Carlos de Lannoy cvdelannoy

Startup founder + bioinformatics postdoc researcher @ TU Delft (NL). Likes single-molecule spectroscopy and nanopores.

cvdelannoy / moment_invariants_are_chirality_invariant.py

Created April 19, 2022 13:01

	import numpy as np
	import prody as pr
	from geometricus import MomentInvariants, SplitType
	import plotly as py
	import plotly.graph_objs as go

	def make_atom_group(atom_list):
	out_group = pr.atomgroup.AtomGroup('Protein')
	out_group.addCoordset(atom_list)

cvdelannoy / dssp_biopython_minimal_example.py

Created July 25, 2019 15:05

Assess accessible surface area for each amino acid in a pdb file

	from Bio.PDB import PDBParser, PDBList
	from Bio.PDB.DSSP import DSSP

	# !! set path to mkdssp binary !! Install: https://github.com/cmbi/xssp (use docker or check dockerfile for install tips)
	mkdssp_path = '/home/carlos/Downloads/xssp-3.0.8/mkdssp'

	pdb_downloader = PDBList()

	# Retrieve an example pdb file (for alpha-synuclein here) and load
	pdb_fn = PDBList().retrieve_pdb_file('1xq8', file_format='pdb')

cvdelannoy / multiprocessing_example.py

Created June 11, 2019 13:26

One way to use python multiprocessing module

	import multiprocessing as mp

	def square(x, out_queue):
	out_queue.put(x ** 2)

	out_list = []

	out_queue = mp.Queue()
	processes = [mp.Process(target=square, args=(x, out_queue)) for x in range(8)]
	for p in processes: p.start()