Amr ALHOSSARY

Here is another question for community discussion: When an amino acid (regardless to being L or D) is the substrate (say in an oligopeptide), is it considered both polymeric and...

I agree to most of your points @josemduarte. D-AminoAcids are not as frequent as L-AminoAcids (at least yet). However, they are aminoacids at the end of the day. They have...

> Is it possible to write your code to use the `Group` interface (e.g. `Group.getAtom("N")` instead of `AminoAcid.getN()`)? I also feel like supporting D-AA is unusual enough that it should...

Sorry closed by mistake

> Does this fix a particular problem or is the motivation solely completeness? It fixes a particular problem. I am searching the PDB for different types of cross links (e.g....

Let's keep this pull request for the implementation discussions, and keep the design discussions to the #993 .

According to the conversation [here](https://stackoverflow.com/questions/41270364/what-does-forktrue-fork-means-in-pom-xml-while-using-maven), it leads to non repeatable compilation operation.

related to #946

Sample code in case someone wants to work on it. ```java URL url; HttpURLConnection httpConnection = null; try { url = new URL("https://scop.berkeley.edu/downloads/parse/dir.des.scope.2.07-stable.txt"); URLConnection connection = url.openConnection(); if (connection instanceof...

Hi @Sounak123, sorry for my late reply. We always welcome new contributors. You will need to create 2 ~~abstract~~ (sorry I mean **static**) methods somewhere in biojava-core, preferably in ```Java...