andersx

from __future__ import print_function
import os
import numpy as np

__EXECUTABLE__ = "/home/andersx/opt/mndo/mndo99_20121112_intel64_ifort-11.1.080_mkl-10.3.12.361"


def write_om2_gradient(coords, species, filename):
    """ Writes an input file to calculate the
        OM2 energy and gradient with MNDO99.

andersx

import numpy as np
from numpy.random import uniform

def simulate(probability):

    n = 1
    while uniform() > probability:
        n += 1
    return n 
    

andersx

! PUBLIC DOMAIN LICENSE 2017 BY ANDERS S. CHRISTENSEN
!
! I WROTE THIS BECAUSE I WAS BORED - I DON'T RECOMMEND
! WRITING FILE PARSERS IN FORTRAN BECAUSE IT IS NOT
! PRODUCTIVE.

program convert
    
    implicit none

andersx

 *******************************************************************************
 ** Site#: 18858        For non-commercial use only    Version 18.012L 64BITS **
 *******************************************************************************
 ** Cite this program as: MOPAC2016, Version: 18.012L, James J. P. Stewart,   **
 ** Stewart Computational Chemistry, web: HTTP://OpenMOPAC.net. Days left: 364**
 *******************************************************************************
 **                                                                           **
 **                                MOPAC2016                                  **
 **                                                                           **
 *******************************************************************************

andersx

#!/usr/bin/env python2
# MIT LICENSE, Anders S. Christensen (c) 2018

import sys
import pybel
import openbabel

NAME = {
    1:  'H'  ,
    2:  'He' ,

andersx

#!/usr/bin/env python2

import sys
sys.path.insert(0,"/home/andersx/dev/qml/fchl_arad/build/lib.linux-x86_64-2.7")
# sys.path.insert(0,"/home/andersx/dev/qml/fchl/build/lib.linux-x86_64-2.7")

import numpy as np

from time import time

andersx

# The MIT License
# 
# Copyright (c) 2010-2018 Anders S. Christensen
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

andersx

# Envoke by
# > pymol -c render_movie.pml <trajectoryfile.xyz>
# > convert -delay 20 -loop 0 mov*.png <outputfile.gif>

# load opt.xyz
show sticks, all
bg_color white
color grey05, elem c
preset.ball_and_stick(selection='all', mode=1)
set ray_trace_mode, 4

andersx

#!/usr/bin/env bash

while :
do
    date
    ssh -t alchemy slurm_node_reserve 24 4320 
    ssh -t alchemy slurm_node_extend 4320

    sleep 60

andersx

import sys

from rdkit import Chem
from rdkit.Chem import AllChem

if __name__ == "__main__":

    # my_smiles = ['C#N', 'C1C(C2C1OC2)O', 'C1C2C3C1C2C3O', 'C1C2COC2C1O', 'C1CC2(C1CC2)O',
    #              'C1CC2(C1NC2)O', 'C1CC2(C1OC2)N', 'C1CC2(C1OC2)O', 'C1CC2C1CC2O']
    my_smiles = ['C#N', 'C1C(C2C1OC2)O']