DOCSLIB.ORG

Open Babel Documentation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Open Babel Documentation Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) Mar 26, 2021 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 11 2.1 Install a binary package......................................... 11 2.2 Compiling Open Babel.......................................... 11 3 obabel - Convert, Filter and Manipulate Chemical Data 19 3.1 Synopsis................................................. 19 3.2 Options.................................................. 19 3.3 Examples................................................. 22 3.4 Format Options.............................................. 24 3.5 Append property values to the title.................................... 24 3.6 Generating conformers for structures.................................. 24 3.7 Filtering molecules from a multimolecule file.............................. 25 3.8 Substructure and similarity searching.................................. 28 3.9 Sorting molecules............................................ 28 3.10 Remove duplicate molecules....................................... 28 3.11 Aliases for chemical groups....................................... 29 3.12 Forcefield energy and minimization................................... 30 3.13 Aligning molecules or substructures................................... 30 3.14 Specifying the speed of 3D coordinate generation............................ 31 4 The Open Babel GUI 33 4.1 Basic operation.............................................. 33 4.2 Options.................................................. 33 4.3 Multiple input files............................................ 34 4.4 Wildcards in filenames.......................................... 34 4.5 Local input................................................ 35 4.6 Output file................................................ 35 4.7 Graphical display............................................. 35 4.8 Using a restricted set of formats..................................... 35 4.9 Other features.............................................. 35 4.10 Example files............................................... 36 5 Tutorial on using the GUI 37 5.1 Converting chemical file formats..................................... 37 i 5.2 Filtering structures............................................ 39 5.3 Substructure and similarity searching a large dataset.......................... 42 6 Molecular fingerprints and similarity searching 45 6.1 Fingerprint format............................................ 45 6.2 Spectrophores™............................................. 50 7 obabel vs Chemistry Toolkit Rosetta 55 7.1 Heavy atom counts from an SD file................................... 55 7.2 Convert a SMILES string to canonical SMILES............................. 55 7.3 Report how many SD file records are within a certain molecular weight range............. 56 7.4 Convert SMILES file to SD file..................................... 56 7.5 Report the similarity between two structures.............................. 56 7.6 Find the 10 nearest neighbors in a data set................................ 56 7.7 Depict a compound as an image..................................... 57 7.8 Highlight a substructure in the depiction................................. 57 7.9 Align the depiction using a fixed substructure.............................. 58 7.10 Perform a substructure search on an SDF file and report the number of false positives......... 59 7.11 Calculate TPSA............................................. 59 7.12 Working with SD tag data........................................ 60 7.13 Unattempted tasks............................................ 61 8 2D Depiction 63 8.1 Molecular graphics............................................ 64 9 3D Structure Generation 65 9.1 Generate a single conformer....................................... 65 9.2 Generate multiple conformers...................................... 67 10 Molecular Mechanics and Force Fields 71 10.1 Generalized Amber Force Field (gaff).................................. 71 10.2 Ghemical Force Field (ghemical).................................... 72 10.3 MMFF94 Force Field (mmff94)..................................... 72 10.4 Universal Force Field (uff)........................................ 73 11 Write software using the Open Babel library 75 11.1 The Open Babel API........................................... 75 11.2 C++.................................................... 76 11.3 Python.................................................. 79 11.4 Java.................................................... 96 11.5 Perl.................................................... 99 11.6 CSharp and OBDotNet.......................................... 102 11.7 Ruby................................................... 105 11.8 Updating to Open Babel 3.0 from 2.x.................................. 105 12 Cheminformatics 101 109 12.1 Cheminformatics Basics......................................... 109 12.2 Representing Molecules......................................... 111 12.3 Substructure Searching with Indexes.................................. 115 12.4 Molecular Similarity........................................... 117 12.5 Chemical Registration Systems..................................... 118 13 Stereochemistry 121 13.1 Accessing stereochemistry information................................. 121 13.2 The Config() object............................................ 122 ii 13.3 Modifying the stereochemistry...................................... 123 13.4 Stereo perception............................................. 124 13.5 Miscellaneous stereo functions in the API................................ 126 14 Handling of aromaticity 127 14.1 How is aromaticity information stored?................................. 127 14.2 Perception of aromaticity........................................ 127 14.3 SMILES reading and writing....................................... 128 14.4 Effect of modifying the structure..................................... 128 15 Radicals and SMILES extensions 131 15.1 The need for radicals and implicit hydrogen to coexist......................... 131 15.2 How Open Babel does it......................................... 131 15.3 In radicals either the hydrogen or the spin multiplicity can be implicit................. 132 15.4 SMILES extensions for radicals..................................... 133 15.5 Other Supported Extensions....................................... 133 16 Contributing to Open Babel 135 16.1 Overview................................................. 135 16.2 Developing Open Babel......................................... 136 16.3 Documentation.............................................. 140 16.4 Adding a new test............................................ 141 16.5 Software Archaeology.......................................... 145 17 Adding plugins 147 17.1 How to add a new file format...................................... 148 17.2 Adding new operations and options................................... 148 17.3 How to add a new descriptor....................................... 150 18 Supported File Formats and Options 153 18.1 Common cheminformatics formats................................... 154 18.2 Utility formats.............................................. 162 18.3 Other cheminformatics formats..................................... 170 18.4 Computational chemistry formats.................................... 173 18.5 Molecular fingerprint formats...................................... 184 18.6 Crystallography formats......................................... 187 18.7 Reaction formats............................................. 189 18.8 Image formats.............................................. 191 18.9 2D drawing formats........................................... 198 18.10 3D viewer formats............................................ 199 18.11 Kinetics and Thermodynamics formats................................. 201 18.12 Molecular dynamics and docking formats................................ 201 18.13 Volume data formats........................................... 205 18.14 JSON formats.............................................. 206 18.15 Miscellaneous formats.......................................... 207 18.16 Biological data formats.......................................... 207 18.17 Obscure formats............................................. 208 19 Descriptors 209 19.1 Numerical descriptors.......................................... 209 19.2 Textual descriptors............................................ 210 19.3 Descriptors for filtering......................................... 211 20 Charge models 213 20.1 Cheminformatics charge models..................................... 213 iii 20.2 Special charge models.......................................... 213 21 Release Notes 215 21.1 Open Babel 3.0.0............................................. 215 21.2 Open Babel 2.4.0............................................. 223 21.3 Open Babel 2.3.1............................................. 226 21.4 Open Babel 2.3.0............................................. 227 21.5 Open Babel 2.2.3............................................. 229 21.6 Open Babel 2.2.2............................................. 229 21.7 Open Babel 2.2.1............................................. 230 21.8 Open Babel 2.2.0............................................
Recommended publications
  • Mercury 2.4 User Guide and Tutorials 2011 CSDS Release

    Mercury 2.4 User Guide and Tutorials 2011 CSDS Release

    Mercury 2.4 User Guide and Tutorials 2011 CSDS Release Copyright © 2010 The Cambridge Crystallographic Data Centre Registered Charity No 800579 Conditions of Use The Cambridge Structural Database System (CSD System) comprising all or some of the following: ConQuest, Quest, PreQuest, Mercury, (Mercury CSD and Materials module of Mercury), VISTA, Mogul, IsoStar, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the foregoing data files, documentation and command procedures (each individually a Component) is a database and copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its licensors and all rights are protected. Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary. When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence. All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence. In particular: • The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location. • The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re- distributed in any form, in whole or in part, to any third party. • Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC.
  • Pyplif HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors

    Pyplif HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors

    molecules Article PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors Enade P. Istyastono 1,* , Nunung Yuniarti 2, Vivitri D. Prasasty 3 and Sudi Mungkasi 4 1 Faculty of Pharmacy, Sanata Dharma University, Yogyakarta 55282, Indonesia 2 Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; [email protected] 3 Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia; [email protected] 4 Department of Mathematics, Faculty of Science and Technology, Sanata Dharma University, Yogyakarta 55282, Indonesia; [email protected] * Correspondence: [email protected]; Tel.: +62-274883037 Abstract: Identification of molecular determinants of receptor-ligand binding could significantly increase the quality of structure-based virtual screening protocols. In turn, drug design process, especially the fragment-based approaches, could benefit from the knowledge. Retrospective virtual screening campaigns by employing AutoDock Vina followed by protein-ligand interaction finger- printing (PLIF) identification by using recently published PyPLIF HIPPOS were the main techniques used here. The ligands and decoys datasets from the enhanced version of the database of useful de- coys (DUDE) targeting human G protein-coupled receptors (GPCRs) were employed in this research since the mutation data are available and could be used to retrospectively verify the prediction. The results show that the method presented in this article could pinpoint some retrospectively verified molecular determinants. The method is therefore suggested to be employed as a routine in drug Citation: Istyastono, E.P.; Yuniarti, design and discovery. N.; Prasasty, V.D.; Mungkasi, S. PyPLIF HIPPOS-Assisted Prediction Keywords: PyPLIF HIPPOS; AutoDock Vina; drug discovery; fragment-based; molecular determi- of Molecular Determinants of Ligand Binding to Receptors.
  • Open Babel Documentation Release 2.3.1

    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

    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.
  • A Java-Based Platform for Evolutionary De Novo Molecular Design

    A Java-Based Platform for Evolutionary De Novo Molecular Design

    Article MoleGear: A Java-Based Platform for Evolutionary De Novo Molecular Design Yunhan Chu and Xuezhong He * Department of Chemical Engineering, Norwegian University of Science and Technology, N-7491 Trondheim, Norway; [email protected] * Correspondence: [email protected]; Tel.: +47-73593942 Received: 25 March 2019; Accepted: 10 April 2019; Published: 11 April 2019 Abstract: A Java-based platform, MoleGear, is developed for de novo molecular design based on the chemistry development kit (CDK) and other Java packages. MoleGear uses evolutionary algorithm (EA) to explore chemical space, and a suite of fragment-based operators of growing, crossover, and mutation for assembling novel molecules that can be scored by prediction of binding free energy or a weighted-sum multi-objective fitness function. The EA can be conducted in parallel over multiple nodes to support large-scale molecular optimizations. Some complementary utilities such as fragment library design, chemical space analysis, and graphical user interface are also integrated into MoleGear. The candidate molecules as inhibitors for the human immunodeficiency virus 1 (HIV-1) protease were designed by MoleGear, which validates the potential capability for de novo molecular design. Keywords: de novo design; evolutionary algorithm; drug molecules; fitness; multi-objective function 1. Introduction Computational chemistry plays an important role in the design of new drug-like molecules [1– 5], catalysts [6–8], and novel solvents of ionic liquids [9–11]. De novo molecular design has been an active research area of drug design/discovery over the last decades, and many approaches such as LUDI [12], LEA3D [13], Flux [14,15], and pharmacophore-linked fragment virtual screening (PFVS) [16] have been developed by using protein and ligand structures.
  • Instructions on Making Pdf Files Containing 3D

    Instructions on Making Pdf Files Containing 3D

    Detailed Instructions for Creating an Embedded Virtual 3-D Image of a Molecule Creating the documents with embedded virtual three-dimensional images may be done fairly easily by repeating the following procedures. Once you have embedded your first image, the use of that image is limited only by your imagination. The following instructions are written in extreme detail with annotated screen shots of the four programs you will use throughout for clarification. Once you are familiar with the procedure embedding a structure of interest should take less than 20 min., limited only by the speed with which you can click a mouse. In practice most of our embedded 3-D images have been created by our undergraduate student collaborators. Step 1. Creating a 2-D image in ChemSketch Using ACD ChemSketch 11.0 Freeware (http://www.acdlabs.com/download/chemsk_download.html ) a two dimensional structure may be drawn as per your specific need (see Figure 1). Once the molecule is drawn, optimized it by clicking the 3-D optimization button then save as an MDL molfile (*.mol). Figure 1: A screen shot of acetone drawn with ChemSketch after 3-D optimization. Step 2. Converting the *.mol file to a *.pdb file using Open Babel The file can now be converted from a .mol file to a .pdb file, Protein Data Bank format, to be properly accessed with the Adobe Acrobat 3D Toolkit 8.1.0. The file conversion is done using Open Babel Graphical User Interface v2.2.0 (openbabel.sourceforge.net) under default settings. Step by step instructions: A.
  • Structural Insight Into Pichia Pastoris Fatty Acid Synthase Joseph S

    Structural Insight Into Pichia Pastoris Fatty Acid Synthase Joseph S

    www.nature.com/scientificreports OPEN Structural insight into Pichia pastoris fatty acid synthase Joseph S. Snowden, Jehad Alzahrani, Lee Sherry, Martin Stacey, David J. Rowlands, Neil A. Ranson* & Nicola J. Stonehouse* Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identifed FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purifed from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identifed several diferences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classifcation, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further eforts to engineer yeast FAS for synthesis of alternate products. Fatty acid synthases (FASs) are critical metabolic enzymes for the endogenous biosynthesis of fatty acids in a diverse range of organisms. Trough iterative cycles of chain elongation, FASs catalyse the synthesis of long-chain fatty acids that can produce raw materials for membrane bilayer synthesis, lipid anchors of peripheral membrane proteins, metabolic energy stores, or precursors for various fatty acid-derived signalling compounds1. In addition to their key physiological importance, microbial FAS systems are also a common target of metabolic engineering approaches, usually with the aim of generating short chain fatty acids for an expanded repertoire of fatty acid- derived chemicals, including chemicals with key industrial signifcance such as α-olefns2–6.
  • JRC QSAR Model Database

    JRC QSAR Model Database

    JRC QSAR Model Database EURL ECVAM DataBase service on ALternative Methods to animal experimentation To promote the development and uptake of alternative and advanced methods in toxicology and biomedical sciences SDF - STRUCTURE DATA FORMAT: How to create from SMILES The European Commission’s science and knowledge service Joint Research Centre Directorate F Health, Consumers & Reference Materials Chemicals Safety & Alternative Methods Unit The European Commission’s science and knowledge service Joint Research Centre EUR 28708 EN This publication is a Tutorial by the Joint Research Centre (JRC), the European Commission’s science and knowledge service. It aims to provide user support. The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication. Contact information Email: [email protected] JRC Science Hub https://ec.europa.eu/jrc JRC107492 EUR 28708 EN PDF ISBN 978-92-79-71294-4 ISSN 1831-9424 doi:10.2760/952280 Print ISBN 978-92-79-71295-1 ISSN 1018-5593 doi:10.2760/668595 Luxembourg: Publications Office of the European Union, 2017 Ispra: European Commission, 2017 © European Union, 2017 The reuse of the document is authorised, provided the source is acknowledged and the original meaning or message of the texts are not distorted. The European Commission shall not be held liable for any consequences stemming from the reuse. How to cite this document: Triebe
  • A Web-Based 3D Molecular Structure Editor and Visualizer Platform

    A Web-Based 3D Molecular Structure Editor and Visualizer Platform

    Mohebifar and Sajadi J Cheminform (2015) 7:56 DOI 10.1186/s13321-015-0101-7 SOFTWARE Open Access Chemozart: a web‑based 3D molecular structure editor and visualizer platform Mohamad Mohebifar* and Fatemehsadat Sajadi Abstract Background: Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimen- sional structures of molecules. Results: With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user- friendly interface is composed. More than 30 packages are used to compose this application which adds enough flex- ibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Conclusions: Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (applica- tion programming interface). JavaScript libraries which allow creation of web pages containing interactive three- dimensional molecular structures has also been made available.
  • Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

    Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

    processes Review Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Outi M. H. Salo-Ahen 1,2,* , Ida Alanko 1,2, Rajendra Bhadane 1,2 , Alexandre M. J. J. Bonvin 3,* , Rodrigo Vargas Honorato 3, Shakhawath Hossain 4 , André H. Juffer 5 , Aleksei Kabedev 4, Maija Lahtela-Kakkonen 6, Anders Støttrup Larsen 7, Eveline Lescrinier 8 , Parthiban Marimuthu 1,2 , Muhammad Usman Mirza 8 , Ghulam Mustafa 9, Ariane Nunes-Alves 10,11,* , Tatu Pantsar 6,12, Atefeh Saadabadi 1,2 , Kalaimathy Singaravelu 13 and Michiel Vanmeert 8 1 Pharmaceutical Sciences Laboratory (Pharmacy), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland; ida.alanko@abo.fi (I.A.); rajendra.bhadane@abo.fi (R.B.); parthiban.marimuthu@abo.fi (P.M.); atefeh.saadabadi@abo.fi (A.S.) 2 Structural Bioinformatics Laboratory (Biochemistry), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland 3 Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; [email protected] 4 Swedish Drug Delivery Forum (SDDF), Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; [email protected] (S.H.); [email protected] (A.K.) 5 Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7 A, FI-90014 Oulu, Finland; andre.juffer@oulu.fi 6 School of Pharmacy, University of Eastern Finland, FI-70210 Kuopio, Finland; maija.lahtela-kakkonen@uef.fi (M.L.-K.); tatu.pantsar@uef.fi
  • Quickly Documentation Release 0.1

    Quickly Documentation Release 0.1

    Quickly Documentation Release 0.1 Michael Spencer March 28, 2016 Contents 1 Offline Reading 3 1.1 Tutorial..................................................3 1.2 QMLify Transpiler............................................5 1.3 Core JS Modules.............................................5 1.4 Distributing your Module........................................8 2 Indices and tables 11 i ii Quickly Documentation, Release 0.1 Quickly is a build tool and QML module with provides an NodeJS-like ES6 environment for Javascript used in QML. The goal of the project is to allow you to write awesome modern ES6 Javascript taking advantage of classes, decorators, arrow functions, and best of all, many of the vast array of NPM packages available using the standard ES6 module imports. You can then take that code and use in directly from QML, just as you would with plain, old, QML-specific Javascript. You can even build a library using ES6 and NPM packages, and then distribute that as a standard QML module or QPM package for other developers to use in regular QML or QML-specific Javascript. For those who would prefer to stick with standard QML-specific Javascript, you can also do that and still use the Quickly library, which gives you promises, the fetch API, and many polyfills. This is great for longtime QML devel- opers or existing projects that just want to drop in some easy-to-use features from modern JS core libraries. Tutorial A quick guide to get you up and running with Quickly. QMLify Transpiler How to use qmlify, the Quickly transpiler. Core JS Modules How to use the core JS modules. Distributing your Module Distributing your awesome new module for other developers to use.
  • Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department

    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).