MOlecular Structural Formula Editor Calculatig Canonical SMILES
LICENSE: MOSFECCS is licensed under the GNU Public License 3. See LICENSE.md
MOSFFECS is a HTML-Javascript application that provides an editor for molecular structural formulae in a window. It is typically installed inside a Moodle course but can also be called by a browser from a local installation on a desktop/laptop.
With MOSFECCS (MOlecular Structural Formula Editor Calculatig Canonical SMILES), users can draw one or several formulae interactively with the mouse or with a stylus (on touch devices). On demand, the program converts the molecular structure into an alphanumeric code (mosfeccs-SMILES) that is bi-unique for the structure and allows to enter the structure(s) into the answer fields of on-line quizzes in on-line learning environments like Moodle.
MOSFECCS also contains a parser that converts SMILES codes into structural formulae ("put SMILES" button).
mosfeccs-SMILES are canonical (bi-unique) and mostly, but not always identical with Daylight-SMILES™. For details see MOSFECCS-SMILES technical manual.
SMILES-extensions to specify lone-pairs, curved arrows, and reaction arrows are specific for MOSFECCS.
MOSFECCS was developed with the didactics of basic organic chemistry in mind. In contrast to most molecular editors that were developed as tools to enter chemical structures for database searches, MOSFECCS does not correct user errors (violations of the laws and conventions of structural theory) and allows to draw "wrong" structures.
MOSFECCS was coded by Bernhard Jaun, Prof. (emeritus since 2013) at the Laboratory of Organic Chemistry ETH-Zurich. So far (2015-2024), it has been used in the context of the courses Organic Chemistry I&II for students of biology, pharmaceutical sciences, health sciences&technology (Prof. Carlo Thilgen) at ETHZ. This course offers the students a comprehensive set of on-line trainings (quizzes, total of ca. 1000 questions) in the e-learning environment Moodle. About half of the questions require the students to draw molecular structures in an editor, convert the structure into alphanumeric code (mosfeccs-SMILES) and enter the result as answer into the quiz. The correctness of the answer is then checked on the server-side of Moodle in the same way as text or numeric answers.
Since 2018, the first-year examinations in Organic Chemistry I&II for BIOL./PHARM./HST (Prof. Thilgen) at ETH are carried out on-line via the Safe Exam Browser (SEB), the Moodle-exam server of ETH, and MOSFECCS as the editor for structural formulae.
As of November 2023, more than 2800 students in 12 first-year examinations have already used MOSFECCS in the exam.
MOSFECCS has been shown to work with the following operation systems and browsers:
Mac OS 13.6.1: Firefox 119.0.1, Chrome 119.0.6045.159, Safari 17.1, SEB 3.3
Windows 10: Firefox 118.0.1, Chrome 119.0, Edge 119.0, SEB 3.5
iOS 14.4.2: Firefox, Chrome, Safari, ETH-Moodle.app
Android: Firefox, Chrome, Samsung Internet, ETH-Moodle.app
Files for installation of MOSFECCS in a Moodle course (main script compiled by Google closure compiler) MOSFECCS_v6_install_in_Moodle.zip.
Consult the file "Installing MOSFECCS in Moodle.pdf" for detailed instructions.
The file "Example_Moodle_Quizz_with_MOSFECCS.xml" can be imported into a Moodle course and contains one quiz with 10 questions that illustrate the use of MOSFECCS and MOSFECCS-SMILES in different Moodle question types.
MOSFECCS can also be installed locally on a computer: download "MOSFECCS_v6_local_install_on computer.zip" to your computer, unzip and open the file MOSFECCS_v6_240311cc.html with your browser.
MOSFECCS_MANUAL.pdf (alternatively, use the HELP button in MOSFECCS)
MOSFECCS-SMILES_technical_Manual: describes the conventions and procedures used by MOSFECCS for calculating canonical SMILES.
This section contains the source code of MOSFECCS and additional tools for development and testing.
MAKEVERSION: The perl script makeversion.pl takes the development version of MOSFECCS source code:
MOSFECCS_v6_SVG_DEV_240311-2.html and generates the production versions:
MOSFECCS_v6_240311.html (source)
MOSFECCS_v6_240311cc.html (compiled)
as well as the testing application mostest_240311-2.js (running under nodeJS).
For a detailed description of making the production versions from the development version see makeversion_Manual.pdf
MOSTEST: mostest_xxxxxx-z.js runs under nodeJS and accepts a file with SMILES-codes (one per line) as input. The SMILES-generator and SMILES-parser of mostest_xxxxxx-z.js are identical to those of MOSFECSS since mostest_xxxxxx-z.js is made by makeversion.pl from MOSFECCS. Each SMILES in the input file is converted into a structure (svg-graphic) by the parser and then the SMILES-code is calculated for the structure. mostest_xxxxxx-y.js compares the input and output SMILES-codes and reports if they are not identical or if an error occurs.
AllTestMols.txt is a testfile with ca 1600 molecules (SMILES-codes) that can be used as input for mostest.js
For BUG reports, suggestions for improvements and other questions related to coding: jaun@ethz.ch
Questions related to the use of MOSFECCS within Moodle quizzes: thilgen@org.chem.ethz.ch