import numpy
import mp3
s = mp3.system()
s.cord = mp3.dcd()
s.cord.setinput("water1000.dcd")
s.labels.getfrompsf("water1000.psf")
s.cord.nextframe()
# return a list of protein atoms:
# make a list containing atom numbers and properties
atoms = [ i for i in xrange(0,s.cord.natoms) if s.labels.data.field('atomtype')[i] == "OSPC" ]
goodatoms = s.cord.frame[atoms]
#print goodatoms
minatoms = goodatoms.argmin(axis=0)
maxatoms = goodatoms.argmax(axis=0)
boxmin = numpy.asarray( [ goodatoms[minatoms[i],i] for i in (0,1,2) ] )
boxmax = numpy.asarray( [ goodatoms[maxatoms[i],i] for i in (0,1,2) ] )
numpy.add(boxmin, -10, boxmin )
numpy.add(boxmax, 10, boxmax )
print boxmin, boxmax
def main():
# Put what you want here.
dcd_to_msd = "/home/richard/research/mp3/tests/water1000.dcd"
psf_name = "/home/richard/research/mp3/tests/water1000.psf"
# Set up the systems, so that you can find the atoms you want below.
cord = mp3.dcd()
cord.setinput(dcd_to_msd)
s = mp3.system(cord=cord, psf=psf_name)
# Find which atoms you want right here.
# First, we find all atoms in the protein, and all in the residues we
# want.
residue_low = 10
residue_high = 20
residues = [i for i in xrange(s.labels.natoms) if
(s.labels.data.field("resnum") >= residue_low and
s.labels.data.field("resnum") <= residue_high) ]
protein = s.labels.findatoms(name="SPCE", field="resname")
# Find alpha carbons, add them all to a set. This is what we align by
alpha_carbons = s.labels.findatoms(name="CA", field="atomtype")
atomset = sets.Set()
atomset |= protein # union update
atomset &= alpha_carbons # intersection update
atomset &= residues
atoms_to_align_by = list(atomset)
# Find all atoms in the residues. Then find all hydrogens, and remove
# the hydrogens from the set
# residues has been defined above
hydrogens = s.labels.findatoms(name="H", field="atomtype")
atomset = sets.Set()
atomset |= protein
atomset &= residues
atomset -= hydrogens
atoms_to_msd = list(atomset)
# Set up our aligned cord, now
#atomlist = range(cord.natoms)
#atoms_to_align_by = atomlist
#atoms_to_msd = atomlist
aligned_cord = mp3.aligncord()
aligned_cord.setcord(s.cord)
aligned_cord.setatoms( atoms_to_align_by )
aligned_cord.init()
s.cord = aligned_cord
msd = Msder(cord=s.cord, window=5, atomlist=atoms_to_msd )
print "beginning correlation"
msd.do_n_msd(5)
print msd.msd()
# Here is some argument parsing, but "optparse" (standard library in 2.3)
# is FAR better.
#
if len(sys.argv) < 3: # do we have enough arguments?
print "%s dcdname pdbname" % sys.argv[0] # usage syntax
dcdname = sys.argv[1] # get the file names
psfname = sys.argv[2]
# I always have trouble thinking of what the names will be.
# "mols" means "the molecules" we want to analyze
mols = mp3.system() # set up the system here
mols.labels.getfrompsf(psfname) # This opens the file, reads it in, closes it
mols.cord = mp3.dcd() # mols.dcd isn't automatically there
# because there can be different types of "containers"
# for it
mols.cord.setfile(dcdname) # Tells it where we are going to be reading from.
# You -no longer- need to call mols.cord.init()
group_of_interest = "OSPC"
print "Seaching for %s groups"%group_of_interest
print '---'
# find out which atoms we want to analyze
atoms_to_analyze = [] # a list to store them in
for i in xrange(0,mols.cord.natoms): # loop over all atoms...