matteoferla

# for details see https://stackoverflow.com/questions/36237477/python-docstrings-to-github-readme-md
# further details in https://blog.matteoferla.com/2019/11/convert-python-docstrings-to-github.html

import re
import shutil
import os
import subprocess

# ## Settings
repo_path = '/Users/👾👾👾/👾👾👾'

matteoferla

This is an experiment. Is a GitHub Gist comment a good way to log publically how I fixed an installation or similar issue?

See comments

matteoferla

from rdkit import mol

def set_to_neutral_pH(mol: Chem):
    """
    Not great, but does the job.
    
    * Protonates amines, but not aromatic bound amines.
    * Deprotonates carboxylic acid, phosphoric acid and sulfuric acid, without ruining esters.
    """
    protons_added = 0

matteoferla

import numpy as np
import pymol2
token_resi = 25 # this present in all chains
filename = '👾👾👾.pse'

coords = {}
with pymol2.PyMOL() as pymol:
    pymol.cmd.load('crysalin_lattice.pse')
    for name in pymol.cmd.get_object_list():
        for chain in pymol.cmd.get_chains(name):

matteoferla

I want Pytorch, Jax and Tensorflow.

Check: nvidia-smi still gives 'NVIDIA-SMI 510.85.02 Driver Version: 510.85.02 CUDA Version: 11.6 '

conda activate base
unset LD_LIBRARY_PATH
unset CUDA_HOME
export NEW_ENV='cuda118redux'
export CONDA_ALWAYS_YES=yes

matteoferla

# ========================
# Sets presents...
# tries to source $HOME/.bashrc
# or $HOME2/.bashrc;
# or a fallback
# ========================

# source /data/xchem-fragalysis/shared/bashrc.sh

# universal fixes

matteoferla

matteoferla

// In NGL it may be handy to show an XYZ system axes / caltrop / cube edge
// the following is called via `addAxis(stage)`

const addAxis = (stage) => {
  let shape = new NGL.Shape("shape", { dashedCylinder: true })
shape.addArrow([ 0, 0, 0 ], [ 10, 0, 0 ], [ 1, 0, 0 ], 1.0);
shape.addText([ 12, 0, 0 ], [ 1, 0, 0 ], 2.5, "x");
shape.addArrow([ 0, 0, 0 ], [ 0, 10, 0 ], [ 0, 1, 0 ], 1.0);
shape.addText([ 0, 12, 0 ], [ 0, 1, 0 ], 2.5, "y");
shape.addArrow([ 0, 0, 0 ], [ 0, 0, 10 ], [ 0, 0, 1 ], 1.0);

matteoferla

I wanted to get the void volume with OpenEye Spicoli for use in OERocs.

But it did not create a usable surface.

This here is for my reference as I am missing something.

Standard reading:

# -----------------------------------

matteoferla