Open Babel Access and Interconvert Chemical Information
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Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al. -
Computer-Assisted Catalyst Development Via Automated Modelling of Conformationally Complex Molecules
www.nature.com/scientificreports OPEN Computer‑assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands Sibo Lin1*, Jenna C. Fromer2, Yagnaseni Ghosh1, Brian Hanna1, Mohamed Elanany3 & Wei Xu4 Simulation of conformationally complicated molecules requires multiple levels of theory to obtain accurate thermodynamics, requiring signifcant researcher time to implement. We automate this workfow using all open‑source code (XTBDFT) and apply it toward a practical challenge: diphosphinoamine (PNP) ligands used for ethylene tetramerization catalysis may isomerize (with deleterious efects) to iminobisphosphines (PPNs), and a computational method to evaluate PNP ligand candidates would save signifcant experimental efort. We use XTBDFT to calculate the thermodynamic stability of a wide range of conformationally complex PNP ligands against isomeriation to PPN (ΔGPPN), and establish a strong correlation between ΔGPPN and catalyst performance. Finally, we apply our method to screen novel PNP candidates, saving signifcant time by ruling out candidates with non‑trivial synthetic routes and poor expected catalytic performance. Quantum mechanical methods with high energy accuracy, such as density functional theory (DFT), can opti- mize molecular input structures to a nearby local minimum, but calculating accurate reaction thermodynamics requires fnding global minimum energy structures1,2. For simple molecules, expert intuition can identify a few minima to focus study on, but an alternative approach must be considered for more complex molecules or to eventually fulfl the dream of autonomous catalyst design 3,4: the potential energy surface must be frst surveyed with a computationally efcient method; then minima from this survey must be refned using slower, more accurate methods; fnally, for molecules possessing low-frequency vibrational modes, those modes need to be treated appropriately to obtain accurate thermodynamic energies 5–7. -
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department Name of FOSS Applications Employability GChemPaint GChemPaint is an editor for 2Dchem- GChemPaint is currently being developed ical structures with a multiple docu- as part of The Chemistry Development ment interface. Kit, and a Standard Widget Tool kit- based GChemPaint application is being developed, as part of Bioclipse. Jmol Jmol applet is used to explore the Jmol is a free, open source molecule viewer structure of molecules. Jmol applet is for students, educators, and researchers used to depict X-ray structures in chemistry and biochemistry. It is cross- platform, running on Windows, Mac OS X, and Linux/Unix systems. For PG Students LaTeX Document markup language and Value addition to academic Skills set. preparation system for Tex typesetting Essential for International paper presentation and scientific journals. For PG student for their project work Scilab Scientific Computation package for Value addition in technical problem numerical computations solving via use of computational methods for engineering problems, Applicable in Chemical, ECE, Electrical, Electronics, Civil, Mechanical, Mathematics etc. For PG student who are taking Physical Chemistry Avogadro Avogadro is a free and open source, Research and Development in Chemistry, advanced molecule editor and Pharmacist and University lecturers. visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc. Spoken Tutorial Project, IIT Bombay Brochure for Commerce and Commerce IT Name of FOSS Applications / Employability LibreOffice – Writer, Calc, Writing letters, documents, creating spreadsheets, tables, Impress making presentations, desktop publishing LibreOffice – Base, Draw, Managing databases, Drawing, doing simple Mathematical Math operations For Commerce IT Students Drupal Drupal is a free and open source content management system (CMS). -
Designing Universal Chemical Markup (UCM) Through the Reusable Methodology Based on Analyzing Existing Related Formats
Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software s t tools and two stage analysis procedure that supplied the necessary information for the n i r development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, P CTfile and XDfile. In addition the following formats were included in the first stage only: e r P CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results: A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. -
Open Data, Open Source and Open Standards in Chemistry: the Blue Obelisk five Years On
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk ¯ve years on Noel M O'Boyle¤1 , Rajarshi Guha2 , Egon L Willighagen3 , Samuel E Adams4 , Jonathan Alvarsson5 , Richard L Apodaca6 , Jean-Claude Bradley7 , Igor V Filippov8 , Robert M Hanson9 , Marcus D Hanwell10 , Geo®rey R Hutchison11 , Craig A James12 , Nina Jeliazkova13 , Andrew SID Lang14 , Karol M Langner15 , David C Lonie16 , Daniel M Lowe4 , J¶er^omePansanel17 , Dmitry Pavlov18 , Ola Spjuth5 , Christoph Steinbeck19 , Adam L Tenderholt20 , Kevin J Theisen21 , Peter Murray-Rust4 1Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, College Road, Cork, Co. Cork, Ireland 2NIH Center for Translational Therapeutics, 9800 Medical Center Drive, Rockville, MD 20878, USA 3Division of Molecular Toxicology, Institute of Environmental Medicine, Nobels vaeg 13, Karolinska Institutet, 171 77 Stockholm, Sweden 4Unilever Centre for Molecular Sciences Informatics, Department of Chemistry, University of Cambridge, Lens¯eld Road, CB2 1EW, UK 5Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden 6Metamolecular, LLC, 8070 La Jolla Shores Drive #464, La Jolla, CA 92037, USA 7Department of Chemistry, Drexel University, 32nd and Chestnut streets, Philadelphia, PA 19104, USA 8Chemical Biology Laboratory, Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA 9St. Olaf College, 1520 St. Olaf Ave., North¯eld, MN 55057, USA 10Kitware, Inc., 28 Corporate Drive, Clifton Park, NY 12065, USA 11Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA 12eMolecules Inc., 380 Stevens Ave., Solana Beach, California 92075, USA 13Ideaconsult Ltd., 4.A.Kanchev str., So¯a 1000, Bulgaria 14Department of Engineering, Computer Science, Physics, and Mathematics, Oral Roberts University, 7777 S. -
Pymol Modelling Workshop
PyMOL Modelling Workshop My website: http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM442/ There you will find links to download the latest educational version of PyMOL as well as a link to my “Introduction to PyMOL”, which in turn has links to other people's PyMOL tutorials. Note also the PyMOL Wiki: http://pymolwiki.org. Structure files can be found by searching the Protein Data Bank (PDB) for structure: easy to remember website http://www.pdb.org. There is also the PDBe (PDB Europe, http://www.pdbe.org) that contains the same databank of structures, but with a different web interface for searching for structures and a different set of tools for analyzing structures. What is in a PDB file? Lots of information in the “header” (the section of the file preceding the actual atomic coordinates) as well as the coordinates for the atoms. When assessing a structure, one needs to take account of the resolution and R-factor, error estimates and missing residues. There is information about the sequence that was used to determine the structure with a sequence database reference. There is also information about the biological unit. In the case of crystal structures the biological unit may need to be generated by applying crystallographic symmetry operators, although there are web sites that also try to provide that information. (e.g. http://www.ebi.ac.uk/msd-srv/pisa/). Warning: One cannot blindly trust a crystal structure to be providing you with a completely accurate picture of reality. Reading the paper that describes the structure is a good start! Outline of PyMOL usage PyMOL is a very powerful, scriptable (customizable) tool for making publication-quality figures and performing analyses on structures. -
Dmol Guide to Select a Dmol3 Task 1
DMOL3 GUIDE MATERIALS STUDIO 8.0 Copyright Notice ©2014 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon and the 3DS logo, CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA and NETVIBES are commercial trademarks or registered trademarks of Dassault Systèmes or its subsidiaries in the U.S. and/or other countries. All other trademarks are owned by their respective owners. Use of any Dassault Systèmes or its subsidiaries trademarks is subject to their express written approval. Acknowledgments and References To print photographs or files of computational results (figures and/or data) obtained using BIOVIA software, acknowledge the source in an appropriate format. For example: "Computational results obtained using software programs from Dassault Systèmes Biovia Corp.. The ab initio calculations were performed with the DMol3 program, and graphical displays generated with Materials Studio." BIOVIA may grant permission to republish or reprint its copyrighted materials. Requests should be submitted to BIOVIA Support, either through electronic mail to [email protected], or in writing to: BIOVIA Support 5005 Wateridge Vista Drive, San Diego, CA 92121 USA Contents DMol3 1 Setting up a molecular dynamics calculation20 Introduction 1 Choosing an ensemble 21 Further Information 1 Defining the time step 21 Tasks in DMol3 2 Defining the thermostat control 21 Energy 3 Constraints during dynamics 21 Setting up the calculation 3 Setting up a transition state calculation 22 Dynamics 4 Which method to use? -
Atomistic Molecular Dynamics Simulation of Graphene- Isoprene Nanocomposites
Atomistic molecular dynamics simulation of graphene- isoprene nanocomposites P Chanlert1, J Wong-Ekkabut2, W Liewrian3,4,5 and T Sutthibutpong3,4,5* 1 Program of Physics, Faculty of Science and Technology, Songkhla Rajabhat University, Songkhla, 90000, Thailand 2 Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand 3 Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand 4 Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand 5 Thailand Center of Excellence in Physics (ThEP Center), Commission on Higher Education, Bangkok 10400, Thailand *email: [email protected] Abstract. A series of atomistic molecular dynamics simulations were performed for 4-mer isoprene molecules confined between graphene sheets with varied graphene separations in order to observe the finite size effects arose from the van der Waals interactions between the isoprene oligomer, forming high density shells at the graphene interfaces. For the small confinement regions, 1.24 nm and 2.21 nm, local density of isoprene at the graphene interface becomes higher than 10 times the bulk density. These results provided the further insights towards the rational design of nanostructures based on graphene sheets and natural rubber polymer. 1. Introduction Composite material is the combination between two materials or more where chemical reaction between these materials is absent. In composites, one with higher quantity is called matrix while those with lesser quantity are called fillers. In general, adding fillers into matrix material enhances both physical and mechanical properties in some ways. -
Conformational Analysis 3D Structures, Conformations and Molecular Surfaces
Conformational Analysis 3D Structures, Conformations and Molecular Surfaces Christof H. Schwab Molecular Networks GmbH Altamira LLC Henkestr. 91 1455 Candlewood Drive 91052 Erlangen, Germany mn-am.com Columbus, Ohio 43235, USA Molecular Networks and Altamira MN-AM Erlangen, Germany Columbus, Ohio, USA Friedrich-Alexander-Universität The Ohio State University 1997 2008 Chemoinformatics 3D structure generation Physicochemical and reaction properties Metabolic reaction knowledge Computational toxicology and risk assessment Database and knowledgebase Predictive models Consulting services 2 Product Lines – Chemoinformatics CORINA Classic CORINA Classic Industry-standard 3D structure generation CORINA Symphony Profiling and managing of chemical datasets Workflows Structure cleaning/processing Descriptor generation (properties and fragments) SYLVIA Estimation of synthetic accessibility of compounds Public tools ChemoTyper (with ToxPrint Chemotypes) https://chemotyper.org, https://toxprint.org 3 Product Lines – Computational Toxicology and Risk Assessment ChemTunes Platform to support decision making in human health and regulatory critical endpoints Toxicity database (all endpoints) "Inventory" concept for compound location ChemTunes ToxGPS Prediction models All human health related endpoints Workflows TTC (thresholds of toxicological concern) Genotoxic Impurities Read-Across (in development) Workflow ICH M7 GTI (in development) 4 3D Structures, Conformations and Molecular Surfaces – Overview 3D structures – why, -
Computational Chemistry
Computational Chemistry as a Teaching Aid Melissa Boule Aaron Harshman Rexford Hoadley An Interactive Qualifying Project Report Submitted to the Faculty of the Worcester Polytechnic Institute In partial fulfillment of the requirements for the Bachelor of Science Degree Approved by: Professor N. Aaron Deskins 1i Abstract Molecular modeling software has transformed the capabilities of researchers. Molecular modeling software has the potential to be a helpful teaching tool, though as of yet its efficacy as a teaching technique has yet to be proven. This project focused on determining the effectiveness of a particular molecular modeling software in high school classrooms. Our team researched what topics students struggled with, surveyed current high school chemistry teachers, chose a modeling software, and then developed a lesson plan around these topics. Lastly, we implemented the lesson in two separate high school classrooms. We concluded that these programs show promise for the future, but with the current limitations of high school technology, these tools may not be as impactful. 2ii Acknowledgements This project would not have been possible without the help of many great educators. Our advisor Professor N. Aaron Deskins provided driving force to ensure the research ran smoothly and efficiently. Mrs. Laurie Hanlan and Professor Drew Brodeur provided insight and guidance early in the development of our topic. Mr. Mark Taylor set-up our WebMO server and all our other technology needs. Lastly, Mrs. Pamela Graves and Mr. Eric Van Inwegen were instrumental by allowing us time in their classrooms to implement our lesson plans. Without the support of this diverse group of people this project would never have been possible. -
Bringing Open Source to Drug Discovery
Bringing Open Source to Drug Discovery Chris Swain Cambridge MedChem Consulting Standing on the shoulders of giants • There are a huge number of people involved in writing open source software • It is impossible to acknowledge them all individually • The slide deck will be available for download and includes 25 slides of details and download links – Copy on my website www.cambridgemedchemconsulting.com Why us Open Source software? • Allows access to source code – You can customise the code to suit your needs – If developer ceases trading the code can continue to be developed – Outside scrutiny improves stability and security What Resources are available • Toolkits • Databases • Web Services • Workflows • Applications • Scripts Toolkits • OpenBabel (htttp://openbabel.org) is a chemical toolbox – Ready-to-use programs, and complete programmer's toolkit – Read, write and convert over 110 chemical file formats – Filter and search molecular files using SMARTS and other methods, KNIME add-on – Supports molecular modeling, cheminformatics, bioinformatics – Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry – Written in C++ but accessible from Python, Ruby, Perl, Shell scripts… Toolkits • OpenBabel • R • CDK • OpenCL • RDkit • SciPy • Indigo • NumPy • ChemmineR • Pandas • Helium • Flot • FROWNS • GNU Octave • Perlmol • OpenMPI Toolkits • RDKit (http://www.rdkit.org) – A collection of cheminformatics and machine-learning software written in C++ and Python. – Knime nodes – The core algorithms and data structures are written in C ++. Wrappers are provided to use the toolkit from either Python or Java. – Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.