Legal Notices¶
Copyright and Trademarks¶
© 1997-2024 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.
Sample Code¶
For all of the code examples and samples within OpenEye documents, the following terms of use apply.
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.
Citation¶
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.
For example:
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.
For example:
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:
OEChem TK
OEDepict TK
FastROCS TK
Grapheme TK
GraphSim TK
Lexichem TK
OEMedChem TK
MolProp TK
Quacpac TK
OEFF TK
OEDocking TK
Omega TK
Shape TK
Spicoli TK
Spruce TK
Szmap TK
Szybki TK
Zap TK
AFITT Application
BROOD Application
EON Application
OEDocking Application
OMEGA Application
PICTO Application
pKa-Prospector Application
QUACPAC Application
ROCS Application
SiteHopper Application
SPRUCE Application
SZMAP Application
SZYBKI Application
VIDA Application
You can use the version number of the individual Application or Toolkit. For example:
SZYBKI Application 2.5.1.2. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.
Szybki TK 2.5.1.2. 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.
For example:
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.
For example:
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.
For example:
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.
Technology Licensing¶
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.
GCC¶
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
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To protect your rights, we need to prevent others from denying you
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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
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Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
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For the developers' and authors' protection, the GPL clearly explains
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Some devices are designed to deny users access to install or run
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Finally, every program is threatened constantly by software patents.
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The precise terms and conditions for copying, distribution and
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TERMS AND CONDITIONS
0. Definitions.
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"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
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A "covered work" means either the unmodified Program or a work based
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To "propagate" a work means to do anything with it that, without
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public, and in some countries other activities as well.
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An interactive user interface displays "Appropriate Legal Notices"
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1. Source Code.
The "source code" for a work means the preferred form of the work
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The "System Libraries" of an executable work include anything, other
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The Corresponding Source need not include anything that users
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The Corresponding Source for a work in source code form is that
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All rights granted under this License are granted for the term of
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You may convey verbatim copies of the Program's source code as you
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You may convey a work based on the Program, or the modifications to
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b) The work must carry prominent notices stating that it is
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"keep intact all notices".
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License to anyone who comes into possession of a copy. This
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A compilation of a covered work with other separate and independent
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You are not required to accept this License in order to receive or
run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
modify any covered work. These actions infringe copyright if you do
not accept this License. Therefore, by modifying or propagating a
covered work, you indicate your acceptance of this License to do so.
10. Automatic Licensing of Downstream Recipients.
Each time you convey a covered work, the recipient automatically
receives a license from the original licensors, to run, modify and
propagate that work, subject to this License. You are not responsible
for enforcing compliance by third parties with this License.
An "entity transaction" is a transaction transferring control of an
organization, or substantially all assets of one, or subdividing an
organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
transaction who receives a copy of the work also receives whatever
licenses to the work the party's predecessor in interest had or could
give under the previous paragraph, plus a right to possession of the
Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
not impose a license fee, royalty, or other charge for exercise of
rights granted under this License, and you may not initiate litigation
(including a cross-claim or counterclaim in a lawsuit) alleging that
any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
11. Patents.
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.
In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License. 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>.
See also