maxmin.py

# GPL v 3.0
# script name: maxmin.py
# written by Naoyuki Miyashita on 12/20/2013
# Naoyuki Miyashita (c) 2013
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
# python maxmin.py filename.pdb ¨selection¨
#-----------------------------------
# Please use prody selection rules in the atom selections.
#
from pylab import *
import numpy as np
import scipy as sp
import lProam
from prody import *
from matplotlib import pyplot as plt
from scipy import stats

#
def argv_read():
    filename     = sys.argv[1]
    sele         = sys.argv[2]
    argv_array=(filename,sele)
    return(argv_array)

def translation(filename,sele):
    # read and setup pdb
    pdb        = lProam.file_read(filename)
    # key coords
    pdb_idx    = pdb.copy()
    pdb_sele   = pdb_idx.select(sele)
    print pdb_sele
    pdb_coord   = pdb_sele.getCoords()
    print pdb_coord
    xara=np.array([])
    yara=np.array([])
    zara=np.array([])
    #
    xara=pdb_coord[:,0]
    yara=pdb_coord[:,1]
    zara=pdb_coord[:,2]
    #print xara
    #
    min_x = np.amin(xara)
    min_y = np.amin(yara)
    min_z = np.amin(zara)

    max_x = np.amax(xara)
    max_y = np.amax(yara)
    max_z = np.amax(zara)

    center_x = (max_x + min_x)*0.5
    center_y = (max_y + min_y)*0.5
    center_z = (max_z + min_z)*0.5

    size_x = max_x - min_x
    size_y = max_y - min_y
    size_z = max_z - min_z

    print "=== MaxMin ========"
    print "min    (x,y,z) = ",min_x, min_y, min_z
    print "max    (x,y,z) = ",max_x, max_y, max_z
    print "size   (x,y,z) = ",size_x, size_y, size_z
    print "center (x,y,z) = ",center_x, center_y, center_z
    print "-------------------"

    return ()


def main_calc():
    #input
    argv_array=argv_read()
    (filename,sele)=argv_array
    #
    translation(filename,sele)
    #
    return()

if __name__ == '__main__':
    main_calc()