Macs in Chemistry

Insanely great science

 

Tutorials, Tips and Tricks

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
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

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.

Meeting Reports

Chemistry on Mobile Devices:- Meeting Report
Cheminformatics for Drug Design:- Meeting Report

--Created by Macs in Chemistry (https://www.macinchem.org)
--Copyright (c) 2011, Chris Swain
--All rights reserved.

--Redistribution and use in source and binary forms, with or without
--modification, are permitted provided that the following conditions are met:

--1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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--THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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--LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
--ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
--(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
--SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.W

Compilations of data analysis tools, reference management software, GPU-accelerated applicationsand spectroscopy software

Updated 21 September 2017 2017