calcDistanceDCD.py

# GPL v 3.0 
# script name: calcDistanceDCD.py
# written by Naoyuki Miyashita on 12/18/2013 
# Naoyuki Miyashita (c) 2013
#
#-----------------------------------
# Use lProam, pylab, numpy
#-----------------------------------
# ussage:
#
# file="new.pdb"
# dcd="test.dcd"
# python calc DistanceDCD.py $file $dcd \
# "resnum 1to2 and name CA" \
# "resnum 4to5 and name CA"
#-----------------------------------
# Please use prody selection rules in the atom selections.
#
from prody import *
from pylab import *
import numpy as np
import lProam
# 

def argv_read():
    filename     = sys.argv[1]         # input.pdb
    dcdfile      = sys.argv[2]         # input.dcd
    selec1 = sys.argv[3]               # "segment A"
    selec2 = sys.argv[4]               # "segment B"
    argv_array=(filename,dcdfile,selec1,selec2)
    return(argv_array)

def get_pdb_center(filename,center_selec):
    #read pdb
    center = np.array([])
    pdb1   = lProam.file_read(filename)
    key_pdb    = pdb1.select(center_selec)
    #setup pdb
    cent = center_selec + " and name CA"
    center = lProam.get_center(key_pdb,center_selec)
    # copy pdb
    return(center)

def main_calc():
    #input
    argv_array=argv_read()
    (filename,dcdfile,select1,select2)=argv_array
    #
    # read and setup pdb
    pdb = lProam.file_read(filename)
    #print pdb
    dcd = lProam.dcd_trj(dcdfile)
    #print dcd
    dcd.link(pdb)
    dcd.setCoords(pdb)
    #(pdb,dcd)=lProam.readFrame(filename,dcdfile)
    #print dcd
    a1 = pdb.select(select1)
    a2 = pdb.select(select2)
    #print a1, a2
    dist = zeros(dcd.numFrames())
    #dist = zeros(arange(dcd))
    for i, frame in enumerate(dcd):
        c1 = calcCenter(a1)
        c2 = calcCenter(a2)
        #dist[i] = calcDistance(a1, a2)
        dist[i] = calcDistance(c1, c2)
        #print "DISTANCE=",dist[i]
        print i," ", dist[i]
    return()

if __name__ == '__main__':
    main_calc()