├── .gitignore ├── CHANGELOG.txt ├── LICENSE.txt ├── MANIFEST ├── README.md ├── TO_DO.txt ├── examples ├── README.md ├── comp_2_files.csv ├── comp_simple_smiles.csv ├── comp_smiles.csv ├── zid_smiles.csv ├── zid_smiles2.csv ├── zid_smiles3.csv └── zinc_ids.csv ├── images ├── add_to_sqlite_1.png ├── comp_2_files.png ├── comp_simple_smiles.png ├── comp_smiles.png ├── insert_id_sqlite_1.png ├── smilite_overview.png ├── sqlite_to_csv_1.png ├── sqlite_to_csv_2.png ├── zid_smiles.png ├── zid_smiles2.png ├── zid_smiles3.png └── zinc_ids.png ├── scripts ├── cmd_line_online_query_scripts │ ├── lookup_smile_str.py │ └── lookup_zincid.py ├── csv_scripts │ ├── comp_2_smile_files.py │ ├── comp_smile_strings.py │ └── gen_zincid_smile_csv.py └── sqlite_scripts │ ├── add_to_sqlite.py │ ├── lookup_single_id.py │ ├── lookup_smile.py │ └── sqlite_to_csv.py ├── setup.py ├── smilite ├── __init__.py └── smilite.py └── test ├── test_get_zinc_smile.py └── test_simplify_smile.py /.gitignore: -------------------------------------------------------------------------------- 1 | *env 2 | *.swo 3 | *.sqlite 4 | gmon.out 5 | __pycache__ 6 | *.pyc 7 | *.o 8 | *.so 9 | *.gcno 10 | *.swp 11 | *.egg-info 12 | *.egg 13 | *~ 14 | build 15 | dist 16 | lib/test 17 | doc/_build 18 | *.log 19 | *env 20 | *ENV 21 | .DS_store 22 | .idea 23 | -------------------------------------------------------------------------------- /CHANGELOG.txt: -------------------------------------------------------------------------------- 1 | **VERSION 2.3.1 (07/25/2020)** 2 | 3 | - Fix bug to allow `zinc15` option in gen_zincid_smile_csv.py script 4 | 5 | **VERSION 2.3.0 (06/10/2020)** 6 | 7 | - Fixes ZINC URL in `lookup_smile_str.py` 8 | - Adds an optional command line parameter (with arguments `zinc15` or `zinc12`) for `lookup_smile_str.py` 9 | 10 | **VERSION 2.2.0** 11 | 12 | - Provides an optional command line argument (zinc15) to use ZINC15 as a backend for downloading SMILES 13 | 14 | **VERSION 2.1.0** 15 | 16 | - Functions and scripts to fetch ZINC IDs corresponding to a SMILE string query 17 | 18 | **VERSION 2.0.1** 19 | 20 | - Progress bar for add_to_sqlite.py 21 | 22 | **VERSION 2.0.0** 23 | 24 | - added SQLite features 25 | 26 | **VERSION 1.3.0** 27 | 28 | - added script and module function to compare SMILE strings across 2 files. 29 | 30 | **VERSION 1.2.0** 31 | 32 | - added Python 2.x support 33 | 34 | **VERSION 1.1.1** 35 | 36 | - PyPrind dependency fix 37 | 38 | **VERSION 1.1.0** 39 | 40 | - added a progress bar (pyprind) to `generate_zincid_smile_csv()` function 41 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /MANIFEST: -------------------------------------------------------------------------------- 1 | # file GENERATED by distutils, do NOT edit 2 | CHANGELOG.txt 3 | LICENSE.txt 4 | README.html 5 | README.md 6 | setup.py 7 | examples/README.md 8 | examples/comp_2_files.csv 9 | examples/comp_simple_smiles.csv 10 | examples/comp_smiles.csv 11 | examples/zid_smiles.csv 12 | examples/zid_smiles2.csv 13 | examples/zid_smiles3.csv 14 | examples/zinc_ids.csv 15 | scripts/cmd_line_online_query_scripts/lookup_smile_str.py 16 | scripts/cmd_line_online_query_scripts/lookup_zincid.py 17 | scripts/csv_scripts/comp_2_smile_files.py 18 | scripts/csv_scripts/comp_smile_strings.py 19 | scripts/csv_scripts/gen_zincid_smile_csv.py 20 | scripts/sqlite_scripts/add_to_sqlite.py 21 | scripts/sqlite_scripts/lookup_single_id.py 22 | scripts/sqlite_scripts/lookup_smile.py 23 | scripts/sqlite_scripts/sqlite_to_csv.py 24 | smilite/__init__.py 25 | smilite/smilite.py 26 | test/test_get_zinc_smile.py 27 | test/test_simplify_smile.py 28 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # smilite 2 | 3 | smilite is a Python module to download and analyze SMILES strings (Simplified Molecular-Input Line-entry System) of chemical compounds from ZINC (a free database of commercially-available compounds for virtual screening, [http://zinc.docking.org](http://zinc.docking.org)). 4 | Now supports both Python 3.x and Python 2.x. 5 | 6 | 7 | ![](https://raw.github.com/rasbt/smilite/master/images/smilite_overview.png) 8 | 9 | #### Sections 10 | 11 | • [Installation](#installation) 12 | • [Simple command line online query scripts](#simple_cmd_scripts) 13 |       - [lookup_zincid.py](#lookup_zincid) 14 |       - [lookup_smile_str.py](#lookup_smile_str) 15 | • [CSV file command line scripts](#csv_scripts) 16 |       - [gen_zincid_smile_csv.py (downloading SMILES)](#gen_zincid) 17 |       - [comp_smile_strings.py (checking for duplicates within 1 file)](#comp_smile) 18 |       - [comp_2_smile_files.py (checking for duplicates across 2 files)](#comp_2_smile) 19 | • [SQLite file command line scripts](#sqlite_scripts) 20 |       - [lookup_single_id.py](#lookup1id) 21 |       - [lookup_smile.py](#lookupsmile) 22 |       - [add_to_sqlite.py](#add_to_sqlite) 23 |       - [sqlite_to_csv.py](#sqlite_to_csv) 24 | • [Changelog](#changelog) 25 | 26 | 27 | 28 | # Installation 29 | 30 | You can use the following command to install smilite: 31 | `pip install smilite` 32 | or 33 | `easy_install smilite` 34 | 35 | Alternatively, you can download the package manually from the Python Package Index [https://pypi.python.org/pypi/smilite](https://pypi.python.org/pypi/smilite), unzip it, navigate into the package, and use the command: 36 | 37 | `python3 setup.py install` 38 | 39 | 40 | 41 | # Simple command line online query scripts 42 | 43 | If you downloaded the smilite package from [https://pypi.python.org/pypi/smilite](https://pypi.python.org/pypi/smilite) or [https://github.com/rasbt/smilite](https://github.com/rasbt/smilite), you can use the command line scripts I provide in the `scripts/cmd_line_online_query_scripts` dir. 44 | 45 | 46 | 47 | ### lookup_zincid.py 48 | 49 | Retrieves the SMILES string and simplified SMILES string for a given ZINC ID 50 | from the online Zinc. It uses [ZINC12](http://zinc.docking.org) as the default backend, and via an additional commandline argument `zinc15`, the [ZINC15](http://zinc15.docking.org) database will be used instead. 51 | 52 | **Usage:** 53 | `[shell]>> python3 lookup_zincid.py ZINC_ID [zinc12/zinc15]` 54 | 55 | **Example (retrieve data from ZINC):** 56 | `[shell]>> python3 lookup_zincid.py ZINC01234567 zinc15` 57 | 58 | **Output example:** 59 | 60 | 
ZINC01234567
 61 | C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O
 62 | CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O
 63 |
64 | 65 | Where 66 | - 1st row: ZINC ID 67 | - 2nd row: SMILES string 68 | - 3rd row: simplified SMILES string 69 | 70 | 71 | 72 | ### lookup_smile_str.py 73 | 74 | Retrieves the corresponding ZINC_IDs for a given SMILES string 75 | from the online ZINC database. 76 | 77 | **Usage:** 78 | `[shell]>> python3 lookup_smile_str.py SMILE_str` 79 | 80 | **Example (retrieve data from ZINC):** 81 | `[shell]>> python3 lookup_smile_str.py "C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O"` 82 | 83 | **Output example:** 84 | 85 | 
ZINC01234567
 86 | ZINC01234568
 87 | ZINC01242053
 88 | ZINC01242055
89 | 90 | 91 | 92 | # CSV file command line scripts 93 | 94 | If you downloaded the smilite package from [https://pypi.python.org/pypi/smilite](https://pypi.python.org/pypi/smilite) or [https://github.com/rasbt/smilite](https://github.com/rasbt/smilite), you can use the command line scripts I provide in the `scripts/csv_scripts` dir. 95 | 96 | 97 | 98 | ### gen_zincid_smile_csv.py (downloading SMILES) 99 | 100 | Generates a ZINC_ID,SMILE_STR csv file from a input file of ZINC IDs. The input file should consist of 1 columns with 1 ZINC ID per row. [ZINC12](http://zinc.docking.org) is used as the default backend, and via an additional commandline argument `zinc15`, the [ZINC15](http://zinc15.docking.org) database can be used instead. 101 | 102 | **Usage:** 103 | `[shell]>> python3 gen_zincid_smile_csv.py in.csv out.csv [zinc12/zinc15]` 104 | 105 | **Example:** 106 | `[shell]>> python3 gen_zincid_smile_csv.py ../examples/zinc_ids.csv ../examples/zid_smiles.csv zinc15` 107 | 108 | **Screen Output:** 109 | 110 | 
Downloading SMILES
111 | 0%                          100%
112 | [##########                    ] | ETA[sec]: 106.525
113 | 114 | **Input example file format:** 115 | ![](https://raw.github.com/rasbt/smilite/master/images/zinc_ids.png) 116 | [zinc_ids.csv](https://raw.github.com/rasbt/smilite/master/examples/zinc_ids.csv) 117 | 118 | **Output example file format:** 119 | ![](https://raw.github.com/rasbt/smilite/master/images/zid_smiles.png) 120 | [zid_smiles.csv](https://raw.github.com/rasbt/smilite/master/examples/zid_smiles.csv) 121 | 122 | 123 | 124 | ### comp_smile_strings.py (checking for duplicates within 1 file) 125 | 126 | Compares SMILES strings within a 2 column CSV file (ZINC_ID,SMILE_string) to identify duplicates. Generates a new CSV file with ZINC IDs of identified duplicates listed in a 3rd-nth column(s). 127 | 128 | **Usage:** 129 | `[shell]>> python3 comp_smile_strings.py in.csv out.csv [simplify]` 130 | 131 | **Example 1:** 132 | `[shell]>> python3 comp_smile_strings.py ../examples/zinc_smiles.csv ../examples/comp_smiles.csv` 133 | 134 | **Input example file format:** 135 | ![](https://raw.github.com/rasbt/smilite/master/images/zid_smiles.png) 136 | [zid_smiles.csv](https://raw.github.com/rasbt/smilite/master/examples/zid_smiles.csv) 137 | 138 | **Output example file format 1:** 139 | ![](https://raw.github.com/rasbt/smilite/master/images/comp_smiles.png) 140 | [comp_smiles.csv](https://raw.github.com/rasbt/smilite/master/examples/comp_smiles.csv) 141 | 142 | Where 143 | - 1st column: ZINC ID 144 | - 2nd column: SMILES string 145 | - 3rd column: number of duplicates 146 | - 4th-nth column: ZINC IDs of duplicates 147 | 148 | **Example 2:** 149 | `[shell]>> python3 comp_smile_strings.py ../examples/zid_smiles.csv ../examples/comp_simple_smiles.csv simplify` 150 | 151 | **Output example file format 2:** ![](https://raw.github.com/rasbt/smilite/master/images/comp_simple_smiles.png) 152 | [comp_simple_smiles.csv](https://raw.github.com/rasbt/smilite/master/examples/comp_simple_smiles.csv) 153 | 154 | 155 | 156 | ### comp_2_smile_files.py (checking for duplicates across 2 files) 157 | 158 | Compares SMILES strings between 2 input CSV files, where each file consists of rows with 2 columns ZINC_ID,SMILE_string to identify duplicate SMILES string across both files. 159 | Generates a new CSV file with ZINC IDs of identified duplicates listed in a 3rd-nth column(s). 160 | 161 | **Usage:** 162 | `[shell]>> python3 comp_2_smile_files.py in1.csv in2.csv out.csv [simplify]` 163 | 164 | **Example:** 165 | `[shell]>> python3 comp_2_smile_files.py ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv ../examples/comp_2_files.csv` 166 | 167 | **Input example file 1:** 168 | ![](https://raw.github.com/rasbt/smilite/master/images/zid_smiles2.png) 169 | [zid_smiles2.csv](https://raw.github.com/rasbt/smilite/master/examples/zid_smiles2.csv) 170 | 171 | **Input example file 2:** 172 | ![](https://raw.github.com/rasbt/smilite/master/images/zid_smiles3.png) 173 | [zid_smiles3.csv](https://raw.github.com/rasbt/smilite/master/examples/zid_smiles3.csv) 174 | 175 | **Output example file format:** 176 | ![](https://raw.github.com/rasbt/smilite/master/images/comp_2_files.png) 177 | [comp_2_files.csv](https://raw.github.com/rasbt/smilite/master/examples/comp_2_files.csv) 178 | 179 | Where: 180 | - 1st column: name of the origin file 181 | - 2nd column: ZINC ID 182 | - 3rd column: SMILES string 183 | - 4th-nth column: ZINC IDs of duplicates 184 | 185 | 186 | 187 | # SQLite file command line scripts 188 | 189 | If you downloaded the smilite package from [https://pypi.python.org/pypi/smilite](https://pypi.python.org/pypi/smilite) or [https://github.com/rasbt/smilite](https://github.com/rasbt/smilite), you can use the command line scripts I provide in the `scripts/sqlite_scripts` dir. 190 | 191 | 192 | 193 | ### lookup_single_id.py 194 | 195 | Retrieves the SMILES string and simplified SMILES string for a given ZINC ID 196 | from a previously built smilite SQLite database or from the online ZINC database. 197 | 198 | **Usage:** 199 | `[shell]>> python3 lookup_single_id.py ZINC_ID [sqlite_file]` 200 | 201 | **Example1 (retrieve data from a smilite SQLite database):** 202 | `[shell]>> python3 lookup_single_id.py ZINC01234567 ~/Desktop/smilite_db.sqlite` 203 | 204 | **Example2 (retrieve data from the ZINC online database):** 205 | `[shell]>> python3 lookup_single_id.py ZINC01234567` 206 | 207 | **Output example:** 208 | 209 | 
ZINC01234567
210 | C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O
211 | CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O
212 |
213 | 214 | Where 215 | - 1st row: ZINC ID 216 | - 2nd row: SMILES string 217 | - 3rd row: simplified SMILES string 218 | 219 | 220 | 221 | ### lookup_smile.py 222 | 223 | Retrieves the ZINC ID(s) for a given SMILES string or simplified SMILES string from a previously built smilite SQLite database. 224 | 225 | **Usage:** 226 | `[shell]>> python3 lookup_smile.py sqlite_file SMILE_STRING [simplify]` 227 | 228 | **Example1 (search for SMILES string):** 229 | `[shell]>> python3 lookup_smile.py ~/Desktop/smilite.sqlite "C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O"` 230 | 231 | **Example2 (search for simplified SMILES string):** 232 | `[shell]>> python3 lookup_smile.py ~/Desktop/smilite.sqlite "CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O" simple` 233 | 234 | **Output example:** 235 | 236 | 
ZINC01234567
237 | C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O
238 | CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O
239 |
240 | 241 | Where 242 | - 1st row: ZINC ID 243 | - 2nd row: SMILES string 244 | - 3rd row: simplified SMILES string 245 | 246 | 247 | 248 | ### add_to_sqlite.py 249 | 250 | Reads ZINC IDs from a CSV file and looks up SMILES strings and simplified SMILES strings from the ZINC online database. Writes those SMILES strings to a smilite SQLite database. A new database will be created if it doesn't exist, yet. 251 | 252 | **Usage:** 253 | `[shell]>> python3 add_to_sqlite.py sqlite_file csv_file` 254 | 255 | **Example:** 256 | `[shell]>> python3 add_to_sqlite.py ~/Desktop/smilite.sqlite ~/Desktop/zinc_ids.csv` 257 | 258 | **Input CSV file example format:** 259 | 260 | 
ZINC01234567
261 | ZINC01234568
262 | ...
263 |
264 | 265 | An example of the smilite SQLite database contents after successful insertion is shown in the image below. ![https://raw.github.com/rasbt/smilite/master/images/add_to_sqlite_1.png](https://raw.github.com/rasbt/smilite/master/images/add_to_sqlite_1.png) 266 | 267 | 268 | 269 | ### sqlite_to_csv.py 270 | 271 | Writes contents of an SQLite smilite database to a CSV file. 272 | 273 | **Usage:** 274 | `[shell]>> python3 sqlite_to_csv.py sqlite_file csv_file` 275 | 276 | **Example:** 277 | `[shell]>> python3 sqlite_to_csv.py ~/Desktop/smilite.sqlite ~/Desktop/zinc_smiles.csv` 278 | 279 | **Input CSV file example format:** 280 | 281 | 
ZINC_ID,SMILE,SIMPLE_SMILE
282 | ZINC01234568,C[C@@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O
283 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O
284 |
285 | 286 | An example of the CSV file contents opened in an spreadsheet program is shown in the image below. ![https://raw.github.com/rasbt/smilite/master/images/sqlite_to_csv_2.png](https://raw.github.com/rasbt/smilite/master/images/sqlite_to_csv_2.png) 287 | 288 | 289 | 290 | 291 | 292 | # Changelog 293 | 294 | **VERSION 2.3.1 (07/25/2020)** 295 | 296 | - Fix bug to allow `zinc15` option in gen_zincid_smile_csv.py script 297 | 298 | **VERSION 2.3.0 (06/10/2020)** 299 | 300 | - Fixes ZINC URL in `lookup_smile_str.py` 301 | - Adds an optional command line parameter (with arguments `zinc15` or `zinc12`) for `lookup_smile_str.py` 302 | 303 | **VERSION 2.2.0** 304 | 305 | * Provides an optional command line argument (zinc15) to use ZINC15 as a backend for downloading SMILES 306 | 307 | **VERSION 2.1.0** 308 | 309 | * Functions and scripts to fetch ZINC IDs corresponding to a SMILES string query 310 | 311 | **VERSION 2.0.1** 312 | 313 | * Progress bar for add_to_sqlite.py 314 | 315 | **VERSION 2.0.0** 316 | 317 | * added SQLite features 318 | 319 | **VERSION 1.3.0** 320 | 321 | * added script and module function to compare SMILES strings across 2 files. 322 | 323 | **VERSION 1.2.0** 324 | 325 | * added Python 2.x support 326 | 327 | **VERSION 1.1.1** 328 | 329 | * PyPrind dependency fix 330 | 331 | **VERSION 1.1.0** 332 | 333 | * added a progress bar (PyPrind) to `generate_zincid_smile_csv()` function -------------------------------------------------------------------------------- /TO_DO.txt: -------------------------------------------------------------------------------- 1 | smilite `smile_to_zincid` extension 2 | =================================== 3 | 4 | 5 | []update version in changelog 6 | []update version in setup.py 7 | []update version in __init__ 8 | [ ]create csv_scripts/gen_smile_zinc_id_csv.py (same output structure as from gen_zincid_smile_csv.py) 9 | [ ]modify sqlite_scripts/lookup_smile.py 10 | [ ]split sqlite_scripts/add_to_sqlite.py into 11 | [ ]sqlite_scripts/add_to_sqlite_from_id.py 12 | [ ]sqlite_scripts/add_to_sqlite_from_smile.py 13 | [ ]add/modify script paths in setup.py data dict 14 | [ ]update README.md 15 | [ ]convert to README.html 16 | [ ]upload smilite code to PyPi 17 | [ ]upload README.html to PyPi 18 | [ ]update documentation on website 19 | -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- 1 | ## Example Files 2 | 3 | #### zinc_ids.csv 4 | CSV file consisting of one column with 1 ZINC ID per row. 5 | Used as input for `smilite.generate_zincid_smile_csv()` to download SMILE strings 6 | from the ZINC online database ([http://zinc.docking.org](http://zinc.docking.org)) and generates a 2-column CSV file with 7 | ZINC_ID,SMILE_str pairs. 8 | This function is implemented in the command line script: [../scripts/gen_zincid_smiles.py](../scripts/gen_zincid_smiles.py). 9 | 10 | #### zid_smiles.csv 11 | A 2-column CSV file with ZINC_ID,SMILE_str pairs that is generated when the function `smilite.generate_zincid_smile_csv()` is invoked or via the command line script: [../scripts/gen_zincid_smiles.py](../scripts/gen_zincid_smiles.py). 12 | 13 | This CSV file can be used as input CSV file to check for SMILE string duplicates via the `smilite.check_duplicate_smiles()` function or the command line script [../scripts/comp_smile_strings.py](../scripts/comp_smile_strings.py). 14 | 15 | #### comp_smiles.csv 16 | A multi-column CSV file where 17 | - 1st column: ZINC ID 18 | - 2nd column: SMILE string 19 | - 3rd column: number of duplicates 20 | - 4th-nth column: ZINC IDs of duplicates 21 | 22 | This CSV file is the output of invoking the `smilite.check_duplicate_smiles()` function 23 | or the command line script [../scripts/comp_smile_strings.py](../scripts/comp_smile_strings.py). 24 | 25 | 26 | #### comp_simple_smiles.csv 27 | 28 | A multi-column CSV file where 29 | - 1st column: ZINC ID 30 | - 2nd column: simplified SMILE string 31 | - 3rd column: number of duplicates 32 | - 4th-nth column: ZINC IDs of duplicates 33 | 34 | This CSV file is the output of invoking the `smilite.check_duplicate_smiles()` function with the additional argument `compare_simplified_smiles=True` 35 | or the command line script [../scripts/comp_smile_strings.py](../scripts/comp_smile_strings.py) with the provided command line argument `simplify`. 36 | -------------------------------------------------------------------------------- /examples/comp_2_files.csv: -------------------------------------------------------------------------------- 1 | file_origin,zinc_id,smile_str,duplicates 2 | examples/zid_smiles2.csv,ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2, 3 | examples/zid_smiles2.csv,ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C, 4 | examples/zid_smiles2.csv,ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,ZINC12345678, 5 | examples/zid_smiles2.csv,ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,ZINC12345678, 6 | examples/zid_smiles3.csv,ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,ZINC12345678,ZINC12345678, 7 | examples/zid_smiles3.csv,ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O, 8 | examples/zid_smiles3.csv,ZINC03245324,c1ccc(c(c1)C#N)Sc2ccccc2C(=O)OCC(=O)Nc3ccc4c(c3)OCCO4, -------------------------------------------------------------------------------- /examples/comp_simple_smiles.csv: -------------------------------------------------------------------------------- 1 | zinc_id,smile_str,duplicates 2 | ZINC03245324,C1CCC(C(C1)CN)SC2CCCCC2C(=O)OCC(=O)NC3CCC4C(C3)OCCO4,0, 3 | ZINC83310457,CC1CCCC(C1N2C(CC(C2C)/C=N\NC(=O)C(=O)NC3CCC(CC3)N(=O)O)C)C,0, 4 | ZINC01234567,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O,0, 5 | ZINC12345678,CC1CCC(CC1C)OCCOC2C(CC(CC2I)/C=N/N3CNNC3)OC,0, 6 | ZINC00029323,COC1CCCC(C1)NC(=O)C2CCCNC2,1,ZINC00029323, -------------------------------------------------------------------------------- /examples/comp_smiles.csv: -------------------------------------------------------------------------------- 1 | zinc_id,smile_str,duplicates 2 | ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,0, 3 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,0, 4 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC,0, 5 | ZINC03245324,c1ccc(c(c1)C#N)Sc2ccccc2C(=O)OCC(=O)Nc3ccc4c(c3)OCCO4,0, 6 | ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,1,ZINC00029323, -------------------------------------------------------------------------------- /examples/zid_smiles.csv: -------------------------------------------------------------------------------- 1 | ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 2 | ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 3 | ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C 4 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 5 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 6 | ZINC03245324,c1ccc(c(c1)C#N)Sc2ccccc2C(=O)OCC(=O)Nc3ccc4c(c3)OCCO4 7 | -------------------------------------------------------------------------------- /examples/zid_smiles2.csv: -------------------------------------------------------------------------------- 1 | ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 2 | ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C 3 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 4 | 5 | -------------------------------------------------------------------------------- /examples/zid_smiles3.csv: -------------------------------------------------------------------------------- 1 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 2 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 3 | ZINC03245324,c1ccc(c(c1)C#N)Sc2ccccc2C(=O)OCC(=O)Nc3ccc4c(c3)OCCO4 4 | -------------------------------------------------------------------------------- /examples/zinc_ids.csv: -------------------------------------------------------------------------------- 1 | ZINC00029323 2 | ZINC00029323 3 | ZINC83310457 4 | ZINC12345678 5 | ZINC01234567 6 | ZINC03245324 7 | -------------------------------------------------------------------------------- /images/add_to_sqlite_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/smilite/48f61df2ccc48b73d30a66cabcbb37b85c189d6c/images/add_to_sqlite_1.png -------------------------------------------------------------------------------- /images/comp_2_files.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/smilite/48f61df2ccc48b73d30a66cabcbb37b85c189d6c/images/comp_2_files.png -------------------------------------------------------------------------------- /images/comp_simple_smiles.png: 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https://raw.githubusercontent.com/rasbt/smilite/48f61df2ccc48b73d30a66cabcbb37b85c189d6c/images/zinc_ids.png -------------------------------------------------------------------------------- /scripts/cmd_line_online_query_scripts/lookup_smile_str.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014 Sebastian Raschka 2 | # 3 | # Retrieves the corresponding ZINC_IDs for a given SMILE string 4 | # from the online ZINC database. 5 | # 6 | # 7 | # Usage: 8 | # [shell]>> python3 lookup_smile_str.py SMILE_str 9 | # 10 | # Example (retrieve data from the ZINC online database): 11 | # [shell]>> python3 lookup_smile_str.py \ 12 | # 'C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O' 13 | # 14 | # 15 | # Output example: 16 | # ZINC01234567 17 | # ZINC01234568 18 | # ZINC01242053 19 | # ZINC01242055 20 | # 21 | 22 | import smilite 23 | import sys 24 | 25 | 26 | def print_usage(): 27 | print('\nUSAGE: python3 lookup_smile_str.py SMILE_str Backend') 28 | print('\n\nUses zinc15 as backend by default' 29 | '\n\nEXAMPLE 1 (retrieve data from ZINC12):\n' 30 | 'python3 lookup_smile_str.py' 31 | ' C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O"' 32 | '\n\nEXAMPLE 2 (retrieve data from ZINC12):\n' 33 | 'python3 lookup_smile_str.py' 34 | ' CCOc1ccc(cc1)N([C@@H](C)C(=O)Nc2ccc(cc2C)Cl)S(=O)(=O)C" zinc12') 35 | 36 | 37 | zinc_id = [None] 38 | 39 | try: 40 | smile_str = sys.argv[1] 41 | 42 | if len(sys.argv) >= 3: 43 | backend = sys.argv[2] 44 | else: 45 | backend = 'zinc15' 46 | 47 | zinc_ids = smilite.get_zincid_from_smile(smile_str, backend=backend) 48 | for zid in zinc_ids: 49 | print(zid) 50 | 51 | except IOError as err: 52 | print('\n\nERROR: {}'.format(err)) 53 | print_usage() 54 | 55 | except IndexError: 56 | print('\n\nERROR: Invalid command line arguments.') 57 | print_usage() 58 | -------------------------------------------------------------------------------- /scripts/cmd_line_online_query_scripts/lookup_zincid.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Retrieves the SMILE string and simplified SMILE string for a given ZINC ID 4 | # from the online ZINC database. 5 | # 6 | # 7 | # Usage: 8 | # [shell]>> python3 lookup_zincid.py ZINC_ID 9 | # 10 | # Example (retrieve data from the ZINC online database): 11 | # [shell]>> python3 lookup_zincid.py ZINC01234567 12 | # 13 | # 14 | # 15 | # Output example: 16 | # ZINC01234567 17 | # C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 18 | # CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 19 | # 20 | # Where 21 | # 1st row: ZINC ID 22 | # 2nd row: SMILE string 23 | # 3rd row: simplified SMILE string 24 | # 25 | 26 | import smilite 27 | import sys 28 | 29 | 30 | def print_usage(): 31 | print('\nUSAGE: python3 lookup_zincid.py ZINC_ID [zinc12 (def.) / zinc15]') 32 | print('\n\nEXAMPLES (retrieve data from ZINC):\n' 33 | '1) python3 lookup_zincid.py ZINC01234567 zinc12\n' 34 | '2) python3 lookup_zincid.py ZINC01234567 zinc15') 35 | 36 | 37 | smile_str = '' 38 | simple_smile_str = '' 39 | 40 | try: 41 | zinc_id = sys.argv[1] 42 | 43 | if len(sys.argv) >= 3: 44 | backend = sys.argv[2] 45 | else: 46 | backend = 'zinc12' 47 | 48 | smile_str = smilite.get_zinc_smile(zinc_id, backend=backend) 49 | if smile_str: 50 | simple_smile_str = smilite.simplify_smile(smile_str) 51 | print('{}\n{}\n{}'.format(zinc_id, smile_str, simple_smile_str)) 52 | 53 | except IOError as err: 54 | print('\n\nERROR: {}'.format(err)) 55 | print_usage() 56 | 57 | except IndexError: 58 | print('\n\nERROR: Invalid command line arguments.') 59 | print_usage() 60 | -------------------------------------------------------------------------------- /scripts/csv_scripts/comp_2_smile_files.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Compares SMILE strings between 2 input CSV files, where each 4 | # file consists of rows with 2 columns ZINC_ID,SMILE_string to # 5 | # identify duplicate SMILE string across both files. 6 | # Generates a new CSV file with ZINC IDs of identified 7 | # duplicates listed in a 3rd-nth column(s). 8 | # 9 | # 10 | # Input example file format: 11 | # ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 12 | # ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 13 | # ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C 14 | # ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 15 | # 16 | # Output example file format: 17 | # file_origin,zinc_id,smile_str,duplicates 18 | # my_file1.csv,ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,1,ZINC00029323, 19 | # my_file1.csv,ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,0, 20 | # my_file1.csv,ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,0, 21 | # my_file2.csv,ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,1,ZINC00029323, 22 | # my_file2.csv,ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,0, 23 | # my_file2.csv,ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,0, 24 | # 25 | # 26 | # 27 | # Where 28 | # 1st column: name of the origin file 29 | # 2nd column: ZINC ID 30 | # 3rd column: SMILE string 31 | # 4th-nth column: ZINC IDs of duplicates 32 | # 33 | # Usage: 34 | # [shell]>> python3 comp_2_smile_files.py in1.csv in2.csv out.csv [simplify] 35 | # 36 | # Example 1: 37 | # [shell]>> python3 comp_2_smile_files.py \ 38 | # ../examples/zid_smiles2.csv \ 39 | # ../examples/zid_smiles3.csv \ 40 | # ../examples/comp_2_files.csv 41 | # 42 | # Example 2: 43 | # [shell]>> python3 comp_2_smile_files.py \ 44 | # ../examples/zid_smiles2.csv \ 45 | # ../examples/zid_smiles3.csv \ 46 | # ../examples/comp_2_files.csv simplify 47 | 48 | 49 | import smilite 50 | import sys 51 | 52 | 53 | def print_usage(): 54 | print('\nUSAGE: python3 comp_2_smile_files.py' 55 | ' in1.csv in2.csv out.csv [simplify]') 56 | print('\nEXAMPLE 1: python3 comp_2_smile_files.py' 57 | ' ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv' 58 | ' ../examples/comp_2_files.csv\n') 59 | print('\nEXAMPLE 2: python3 comp_2_smile_files.py' 60 | ' ../examples/zid_smiles2.csv ../examples/zid_smiles3.csv' 61 | ' ../examples/comp_2_files.csv simplify\n') 62 | 63 | 64 | try: 65 | in_csv1 = sys.argv[1] 66 | in_csv2 = sys.argv[2] 67 | out_csv = sys.argv[3] 68 | simplify = False 69 | 70 | if len(sys.argv) > 4: 71 | simplify = True 72 | 73 | smilite.comp_two_csvfiles(in_csv1, in_csv2, 74 | out_csv, compare_simplified_smiles=simplify) 75 | 76 | except IOError as err: 77 | print('\n\nERROR: {}'.format(err)) 78 | print_usage() 79 | 80 | except IndexError: 81 | print('\n\nERROR: Invalid command line arguments.') 82 | print_usage() 83 | -------------------------------------------------------------------------------- /scripts/csv_scripts/comp_smile_strings.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Compares SMILE strings within a 2 column CSV file (ZINC_ID,SMILE_string) to 4 | # identify duplicates. Generates a new CSV file with ZINC IDs of identified 5 | # duplicates listed in a 3rd-nth column(s). 6 | # 7 | # 8 | # Input example file format: 9 | # ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 10 | # ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2 11 | # ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C 12 | # ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 13 | # 14 | # Output example file format: 15 | # zinc_id,smile_str,duplicates 16 | # ZINC00029323,COc1cccc(c1)NC(=O)c2cccnc2,1,ZINC00029323, 17 | # ZINC83310457,Cc1cccc(c1n2c(cc(c2C)/C=N\NC(=O)C(=O)Nc3ccc(cc3)[N+](=O)[O-])C)C,0, 18 | # ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,0, 19 | # 20 | # Where 21 | # 1st column: ZINC ID 22 | # 2nd column: SMILE string 23 | # 3rd column: number of duplicates 24 | # 4th-nth column: ZINC IDs of duplicates 25 | # 26 | # Usage: 27 | # [shell]>> python3 comp_smile_strings.py in.csv out.csv [simplify] 28 | # 29 | # Example 1: 30 | # [shell]>> python3 gen_zincid_smile_csv.py \ 31 | # ../examples/zinc_ids.csv \ 32 | # ../examples/zid_smiles.csv 33 | # 34 | # Example 2: 35 | # [shell]>> python3 comp_smile_strings.py \ 36 | # ../examples/zid_smiles.csv \ 37 | # ../examples/comp_simple_smiles.csv simplify 38 | 39 | 40 | import smilite 41 | import sys 42 | 43 | 44 | def print_usage(): 45 | print('\nUSAGE: python3 comp_smile_strings.py in.csv out.csv [simplify]') 46 | print('\nEXAMPLE 1: python3 comp_smile_strings.py' 47 | ' ../examples/zid_smiles.csv ../examples/comp_smiles.csv\n') 48 | print('\nEXAMPLE 2: python3 comp_smile_strings.py' 49 | ' ../examples/zid_smiles.csv' 50 | ' ../examples/comp_simple_smiles.csv simplify\n') 51 | 52 | 53 | try: 54 | in_csv = sys.argv[1] 55 | out_csv = sys.argv[2] 56 | simplify = False 57 | 58 | if len(sys.argv) > 3: 59 | simplify = True 60 | 61 | smilite.check_duplicate_smiles(in_csv, out_csv, 62 | compare_simplified_smiles=simplify) 63 | 64 | except IOError as err: 65 | print('\n\nERROR: {}'.format(err)) 66 | print_usage() 67 | 68 | except IndexError: 69 | print('\n\nERROR: Invalid command line arguments.') 70 | print_usage() 71 | -------------------------------------------------------------------------------- /scripts/csv_scripts/gen_zincid_smile_csv.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Generates a ZINC_ID,SMILE_STR csv file from a input file of 4 | # ZINC IDs. The input file should consist of 1 columns with 1 ZINC ID per row. 5 | # 6 | # Input example file format: 7 | # ZINC0000123456 8 | # ZINC0000234567 9 | # ... 10 | # 11 | # Output example file format: 12 | # ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 13 | # ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 14 | # ... 15 | # 16 | # Usage: 17 | # [shell]>> python3 gen_zincid_smile_csv.py \ 18 | # in.csv out.csv [zinc12 (default) / zinc15] 19 | # 20 | # Example: 21 | # [shell]>> python3 gen_zincid_smile_csv.py \ 22 | # ../examples/zinc_ids.csv ../examples/zid_smiles.csv zinc15 23 | 24 | 25 | import smilite 26 | import sys 27 | 28 | 29 | def print_usage(): 30 | print('\nUSAGE: python3 gen_zincid_smile_csv.py' 31 | ' in.csv out.csv [zinc12 (default) / zinc15]') 32 | print('\nEXAMPLE: python3 gen_zincid_smile_csv.py ' 33 | '../examples/zinc_ids.csv ../examples/zid_smiles.csv zinc12\n') 34 | 35 | 36 | try: 37 | in_csv = sys.argv[1] 38 | out_csv = sys.argv[2] 39 | 40 | if len(sys.argv) >= 4: 41 | backend = sys.argv[3] 42 | else: 43 | backend = 'zinc12' 44 | 45 | smilite.generate_zincid_smile_csv(in_csv, out_csv, 46 | print_progress_bar=True, 47 | backend=backend) 48 | 49 | except IOError as err: 50 | print('\n\nERROR: {}'.format(err)) 51 | print_usage() 52 | 53 | except IndexError: 54 | print('\n\nERROR: Invalid command line arguments.') 55 | print_usage() 56 | -------------------------------------------------------------------------------- /scripts/sqlite_scripts/add_to_sqlite.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Reads ZINC IDs from a CSV file and looks up SMILE strings 4 | # and simplified SMILE strings 5 | # from the ZINC online database. Writes those SMILE strings 6 | # to a smilite SQLite database. 7 | # A new database will be created if it doesn't exist, yet. 8 | # 9 | # Usage: 10 | # [shell]>> python3 add_to_sqlite.py sqlite_file csv_file 11 | # 12 | # Example: 13 | # [shell]>> python3 add_to_sqlite.py 14 | # ~/Desktop/smilite.sqlite ~/Desktop/zinc_ids.csv 15 | # 16 | # 17 | # Input CSV file example format: 18 | # ZINC01234567 19 | # ZINC01234568 20 | # ... 21 | # 22 | # 23 | # 24 | 25 | import smilite 26 | import sys 27 | import os 28 | import pyprind 29 | 30 | 31 | def print_usage(): 32 | print('\nUSAGE: python3 add_to_sqlite.py sqlite_file csv_file') 33 | print('\nEXAMPLE:\n' 34 | 'python3 add_to_sqlite.py' 35 | ' ~/Desktop/smilite.sqlite ~/Desktop/zinc_ids.csv') 36 | 37 | 38 | try: 39 | sqlite_file = sys.argv[1] 40 | csv_file = sys.argv[2] 41 | if not os.path.exists(sqlite_file): 42 | smilite.create_sqlite(sqlite_file) 43 | with open(csv_file, 'r') as in_csv: 44 | all_lines = in_csv.readlines() 45 | pbar = pyprind.ProgBar(len(all_lines), title='Downloading SMILES') 46 | for line in all_lines: 47 | pbar.update() 48 | line = line.strip() 49 | if line: 50 | zinc_id = line.split(',')[0] 51 | smilite.insert_id_sqlite(sqlite_file, zinc_id) 52 | 53 | except IOError as err: 54 | print('\n\nERROR: {}'.format(err)) 55 | print_usage() 56 | 57 | 58 | except IndexError: 59 | print('\n\nERROR: Invalid command line arguments.') 60 | print_usage() 61 | -------------------------------------------------------------------------------- /scripts/sqlite_scripts/lookup_single_id.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Retrieves the SMILE string and simplified SMILE string for a given ZINC ID 4 | # from a previously built smilite SQLite database 5 | # or from the online ZINC database. 6 | # 7 | # 8 | # Usage: 9 | # [shell]>> python3 lookup_single_id.py ZINC_ID [sqlite_file] 10 | # 11 | # Example 1 (retrieve data from a smilite SQLite database): 12 | # [shell]>> python3 lookup_single_id.py 13 | # ZINC01234567 \ 14 | # ~/Desktop/smilite_db.sqlite 15 | # 16 | # Example 2 (retrieve data from the ZINC online database): 17 | # [shell]>> python3 lookup_single_id.py ZINC01234567 18 | # 19 | # 20 | # 21 | # Output example: 22 | # ZINC01234567 23 | # C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 24 | # CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 25 | # 26 | # Where 27 | # 1st row: ZINC ID 28 | # 2nd row: SMILE string 29 | # 3rd row: simplified SMILE string 30 | # 31 | 32 | import smilite 33 | import sys 34 | 35 | 36 | def print_usage(): 37 | print('\nUSAGE: python3 lookup_single_id.py ZINC_ID [sqlite_file]') 38 | print('\n\nEXAMPLE1 (retrieve data from a smilite SQLite database):\n' 39 | 'python3 lookup_single_id.py ZINC01234567 ' 40 | '~/Desktop/smilite_db.sqlite') 41 | print('\n\nEXAMPLE2 (retrieve data from the ZINC online database):\n' 42 | 'python3 lookup_single_id.py ZINC01234567\n') 43 | 44 | 45 | smile_str = '' 46 | simple_smile_str = '' 47 | 48 | try: 49 | zinc_id = sys.argv[1] 50 | 51 | if len(sys.argv) > 2: 52 | sqlite_file = sys.argv[2] 53 | lookup_result = smilite.lookup_id_sqlite(sqlite_file, zinc_id) 54 | try: 55 | smile_str, simple_smile_str = lookup_result[1], lookup_result[2] 56 | except IndexError: 57 | pass 58 | 59 | else: 60 | smile_str = smilite.get_zinc_smile(zinc_id) 61 | if smile_str: 62 | simple_smile_str = smilite.simplify_smile(smile_str) 63 | 64 | print('{}\n{}\n{}'.format(zinc_id, smile_str, simple_smile_str)) 65 | 66 | except IOError as err: 67 | print('\n\nERROR: {}'.format(err)) 68 | print_usage() 69 | 70 | except IndexError: 71 | print('\n\nERROR: Invalid command line arguments.') 72 | print_usage() 73 | -------------------------------------------------------------------------------- /scripts/sqlite_scripts/lookup_smile.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Retrieves the ZINC ID(s) for a given SMILE sting or simplified SMILE string 4 | # from a previously built smilite SQLite database. 5 | # 6 | # 7 | # Usage: 8 | # [shell]>> python3 lookup_smile.py sqlite_file SMILE_STRING [simplify] 9 | # 10 | # Example 1 (search for SMILE string): 11 | # [shell]>> python3 lookup_smile.py ~/Desktop/smilite.sqlite \ 12 | # "C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O" 13 | # 14 | # Example 2 (search for simplified SMILE string): 15 | # [shell]>> python3 lookup_smile.py ~/Desktop/smilite.sqlite \ 16 | # "CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O" simple 17 | # 18 | # 19 | # 20 | # Output example: 21 | # ZINC01234567 22 | # C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 23 | # CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 24 | # 25 | # Where 26 | # 1st row: ZINC ID 27 | # 2nd row: SMILE string 28 | # 3rd row: simplified SMILE string 29 | # 30 | 31 | import smilite 32 | import sys 33 | 34 | 35 | def print_usage(): 36 | print('\nUSAGE: python3 lookup_smile.py ' 37 | 'sqlite_file SMILE_STRING [simplify]') 38 | print('\n\nEXAMPLE1 (search for SMILE string):\n' 39 | 'python3 lookup_smile.py ~/Desktop/smilite.sqlite ' 40 | '"C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O"') 41 | print('\n\nEXAMPLE2 (search for simplified SMILE string):\n' 42 | 'python3 lookup_smile.py ~/Desktop/smilite.sqlite ' 43 | '"CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O simple\n"') 44 | 45 | 46 | zinc_id = '' 47 | simple_smile = False 48 | 49 | try: 50 | sqlite_file = sys.argv[1] 51 | smile = sys.argv[2] 52 | if len(sys.argv) > 3: 53 | simple_smile = True 54 | 55 | result = smilite.lookup_smile_sqlite(sqlite_file, smile, simple_smile) 56 | for i in result: 57 | if isinstance(i, list): 58 | for j in i: 59 | print(j) 60 | else: 61 | print(i) 62 | 63 | 64 | except IOError as err: 65 | print('\n\nERROR: {}'.format(err)) 66 | print_usage() 67 | 68 | except IndexError: 69 | print('\n\nERROR: Invalid command line arguments.') 70 | print_usage() 71 | -------------------------------------------------------------------------------- /scripts/sqlite_scripts/sqlite_to_csv.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # Writes contents of an SQLite smilite database to a CSV file. 4 | # 5 | # Usage: 6 | # [shell]>> python3 sqlite_to_csv.py sqlite_file csv_file 7 | # 8 | # Example: 9 | # [shell]>> python3 sqlite_to_csv.py ~/Desktop/smilite.sqlite ~/Desktop/zinc_smiles.csv 10 | # 11 | # Output CSV file example: 12 | # ZINC_ID,SMILE,SIMPLE_SMILE 13 | # ZINC01234568,C[C@@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 14 | # ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 15 | # 16 | 17 | import smilite 18 | import sys 19 | import os 20 | 21 | def print_usage(): 22 | print('\nUSAGE: python3 sqlite_to_csv.py sqlite_file csv_file') 23 | print('\nEXAMPLE:\n'\ 24 | 'python3 sqlite_to_csv.py ~/Desktop/smilite.sqlite ~/Desktop/zinc_smiles.csv') 25 | 26 | try: 27 | sqlite_file = sys.argv[1] 28 | csv_file = sys.argv[2] 29 | smilite.sqlite_to_csv(sqlite_file, csv_file) 30 | 31 | except IOError as err: 32 | print('\n\nERROR: {}'.format(err)) 33 | print_usage() 34 | 35 | except IndexError: 36 | print('\n\nERROR: Invalid command line arguments.') 37 | print_usage() 38 | 39 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | 3 | setup(name='smilite', 4 | version='2.3.0', 5 | description='smilite is a Python module to download' 6 | ' and analyze SMILE strings', 7 | author='Sebastian Raschka', 8 | author_email='se.raschka@gmail.com', 9 | url='https://github.com/rasbt/smilite', 10 | packages=['smilite'], 11 | package_data={'': ['LICENSE.txt', 12 | 'README.md', 13 | 'CHANGELOG.txt']}, 14 | install_requires=['PyPrind>=2.3.1'], 15 | license='GPLv3', 16 | platforms='any', 17 | classifiers=[ 18 | 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 19 | 'Development Status :: 5 - Production/Stable', 20 | 'Programming Language :: Python :: 3', 21 | 'Environment :: Console', 22 | ], 23 | long_description=""" 24 | 25 | smilite is a Python module to download and analyze SMILE strings 26 | (Simplified Molecular-Input Line-entry System) 27 | of chemical compounds from ZINC 28 | (a free database of commercially-available compounds for virtual screening, 29 | http://zinc.docking.org). 30 | 31 | Source repository: https://github.com/rasbt/smilite 32 | 33 | """) 34 | -------------------------------------------------------------------------------- /smilite/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # A small module to retrieve SMILE strings 4 | # (Simplified molecular-input line-entry system) from the ZINC online 5 | # database (http://zinc.docking.org) 6 | 7 | from .smilite import get_zinc_smile 8 | from .smilite import generate_zincid_smile_csv 9 | from .smilite import simplify_smile 10 | from .smilite import check_duplicate_smiles 11 | from .smilite import comp_two_csvfiles 12 | from .smilite import create_id_smile_list 13 | from .smilite import create_sqlite 14 | from .smilite import insert_id_sqlite 15 | from .smilite import lookup_id_sqlite 16 | from .smilite import lookup_smile_sqlite 17 | from .smilite import sqlite_to_dict 18 | from .smilite import sqlite_to_csv 19 | from .smilite import get_zincid_from_smile 20 | 21 | __version__ = '2.3.1' 22 | 23 | -------------------------------------------------------------------------------- /smilite/smilite.py: -------------------------------------------------------------------------------- 1 | # Copyright 2014-2020 Sebastian Raschka 2 | # 3 | # smilite is a Python module to download and analyze SMILE strings 4 | # (Simplified Molecular-Input Line-entry System) of chemical compounds 5 | # from ZINC (a free database of commercially-available compounds 6 | # for virtual screening: 7 | # http://zinc.docking.org 8 | # Now supports both Python 3.x and Python 2.x. 9 | 10 | import sys 11 | import sqlite3 12 | import os 13 | import pyprind 14 | 15 | # Load Python version specific modules 16 | if sys.version_info[0] == 3: 17 | import urllib.request 18 | import urllib.parse 19 | else: 20 | import urllib 21 | 22 | 23 | def get_zinc_smile(zinc_id, backend='zinc12'): 24 | """ 25 | Gets the corresponding SMILE string for a ZINC ID query from 26 | the ZINC online database. Requires an internet connection. 27 | 28 | Keyword arguments: 29 | zinc_id (str): A valid ZINC ID, e.g. 'ZINC00029323' 30 | backend (str): zinc12 or zinc15 31 | 32 | Returns the SMILE string for the corresponding ZINC ID. 33 | E.g., 'COc1cccc(c1)NC(=O)c2cccnc2' 34 | 35 | """ 36 | if backend not in {'zinc12', 'zinc15'}: 37 | raise ValueError("backend must be 'zinc12' or 'zinc15'") 38 | 39 | stripped_id = zinc_id.strip('ZINC') 40 | 41 | if backend == 'zinc12': 42 | min_len = 8 43 | base_path = 'http://zinc.docking.org/substance/' 44 | line_lookup = ('Draw' 48 | 49 | else: 50 | min_len = 12 51 | base_path = 'http://zinc15.docking.org/substances/' 52 | line_lookup = 'id="substance-smiles-field" readonly value="' 53 | first_linesplit = line_lookup 54 | second_linesplit = '">' 55 | 56 | while len(stripped_id) < min_len: 57 | stripped_id = '0' + stripped_id 58 | 59 | smile_str = None 60 | 61 | try: 62 | if sys.version_info[0] == 3: 63 | response = urllib.request.urlopen( 64 | '{}{}' 65 | .format(base_path, stripped_id)) 66 | else: 67 | response = urllib.urlopen('{}{}' 68 | .format(base_path, stripped_id)) 69 | except urllib.error.HTTPError: 70 | print('Invalid ZINC ID {}'.format(zinc_id)) 71 | response = [] 72 | for line in response: 73 | line = line.decode(encoding='UTF-8').strip() 74 | if line_lookup in line: 75 | line = (line.split(first_linesplit)[-1] 76 | .split(second_linesplit)[0]) 77 | if sys.version_info[0] == 3: 78 | smile_str = urllib.parse.unquote(line) 79 | else: 80 | smile_str = urllib.unquote(line) 81 | break 82 | return smile_str 83 | 84 | 85 | def get_zincid_from_smile(smile_str, backend='zinc15'): 86 | """ 87 | Gets the corresponding ZINC ID(s) for a SMILE string query from 88 | the ZINC online database. Requires an internet connection. 89 | 90 | Keyword arguments: 91 | smile_str (str): A valid SMILE string, e.g., 92 | C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O' 93 | backend (str): Specifies the database backend, "zinc12" or "zinc15" 94 | 95 | Returns the SMILE string for the corresponding ZINC ID(s) in a list. 96 | E.g., ['ZINC01234567', 'ZINC01234568', 'ZINC01242053', 'ZINC01242055'] 97 | 98 | """ 99 | 100 | if backend not in {'zinc12', 'zinc15'}: 101 | raise ValueError("backend must be 'zinc12' or 'zinc15'") 102 | 103 | stripped_smile = smile_str.strip() 104 | encoded_smile = urllib.parse.quote(stripped_smile) 105 | 106 | if backend == 'zinc12': 107 | url_part1 = 'http://zinc12.docking.org/results?structure.smiles=' 108 | url_part3 = '&structure.similarity=1.0' 109 | elif backend == 'zinc15': 110 | url_part1 = 'http://zinc.docking.org/substances/search/?q=' 111 | url_part3 = '' 112 | else: 113 | raise ValueError("Backend must be 'zinc12' or 'zinc15'. " 114 | "Got %s" % (backend)) 115 | 116 | zinc_ids = [] 117 | 118 | try: 119 | if sys.version_info[0] == 3: 120 | #smile_url = urllib.request.pathname2url(encoded_smile) 121 | response = urllib.request.urlopen('{}{}{}' 122 | .format(url_part1, 123 | encoded_smile, 124 | url_part3)) 125 | else: 126 | #smile_url = urllib.pathname2url(encoded_smile) 127 | response = urllib.urlopen('{}{}{}' 128 | .format(url_part1, 129 | encoded_smile, 130 | url_part3)) 131 | except urllib.error.HTTPError: 132 | print('Invalid SMILE string {}'.format(smile_str)) 133 | response = [] 134 | for line in response: 135 | line = line.decode(encoding='UTF-8').strip() 136 | 137 | if backend == 'zinc15': 138 | if line.startswith('')[-2].split('>')[-1] 148 | if sys.version_info[0] == 3: 149 | zinc_id = urllib.parse.unquote(line) 150 | else: 151 | zinc_id = urllib.unquote(line) 152 | zinc_id = 'ZINC' + (8-len(zinc_id)) * '0' + zinc_id 153 | zinc_ids.append(str(zinc_id)) 154 | return zinc_ids 155 | 156 | 157 | def generate_zincid_smile_csv(zincid_list, out_file, 158 | print_progress_bar=True, backend='zinc12'): 159 | """ 160 | Generates a CSV file of ZINC_ID,SMILE_string entries 161 | by querying the ZINC online database. 162 | 163 | Keyword arguments: 164 | zincid_list (str): Path to a UTF-8 or ASCII formatted file 165 | that contains 1 ZINC_ID per row. E.g., 166 | ZINC0000123456 167 | ZINC0000234567 168 | [...] 169 | out_file (str): Path to a new output CSV file that will be written. 170 | print_prgress_bar (bool): Prints a progress bar to the screen if True. 171 | 172 | """ 173 | id_smile_pairs = [] 174 | with open(zincid_list, 'r') as infile: 175 | all_lines = infile.readlines() 176 | if print_progress_bar: 177 | pbar = pyprind.ProgBar(len(all_lines), title='Downloading SMILES') 178 | for line in all_lines: 179 | line = line.strip() 180 | id_smile_pairs.append((line, get_zinc_smile(line, 181 | backend=backend))) 182 | if print_progress_bar: 183 | pbar.update() 184 | with open(out_file, 'w') as out: 185 | for p in id_smile_pairs: 186 | out.write('{},{}\n'.format(p[0], p[1])) 187 | 188 | 189 | def check_duplicate_smiles(zincid_list, out_file, 190 | compare_simplified_smiles=False): 191 | """ 192 | Scans a ZINC_ID,SMILE_string CSV file for duplicate SMILE strings. 193 | 194 | Keyword arguments: 195 | zincid_list (str): Path to a UTF-8 or ASCII formatted file that 196 | contains 1 ZINC_ID + 1 SMILE String per row. 197 | E.g., 198 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 199 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 200 | [...] 201 | out_file (str): Path to a new output CSV file that will be written. 202 | compare_simplified_smiles (bool): If true, S 203 | SMILE strings will be simplified for the comparison. 204 | 205 | """ 206 | smile_dict = dict() 207 | with open(zincid_list, 'r') as infile: 208 | all_lines = infile.readlines() 209 | for line in all_lines: 210 | line = line.strip().split(',') 211 | if len(line) == 2: 212 | zinc_id, smile_str = line 213 | if compare_simplified_smiles: 214 | smile_str = simplify_smile(smile_str) 215 | if smile_str not in smile_dict: 216 | smile_dict[smile_str] = [zinc_id] 217 | else: 218 | smile_dict[smile_str].append(zinc_id) 219 | 220 | with open(out_file, 'w') as out: 221 | out.write('zinc_id,smile_str,duplicates') 222 | for entry in smile_dict: 223 | out.write('\n{},{},{},'.format( 224 | smile_dict[entry][0], entry, len(smile_dict[entry]) - 1)) 225 | for duplicate in smile_dict[entry][1:]: 226 | out.write(duplicate + ',') 227 | print('\nResults written to', out_file) 228 | 229 | 230 | def create_id_smile_list(id_smile_csv, simplify_smiles=False): 231 | """ 232 | Reads in a CSV file and returns a list of [ZINC_ID,SMILE_STR] sublists. 233 | 234 | Keyword arguments: 235 | id_smile_csv (str): Path to a UTF-8 or ASCII formatted file that 236 | contains 1 ZINC_ID + 1 SMILE String per row. 237 | E.g., 238 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 239 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 240 | [...] 241 | simplify_smiles (bool): If true, SMILE strings will be simplified. 242 | 243 | """ 244 | smile_list = [] 245 | with open(id_smile_csv, 'r') as infile: 246 | all_lines = infile.readlines() 247 | for line in all_lines: 248 | line = line.strip().split(',') 249 | if len(line) == 2: 250 | zinc_id, smile_str = line 251 | if simplify_smiles: 252 | smile_str = simplify_smile(smile_str) 253 | smile_list.append([zinc_id, smile_str]) 254 | return smile_list 255 | 256 | 257 | def comp_two_csvfiles(zincid_list1, zincid_list2, out_file, 258 | compare_simplified_smiles=False): 259 | """ 260 | Compares SMILE strings across two ZINC_ID CSV files for duplicates 261 | (does not check for duplicates within each file). 262 | 263 | Keyword arguments: 264 | zincid_list1 (str): Path to a UTF-8 or ASCII formatted file that 265 | contains 1 ZINC_ID + 1 SMILE String per row. 266 | E.g., 267 | ZINC12345678,Cc1ccc(cc1C)OCCOc2c(cc(cc2I)/C=N/n3cnnc3)OC 268 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O 269 | [...] 270 | zincid_list2 (str): Second ZINC_ID list file, similarly 271 | out_file (str): Path to a new output CSV file that will be written. 272 | compare_simplified_smiles (bool): If true, 273 | SMILE strings will be simplified for the comparison. 274 | 275 | """ 276 | smile_list1 = create_id_smile_list(zincid_list1, compare_simplified_smiles) 277 | smile_list2 = create_id_smile_list(zincid_list2, compare_simplified_smiles) 278 | 279 | with open(out_file, 'w') as out: 280 | out.write('file_origin,zinc_id,smile_str,duplicates') 281 | for entry in smile_list1: 282 | out.write('\n{},{},{},'.format( 283 | zincid_list1, entry[0], entry[1])) 284 | for comp in smile_list2: 285 | if comp[1] == entry[1]: # if SMILES are similar 286 | out.write(comp[0] + ',') 287 | for entry in smile_list2: 288 | out.write('\n{},{},{},'.format( 289 | zincid_list2, entry[0], entry[1])) 290 | for comp in smile_list1: 291 | if comp[1] == entry[1]: # if SMILES are similar 292 | out.write(comp[0] + ',') 293 | print('\nResults written to', out_file) 294 | 295 | 296 | def simplify_smile(smile_str): 297 | """ 298 | Simplifies a SMILE string by removing hydrogen atoms (H), 299 | chiral specifications ('@'), charges (+ / -), '#'-characters, 300 | and square brackets ('[', ']'). 301 | 302 | Keyword Arguments: 303 | smile_str (str): A smile string, e.g., C[C@H](CCC(=O)NCCS(=O)(=O)[O-]) 304 | 305 | Returns a simplified SMILE string, e.g., CC(CCC(=O)NCCS(=O)(=O)O) 306 | 307 | """ 308 | remove_chars = ['@', '-', '+', 'H', '[', ']', '#'] 309 | stripped_smile = [] 310 | for sym in smile_str: 311 | if sym.isalpha(): 312 | sym = sym.upper() 313 | if sym not in remove_chars: 314 | stripped_smile.append(sym) 315 | return "".join(stripped_smile) 316 | 317 | 318 | def create_sqlite(sqlite_file): 319 | """ 320 | Creates a new SQLite database file if it doesn't exist yet. 321 | The database created will consists of 3 columns: 322 | 1) 'zinc_id' (ZINC ID as Primary Key) 323 | 2) 'smile' (SMILE string obtained from the ZINC online db) 324 | 3) 'simple_smile' (simplified SMILE string, 325 | see smilite.simplify_smile()) 326 | 327 | Keyword arguments: 328 | sqlite_file (str): Path to the new SQLite database file. 329 | 330 | """ 331 | if not os.path.exists(sqlite_file): 332 | # open connection to a sqlite file object 333 | conn = sqlite3.connect(sqlite_file) 334 | c = conn.cursor() 335 | 336 | # creating a new SQLite table with 3 columns 337 | c.execute('CREATE TABLE smilite (zinc_id TEXT PRIMARY KEY,' 338 | ' smile TEXT, simple_smile TEXT)') 339 | 340 | # commit changes and close the connection to the sqlite file object. 341 | conn.commit() 342 | conn.close() 343 | 344 | 345 | def insert_id_sqlite(sqlite_file, zinc_id, backend='zinc12'): 346 | """ 347 | Inserts a new ZINC ID into an existing SQLite database if the ZINC ID 348 | isn't contained in the database, yet. Obtains the SMILE string from the 349 | ZINC online database and adds it to the new ZINC ID database entry together 350 | with an simplified SMILE string. 351 | 352 | Example database entry: 353 | zinc_id,smile,simple_smile 354 | "ZINC01234567","C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O","CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O" 355 | 356 | Keyword arguments: 357 | sqlite_file (str): Path to an existing SQLite database file 358 | zinc_id (str): A valid ZINC ID 359 | 360 | Returns True if insertion was successful, else returns False. 361 | 362 | """ 363 | success = False 364 | if os.path.exists(sqlite_file): 365 | # open connection to a sqlite file object 366 | conn = sqlite3.connect(sqlite_file) 367 | c = conn.cursor() 368 | 369 | # get smile string and simplified smile string 370 | smile_str = get_zinc_smile(zinc_id, backend=backend) 371 | if smile_str: 372 | simple_smile = simplify_smile(smile_str) 373 | 374 | # insert data into database 375 | if smile_str and simple_smile: 376 | c.execute('INSERT OR IGNORE INTO smilite (zinc_id, smile,' 377 | ' simple_smile) VALUES (?, ?, ?)', 378 | (zinc_id, smile_str, simple_smile)) 379 | success = True 380 | 381 | # commit changes and close the connection to the sqlite file object. 382 | conn.commit() 383 | conn.close() 384 | return success 385 | 386 | else: 387 | return success 388 | 389 | 390 | def lookup_id_sqlite(sqlite_file, zinc_id): 391 | """ 392 | Looks up an ZINC ID in an existing SQLite database file. 393 | 394 | Keyword arguments: 395 | sqlite_file (str): Path to an existing SQLite database file 396 | zinc_id (str): A valid ZINC ID 397 | 398 | Returns a list with the ZINC ID, SMILE string, and simplified SMILE 399 | string or an empty list if ZINC ID could not be found. 400 | Example returned list: 401 | ['ZINC01234567', 'C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O', 402 | 'CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O'] 403 | 404 | """ 405 | result = [] 406 | if os.path.exists(sqlite_file): 407 | 408 | # open connection to a sqlite file object 409 | conn = sqlite3.connect(sqlite_file) 410 | c = conn.cursor() 411 | 412 | c.execute('SELECT * FROM smilite WHERE zinc_id=?', (zinc_id,)) 413 | all_rows = c.fetchall() 414 | try: 415 | result = [i for i in all_rows[0]] 416 | except IndexError: 417 | pass 418 | 419 | # close the connection to the sqlite file object. 420 | conn.close() 421 | 422 | return result 423 | 424 | 425 | def lookup_smile_sqlite(sqlite_file, smile_str, simple_smile=False): 426 | """ 427 | Looks up an ZINC ID for a given SMILE string in an existing 428 | SQLite database file. 429 | 430 | Keyword arguments: 431 | sqlite_file (str): Path to an existing SQLite database file 432 | smile_str (str): A SMILE string to query the database 433 | simple_smile (bool): Queries simplified smile strings in the 434 | database if true 435 | 436 | Returns a list with the ZINC ID, SMILE string, and simplified SMILE 437 | string or an empty list if SMILE string could not be found. 438 | Example returned list: 439 | ['ZINC01234567', 'C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O', 440 | 'CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O'] 441 | If multiple ZINC IDs match the query SMILE string, a list of sublists 442 | is returned. 443 | 444 | """ 445 | result = [] 446 | if os.path.exists(sqlite_file): 447 | 448 | # open connection to a sqlite file object 449 | conn = sqlite3.connect(sqlite_file) 450 | c = conn.cursor() 451 | 452 | if simple_smile: 453 | c.execute('SELECT * FROM smilite WHERE simple_smile=?', 454 | (smile_str,)) 455 | else: 456 | c.execute('SELECT * FROM smilite WHERE smile=?', (smile_str,)) 457 | all_rows = c.fetchall() 458 | try: 459 | for i in all_rows: 460 | result.append([j for j in i]) 461 | except IndexError: 462 | pass 463 | 464 | # close the connection to the sqlite file object. 465 | conn.close() 466 | 467 | return result 468 | 469 | 470 | def sqlite_to_dict(sqlite_file): 471 | """ 472 | Returns contents of an SQLite smilite database as Python dictionary object. 473 | 474 | Keyword arguments: 475 | sqlite_file (str): Path to an existing SQLite database file 476 | 477 | Returns an SQLite smilite database as Python dictionary object with 478 | ZINC IDs as keys and corresponding 479 | [SMILE_string, Simple_SMILE_string] lists as values. 480 | 481 | Example returned dictionary: 482 | { 483 | 'ZINC01234568': ['C[C@@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O', 484 | 'CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O'], 485 | 'ZINC01234567': ['C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O', 486 | 'CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O'] 487 | } 488 | 489 | """ 490 | result = {} 491 | if os.path.exists(sqlite_file): 492 | 493 | # open connection to a sqlite file object 494 | conn = sqlite3.connect(sqlite_file) 495 | c = conn.cursor() 496 | 497 | c.execute('SELECT * FROM smilite') 498 | all_rows = c.fetchall() 499 | try: 500 | result = {i[0]: [i[1], i[2]] for i in all_rows} 501 | except IndexError: 502 | pass 503 | 504 | # close the connection to the sqlite file object. 505 | conn.close() 506 | 507 | return result 508 | 509 | 510 | def sqlite_to_csv(sqlite_file, csv_file): 511 | """ 512 | Writes contents of an SQLite smilite database to a CSV file. 513 | 514 | Keyword arguments: 515 | sqlite_file (str): Path to an existing SQLite database file 516 | csv_file (str): Path to the output CSV file 517 | 518 | Example output CSV file contents: 519 | 520 | ZINC_ID,SMILE,SIMPLE_SMILE 521 | ZINC01234567,C[C@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 522 | ZINC01234568,C[C@@H]1CCCC[NH+]1CC#CC(c2ccccc2)(c3ccccc3)O,CC1CCCCN1CCCC(C2CCCCC2)(C3CCCCC3)O 523 | ... 524 | 525 | """ 526 | zinc_dict = sqlite_to_dict(sqlite_file) 527 | with open(csv_file, 'a') as out_csv: 528 | out_csv.write('ZINC_ID,SMILE,SIMPLE_SMILE\n') 529 | for k in zinc_dict.keys(): 530 | line = '{},{}\n'.format(k, ",".join(zinc_dict[k])) 531 | out_csv.write(line) 532 | -------------------------------------------------------------------------------- /test/test_get_zinc_smile.py: -------------------------------------------------------------------------------- 1 | # Sebastian Raschka, 02/2014 2 | 3 | import smilite 4 | 5 | def test_get_zinc_smile(): 6 | out = smilite.get_zinc_smile('ZINC00029323') 7 | assert out == 'COc1cccc(c1)NC(=O)c2cccnc2' 8 | 9 | -------------------------------------------------------------------------------- /test/test_simplify_smile.py: -------------------------------------------------------------------------------- 1 | # Sebastian Raschka, 02/2014 2 | 3 | import smilite 4 | 5 | def test_simplify_smile(): 6 | out = smilite.simplify_smile('C[C@H](CCC(=O)NCCS(=O)(=O)[O-])') 7 | assert out == 'CC(CCC(=O)NCCS(=O)(=O)O)' 8 | 9 | --------------------------------------------------------------------------------