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
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
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

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
Building HERG Random Forest model Jupyter Notebook Build model and pickle. Requires data set from GitHub https://github.com/AGPreissner/Publications
Single molecule HERG Random Forest prediction Jupyter Notebook Also fingerprint contribution

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.
--2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

--THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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--WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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--(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
--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 22 September 2018