ISDementyev

from glob import glob

def decode_encode_pdb(input_file, output_file):
    with open(input_file, 'r', encoding='utf-8') as file:
        lines = file.readlines()
    
    decoded_lines = [line.encode('utf-8').decode('utf-8', 'replace') for line in lines]

    with open(output_file, 'w', encoding='utf-8') as file:
        file.writelines(decoded_lines)

ISDementyev

# Run using the terminal command: pymol loadpdb.py

from glob import glob
from pymol import cmd

files = glob("*.pdb")

for pdb in files:
  cmd.load(pdb, object=pdb[:-4])

ISDementyev

#!/bin/bash

pdbs=$(ls *.pdb)

for pdb in $pdbs
do
        prefix=${pdb:0:4}
        grep -vf residues.txt $pdb > $prefix-ensemble-nores.pdb
done

ISDementyev

int CharToInt(char Digit)
{
  return (int)Digit - 48;
}

int main()
{
  int Int6 = CharToInt('6');
  printf("Int: %d", Int6);
  return 0;

ISDementyev

# Add this keyword into plt.hist: weights=np.ones(len(data)) / len(data)
# Also make sure that density=False

ISDementyev

# assuming you already have com coordinates, com1 and com2, which can be generated using centerofmass and appropriate input

pseudoatom com1_particle, pos=com1
pseudoatom com2_particle, pos=com2

dist distance_com, com1_particle, com2_particle

save file.pse

ISDementyev

#!/bin/bash

c=".c"

for i in {1..10} ; do echo "#include <stdio.h>" > file$i$c 
# the loop takes the #include statement and appends it into the first line of each file; done to avoid writing it out every time.

ISDementyev

resdict = {"ALA": "A","CYS": "C","ASP": "D","GLU": "E","PHE": "F","GLY": "G","HIS": "H","ILE": "I","LYS": "K","LEU": "L","MET": "M","ASN": "N","PRO": "P","GLN": "Q","ARG": "R","SER": "S","THR": "T","VAL": "V","TRP": "W","TYR": "Y"}
resdict_inv = {one_let: three_let for three_let, one_let in resdict.items()}

ISDementyev

import matplotlib.pyplot as plt

plt.style.use('seaborn') # I personally prefer seaborn for the graph style, but you may choose whichever you want.
params = {"ytick.color" : "black",
          "xtick.color" : "black",
          "axes.labelcolor" : "black",
          "axes.edgecolor" : "black",
          "text.usetex" : True,
          "font.family" : "serif",
          "font.serif" : ["Computer Modern Serif"]}

ISDementyev

# %%file build_dimer.py
import os
from PeptideBuilder import Geometry
import PeptideBuilder
import Bio.PDB
from simtk.unit import *
from simtk.openmm.app import *
import numpy as np

def buildPeptide(peptide, customAngles=False, phi=-40, psi=60, omega=180):