0 0 0 0 0 0
|
177 |
+
-2.3260 -3.0022 2.4429 H 0 0 0 0 0 0 0 0 0 0 0 0
|
178 |
+
-3.5643 4.2999 0.6616 H 0 0 0 0 0 0 0 0 0 0 0 0
|
179 |
+
-2.9530 -4.4872 0.5586 H 0 0 0 0 0 0 0 0 0 0 0 0
|
180 |
+
1 10 1 0
|
181 |
+
1 35 1 0
|
182 |
+
2 5 1 0
|
183 |
+
2 8 1 0
|
184 |
+
2 9 1 0
|
185 |
+
3 4 1 0
|
186 |
+
3 6 1 0
|
187 |
+
3 7 1 0
|
188 |
+
3 23 1 0
|
189 |
+
4 5 1 0
|
190 |
+
4 10 1 0
|
191 |
+
4 24 1 1
|
192 |
+
5 25 1 0
|
193 |
+
5 26 1 0
|
194 |
+
6 8 1 0
|
195 |
+
6 27 1 0
|
196 |
+
6 28 1 0
|
197 |
+
7 9 1 0
|
198 |
+
7 29 1 0
|
199 |
+
7 30 1 0
|
200 |
+
8 31 1 0
|
201 |
+
8 32 1 0
|
202 |
+
9 33 1 0
|
203 |
+
9 34 1 0
|
204 |
+
10 11 1 0
|
205 |
+
10 12 1 0
|
206 |
+
11 13 2 0
|
207 |
+
11 15 1 0
|
208 |
+
12 14 2 0
|
209 |
+
12 16 1 0
|
210 |
+
13 17 1 0
|
211 |
+
13 36 1 0
|
212 |
+
14 18 1 0
|
213 |
+
14 37 1 0
|
214 |
+
15 19 2 0
|
215 |
+
15 38 1 0
|
216 |
+
16 20 2 0
|
217 |
+
16 39 1 0
|
218 |
+
17 21 2 0
|
219 |
+
17 40 1 0
|
220 |
+
18 22 2 0
|
221 |
+
18 41 1 0
|
222 |
+
19 21 1 0
|
223 |
+
19 42 1 0
|
224 |
+
20 22 1 0
|
225 |
+
20 43 1 0
|
226 |
+
21 44 1 0
|
227 |
+
22 45 1 0
|
228 |
+
M END
|
229 |
+
> <compoud_name> (2)
|
230 |
+
H1_Quifenadine
|
231 |
+
|
232 |
+
> <SMILES> (2)
|
233 |
+
[H]OC(c1c([H])c([H])c([H])c([H])c1[H])(c1c([H])c([H])c([H])c([H])c1[H])C1([H])C([H])([H])N2C([H])([H])C([H])([H])C1([H])C([H])([H])C2([H])[H]
|
234 |
+
|
235 |
+
> <cid> (2)
|
236 |
+
65600
|
237 |
+
|
238 |
+
> <category> (2)
|
239 |
+
N
|
240 |
+
|
241 |
+
> <inchi> (2)
|
242 |
+
InChI=1S/C20H23NO/c22-20(17-7-3-1-4-8-17,18-9-5-2-6-10-18)19-15-21-13-11-16(19)12-14-21/h1-10,16,19,22H,11-15H2/t19-/m1/s1
|
243 |
+
|
244 |
+
> <Energy> (2)
|
245 |
+
84.891
|
246 |
+
|
247 |
+
$$$$
|
248 |
+
H1_Rupatadine
|
249 |
+
RDKit 3D
|
250 |
+
|
251 |
+
56 60 0 0 0 0 0 0 0 0999 V2000
|
252 |
+
6.5298 3.3080 0.0562 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
253 |
+
-2.1780 1.1440 -0.1081 N 0 0 0 0 0 0 0 0 0 0 0 0
|
254 |
+
1.8055 -2.5028 1.6263 N 0 0 0 0 0 0 0 0 0 0 0 0
|
255 |
+
-6.5347 -0.2932 -1.5666 N 0 0 0 0 0 0 0 0 0 0 0 0
|
256 |
+
0.4984 0.2017 0.7391 C 0 0 0 0 0 0 0 0 0 0 0 0
|
257 |
+
-0.7596 -0.6401 0.9176 C 0 0 0 0 0 0 0 0 0 0 0 0
|
258 |
+
0.1325 1.6779 0.6992 C 0 0 0 0 0 0 0 0 0 0 0 0
|
259 |
+
-1.8276 -0.2907 -0.1321 C 0 0 0 0 0 0 0 0 0 0 0 0
|
260 |
+
-0.9697 1.9571 -0.3378 C 0 0 0 0 0 0 0 0 0 0 0 0
|
261 |
+
1.7535 -0.3064 0.5966 C 0 0 0 0 0 0 0 0 0 0 0 0
|
262 |
+
-3.2065 1.4670 -1.1132 C 0 0 0 0 0 0 0 0 0 0 0 0
|
263 |
+
2.9347 0.5760 0.4016 C 0 0 0 0 0 0 0 0 0 0 0 0
|
264 |
+
1.9383 -1.7730 0.4937 C 0 0 0 0 0 0 0 0 0 0 0 0
|
265 |
+
3.7669 0.4917 -0.7359 C 0 0 0 0 0 0 0 0 0 0 0 0
|
266 |
+
3.6248 -0.5108 -1.8705 C 0 0 0 0 0 0 0 0 0 0 0 0
|
267 |
+
2.3939 -1.4219 -1.9523 C 0 0 0 0 0 0 0 0 0 0 0 0
|
268 |
+
2.2514 -2.3194 -0.7533 C 0 0 0 0 0 0 0 0 0 0 0 0
|
269 |
+
-4.5656 0.8945 -0.7963 C 0 0 0 0 0 0 0 0 0 0 0 0
|
270 |
+
3.2715 1.4705 1.4385 C 0 0 0 0 0 0 0 0 0 0 0 0
|
271 |
+
4.8769 1.3617 -0.8210 C 0 0 0 0 0 0 0 0 0 0 0 0
|
272 |
+
2.4290 -3.7014 -0.8308 C 0 0 0 0 0 0 0 0 0 0 0 0
|
273 |
+
4.3729 2.3200 1.3344 C 0 0 0 0 0 0 0 0 0 0 0 0
|
274 |
+
5.1670 2.2679 0.1982 C 0 0 0 0 0 0 0 0 0 0 0 0
|
275 |
+
-5.1566 1.0467 0.4633 C 0 0 0 0 0 0 0 0 0 0 0 0
|
276 |
+
-5.3042 0.2290 -1.7686 C 0 0 0 0 0 0 0 0 0 0 0 0
|
277 |
+
2.2947 -4.4730 0.3198 C 0 0 0 0 0 0 0 0 0 0 0 0
|
278 |
+
1.9875 -3.8347 1.5112 C 0 0 0 0 0 0 0 0 0 0 0 0
|
279 |
+
-6.4311 0.5316 0.7094 C 0 0 0 0 0 0 0 0 0 0 0 0
|
280 |
+
-7.0633 -0.1364 -0.3325 C 0 0 0 0 0 0 0 0 0 0 0 0
|
281 |
+
-7.0626 0.6338 2.0605 C 0 0 0 0 0 0 0 0 0 0 0 0
|
282 |
+
-0.5731 -1.7154 0.8560 H 0 0 0 0 0 0 0 0 0 0 0 0
|
283 |
+
-1.1596 -0.4557 1.9235 H 0 0 0 0 0 0 0 0 0 0 0 0
|
284 |
+
-0.2119 1.9818 1.6961 H 0 0 0 0 0 0 0 0 0 0 0 0
|
285 |
+
0.9793 2.3217 0.4489 H 0 0 0 0 0 0 0 0 0 0 0 0
|
286 |
+
-1.4699 -0.5848 -1.1284 H 0 0 0 0 0 0 0 0 0 0 0 0
|
287 |
+
-2.7127 -0.8992 0.0866 H 0 0 0 0 0 0 0 0 0 0 0 0
|
288 |
+
-1.2287 3.0211 -0.2712 H 0 0 0 0 0 0 0 0 0 0 0 0
|
289 |
+
-0.5727 1.7824 -1.3473 H 0 0 0 0 0 0 0 0 0 0 0 0
|
290 |
+
-2.8776 1.1445 -2.1102 H 0 0 0 0 0 0 0 0 0 0 0 0
|
291 |
+
-3.3405 2.5558 -1.1674 H 0 0 0 0 0 0 0 0 0 0 0 0
|
292 |
+
3.6660 0.0536 -2.8120 H 0 0 0 0 0 0 0 0 0 0 0 0
|
293 |
+
4.5182 -1.1506 -1.8447 H 0 0 0 0 0 0 0 0 0 0 0 0
|
294 |
+
2.4771 -2.0361 -2.8582 H 0 0 0 0 0 0 0 0 0 0 0 0
|
295 |
+
1.4795 -0.8292 -2.0837 H 0 0 0 0 0 0 0 0 0 0 0 0
|
296 |
+
2.6674 1.5029 2.3444 H 0 0 0 0 0 0 0 0 0 0 0 0
|
297 |
+
5.5326 1.3154 -1.6888 H 0 0 0 0 0 0 0 0 0 0 0 0
|
298 |
+
2.6741 -4.1805 -1.7747 H 0 0 0 0 0 0 0 0 0 0 0 0
|
299 |
+
4.6043 3.0064 2.1437 H 0 0 0 0 0 0 0 0 0 0 0 0
|
300 |
+
-4.6110 1.5606 1.2526 H 0 0 0 0 0 0 0 0 0 0 0 0
|
301 |
+
-4.9162 0.0859 -2.7735 H 0 0 0 0 0 0 0 0 0 0 0 0
|
302 |
+
2.4295 -5.5486 0.2902 H 0 0 0 0 0 0 0 0 0 0 0 0
|
303 |
+
1.8762 -4.3969 2.4339 H 0 0 0 0 0 0 0 0 0 0 0 0
|
304 |
+
-8.0471 -0.5796 -0.2022 H 0 0 0 0 0 0 0 0 0 0 0 0
|
305 |
+
-8.1536 0.6818 1.9793 H 0 0 0 0 0 0 0 0 0 0 0 0
|
306 |
+
-6.7913 -0.2348 2.6683 H 0 0 0 0 0 0 0 0 0 0 0 0
|
307 |
+
-6.7355 1.5422 2.5773 H 0 0 0 0 0 0 0 0 0 0 0 0
|
308 |
+
1 23 1 0
|
309 |
+
2 8 1 0
|
310 |
+
2 9 1 0
|
311 |
+
2 11 1 0
|
312 |
+
3 13 2 0
|
313 |
+
3 27 1 0
|
314 |
+
4 25 2 0
|
315 |
+
4 29 1 0
|
316 |
+
5 6 1 0
|
317 |
+
5 7 1 0
|
318 |
+
5 10 2 3
|
319 |
+
6 8 1 0
|
320 |
+
6 31 1 0
|
321 |
+
6 32 1 0
|
322 |
+
7 9 1 0
|
323 |
+
7 33 1 0
|
324 |
+
7 34 1 0
|
325 |
+
8 35 1 0
|
326 |
+
8 36 1 0
|
327 |
+
9 37 1 0
|
328 |
+
9 38 1 0
|
329 |
+
10 12 1 0
|
330 |
+
10 13 1 0
|
331 |
+
11 18 1 0
|
332 |
+
11 39 1 0
|
333 |
+
11 40 1 0
|
334 |
+
12 14 2 0
|
335 |
+
12 19 1 0
|
336 |
+
13 17 1 0
|
337 |
+
14 15 1 0
|
338 |
+
14 20 1 0
|
339 |
+
15 16 1 0
|
340 |
+
15 41 1 0
|
341 |
+
15 42 1 0
|
342 |
+
16 17 1 0
|
343 |
+
16 43 1 0
|
344 |
+
16 44 1 0
|
345 |
+
17 21 2 0
|
346 |
+
18 24 2 0
|
347 |
+
18 25 1 0
|
348 |
+
19 22 2 0
|
349 |
+
19 45 1 0
|
350 |
+
20 23 2 0
|
351 |
+
20 46 1 0
|
352 |
+
21 26 1 0
|
353 |
+
21 47 1 0
|
354 |
+
22 23 1 0
|
355 |
+
22 48 1 0
|
356 |
+
24 28 1 0
|
357 |
+
24 49 1 0
|
358 |
+
25 50 1 0
|
359 |
+
26 27 2 0
|
360 |
+
26 51 1 0
|
361 |
+
27 52 1 0
|
362 |
+
28 29 2 0
|
363 |
+
28 30 1 0
|
364 |
+
29 53 1 0
|
365 |
+
30 54 1 0
|
366 |
+
30 55 1 0
|
367 |
+
30 56 1 0
|
368 |
+
M END
|
369 |
+
> <compoud_name> (3)
|
370 |
+
H1_Rupatadine
|
371 |
+
|
372 |
+
> <SMILES> (3)
|
373 |
+
[H]c1nc2c(c([H])c1[H])C([H])([H])C([H])([H])c1c([H])c(Cl)c([H])c([H])c1C2=C1C([H])([H])C([H])([H])N(C([H])([H])c2c([H])nc([H])c(C([H])([H])[H])c2[H])C([H])([H])C1([H])[H]
|
374 |
+
|
375 |
+
> <cid> (3)
|
376 |
+
133017
|
377 |
+
|
378 |
+
> <category> (3)
|
379 |
+
N
|
380 |
+
|
381 |
+
> <inchi> (3)
|
382 |
+
InChI=1S/C26H26ClN3/c1-18-13-19(16-28-15-18)17-30-11-8-20(9-12-30)25-24-7-6-23(27)14-22(24)5-4-21-3-2-10-29-26(21)25/h2-3,6-7,10,13-16H,4-5,8-9,11-12,17H2,1H3
|
383 |
+
|
384 |
+
> <Energy> (3)
|
385 |
+
119.976
|
386 |
+
|
387 |
+
$$$$
|
sample_input_smiles.csv
ADDED
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
OC(=O)CCCN1CCC(OC(c2ncccc2)c2ccc(Cl)cc2)CC1
|
2 |
+
OC(c1ccccc1)(c1ccccc1)C1CN2CCC1CC2
|
3 |
+
c1nc2c(cc1)CCc1cc(Cl)ccc1C2=C1CCN(Cc2cncc(C)c2)CC1
|
4 |
+
C1=CC=C2C(=C1)C=CC3=CC=CC=C3N2C(=O)N
|
5 |
+
CC(=O)Oc1ccccc1C(=O)O
|
6 |
+
CC(=O)Oc1c(cc(cc1)Cl)C(=O)OC(=O)c1c(ccc(c1)Cl)OC(=O)C
|
utils.py
ADDED
@@ -0,0 +1,155 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
import itertools as it
|
2 |
+
import os
|
3 |
+
|
4 |
+
import joblib
|
5 |
+
import numpy as np
|
6 |
+
import pandas as pd
|
7 |
+
import pkg_resources
|
8 |
+
import streamlit as st
|
9 |
+
from b3clf.descriptor_padel import compute_descriptors
|
10 |
+
from b3clf.geometry_opt import geometry_optimize
|
11 |
+
from b3clf.utils import get_descriptors, scale_descriptors, select_descriptors
|
12 |
+
|
13 |
+
|
14 |
+
@st.cache_resource()
|
15 |
+
def load_all_models():
|
16 |
+
"""Get b3clf fitted classifier"""
|
17 |
+
clf_list = ["dtree", "knn", "logreg", "xgb"]
|
18 |
+
sampling_list = [
|
19 |
+
"borderline_SMOTE",
|
20 |
+
"classic_ADASYN",
|
21 |
+
"classic_RandUndersampling",
|
22 |
+
"classic_SMOTE",
|
23 |
+
"kmeans_SMOTE",
|
24 |
+
"common",
|
25 |
+
]
|
26 |
+
|
27 |
+
model_dict = {}
|
28 |
+
package_name = "b3clf"
|
29 |
+
|
30 |
+
for clf_str, sampling_str in it.product(clf_list, sampling_list):
|
31 |
+
# joblib_fpath = os.path.join(
|
32 |
+
# dirname, "pre_trained", "b3clf_{}_{}.joblib".format(clf_str, sampling_str))
|
33 |
+
# pred_model = joblib.load(joblib_fpath)
|
34 |
+
joblib_path_str = f"pre_trained/b3clf_{clf_str}_{sampling_str}.joblib"
|
35 |
+
with pkg_resources.resource_stream(package_name, joblib_path_str) as f:
|
36 |
+
pred_model = joblib.load(f)
|
37 |
+
|
38 |
+
model_dict[clf_str + "_" + sampling_str] = pred_model
|
39 |
+
|
40 |
+
return model_dict
|
41 |
+
|
42 |
+
|
43 |
+
@st.cache_resource
|
44 |
+
def predict_permeability(
|
45 |
+
clf_str, sampling_str, _models_dict, mol_features, info_df, threshold="none"
|
46 |
+
):
|
47 |
+
"""Compute permeability prediction for given feature data."""
|
48 |
+
# load the model
|
49 |
+
# pred_model = load_all_models()[clf_str + "_" + sampling_str]
|
50 |
+
pred_model = _models_dict[clf_str + "_" + sampling_str]
|
51 |
+
|
52 |
+
# load the threshold data
|
53 |
+
package_name = "b3clf"
|
54 |
+
with pkg_resources.resource_stream(package_name, "data/B3clf_thresholds.xlsx") as f:
|
55 |
+
df_thres = pd.read_excel(f, index_col=0, engine="openpyxl")
|
56 |
+
|
57 |
+
# default threshold is 0.5
|
58 |
+
label_pool = np.zeros(mol_features.shape[0], dtype=int)
|
59 |
+
|
60 |
+
if type(mol_features) == pd.DataFrame:
|
61 |
+
if mol_features.index.tolist() != info_df.index.tolist():
|
62 |
+
raise ValueError("Features_df and Info_df do not have the same index.")
|
63 |
+
|
64 |
+
# get predicted probabilities
|
65 |
+
info_df.loc[:, "B3clf_predicted_probability"] = pred_model.predict_proba(
|
66 |
+
mol_features
|
67 |
+
)[:, 1]
|
68 |
+
# get predicted label from probability using the threshold
|
69 |
+
mask = np.greater_equal(
|
70 |
+
info_df["B3clf_predicted_probability"].to_numpy(),
|
71 |
+
# df_thres.loc[clf_str + "-" + sampling_str, threshold])
|
72 |
+
df_thres.loc["xgb-classic_ADASYN", threshold],
|
73 |
+
)
|
74 |
+
label_pool[mask] = 1
|
75 |
+
|
76 |
+
# save the predicted labels
|
77 |
+
info_df["B3clf_predicted_label"] = label_pool
|
78 |
+
info_df.reset_index(inplace=True)
|
79 |
+
|
80 |
+
return info_df
|
81 |
+
|
82 |
+
|
83 |
+
@st.cache_resource
|
84 |
+
def generate_predictions(
|
85 |
+
input_fname: str = None,
|
86 |
+
sep: str = "\s+|\t+",
|
87 |
+
clf: str = "xgb",
|
88 |
+
_models_dict: dict = None,
|
89 |
+
keep_sdf: str = "no",
|
90 |
+
sampling: str = "classic_ADASYN",
|
91 |
+
time_per_mol: int = 120,
|
92 |
+
mol_features: pd.DataFrame = None,
|
93 |
+
info_df: pd.DataFrame = None,
|
94 |
+
):
|
95 |
+
"""
|
96 |
+
Generate predictions for a given input file.
|
97 |
+
"""
|
98 |
+
if mol_features is None and info_df is None:
|
99 |
+
# mol_tag = os.path.splitext(uploaded_file.name)[0]
|
100 |
+
# uploaded_file = uploaded_file.read().decode("utf-8")
|
101 |
+
mol_tag = os.path.basename(input_fname).split(".")[0]
|
102 |
+
internal_sdf = f"{mol_tag}_optimized_3d.sdf"
|
103 |
+
|
104 |
+
# Geometry optimization
|
105 |
+
# Input:
|
106 |
+
# * Either an SDF file with molecular geometries or a text file with SMILES strings
|
107 |
+
|
108 |
+
geometry_optimize(input_fname=input_fname, output_sdf=internal_sdf, sep=sep)
|
109 |
+
|
110 |
+
df_features = compute_descriptors(
|
111 |
+
sdf_file=internal_sdf,
|
112 |
+
excel_out=None,
|
113 |
+
output_csv=None,
|
114 |
+
timeout=None,
|
115 |
+
time_per_molecule=time_per_mol,
|
116 |
+
)
|
117 |
+
|
118 |
+
# Get computed descriptors
|
119 |
+
mol_features, info_df = get_descriptors(df=df_features)
|
120 |
+
|
121 |
+
# Select descriptors
|
122 |
+
mol_features = select_descriptors(df=mol_features)
|
123 |
+
|
124 |
+
# Scale descriptors
|
125 |
+
mol_features.iloc[:, :] = scale_descriptors(df=mol_features)
|
126 |
+
|
127 |
+
# this is problematic for using the same file for calculation
|
128 |
+
if os.path.exists(internal_sdf) and keep_sdf == "no":
|
129 |
+
os.remove(internal_sdf)
|
130 |
+
|
131 |
+
# Get classifier
|
132 |
+
# clf = get_clf(clf_str=clf, sampling_str=sampling)
|
133 |
+
# Get classifier
|
134 |
+
result_df = predict_permeability(
|
135 |
+
clf_str=clf,
|
136 |
+
sampling_str=sampling,
|
137 |
+
_models_dict=_models_dict,
|
138 |
+
mol_features=mol_features,
|
139 |
+
info_df=info_df,
|
140 |
+
threshold="none",
|
141 |
+
)
|
142 |
+
|
143 |
+
# Get classifier
|
144 |
+
display_cols = [
|
145 |
+
"ID",
|
146 |
+
"SMILES",
|
147 |
+
"B3clf_predicted_probability",
|
148 |
+
"B3clf_predicted_label",
|
149 |
+
]
|
150 |
+
|
151 |
+
result_df = result_df[
|
152 |
+
[col for col in result_df.columns.to_list() if col in display_cols]
|
153 |
+
]
|
154 |
+
|
155 |
+
return mol_features, info_df, result_df
|