Copyright and Trademarks¶
© 1997-2023 Cadence Design Systems, Inc. (Cadence), 2655 Seely Ave., San Jose, CA 95134, USA. All rights reserved.
OpenEye, Lexichem, ROCS, Grapheme, and Orion are registered trademarks of Cadence Design Systems, Inc.
This material contains proprietary information of Cadence Design Systems, Inc. Use of copyright notice is precautionary only and does not imply publication or disclosure.
The information supplied in this document is believed to be true, but no liability is assumed for its use or the infringement of the rights of others resulting from its use. Information in this document is subject to change without notice and does not represent a commitment on the part of Cadence Design Systems, Inc.
This package is sold/licensed/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out, or otherwise circulated without Cadence Design Systems’ prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying documentation, may be reproduced, stored in a retrieval system on optical or magnetic disk, tape, CD, DVD or other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying recording, or otherwise for any purpose other than for the purchaser’s personal use without a legal agreement or other written permission granted by Cadence.
This product should not be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation, or communication of aircraft or ground support equipment. Cadence Design Systems, Inc., shall not be liable, in whole or in part, for any claims arising from such use, including death, bankruptcy or outbreak of war.
Windows is a registered trademark of Microsoft Corporation. Apple, OS X, macOS, and Macintosh are registered trademarks of Apple Inc. UNIX is a registered trademark of the Open Group. Linux is a registered trademark of Linus Torvalds. Red Hat is a registered trademark of Red Hat, Inc. SUSE, SLED, and SLES are registered trademarks of Novell, Inc. Ubuntu is a registered trademark of Canonical Ltd.
SYBYL is a registered trademark of Certara, L.P. MDL, BIOVIA and ISIS are registered trademarks of Dassault Systemes and/or its affiliates. SMARTS and SMIRKS are registered trademarks of Daylight Chemical Information Systems, Inc. MacroModel is a registered trademark of Schrodinger, LLC.
Python is a registered trademark of the Python Software Foundation. Django is a registered trademark of the Django Software Foundation. Java is a registered trademark of Oracle and/or its affiliates.
Other products and software packages referenced in this document are trademarks and registered trademarks of their respective vendors or manufacturers.
TERMS FOR USE OF SAMPLE CODE
The software below (“Sample Code”) is provided to current licensees or subscribers of OpenEye products or SaaS offerings (each a “Customer”). Customer is hereby permitted to use, copy, and modify the Sample Code, subject to these terms. OpenEye claims no rights to Customer’s modifications. Modification of Sample Code is at Customer’s sole and exclusive risk. Sample Code may require Customer to have a then current license or subscription to the applicable OpenEye offering.
THE SAMPLE CODE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
In no event shall OpenEye be liable for any damages or liability in connection with the Sample Code or its use.
Orion ® Floes¶
To cite use of an Orion-based floe package, please use the following:
OpenEye <package-name> <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
OpenEye Classic Floes 0.11.2. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
The version number for a floe package is displayed on the first page of the package’s release notes. For example: https://docs.eyesopen.com/floe/modules/classic-floes/docs/source/releasenotes.html.
Toolkits and Applications¶
To cite OpenEye toolkits or applications used in your work, please use the following:
OpenEye Toolkits [or Applications] <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
OpenEye Toolkits 2023.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
The Applications and Toolkits are released as a package, multiple times per year. The first part of the version number designates the calendar year. The version number appears on the summary document for the package.
If you want to cite an individual application or toolkit, you can use the syntax:
<product name> <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
where <product name> is:
You can use the version number of the individual Application or Toolkit. For example:
SZYBKI Application 220.127.116.11. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com. Szybki TK 18.104.22.168. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
The first documentation pages give the product names and version numbers, as in https://docs.eyesopen.com/applications/szybki/index.html and https://docs.eyesopen.com/toolkits/python/szybkitk/index.html.
OpenEye Web Services¶
To cite use of the Macromolecular Data Service (MMDS) web service, please use the syntax:
Macromolecular Data Service <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
Macromolecular Data Service 1.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
The MMDS version number appears on the web service’s release notes.
To cite use of the FastROCS TM server, please use the syntax:
FastROCS <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
FastROCS 1.4.4. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
The FastROCS version number appears on the web service’s release notes.
To cite use of the Molecules as a Service (MaaS) web service, please use the syntax:
MaaS <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
MaaS 1.0. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
The MaaS version number appears on the web service’s release notes.
OpenEye products use the following technology under license.
Some of the open source technologies we use are licensed under the GNU Public License (GPL) version 2 or 3. In all instances, these technologies are communicated with using the “at arms length” principle, using pipes and command line arguments.
While the software is in some instances assembled into a container, that assembly does not invoke the GPL copyleft scope. For each Floe package where these are used, the environment log clearly details the installed programs and their version numbers. With the links below for each technology, the source for each of those programs is available.
On the Linux platform, The OpenEye toolkits are linked with the GCC libraries using an eligible compilation process under the terms of the GCC RUNTIME LIBRARY EXCEPTION (see below).
The OpenEye toolkits are NOT open source software and are NOT governed by GPL or other open source licenses. Your right to use the toolkits are governed by the OpenEye license which is binding to You.
For certain Linux distributions, GCC library components are included as object files. Your rights to use GCC library components (libstdc++, libgcc, and libgomp) included with these distributions are governed by the GPLv3 license as follows:
The components libstdc++, libgcc, and libgomp are part of GCC.
GCC is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
GCC is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with GCC (see below). If not, see Licenses GNU Project .
Per GPLv3, section 6d, the source for GCC is available for download from the following location: GNU. The GCC library components included here are from version gcc-4.9.3 and are built using the standard instructions at Installing GCC.
GCC RUNTIME LIBRARY EXCEPTION¶
Version 3.1, 31 March 2009 Copyright © 2009 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This GCC Runtime Library Exception ("Exception") is an additional permission under section 7 of the GNU General Public License, version 3 ("GPLv3"). It applies to a given file (the "Runtime Library") that bears a notice placed by the copyright holder of the file stating that the file is governed by GPLv3 along with this Exception. When you use GCC to compile a program, GCC may combine portions of certain GCC header files and runtime libraries with the compiled program. The purpose of this Exception is to allow compilation of non-GPL (including proprietary) programs to use, in this way, the header files and runtime libraries covered by this Exception. 0. Definitions. A file is an "Independent Module" if it either requires the Runtime Library for execution after a Compilation Process, or makes use of an interface provided by the Runtime Library, but is not otherwise based on the Runtime Library. "GCC" means a version of the GNU Compiler Collection, with or without modifications, governed by version 3 (or a specified later version) of the GNU General Public License (GPL) with the option of using any subsequent versions published by the FSF. "GPL-compatible Software" is software whose conditions of propagation, modification and use would permit combination with GCC in accord with the license of GCC. "Target Code" refers to output from any compiler for a real or virtual target processor architecture, in executable form or suitable for input to an assembler, loader, linker and/or execution phase. Notwithstanding that, Target Code does not include data in any format that is used as a compiler intermediate representation, or used for producing a compiler intermediate representation. The "Compilation Process" transforms code entirely represented in non-intermediate languages designed for human-written code, and/or in Java Virtual Machine byte code, into Target Code. Thus, for example, use of source code generators and preprocessors need not be considered part of the Compilation Process, since the Compilation Process can be understood as starting with the output of the generators or preprocessors. A Compilation Process is "Eligible" if it is done using GCC, alone or with other GPL-compatible software, or if it is done without using any work based on GCC. For example, using non-GPL-compatible Software to optimize any GCC intermediate representations would not qualify as an Eligible Compilation Process. 1. Grant of Additional Permission. You have permission to propagate a work of Target Code formed by combining the Runtime Library with Independent Modules, even if such propagation would otherwise violate the terms of GPLv3, provided that all Target Code was generated by Eligible Compilation Processes. You may then convey such a combination under terms of your choice, consistent with the licensing of the Independent Modules. 2. No Weakening of GCC Copyleft. The availability of this Exception does not imply any general presumption that third-party software is unaffected by the copyleft requirements of the license of GCC.
GNU GENERAL PUBLIC LICENSE¶
GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it. For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions. Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. 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You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. <one line to give the program's name and a brief idea of what it does.> Copyright (C) <year> <name of author> This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: <program> Copyright (C) <year> <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>. The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.