Vignir Isberg

For loops in Javascript

Thu, 01 Dec 2016 21:00:00 +0000

I have been writing some Javascript code lately. As a fan of Python, I was hoping that modern Javascript offered an equivalent to Python’s for x in y construct. After much reading and some confusion, I now know that JS offers many ways to do a for loop, and that these differ in non-intuitive ways. So, here is an overview of the for loops I’ve encountered.

The classic C-style loop with a counter and a condition

This style of loop is common in other languages, and will be familiar to many. The syntax is verbose and error prone. Not recommended.

var arr = [1,2,3];
for (var i=0; arr.length>i;i++) {
  console.log(i);
}
// Output:
// 1
// 2
// 3

The for .. of loop

Although somewhat awkwardly named, this is very similar to Python’s for x in y, and exactly was I was looking for. Recommended for most purposes, but only works in browsers compatible with ES2015, and thus only safe to use if you compile your code with Babel (or something similar).

let arr = [1,2,3];
for (let i of arr) {
  console.log(i);
}
// Output:
// 1
// 2
// 3

The for .. in loop

Looks good, but might not work as you expect. for .. in loops over the properties of an object, in arbitrary order. Stay away from this one unless you know what you are doing!

let arr = [1,2,3];
for (let i in arr) {
  console.log(i);
}
// Output:
// 0 (array index, not value!)
// 1
// 2

The forEach loop

forEach is not a statement, but a method of an Array object. Nonetheless, it can serve as a for loop, and allows one to apply a function to each element for an array. forEach does differ from a loop statement in that a break statement has no effect inside of a forEach loop. The only way to break out of forEach is to throw an exception.

let arr = [1,2,3];
arr.forEach(i => console.log(i));
// Output:
// 1
// 2
// 3

Map

Like forEach, map is an Array method. It works like forEach, but returns a new array, with the provided function applied to each element of the original array.

let arr = [1,2,3];
console.log(arr.map(i => i*2));
// Output
// [2, 4, 6]

Multiple languages and compose key on OS X

Sat, 06 Feb 2016 22:15:00 +0000

I speak three languages, and I write in all three almost every day.

Two of these languages, Icelandic and Danish, have special characters that are not found on standard English keyboards, and thus require their own keyboard layout. Switching between keyboard layouts depending on what you are writing is a terrible user experience, and nobody should have to deal with that.

Imagine my joy when I discovered the compose key, which allowed me to write in all three languages on my English keyboard layout. By using the compose key to combine two or more characters into one, I could type compose, /, o and get ø, or compose, a, e and get æ.

The problem is that only Linux has a built in compose key. There is a solution for Windows, but it’s more complicated on OS X. I used an app called Ukelele to create a custom keyboard layout with key sequences that emulated a compose key, and used that for years. However, this solution stopped working when I upgraded to OS X El Capitan recently.

Turns out that there is now a better solution. It’s still not as easy as on Linux and Windows, but using Karabiner with custom key mappings essentially gives you a compose key on OS X. I found a repository on GitHub by gnarf that provides exactly that, with nice example mappings for various emoji and the like. I forked and modified the mappings to include Nordic and German characters, and my compose key is working again.

Find my mappings on GitHub.

GPCRdb published in Nucleic Acids Research

Sun, 17 Jan 2016 09:33:51 +0000

A new paper is out in Nucleic Acids Res. that describes a major new release of GPCRdb.

The new release has been completely re-written and consolidated into an integrated system using Python 3, Django and PostgeSQL.

GPCRdb is now open source and the source code and source data are available on BitBucket. A virtual machine config for development is provided in the documentation, making it easy for anyone to start contributing to the project.

Read the paper HERE.

Generic GPCR residue numbering

Tue, 28 Apr 2015 09:33:51 +0000

A paper on generic residue numbering schemes for GPCRs has been published in Trends Pharmacol. Sci.

The paper reviews commonly used generic numbering schemes, and introduces a novel, structure-based scheme that accounts for structural irregularities revealed by recent GPCR crystal structures.

Complementary tools to look up generic numbers and number PDB structures can be found in GPCRdb.

Read the paper HERE.

New fragment-based pharmacophore method published

Thu, 01 Jan 2015 09:33:51 +0000

A paper describing a novel pharmacophore method for G protein-coupled receptors has been published in Methods.

The method uses residue-ligand fragments from X-ray crystal structures to build pharmacophore models for GPCRs, and even allows for modeling of receptors with no structural or ligand data available.

Read the paper HERE.

GPCR Dock 2013

Tue, 05 Aug 2014 09:33:51 +0000

The results of GPCR Dock 2013 have been published.

GPCR Dock is a protein modeling evaluation where modelers around the world try to predict the structure of an upcoming crystal structure of a G protein-coupled receptors in complex with ligands. In the 2013 evaluation, the structures were of 5-hydroxytryptamine receptors 1B and 2B, and the smoothened receptor.

I participated as a member of the Gloriam group, and our structural model of 5-HT1B ranked 1st in overall protein structure, and 3rd in protein-ligand complex prediction.

View the results HERE.

Previous GPCR Dock results can be found HERE (2010) and HERE (2008).

Ph.D. degree

Wed, 14 May 2014 09:33:51 +0000

I defended my Ph.D. thesis on May 6th, and have now been awarded a Ph.D. in Health and Medical Sciences.

The title of the thesis is: “G Protein-Coupled Receptor Modeling, Ligand Identification and Database Development”

The assessment committee members were: Associate Professor Lars Olsen (chairperson), University of Copenhagen, DK Professor Ad IJzerman, Leiden University, NL Dr. Christopher Southan, University of Edinburgh, UK

First endogenous ligands of GPR139 published

Wed, 14 May 2014 09:33:51 +0000

A new paper is out in J. Chem. Inf. Model.

The paper describes the discovery of the first putative endogenous agonists of GPR139, an orphan G protein-coupled receptor.

Read it HERE.

GPCRDB paper published

Tue, 03 Dec 2013 09:33:51 +0000

A new paper is out in Nucleic Acids Res.

The paper describes an update to the GPCRDB, including novel alignments and models. In addition, a new section of GPCRDB, GPCRDB Tools is now available. The tools provide new ways of visualizing and analyzing the data from the GPCRDB, and allow for alignments and similarity calculations of subsets of sequences and sequence positions, well as interactive diagrams that can be exported for publication.

Read it HERE (open access).

5-HT₂ SAR paper out

Thu, 07 Nov 2013 09:33:51 +0000

A new paper is out in PLOS ONE.

The paper describes the synthesis of novel 5-HT₂ receptor agonists with a detailed SAR analysis.

Read it HERE (open access).

Vignir Isberg

For loops in Javascript

The classic C-style loop with a counter and a condition

The for .. of loop

The for .. in loop

The forEach loop

Map

Multiple languages and compose key on OS X

GPCRdb published in Nucleic Acids Research

Generic GPCR residue numbering

New fragment-based pharmacophore method published

GPCR Dock 2013

Ph.D. degree

First endogenous ligands of GPR139 published

GPCRDB paper published

5-HT2 SAR paper out

5-HT₂ SAR paper out