For the desktop the OS X Molecular DataSheet (XMDS) is an interactive cheminformatics tool for viewing and editing molecular structures, chemical reactions and data. It is designed to be instantly intuitive to anyone who has used a Mac, a spreadsheet and any chemical structure sketcher. Mac Compatibility The 64 bit version is expected to work on Mac OS X 10.15 (Catalina) and newer. The 32 bit version of Vina is expected to work on Mac OS X from 10.4 (Tiger) through 10.14 (Mojave). Installing tar xzvf autodockvina112mac64bit.tgz # 64 bit tar xzvf autodockvina112mac.tgz #.
Preview:- Tips and tricks for using Preview
PYMOL:- Using PYMOL with Plugins
Automator workflow:- Combining PDFs
Spotlight:- Tips and tricks for using Spotlight
ChemBioDraw:- Using HotKeys in ChemBioDraw
Knime:- Knime Tutorial
Safari Extensions:- A Tutorial showing how to create a Safari Extension
ChemDoodle Web Components:-Exploring ChemDoodle Web Components
Protein Data Bank Demo and Canvas Technology Analysis Building a PDB query tool
ChemDoodle Web Components 3.0 3D ChemDoodle Web Components with WebGL
ChemDoodle_Protein_ribbon:- Creating Protein Ribbons using ChemDoodle and Web GL
Applescript:- A series of Applescript tutorials
Using Flot and ChemSpider:- Creating interactive plots
Using Flot and ChemDoodle Web Components:- Creating interactive plots
Using Flot and Chemical Identifier Resolver:- Creating interactive plots
Getting data from a dead Mac:- Removing hard drives and installing in external enclosure
Using PTHPasteboard Pro 4:- Multiple clipboards and modifying text on the clipboard
Scripting Vortex:- Calculating molecular properties using OpenBabel
Scripting Vortex 2:- Calculating molecular properties using filter-it
Scripting Vortex 3:- Calculating molecular properties using the ChemAxon cxcalc
Scripting Vortex 4:- Calculating molecular properties using CCG MOE
Scripting Vortex 5:- Calculating molecular similarities using OpenBabel
Scripting Vortex 6:- Filtering molecules using filter-it
Scripting Vortex 7:- Calculating molecular properties using MayaChemTools
Scripting Vortex 8:- Molecular shape matching
Scripting Vortex 9:- 2D depiction of 3D structures
Scripting Vortex 10:- Interacting with the user
Scripting Vortex 11:- Using a web service
Scripting Vortex 12:- JSON import
Scripting Vortex 13:- Using OpenBabel fastsearch
Scripting Vortex 14:- Interacting with MOE using SOAP
Scripting Vortex 15:- Interacting with MOE using the listener
Scripting Vortex 16:-Using predictive models on OCHEM
Scripting Vortex 17:-Using MOE to dock ligands selected in Vortex
Scripting Vortex 18:-Using Un1Chem from within Vortex
Scripting Vortex 19:-Implementing a CNS penetration algorithm
Scripting Vortex 20:-Adding images to Vortex
Scripting Vortex 21:-Displaying web pages in Vortex
Scripting Vortex 22:-Matching muliple SMARTS queries such as PAINS
Scripting Vortex 23:-Accessing ChEMBL web services.
Scripting Vortex 24:- Substructure searching very large compound collections.
Scripting Vortex 25:- Scripting literature searches
Scripting Vortex 26:- Importing Open Source Malaria Project data
Scripting Vortex 27:- Flagging duplicate molecules
Scripting Vortex 28:- Flagging duplicate molecules, version 2
Scripting Vortex 29:- Flagging Potential Aggregators
Scripting Vortex 30:- Getting UniChem data from ChEMBL
Scripting Vortex 31:- Flexible UniChem Search
Scripting Vortex 32:- Dealing with Greek characters in column names
Scripting Vortex 33:- Accessing ZINC supplier information
Scripting Vortex 34:- Analysis of Categories
Scripting Vortex 35:- Several ways of scripting Name to Structure
Scripting Vortex 36:- Getting PDB information
Scripting Vortex 37:- Annotating Functional Groups
Scripting Vortex 38:- Accessing Jupyter Notebook model from Vortex
Scripting Vortex 39:- Predicting sites of metabolism
Scripting Vortex 40:- Interacting with RCSB Protein Data Bank
Scripting Vortex 41:- Flagging potential Kinase Inhibitors
Scripting Vortex 42:- Implementing AB-MPS scoring
Scripting Vortex 43:- Accessing a Jupyter Notebook HERG model from Vortex
Scripting Vortex 44:- Making a Random selection
Scripting Vortex 45:- Rescoring Docking using RF-Score-VS
Scripting Vortex 46:- Counting Identical structures in two datasets
Scripting Vortex 47:- Determining the Amino Acids in a collection of peptides
Scripting Vortex 48:- A Vortex script to calculate the Blood-Brain Barrier (BBB) SCORE
Scripting Vortex 49:- A selection of scripts to help with cluster analysis
Calculation Fields in Vortex:- Using Calculation Fields in Vortex to construct algorithms
A 3D viewer in Vortex:- Viewing Docking results in Vortex using Astex Viewer
Scripting a web service:- Scripting the Organic Chemistry Reference Resolver
Scripting CIR:- Scripting the Chemical Identifier Resolver
Searching eMolecules:- Using ChemBioDraw as the drawing package to search eMolecules
Scripting ChemBioDraw:- Scripting ChemBioDraw to convert cdx to png
Remote Printing:- Printing from your iPad/iPhone using a folder action
Export Notes to Evernote:- A service to automate export notes to Evernote
Cheminformatics on a Mac:- A talk I gave at the Cambridge University Cheminformatics Group Meeting
Marvin web-service:- Accessing the Chemical Identifier Resolver from Marvin
PAINS filter:-A Pan Assay Interference Compounds Filter for filter-it
LigPlot+:-Running LigPlot+ under Mac OS X
eFindSite:-Compiling eFindSite under Mac OS X
Decoy Finder:-Installing Decoy Finder under Mac OS X
3D Printing:-3D Printing resource for chemists
Cheminformatics:-Installing cheminformatics tools on a Mac
Python, Chemistry and a Mac 1:- Setting up iPython notebook
Installing ACPC:- Installing the Linux application ACPC under Mac OSX
Lilly-MedChem Rules:- Compiling and Installing 'Lilly-MedChem Rules'
Fortan on a Mac:- A compilation of Fortran resources and instructions for the Mac
Plane of Best Fit:- Compiling Plane of Best Fit algorithm.
MedChem Wizard:- MedChem wizard knime tutorial.
Installing Checkmol:- Installing Checkmol under Mac OSX.
Clustering:- Options for clustering large datasets
Docking:- A workflow for docking/virtual screening initial studies
Docking:- A workflow for docking/virtual screening, running the docking and analysis of results
Bioconda:- Creating a Bioconda recipe
Augmented Reality:- How to display a protein in augmted reality
Unix Tips:- Unix commands for helping deal with very large files
Safari Exrensions:- Reenabling Extensions after Safari 12 update
Python Data Science Libraries:- Open Source Python Data Science Libraries
Cheminformatics Tookits:- Open Source Cheminformatics Tookits
fp2sim:- Using the Python 3 library fp2sim for similarity searches
Chemistry in FileMaker:- Adding substructure searching to a FileMaker Pro Database
Writing Python with Xcode:- How to configure Xcode to write Python code
Jupyter (aka iPython) Notebooks
Open Source Malaria an iPython Notebook:- Accessing Open Source Malaria Data using an iPython Notebook.Calc Props iPython Notebook:- iPython Notebook to calc physicochemical properties.
ChEMBL models iPython Notebook:- iPython Notebook using ChEMBL predictive models.
AMES model Jupyter Notebook:- Predicting AMES activity using Random Forest model.
Conformation Jupyter Notebook:- Generating conformations for use in Docking
Downloading from the RCSB Protein Data Bank using PythonAn alternative to RCSB java start
Description of Building HERG Random Forest model Jupyter Notebook Build model and pickle. Requires data set from GitHub https://github.com/AGPreissner/Publications. Download the notebook Building HERG Random Forest model Jupyter Notebook
Description of Single molecule HERG Random Forest prediction Jupyter Notebook and fingerprint contribution
Download the notebook Single molecule HERG Random Forest prediction Jupyter Notebook
Enhancing a Jupyter Notebook Embeding LaTeX or MatML in a Jupyter Notebook
Chemically Bonded (itch) Mac Os Catalina
fp2sim:- Using the Python 3 library fp2sim for similarity searches
HELM:- HELM notation in Jupyter Notebook
Wordcloud:- Jupyter notebook to create Wordcloud of tweets
Molecular Similarity Notebook:- Jupyter notebook to create similarity matrix
Interactive plots notebook:- Jupyter notebook showing interactive plots including displaying structure on tooltip
IBM RXN notebook:- Jupyter notebook showing how to interact with AI assisted retrosynthesis web service
Docking notebook:- Jupyter Notebook for docking either locally or using Colab
Meeting Reports
Chemistry on Mobile Devices:- Meeting ReportCheminformatics for Drug Design:- Meeting Report
--Created by Macs in Chemistry (https://www.macinchem.org).
--Copyright (c) 2019, Chris Swain
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--LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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--(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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Compilations of data analysis tools, reference management software, GPU-accelerated applicationsand spectroscopy software
Chemically Bonded (itch) Mac Os 11
- Download the latest version from https://itch.io/app
- Open
Install itch.app
If it doesn't launch the first time - try a second time. We're lookinginto that particular issue.
Note: before v25, itch used to install in /Applications/itch.app. It now installsper-user, in ~/Applications/itch.app. You might want to remove the former before(or after) installing itch v25.
Verifying the app
All our OSX binaries are signed by a Developer ID certificate to the name of Amos Wenger, and you can verify them by running the following command in a terminal:
...where ~/Applications/itch.app is the full path to the .app. If the app is correctly signed, you should see the following terminal output:
Updating
When a new version of the app becomes available, 'A new version is available'shows up in the top right corner.
Clicking it allows you to restart into the new version.
Uninstalling
You can uninstall the app by dragging itch.app out of your ~/Applications folder and into the Trash.
This won't remove your library, which resides at ~/Library/Application Support/itch,
along with any additional install locations you have added from the app.
If you really want to uninstall everything, you'll need to delete that folder as well.