def get_origin_translation(asu_prmtop_file_name, asu_rst7_file_name): rst7 = raf.rst7(asu_rst7_file_name) coords = rst7.Get_Coords() UCbox = rst7.Get_Box() u,invu = raf.CompXfrm(UCbox) masses = raf.prmtop(asu_prmtop_file_name).Get_Masses() com = raf.COM(coords,masses) frac_com = dot(u, com) origin_translation = array([0.5, 0.5, 0.5]) - frac_com return u, origin_translation
def get_origin_translation(asu_prmtop_file_name, asu_rst7_file_name):
rst7 = raf.rst7(asu_rst7_file_name)
coords = rst7.Get_Coords()
UCbox = rst7.Get_Box()
u, invu = raf.CompXfrm(UCbox)
masses = raf.prmtop(asu_prmtop_file_name).Get_Masses()
com = raf.COM(coords, masses)
frac_com = dot(u, com)
origin_translation = array([0.5, 0.5, 0.5]) - frac_com
return u, origin_translation
#! /usr/bin/env python
import ReadAmberFiles as raf
iprmtop=raf.prmtop('/net/casegroup2/u2/pjanowsk/Case/4lzt/4lzt_ff12SB/4lztSh_new.prmtop')
masses=iprmtop.Get_Masses()
totalmass=sum(masses)
irst7=raf.rst7('/net/casegroup2/u2/pjanowsk/Case/4lzt/4lzt_ff12SB/4lztSh.rst7')
box=irst7.Get_Box()
volume=raf.Get_volume(box)
density= totalmass/volume*10/6.022
print "density: %8.3f g/cm^3" %density
#mass-weighted covariance matrix is already calculated
cv=genfromtxt('mwcvmat.dat')
l,v=linalg.eig(cv)
s=argsort(l)[::-1]
#convert eigenvalues to frequencies in cm-1
f=zeros((nmodes))
for i in range(len(l)):
if l[i]<0: f[i]= -108.587*sqrt(-0.6/l[i])
elif l[i]>0: f[i]= 108.587*sqrt(0.6/l[i])
else: f[i]=0
l[s]
v[:,s] #sort columns
#get masses and un-mass weigh the modes
m=raf.prmtop("na.prmtop").Get_Masses()
m=[[i]*3 for i in m]
m=[item for sublist in m for item in sublist]
for vec in range(v.shape[1]):
v[:,vec]=v[:,vec]/sqrt(m)
#calculate rmsf fluctuations along modes
CNST=2.776904e-11 #tkbc2*avogadro's
CONT=1.591549e+07 #(ang/cm / 2pi)
for atom in range(natoms):
sum, sumx, sumy, sumz=0,0,0,0
for mode in range(nmodes):
# mass aligns with the experimental center of mass. #
# #
#======================================================================#
parser = argparse.ArgumentParser()
parser.add_argument("-p", "--AsuTopology", help="Amber single ASU topology file")
parser.add_argument("-pdb", "--AsuPDB", help="Single ASU PDB file")
parser.add_argument("-pdbs", "--PdbWithSymmetry", help="PDB file containing SMTRY and CRYST1 records")
parser.add_argument("-prop", help="Propagation used to create the supercell. Format: \"x y z\"")
args = parser.parse_args()
############################################
# SETUP #
############################################
topo = raf.prmtop(args.AsuTopology)
pdb = raf.pdb(args.AsuPDB)
masses=topo.Get_Masses()
xtal_com=raf.COM(pdb.Get_Coords(),masses)
ix=int(args.prop.split()[0])
iy=int(args.prop.split()[1])
iz=int(args.prop.split()[2])
pdbs = raf.pdb(args.PdbWithSymmetry)
smtry,tr =pdbs.Get_SMTRY()
asymunits=len(smtry)
###########################################
# MAIN #
###########################################
i=1 #counter for the names of the unitcell trajectories
def GenNM(obj, nmids, mode, inp=None, amp=50., nframes=20, dump_file=False, \
prmtop=None):
nmids=[int(i) for i in nmids.split()]
amp = float(amp)
nframes=int(nframes)
mode=int(mode)
stored.NMA = {}
stored.NMA[obj] = {}
if mode==1:
if not inp:
print "Please specify cpptraj covariance matrix file"
return 0
if (not prmtop):
print "Please specify prmtop file for proper mass reweighing of vectors."
return 0
print "Attempting to read mwcov matrix %s" %inp
mwcvmat=genfromtxt(inp)
print "Diagonalizing covariance matrix."
w,v = linalg.eig(mwcvmat)
#sort from largest eigenvvalue to smallest
si=argsort(w)[::-1]
w=w[si]
v=v[:,si]
#convert to cm-1
for i in range(len(w)):
if w[i]<0: w[i]= -108.587*sqrt(-0.6/w[i])
elif w[i]>0: w[i]= 108.587*sqrt(0.6/w[i])
else: w[i]=0
#get masses and un-mass weigh the modes
m=raf.prmtop(prmtop).Get_Masses()
m=[[i]*3 for i in m]
m=[item for sublist in m for item in sublist]
for vec in range(v.shape[1]):
v[:,vec]=v[:,vec]/sqrt(m)
#store
stored.NMA[obj]['w'] = w
stored.NMA[obj]['v'] = v
elif mode==2:
if not inp:
print "Please specify evecs frequency/eigenvector file"
return 0
print "Attempting to read evecs file %s" %inp
stored.NMA[obj]['w'], stored.NMA[obj]['v'] = ReadEvecs(inp)
elif mode==3:
if not inp:
print "Please specify pickled normal mode object"
return 0
print "Attempting to read pickle file %s" %inp
stored.NMA[obj]=pickle.load( open(inp,"rb"))
if dump_file:
print "Dumping eigenvalues and modes to pickle file."
pickle.dump(stored.NMA[obj], open(dump_file,"wb") )
w = stored.NMA[obj]['w']
v = stored.NMA[obj]['v']
print "%7s%20s%20s" % ('NMID', 'f Hz', 'f cm^-1')
for i in range(min(w.size,20)):
print "%7d%20.5e\t%20.5f" % (i, w[i]*2.99792458e10, w[i]),
if i in nmids:
print "*"
else:
print ""
for nmid in nmids:
newobj = "%s-nm_%d" % (obj, nmid)
cmd.delete(newobj)
nm = real(v[:,nmid])
nm *= amp/sqrt((nm**2).sum())
for ifr in range(nframes):
cmd.create(newobj, obj, 1, ifr+1)
stored.nm = nm*sin(2.*pi*ifr/nframes)
cmd.alter_state(ifr+1, newobj, "x,y,z = x+stored.nm[(ID-1)*3], y+stored.nm[(ID-1)*3+1], z+stored.nm[(ID-1)*3+2]")
