amrhamedp’s gists

amrhamedp / virtual_site_comparison

Created January 4, 2022 20:32

virtual_site_comparison

	<mdtraj.Trajectory with 1 frames, 40585 atoms, 12844 residues, and unitcells>
	[Vec3(x=9.059788703918457, y=0.0, z=0.0), Vec3(x=0.0, y=5.983500957489014, z=0.0), Vec3(x=0.0, y=0.0, z=7.570346832275391)] nm
	-133850.6219610522
	<class 'simtk.openmm.openmm.HarmonicBondForce'> 640.2855721759976
	<class 'simtk.openmm.openmm.HarmonicAngleForce'> 1742.1832987272935
	<class 'simtk.openmm.openmm.CustomTorsionForce'> 783.5984530913894
	<class 'simtk.openmm.openmm.NonbondedForce'> -155693.45684747622
	<class 'simtk.openmm.openmm.CustomNonbondedForce'> 18676.809925262485
	<class 'simtk.openmm.openmm.MonteCarloBarostat'> 0.0
	<mdtraj.Trajectory with 1 frames, 40585 atoms, 12844 residues, and unitcells>

amrhamedp / desmond_openmm.py

Last active December 3, 2021 14:14

desmond_openmm.py

	from __future__ import print_function
	from simtk.openmm import app
	import simtk.openmm as mm
	from simtk import unit
	from sys import stdout
	import parmed
	import sys
	import simtk.unit as units
	from MDAnalysis.coordinates.DCD import DCDFile

amrhamedp / decompose.py

Created December 2, 2021 20:11

	from __future__ import print_function
	from simtk.openmm import app
	import simtk.openmm as mm
	from simtk import unit
	from sys import stdout
	import parmed
	import sys
	import simtk.unit as units
	from MDAnalysis.coordinates.DCD import DCDFile

amrhamedp / ex.py

Created December 1, 2021 22:49

	from MDAnalysis.coordinates.DCD import DCDFile
	dms = app.DesmondDMSFile('a.dms')
	system = dms.createSystem(nonbondedMethod=app.PME,
	nonbondedCutoff=9.0*unit.angstroms,OPLS=True)
	import simtk.openmm as openmm
	system.addForce(openmm.MonteCarloBarostat(1 * units.bar, 300*unit.kelvin))
	integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds,
	2.0*unit.femtoseconds)
	integrator.setConstraintTolerance(0.00001)
	platform = mm.Platform.getPlatformByName('CUDA')

amrhamedp / numpy-sqlite3.py

Created December 27, 2017 06:10 — forked from pnavarro-algometrics/numpy-sqlite3.py

Insert numpy array into a sqlite3 database

	import sqlite3
	import numpy

	# Array of 4 columns and 100 rows
	data = numpy.random.rand(100, 4)

	# Create a sample database
	conn = sqlite3.connect('/tmp/sample.db')
	cursor = conn.cursor()

amrhamedp / conf_gen.py

Created July 29, 2017 14:38 — forked from tdudgeon/conf_gen.py

Conformer generation using RDKit

	import sys
	from rdkit import Chem
	from rdkit.Chem import AllChem, TorsionFingerprints
	from rdkit.ML.Cluster import Butina


	def gen_conformers(mol, numConfs=100, maxAttempts=1000, pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, enforceChirality=True):
	ids = AllChem.EmbedMultipleConfs(mol, numConfs=numConfs, maxAttempts=maxAttempts, pruneRmsThresh=pruneRmsThresh, useExpTorsionAnglePrefs=useExpTorsionAnglePrefs, useBasicKnowledge=useBasicKnowledge, enforceChirality=enforceChirality, numThreads=0)
	return list(ids)

amrhamedp / FileRead.cpp

Created July 29, 2017 05:09 — forked from skymarionsky/FileRead.cpp

read file and do something line by line with c++

	#include <iostream>
	#include <fstream>
	#include <sstream>

	using namespace std;

	int main(int argc, char* argv[])
	{
	ifstream file(argv[1]); // pass file name as argment
	string linebuffer;

amrhamedp / 0_reuse_code.js

Created April 17, 2017 06:53

Here are some things you can do with Gists in GistBox.

	// Use Gists to store code you would like to remember later on
	console.log(window); // log the "window" object to the console

amr abdallah amrhamedp