3 |
4 |
5 |
6 |
7 | 
8 | [](license)
9 | [](license)
10 |
11 | ### A toolkit for ligand-based virtual screening
12 |
13 |
14 | Screenlamp is a Python package for facilitating ligand-based virtual screening workflows and toolkits with hypothesis-driven filtering steps.
15 |
16 | **The official documentation is available at https://psa-lab.github.io/screenlamp.**
17 |
18 |
19 | ## About
20 |
21 | The screenlamp toolkit was developed in the [Protein Structure Analysis & Design Laboratory](http://www.kuhnlab.bmb.msu.edu) at Michigan State University. For additional information about screenlamp, please refer to the accompanying research publication, which is currently under revision:
22 |
23 | - Raschka, Sebastian, Anne M. Scott, Nan Liu, Santosh Gunturu, Mar Huertas, Weiming Li, and Leslie A. Kuhn (2018). "Enabling the hypothesis-driven prioritization of ligand candidates in big databases:
24 | Screenlamp and its application to GPCR inhibitor discovery for invasive species control". *Journal of Computer-Aided Molecular Design* 32: 415.
25 | [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/01/17/249151)]
26 | [[Journal article](https://link.springer.com/article/10.1007/s10822-018-0100-7)]
27 |
28 |
29 | Screenlamp is research software and has been made available to other researchers under a permissive [Apache v2 open source license](license). If you use screenlamp in your scientific projects or any derivative work, the authors of the screenlamp software must be acknowledged and the publication listed above should be cited.
30 |
31 |
32 | # Contact
33 |
34 | If you encounter bugs or other technical issues with the screenlamp software package, please send an email to [kuhnlab@msu.edu](mailto:kuhnlab@msu.edu) or use the [Issue Tracker](https://github.com/psa-lab/screenlamp/issues). For questions about the [screenlamp research article](cite/index.html), please contact the publisher or [corresponding author](mailto:kuhnl@msu.edu) directly instead.
35 |
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/docs/argparse_to_md.py:
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1 | # Tool to generate a markdown documentation
2 | # from argparse scripts.
3 | #
4 | # usage: python argparse_to_md.py scipts/ > doc.md
5 | #
6 | # Copyright (C) 2017 Sebastian Raschka
7 | # License: MIT
8 | #
9 | # Author: Sebastian Raschka Sebastian Raschka et al. 2017. 28 | 29 | pages: 30 | - Home: index.md 31 | - Installation: installation.md 32 | - User Documentation: 33 | - Overview: user_guide/doc-overview.md 34 | - Tools: user_guide/tools.md 35 | - Toolkit Tutorial: user_guide/tools-tutorial-1.md 36 | - Pipeline Tutorial: user_guide/pipeline-tutorial-1.md 37 | - About: 38 | - Contact: contact.md 39 | - Release Notes: changelog.md 40 | - License: license.md 41 | - Citing screenlamp: cite.md 42 | -------------------------------------------------------------------------------- /docs/sources/changelog.md: -------------------------------------------------------------------------------- 1 | # Release Notes 2 | 3 | ### Version 1.0.0 (2017-10-31) 4 | 5 | - First release 6 | 7 | ##### Downloads 8 | 9 | - [Source code (zip)](https://github.com/psa-lab/screenlamp/archive/v1.0.0.zip) 10 | - [Source code (tar.gz)](https://github.com/psa-lab/screenlamp/archive/v1.0.0.tar.gz) 11 | -------------------------------------------------------------------------------- /docs/sources/cite.md: -------------------------------------------------------------------------------- 1 | # Citing screenlamp 2 | 3 | Screenlamp is research software and has been made available to other researchers under a permissive [Apache v2 open source license](license). If you use screenlamp in your scientific projects or any derivative work, the authors of the screenlamp software must be acknowledged and the following publication should be cited: 4 | 5 | - Raschka, Sebastian, Anne M. Scott, Nan Liu, Santosh Gunturu, Mar Huertas, Weiming Li, and Leslie A. Kuhn (2018). "Enabling the hypothesis-driven prioritization of ligand candidates in big databases: 6 | Screenlamp and its application to GPCR inhibitor discovery for invasive species control". *Journal of Computer-Aided Molecular Design* 32: 415. 7 | [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/01/17/249151)] 8 | [[Journal article](https://link.springer.com/article/10.1007/s10822-018-0100-7)] 9 | 10 | 11 | 12 | ### BibTeX Entry 13 | 14 | ```tex 15 | @article{raschka2018, 16 | title={Enabling the hypothesis-driven prioritization of ligand 17 | candidates in big databases: Screenlamp and its application to GPCR 18 | inhibitor discovery for invasive species control}, 19 | volume={32}, 20 | DOI={10.1007/s10822-018-0100-7}, 21 | number={3}, 22 | journal={Journal of Computer-Aided Molecular Design}, 23 | author={Raschka, Sebastian and Scott, Anne M. 24 | and Liu, Nan and Gunturu, Santosh and Huertas, 25 | Mar and Li, Weiming and Kuhn, Leslie A.}, 26 | year={2018}, 27 | month={Mar}, 28 | pages={415–433} 29 | } 30 | 31 | ``` 32 | 33 | -------------------------------------------------------------------------------- /docs/sources/contact.md: -------------------------------------------------------------------------------- 1 | # Contact 2 | 3 | If you encounter bugs or other technical issues with the screenlamp software package, please send an email to [kuhnlab@msu.edu](mailto:kuhnlab@msu.edu) or use the [Issue Tracker](https://github.com/psa-lab/screenlamp/issues). For questions about the [screenlamp research article](cite/index.html), please contact the publisher or [corresponding author](mailto:kuhnl@msu.edu) directly instead. 4 | -------------------------------------------------------------------------------- /docs/sources/extra.css: -------------------------------------------------------------------------------- 1 | h1, h2, h3, h4 { 2 | padding-top: 2em; 3 | padding-bottom: 0.5em; 4 | } 5 | 6 | h5, h6 { 7 | padding-top: 1em; 8 | padding-bottom: 0.2em; 9 | } 10 | -------------------------------------------------------------------------------- /docs/sources/images/automated-pipeline-flowchart.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/automated-pipeline-flowchart.jpg -------------------------------------------------------------------------------- /docs/sources/images/automated-pipeline-flowchart.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/automated-pipeline-flowchart.pdf -------------------------------------------------------------------------------- /docs/sources/images/logo-transparent-bg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/logo-transparent-bg.png -------------------------------------------------------------------------------- /docs/sources/images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/logo.png -------------------------------------------------------------------------------- /docs/sources/images/obtaining-screenlamp-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/obtaining-screenlamp-2.png -------------------------------------------------------------------------------- /docs/sources/images/obtaining-screenlamp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/obtaining-screenlamp.png -------------------------------------------------------------------------------- /docs/sources/images/toolkit-tutorial/dataset-overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/images/toolkit-tutorial/dataset-overview.png -------------------------------------------------------------------------------- /docs/sources/index.md: -------------------------------------------------------------------------------- 1 |
2 |
3 | 4 |
5 | 
6 |
7 |
8 |
9 |
10 | 
11 | [](license)
12 | [](license)
13 |
14 | ### A toolkit for ligand-based virtual screening
15 |
16 |
17 | Screenlamp is a Python package for facilitating ligand-based virtual screening workflows and toolkits with hypothesis-driven filtering steps.
18 |
19 |
20 | ## About
21 |
22 | The screenlamp toolkit was developed in the [Protein Structure Analysis & Design Laboratory](http://www.kuhnlab.bmb.msu.edu) at Michigan State University. For additional information about screenlamp, please refer to the accompanying research publication, which is currently under revision:
23 |
24 | - Raschka, Sebastian, Anne M. Scott, Nan Liu, Santosh Gunturu, Mar Huertas, Weiming Li, and Leslie A. Kuhn (2018). "Enabling the hypothesis-driven prioritization of ligand candidates in big databases:
25 | Screenlamp and its application to GPCR inhibitor discovery for invasive species control". *Journal of Computer-Aided Molecular Design* 32: 415.
26 | [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/01/17/249151)]
27 | [[Journal article](https://link.springer.com/article/10.1007/s10822-018-0100-7)]
28 |
29 |
30 |
31 | Screenlamp is research software and has been made available to other researchers under a permissive [Apache v2 open source license](license). If you use screenlamp in your scientific projects or any derivative work, the authors of the screenlamp software must be acknowledged and the publication listed above should be cited.
32 |
33 |
34 |
35 |
--------------------------------------------------------------------------------
/docs/sources/installation.md:
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1 | # Installing screenlamp
2 |
3 | ---
4 |
5 | ## Obtaining screenlamp
6 |
7 | You can download the latest version of screenlamp from the [GitHub repository](https://github.com/psa-lab/screenlamp) by clicking on "Download ZIP" or download the latest stable release from the ["release" list](https://github.com/psa-lab/screenlamp/releases):
8 |
9 | [](https://github.com/psa-lab/screenlamp)
10 |
11 | ## Setting up your Python environment for screenlamp
12 |
13 | Python package dependencies of screenlamp are listed in the `requirements.txt` file located in the screenlamp directory. To install all of these dependencies most conveniently, you can execute the following command:
14 |
15 | pip install -r requirements.txt
16 |
17 | The the main modules of screenlamp are located in the `tools/` subdirectory, and after satisfying the Python package requirements (see [`requirements.txt`](https://github.com/psa-lab/screenlamp/blob/master/requirements.txt)), they are ready to use. If you haven't used screenlamp before, it is recommended that to read the screenlamp [tutorial](user_guide/doc-overview.md).
18 |
19 | ## Other software requirements
20 |
21 | Certain submodules within screenlamp require external software to sample low-energy conformations of molecules and to generate pair-wise overlays. The tools that are currently being used in the [pre-built, automated screening pipeline](user_guide/pipeline-tutorial-1/) are [OpenEye OMEGA](https://www.eyesopen.com/omega) and [OpenEye ROCS](https://www.eyesopen.com/rocs) to accomplish those tasks. However, screenlamp does not strictly require OMEGA and ROCS, and you are free to use any open source alternative that provided that the output files are compatible with screenlamp tools, which uses the MOL2 file format.
22 |
23 | If you don't have access to OpenEye toolkits, yet, you can visit the [OpenEye website](https://www.eyesopen.com/licensing-philosophy) for more details on their licensing terms (for example, OpenEye offers a free licensing model for academics engaged in public domain research or teaching).
24 |
25 | ## Obtaining older versions of screenlamp
26 |
27 | To obtain one of the previous versions of screenlamp, please see the [Release Notes](changelog), which contains download links for all release versions of screenlamp.
28 |
29 | ### Development version
30 |
31 | You can download the latest development version of screenlamp as [ZIP](https://github.com/psa-lab/screenlamp/archive/master.zip) file directly from GitHub:
32 |
33 | [](https://github.com/psa-lab/screenlamp)
34 |
35 |
6 | 36 | 37 | Alternatively, you can clone the screenlamp development version to your local machine by executing the following command: 38 | 39 | git clone https://github.com/psa-lab/screenlamp.git 40 | -------------------------------------------------------------------------------- /docs/sources/license.md: -------------------------------------------------------------------------------- 1 | 2 | ########################################################################## 3 | 4 | Apache License 5 | Version 2.0, January 2004 6 | http://www.apache.org/licenses/ 7 | 8 | ########################################################################## 9 | 10 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 11 | 12 | 1. 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182 |
183 | 184 | END OF TERMS AND CONDITIONS 185 | 186 | 187 | Copyright 2017 Michigan State University 188 | 189 | The screenlamp software was developed by Sebastian Raschka 190 | and Leslie A. Kuhn in the Protein Structure Lab 191 | (http://www.kuhnlab.bmb.msu.edu) at Michigan State University. 192 | 193 | Licensed under the Apache License, Version 2.0 (the "License"); 194 | you may not use this file except in compliance with the License. 195 | You may obtain a copy of the License at 196 | 197 | http://www.apache.org/licenses/LICENSE-2.0 198 | 199 | Unless required by applicable law or agreed to in writing, software 200 | distributed under the License is distributed on an "AS IS" BASIS, 201 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 202 | See the License for the specific language governing permissions and 203 | limitations under the License. -------------------------------------------------------------------------------- /docs/sources/user_guide/doc-overview.md: -------------------------------------------------------------------------------- 1 | # Overview 2 | 3 | The screenlamp toolkit is designed in a modular way to provide the building blocks for constructing efficient and flexible virtual screening pipelines. The user documentation consists of three parts: 4 | 5 | 1. [Tools](tools): An overview of the different tools within screenlamp and a summary of their usage commands. 6 | 2. [Toolkit Tutorial](tools-tutorial-1): An example showing how to combine the different tools summarized in the Toolkit API to perform a typical virtual screening run. 7 | 3. [Pipeline Tutorial](pipeline-tutorial-1): A preconstructed, automated virtual pipeline based on the tools listed in the Toolkit API and the virtual screening run explained in the Toolkit Tutorial. 8 | 9 | If you are new to screenlamp and would like to get a top-down perspective of what you can do with this toolkit, I recommend starting with the [Pipeline Tutorial](pipeline-tutorial-1), which presents you with an automated virtual screening run on a small example dataset. To construct your own virtual screening pipelines and see how the different modules within screenlamp can be used in tandem, please read the [Toolkit Tutorial](tools-tutorial-1). While reading through the tutorials, the [Tools](tools) page can be used as a reference for more detailed descriptions of the tools that are available within screenlamp. -------------------------------------------------------------------------------- /docs/sources/user_guide/images/tools-tutorial-1/3kpzs-keto-sulfur.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/user_guide/images/tools-tutorial-1/3kpzs-keto-sulfur.png -------------------------------------------------------------------------------- /docs/sources/user_guide/images/tools-tutorial-1/5-mol2ids.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/user_guide/images/tools-tutorial-1/5-mol2ids.png 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https://raw.githubusercontent.com/rasbt/screenlamp/c0da04fa00472890880b0817bd1f61d013638c9b/docs/sources/user_guide/images/tools-tutorial-1/zincdata-spreadsheat.png -------------------------------------------------------------------------------- /docs/sources/user_guide/pipeline-tutorial-1.md: -------------------------------------------------------------------------------- 1 | # Tutorial on Using a Pre-constructed Screenlamp Pipeline 2 | 3 | ## Overview 4 | 5 | This tutorial explains how to use a pre-built screenlamp pipeline to perform an automated virtual screening on a small example dataset. 6 | 7 | In this particular screening pipeline, we are searching for mimics of a query molecule that contain a keto-group and sulfur atom in a specified distance to each other (13-20 angstroms) and have a high overall chemical and volumetric similarity towards the query. Then, we are selecting a subset of database molecules where the keto-group of the query molecule overlays with a keto-group in the database molecules, and where the sulfur atom in the query overlays with a sulfur atom in the database molecules. The overall virtual screening pipeline is summarized in the flowchart below. For more details on the individual screening steps, please see the [Toolkit Tutorial](./tools-tutorial-1), which walks you through these steps using the same database and approach. 8 | 9 |  10 | 11 | (A higher-resolution PDF version of this flowchart is available [here](https://github.com/rasbt/screenlamp/blob/master/docs/sources/images/automated-pipeline-flowchart.pdf).) 12 | 13 | ### Requirements 14 | 15 | Before you continue with the tutorial, please see the [setup instructions](../installation/index.html#other-software-requirements) for screenlamp if this is your first screening run. 16 | 17 | 18 | ## Obtaining and Preparing the Dataset 19 | 20 | 21 | ### MOL2 Input Files 22 | 23 | The automated screenlamp pipeline that is being used in this tutorial is compatible with Tripos MOL2 files of arbitrary database origin and size. A typical use case for this pipeline would be the screening of all ~18,000,000 *Drug-Like* molecules from [ZINC](http://zinc.docking.org), which is available in MOL2 format on ZINC [here](http://zinc.docking.org/subsets/drug-like). Please note that screenlamp supports both Tripos MOL2 (`*.mol2`) files and gzipped Tripos MOL2 files (`*.mol2.gz`) out of the box. Thus, if your input dataset is in gzipped format, you can use it right away without having to make any adjustments or decompressing it. However, please note that the decompressing and compressing operations that are performed when working with gzipped files have an additional toll on computational performance. 24 | 25 | **Please keep in mind that this screening pipeline with 18,000,000 input molecules and the preconfigured settings takes about a day to complete on a multi-core desktop computer**. Thus, it is recommended to work through this tutorial using a smaller dataset. With kind permission from John Irwin and the ZINC team, we recommend using a random subset of 70,000 small molecules that we prepared for this tutorial. It takes approximately 10 minutes for a multi-core Desktop computer to execute all steps in the automated, virtual screening pipeline described earlier. This subset from ZINC is split into 7 multi-MOL2 file with 10,000 molecules each: `partition_mol2_1.mol2` to `partition_mol2_7.mol2`. 26 | 27 | For this tutorial, please download the dataset by clicking the following link and unzip it on your machine that you are using for the virtual screening run: [https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/partition_1-7.zip](https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/partition_1-7.zip) 28 | 29 | ### data table for Prefiltering 30 | 31 | For this particular tutorial, you'll also need a data table containing general information about these molecules. Although the partitions you downloaded above are only a small, modified subset of [ZINC](http://zinc.docking.org) molecules, we are going to use the full ~18,000,000 molecule Drug-like table available for download at [http://zinc.docking.org/subsets/drug-like](http://zinc.docking.org/subsets/drug-like). To download the tab-separated table, click on the [Properties](http://zinc.docking.org/db/bysubset/3/3_prop.xls) link on the [ZINC Drug-like](http://zinc.docking.org/subsets/drug-like) page. Please note that the size of the data table is about ~1.8 Gb, and thus, the download may take a while depending on your internet connection. Alternatively, a smaller data table containing only ~170,000 molecules, please use the following link: [https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/small_table_p1-7.txt](https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/small_table_p1-7.txt) 32 | 33 | 34 | ### Query Molecule 35 | 36 | The third data file you'll need for ligand-based virtual screening is the query molecule. For this tutorial, please download the following multi-conformer MOL2 file: [https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/3kpzs_query.mol2](https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/3kpzs_query.mol2) 37 | 38 | ## Editing the Configuration File 39 | 40 | Once you obtained the database molecules (mol2 partitions), the data table of molecular properties, and the query molecule, you can prepare the configuration file that stores the information about your local file paths and screening settings. 41 | 42 | As your configuration file template, you can use the following YAML file the [`screenlamp/tools/pipelines/pipeline-example-1-config.yaml`](https://github.com/rasbt/screenlamp/blob/master/tools/pipelines/pipeline-example-1-config.yaml), create a local copy of it and modify the file paths according to your system's configuration. 43 | 44 | ## Running the Automated Screening Pipeline 45 | 46 | After you customized your configuration file, you start the screening pipeline as shown in the example command snippet below: 47 | 48 | ```bash 49 | python path/to/screenlamp/tools/pipelines/pipeline-example-1.py --config_file /path/to/your/config/pipeline-example-1-config.yaml --incremental true 50 | ``` 51 | 52 | By setting `--incremental true`, you will be prompted to confirm each step by pressing enter, which is recommended for the first time use. 53 | 54 | For your reference, a zip archive of all files being generated via the execution of the screenlamp pipeline can be obtained via the following download link: [https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/pipeline-tutorial_1_outputs.zip](https://sebastianraschka.com/datasets/screenlamp/pipeline-tutorial_1/pipeline-tutorial_1_outputs.zip). 55 | 56 | ## Canceling and Resuming a Screening Run 57 | 58 | Note that throughout the screening pipeline execution, you will see a short description of the commands being executed. Also, the current pipeline step being executed will be shown in the terminal window. In case you cancel the or abort a screening run, you can resume it at the last step being executed using the `--start_at_step` flag. For example, if you quit the screening run at Step 2 by pressing CTRL+C 59 | 60 | ``` 61 | ################################################ 62 | Step 02: PREFILTER BY FUNCTIONAL GROUP PRESENCE 63 | ################################################ 64 | 65 | Running command: 66 | python /Users/sebastian/code/screenlamp/tools/funcgroup_presence_to_id.py --input /Users/sebastian/Desktop/screenlamp_pipe/01_selected-mol2s --output /Users/sebastian/Desktop/screenlamp_pipe/02_3keto-and-sulfur-mol2ids.txt --selection ((atom_type == 'S.3') | (atom_type == 'S.o2')) --> (atom_type == 'O.2') --processes 0 67 | 68 | Press Enter to proceed or CTRL+C to quit 69 | ``` 70 | 71 | you can resume the run by using `--start_at_step 2` as shown in the example below: 72 | 73 | ```bash 74 | python path/to/screenlamp/tools/pipelines/pipeline-example-1.py --config_file /path/to/your/config/pipeline-example-1-config.yaml --incremental true --start_at_step 2 75 | ``` 76 | 77 | 78 | 79 | 80 | -------------------------------------------------------------------------------- /docs/sources/user_guide/tools: -------------------------------------------------------------------------------- 1 | ../../../tools/ -------------------------------------------------------------------------------- /docs/united/_LICENSE: -------------------------------------------------------------------------------- 1 | Copyright © 2015, Dougal Matthews. 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1 | body {
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5 | /*
6 | * The code below adds some padding to the top of the current anchor target so
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14 | * See