Molsoft Knime Nodes

FeatureVersion 1.0.0.99 by MOLSOFT

Installation

To use this feature in KNIME, install Molsoft Knime Nodes from the following update site:

KNIME 4.3

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Descriptionhttp://www.molsoft.com/browser/knime.html

KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. Currently we have KNIME nodes for the following ICM functions: * MolConvertTo3D: 2d3d conversion * MolConfGen : Conformation generator (_confGen) * MolAPFSuperimpose : Flexible APF superposition (_chemSuper) * MolIcmDock : Small Molecule Docking (_dockScan and _dockProjPrep) * MolScreen : is a set of high quality 2D fingerprint and 3D pharmacophore models (_molScreen) * MolView : View the results * MolCalcProp : Calculates various molecular properties * MolStandardize : Removes salts, excplicitly drawn hydrogen, standardize chemical groups drawing, apply 2D decpition and assign formal charges What's new in the 1.0.0.76 release: * Fixed compatibility issues with KNIME 3.x platform * Fixed compatibility issues with MacOSX What's new in the 1.0.0.24 release: * Added MolCalcProp and MolStandardize nodes What's new in the 1.0.0.20 release: * Fixed bug in MolDockProjPrep when reading multiple receptors from ICB * MolDockProjPrep allows to select ligand which is in the separate object * MolView can be connected to MolDockProjPrep. (View and change settings of the project) What's new in the 1.0.0.19 release: * Added "Covalent Docking' support for MolIcmDockPrep node (ICM 3.8-1 or grerater is required) * Added MolScreen node (is a set of high quality 2D fingerprint and 3D pharmacophore models for a broad range of pharmacology and toxicology targets) http://molsoft.com/molscreen.html * Added "Output Type" for MolIcmDock node. It allows to choose between SDF and interactive ICM HitList. The last option can be viewable with MolView node. * Added MolView node. Connect this node to the output of other Molsoft nodes. (MolScreen, MolIcmDock, etc)

Copyrighthttp://www.molsoft.com

(c) Copyright 2013, MolSoft L.L.C. ALL RIGHTS RESERVED

Licensehttp://www.molsoft.com/knime/license.txt

Molsoft KNIME Nodes End User License Agreement Background The Molsoft KNIME Nodes collection of KNIME (Konstanz Information Miner) nodes developed by Molsoft LLC allows KINME users to use Molsoft ICM-Pro functionality within the KNIME graphical workbench. The Molsoft KNIME Nodes is currently provided as a free product to current ICM-Pro users who accept the terms and conditions and limitations on use set forth in this End User License Agreement. ACCEPTANCE OF TERMS - "MOLSOFT KNIME NODES" USER'S LICENSE. NOTICE TO USER: PLEASE READ THIS AGREEMENT CAREFULLY. BY INSTALLING OR USING ALL OR ANY PORTION OF THE MOLSOFT KNIME NODES SOFTWARE YOU ACCEPT ALL THE TERMS AND CONDITIONS OF THIS AGREEMENT. UPON ACCEPTANCE OF THIS AGREEMENT, THIS AGREEMENT IS ENFORCEABLE AGAINST YOU AND ANY ENTITY THAT OBTAINED THE "MOLSOFT KNIME NODES" SOFTWARE AND ON WHOSE BEHALF IT IS USED. IF YOU DO NOT AGREE, DO NOT USE THIS SOFTWARE. 1. DEFINITIONS. 1.1 "Molsoft KNIME Nodes" or "Software" means (a) the contents of the "Molsoft KNIME Nodes" computer software files, whether delivered electronically or on media, with which this Agreement is provided; (b) related explanatory written materials or files for the ActiveICM Software ("Documentation"); and (c) any modified versions, additions, or later copies of the Software that you obtain (collectively, "Updates"). 1.2 "Use" or "Using" means to access, install, download, copy or otherwise benefit from using the functionality of the Software. 1.3 "Molsoft" means Molsoft LLC, a California Limited Liability Company, 11999 Sorrento Valley Rd., Ste. 209, San Diego, California 92121-1334 USA. 2. SOFTWARE LICENSE. As long as you have a valid ICM-Pro license and agree to comply with the terms of this End User License Agreement (the "Agreement") including the restrictions herein, Molsoft grants to you a limited, non-exclusive, internal-use-only, non-transferable, non- assignable, non-sublicensable license to install and use the "Molsoft KNIME Nodes" software. 2.2 Distribution Prohibited. This license does not grant you the right to rent, lease, loan, sell, transfer, display, distribute, disclose or make the Software available to third parties or to use the Software, or any portion thereof, in a service bureau, in time-sharing or outsourcing services, or otherwise use the Software for the benefit of third parties. You may not modify, copy, distribute, transmit, display, perform, reproduce, publish, or license the Software. You may not create derivative works from the Software including but not limited to applications that may be viewed using other software programs, products or on other devices. 2.3 User Responsibilities and Security. Users are entirely responsible for maintaining the confidentiality of the Software and for any and all activities that occur from Use of the Software. Users agree to notify Molsoft immediately of any unauthorized Use of the Software or any other breach of security. 3. INTELLECTUAL PROPERTY OWNERSHIP. The Software, related Host Applications, and any copies that you are authorized by Molsoft to make are the intellectual property of and are owned by Molsoft LLC. The structure, organization and code of the Software and related Host Applications are the valuable trade secrets and confidential information of Molsoft LLC. The Software is protected by copyright, including without limitation by United States Copyright Law, by patent law, by international treaty provisions and by the applicable laws in the country in which it is being used. You may not copy the Software, except as set forth in Section 2 ("Software License"). Any copies that you are permitted to make pursuant to this Agreement must contain the same copyright, patent pending, and other proprietary notices that appear on or in the Software. You agree not to modify, adapt or translate the Software. You also agree not to reverse engineer, decompile, disassemble or otherwise attempt to discover the source code of the Software. Any information supplied by Molsoft or obtained by you, as permitted hereunder, may only be used by you for the purpose described herein and may not be disclosed to any third party or used to create any software that is substantially similar to the expression of the Software. Requests for information should be directed to the Molsoft Customer Support Department. Trademarks shall be used in accordance with accepted trademark practice, including identification of trademarks owners' names. Trademarks can only be used to identify printed output produced by the Software and such use of any trademark does not give you any rights of ownership in that trademark. Except as expressly stated above, this Agreement does not grant you any intellectual property rights in the Software. 4. TRANSFER. You may not rent, lease, sublicense or authorize all or any portion of the Software to be copied onto another user's Computer except as may be expressly permitted herein. You may, however, transfer all your rights to Use the Software to another person or legal entity provided that: (a) you also transfer to each this Agreement, the Software and all other software or hardware bundled or pre-installed with the Software, including all copies, Updates and prior versions, to such person or entity; (b) you retain no copies, including backups and copies stored on a computer; and (c) the receiving party accepts the terms and conditions of this Agreement and any other terms and conditions upon which you legally purchased a license to the Software. Notwithstanding the foregoing, you may not transfer education, pre-release, trial, or not- 5. NO WARRANTY. Unless otherwise specified, the Software is being delivered to you "AS IS," and Molsoft makes no warranty as to its use or performance. MOLSOFT DOES NOT AND CANNOT WARRANT THE PERFORMANCE OR RESULTS YOU MAY OBTAIN BY USING THE SOFTWARE. EXCEPT FOR ANY WARRANTY, CONDITION, REPRESENTATION OR TERM THE EXTENT OF WHICH THE SAME CANNOT OR MAY NOT BE EXCLUDED OR LIMITED BY THE LAW APPLICABLE TO YOU IN YOUR JURISDICTION, MOLSOFT MAKES NO WARRANTIES, CONDITIONS, REPRESENTATIONS, OR TERMS (EXPRESS OR IMPLIED WHETHER BY STATUTE, COMMON LAW, CUSTOM, USAGE OR OTHERWISE) AS TO ANY MATTER INCLUDING BUT NOT LIMITED TO NONINFRINGEMENT OF THIRD PARTY RIGHTS, MERCHANTABILITY, INTEGRATION, SATISFACTORY QUALITY, OR FITNESS FOR ANY PARTICULAR PURPOSE. 6. LIMITATION OF LIABILITY. TO THE MAXIMIUM EXTENT PERMITTED BY LAW, IN NO EVENT WILL MOLSOFT BE LIABLE TO YOU FOR ANY DAMAGES, CLAIMS OR COSTS WHATSOEVER, OR FOR ANY CONSEQUENTIAL, INDIRECT, INCIDENTAL DAMAGES, OR FOR ANY LOST PROFITS OR LOST SAVINGS, EVEN IF A MOLSOFT REPRESENTATIVE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH LOSS, DAMAGES, CLAIMS OR COSTS, OR FOR ANY CLAIM BY ANY THIRD PARTY. THE FOREGOING LIMITATIONS AND EXCLUSIONS APPLY TO THE EXTENT PERMITTED BY APPLICABLE LAW IN YOUR JURISDICTION. MOLSOFT'S AGGREGATE LIABILITY AND THAT OF ITS SUPPLIERS UNDER OR IN CONNECTION WITH THIS AGREEMENT SHALL BE LIMITED TO THE AMOUNT ACTUALLY PAID BY YOU FOR THE SOFTWARE, IF ANY. Molsoft is acting on behalf of its suppliers for the purpose of disclaiming, excluding and/or limiting obligations, warranties and liability as provided in this Agreement, but in no other respects and for no other purpose. For further information, please see the jurisdiction specific information at the end of this Agreement, if any, or contact Molsoft's Customer Support Department. 7. GOVERNING LAW. This Agreement will be governed by and construed in accordance with the substantive laws in force in the State of California. The courts of San Diego County, California shall each have non-exclusive jurisdiction over all disputes relating to this Agreement. This Agreement will not be governed by the conflict of law rules of any jurisdiction or the United Nations Convention on Contracts for the International Sale of Goods, the application of which is expressly excluded. 8. GENERAL PROVISIONS. If any part of this Agreement is found void and unenforceable, it will not affect the validity of the balance of the Agreement, which shall remain valid and enforceable according to its terms. This Agreement shall not prejudice the statutory rights of any party dealing as a consumer. This Agreement may only be modified by a writing signed by an authorized officer of Molsoft. Upgrades may be licensed to you by Molsoft with additional or different terms. This is the entire agreement between Molsoft and you relating to the Software, and it supersedes any prior representations, discussions, undertakings, communications or advertising relating to the Software. 9. COMPLIANCE WITH LICENSES. If you are a business or organization, you agree that upon request from Molsoft or Molsoft's authorized representative, you will within thirty (30) days fully document and certify that use of any and all Molsoft Software at the time of the request is in conformity with your valid licenses from Molsoft. 10. TRADEMARKS. Molsoft and Molsoft ICM are either registered trademarks or trademarks of Molsoft LLC in the United States and/or other countries. KNIME is a trademark of KNIME.com AG. The names of actual companies and products mentioned herein may be the trademarks of their respective owners. 11. COPYRIGHT NOTICE. Copyright (c) 2013 Molsoft LLC, 11199 Sorrento Valley Rd., Ste. 209, San Diego, CA 92121-1334 U.S.A. All rights reserved. Any rights not expressly granted herein are reserved. Molsoft KNIME Nodes EULA (Revised 11-07-13)

Content

The feature Molsoft Knime Nodes consists of 2 items: