matteoferla

%%javascript
//hack to fix export
require.config({
  paths: {
    d3: 'https://cdnjs.cloudflare.com/ajax/libs/d3/5.9.2/d3',
    jquery: 'https://code.jquery.com/jquery-3.4.1.min',
    plotly: 'https://cdn.plot.ly/plotly-latest.min'
  },

  shim: {

matteoferla

%%javascript
//remember to append <script src="https://cdn.plot.ly/plotly-1.2.0.min.js"></script> to head or top of body.
//output_subarea output_html rendered_html
let index = 0; //or whatever is the number of the graph.
//$('.plotly-graph-div').map((i,el) => element.append('<p>'+$(el).attr('id')+'</p>'))
let chart = $('.plotly-graph-div').eq(index).parent();
/// optionally one could change the dimensions for the .plotly-graph-div and svg elements.
//chart.children('.plotly-graph-div').css('height','525px');
//chart.children('.plotly-graph-div').css('width','100%');
let codeEl = $('<pre id="plotText"><code></code></pre>');

matteoferla

import wikitextparser as wtp
import re


####### code to convert template to dictionary
def arg_to_val(arg):
    val = arg.value
    for t in arg.templates:
        tval = t.arguments[0].value
        if t.normal_name() in ('nowrap', 'val'):

matteoferla

import requests, re, csv, pickle
import wikitextparser as wtp

class WikicatParser():
    """
    Gets all the pages recursively within a category and parser the content (via a suplied function) and gets pageviews.
    >>>pages = WikicatParser(cat_name, custom_page_parser=my_function, extra_fields=[], forbidden_categories_keywords=[...]).get_pages_recursively()
    >>>print(pages.data)
    >>>pandas.DataFrame.from_records(list(pages.data.values()))
    custom_page_parser is for content mining. a function that given wiki text returns a dictionary of whatever it mined.

matteoferla

from IPython.display import display, HTML
import uuid

class Progress:
    """
    Add a progressbar.
    Using https://getbootstrap.com/docs/4.3/components/progress/ not the HTML5 one.
    Note that Jupyter uses an older version: 3.4 (https://getbootstrap.com/docs/3.4/components/), but I doubt this will be so for long hence the color via style.
    Two uses different uses.
    

matteoferla

from __future__ import annotations
from dataclasses import dataclass
from typing import List
import pyrosetta

@dataclass
class GapData:
    chain: str
    start: int # PDB index of first missing residue
    previous: int # PDB index of the preceeding present residue

matteoferla

# A raspberry pi has a green and a blue LED connected to D23 and D24

# ============== imports =========================================
from apscheduler.schedulers.background import BackgroundScheduler
from functools import partial
from datetime import datetime
import digitalio
import board
import time

matteoferla

# NGLView is a great way to see a set of rdkit.Chem molecules in 3D.
# Right clicking gives green spheres by default. Right clicking on a sphere removes it. So nice way to keep track

# the `ModNGL` object contains the dynamic property `picked_atoms` which lists the atoms that were clicked.
# Clicked twice is removed. However, there is no way to determine the button integer (left, middle, wheel, right).

# Before loading the mols from rdkit it would be nice to fill the PDB info.
# As seen in https://blog.matteoferla.com/2020/03/atom-names-purely-in-rdkit.html
# once one has the atom names one can delete the atoms off a ``rdkit.Chem.RWMol`` making it nice and clear for Fragmenstein.

matteoferla

from rdkit import Chem
from rdkit.Chem import AllChem

class DummyMasker:
    """
    A context manager that allows operations on a mol containing dummy atoms (R/*) that
    otherwise would raise an RDKit error.
    It simply masks and unmasks the dummy atoms.
    
    >>> mol = Chem.MolFromSmiles('*CCC(C)C')

matteoferla

"""
In the docstring for a class the variables can be defined with ``:var xxx:``,  ``:ivar xxx:`` and  ``:cvar xxx:``.
This prints a block for a given class instance to make it easier.
Dynamic attributes will be marked as class variables.
Private attributes will not show.

NB. Writing  ``#:`` is probably easier and saner, but has to be done during coding...
"""

def sphinxify_vars(obj):