wjiang

import numpy as np
import matplotlib.pyplot as plt
import mrcfile
import random

#################################################################################################

nanodisc_diameter = 170	# Angstrom, change this value for nanodisc of different sizes

#################################################################################################

wjiang

import numpy as np
import matplotlib.pyplot as plt
import mrcfile

n = 64	# 3D map size in pixels
distance_ringcenter_to_boxcenter = n/2.0 * 0.5
radius_ring = distance_ringcenter_to_boxcenter * 0.1

def buildTorus(n, distance_ringcenter_to_boxcenter, radius_ring):
	# http://mathworld.wolfram.com/Torus.html

wjiang

#!/usr/bin/env python

# by Wen Jiang @ Purdue University

import sys, argparse
import pandas as pd
import numpy as np

def main():
    args = parse_command_line()

wjiang

import os, sys, random, math
import pandas as pd
import EMAN2

try:
    mapFile, lstFile, nHelices, twist, maxTilt, maxShift = sys.argv[1:]
    projFile = os.path.splitext(lstFile)[0]+".mrcs"
    nHelices = int(nHelices)
    twist = float(twist)
    maxTilt = float(maxTilt)

wjiang

#!/usr/bin/env python

import os, sys, argparse

def main():
    args = parse_command_line()
    try:
        nodesCompressed = os.environ.get("SLURM_JOB_NODELIST").split(",")
    except:
        print("ERROR: environment variable SLURM_JOB_NODELIST does not exist")

wjiang

#!/usr/bin/env python

# by Wen Jiang @ Purdue University

import sys, argparse
try:
    import pandas as pd
    import numpy as np
    import scipy
except:

wjiang

from EMAN2 import *

sym = "icos"

xf = Transform()
xf.to_identity()
nsym=xf.get_nsym(sym)
for i in range(nsym):
	e = xf.get_sym(sym, i)
	m = e.get_params("matrix")

wjiang

import os, sys
import numpy as np
import mrcfile

if len(sys.argv)!=2:
    print(f"Usage: {sys.argv[0]} <mrc file>")
    sys.exit(-1)

imageFile = sys.argv[1]
prefix = os.path.splitext(imageFile)[0]

wjiang

#!/usr/bin/env python

import sys, mrcfile
import numpy as np
from skimage.io import imsave

if len(sys.argv)!=3:
    print(f"Usage: {sys.argv[0]} <input.mrc> <outputPrefix>")
    sys.exit(-1)