baoilleach

import math
import pybel

def sqr_dist(a, b):
    ac = a.coords
    bc = b.coords
    return (ac[0]-bc[0])**2 + (ac[1]-bc[1])**2 + (ac[2]-bc[2])**2

# Definitions taken from
#    http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html

rmcgibbo

from __future__ import division
import numpy  as np
import IPython as ip
import matplotlib.pyplot as pp
import warnings
from collections import namedtuple
import scipy.optimize

#symbolic algebra
import theano

andersx

import openbabel as ob

# Standard openbabel molecule load
conv = ob.OBConversion()
conv.SetInAndOutFormats('xyz','xyz')
mol = obOBMol()
conv.ReadFile(mol,'my_mol.xyz')

# Define constraints
constraints = ob.OBFFConstraints()

scientificprotocols

Authors: Giorgio Pochetti & Roberta Montanari

Abstract

It could be very useful in drug development to determine the relative affinities of a ligand that can bind to a protein with two (or more) different and specific binding sites. X-ray crystallography is a very powerful technique to determine the locations and describe the features of each binding site but it is unuseful to establish their relative affinities. Moreover, the stoichiometry of binding observed in the crystal structure of a complex could be an artifact of the crystallization conditions.

On the contrary, isothermal titration calorimetry (ITC) can be used to assign the correct stoichiometry of the association, depending on the initial and final concentration ratio between ligand and protein, and to establish the affinity for each specific binding site, if combined with structural information from X-ray crystallography.

platinhom

This gist contains some scripts for Amber.

• anteligand.sh: Use antechamber to prepare a ligand for Amber
• complex_tleap.sh: Use tleap to prepare a ligand-protein complex input parameter file (Amber14)
• checkPDBID_MDprep.sh: After running many preparation jobs for PDB ligand-protein complexes, you should check whether the preparation is done.
• rename_water.py: rename water to HOH O,H1,H2 for PDB/PQR

Maybe need some other tools installed, such as pdb2pqr and g09 and so on.

GeauxEric

import math
import pybel


def squared_distance(coordsA, coordsB):
    """Find the squared distance between two 3-tuples"""
    sqrdist = sum((a - b)**2 for a, b in zip(coordsA, coordsB))
    return sqrdist

jFransham

Achieving warp speed with Rust

Contents:

• Number one optimization tip: don't
• Never optimize blindly
• Don't bother optimizing one-time costs
• Improve your algorithms
• CPU architecture primer
• Keep as much as possible in cache
• Keep as much as possible in registers

PatWalters

#!/usr/bin/env python

import sys
from prody import *
from rdkit import Chem
from rdkit.Chem import AllChem
from io import StringIO
import pypdb

HadrienG2

Hello, Rust community!

My name is Hadrien and I am a software performance engineer in a particle physics lab. My daily job is to figure out ways to make scientific software use hardware more efficiently without sacrificing its correctness, primarily by adapting old-ish codebases to the changes that occured in the software and computing landscape since the days where they were designed:

• CPU clock rates and instruction-level parallelism stopped going up, so optimizing code is now more important.
• Multi-core CPUs went from an exotic niche to a cheap commodity, so parallelism is not optional anymore.
• Core counts grow faster than RAM prices go down, so multi-processing is not enough anymore.
• SIMD vectors become wider and wider, so vectorization is not a gimmick anymore.

realvjy

// Lines
float hash( float n ) {
    return fract(sin(n)*753.5453123);
}

// Slight modification of iq's noise function.
float noise(vector_float2 x )
{
    vector_float2 p = floor(x);
    vector_float2 f = fract(x);