getSegment.py

# GPL v 3.0
# script name: getSegment.py
# written by Naoyuki Miyashita on 1/06/2014
# Naoyuki Miyashita (c) 2014
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
# setupTMDimerPosition.py input.pdb output.pdb distance \
#      "center: selection" \
#      "upper or lower center: selection" \
#      "interface: selection" \
#      alpha_angle rho1_angle
#-----------------------------------
# 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]
    outfile      = sys.argv[2]
    seg      = sys.argv[3]
    key      = sys.argv[4]
    num      = int(sys.argv[5])
    argv_array=(filename,outfile,seg,key,num)
    return(argv_array)

def translation(filename,outfile,seg,key,num):
    # read and setup pdb
    pdb        = lProam.file_read(filename)
    # key coords
    pdb_idx    = pdb.copy()
    pdb_sel    = pdb_idx.select(seg)
    if key == "reset":
        resnum = pdb_sel.getResnums()
        print resnum
        resmax = np.amax(resnum)
        resmin = np.amin(resnum)
        diff = resmax - resmin + 1
        resnum = resnum - resmin +1 + num
        #resnum = resnum - resmin + 1
        pdb_sel.setResnums(resnum)
    elif key == "wreset":
        resnum = pdb_sel.getResnums()
        nlen = len(resnum)
        print resnum,nlen
        resnum1 = range(1,nlen)
        print resnum1
        pdb_sel.setResnums(resnum1)
    #pdb_sel    = pdb_idx.select('segment WA')
    #
    lProam.file_write(outfile,pdb_sel)
    return ()


def main_calc():
    #input
    argv_array=argv_read()
    (filename,outfile,seg,key,num)=argv_array
    #
    translation(filename,outfile,seg,key,num)
    #
    return()

if __name__ == '__main__':
    main_calc()