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
def center_frac_coords(frac_crds, parm, s, e):
coords = frac_crds[s:e, :]
masses = parm.parm_data['MASS'][s:e]
com = raf.COM(coords, masses)
shift = array([0.5, 0.5, 0.5]) - com
cntred_frac_crds = frac_crds + shift
return cntred_frac_crds
def run(nmodes, ipdb_name, ievecs_name, ofile_name):
#Get info from pdb
ipdb=raf.pdb(ipdb_name)
name=ipdb_name.rstrip('.pdb')
atomnames=ipdb.Get_AtomNames()
resnames=ipdb.Get_ResidueNames()
resids=ipdb.Get_ResidueNumbers()
bfactors=ipdb.Get_Bfactors()
coordinates=ipdb.Get_Coords()
#Write info from pdb to nmd file
ofile=open(ofile_name, 'w')
ofile.write('nmwiz_load %s\n' %ofile_name)
print('name %s' %name, file=ofile)
print('atomnames ', end="",file=ofile)
print (*atomnames, file=ofile)
print('resnames ', end="",file=ofile)
print (*resnames, file=ofile)
print('resids ', end="",file=ofile)
print (*resids, file=ofile)
print('bfactors ', end="",file=ofile)
print (*bfactors, file=ofile)
print('coordinates ', end="", file=ofile)
print(*["%8.3f " %xyz for atom in coordinates for xyz in atom], end="", file=ofile)
#This would've been the python2.x way of doing it:
#~ for atom in coordinates:
#~ for coordinate in atom:
#~ ofile.write("%8.3f " %coordinate)
print ('', file=ofile)
#Get modes from evecs file and write to nmd file
vecfile=open(ievecs_name, 'r')
line=''
while line[0:5]!=' ****':
line=vecfile.readline()
for i in range(nmodes):
mode_number, freq=vecfile.readline().strip().split()
assert int(mode_number)== i+1
mode=[]
line=vecfile.readline()
while line[0:5]!=' ****':
for i in line.strip().split():
mode.append(float(i))
line=vecfile.readline()
amplitude=(1/float(freq))
print('mode %2d %12.10f ' %(int(mode_number), amplitude), end="", file=ofile)
print(*["%12.5f " %fluc for fluc in mode], end="", file=ofile)
print ('', file=ofile)
vecfile.close()
#! /usr/bin/python
import ReadAmberFiles as raf
apdb=raf.pdb('vAla3_minimized.pdb')
box=apdb.Get_Box()
coords=apdb.Get_Coords()
natoms=natoms= len(apdb.ATOMlines)
raf.printrst7(coords, box, natoms, 'vAla3_minimized.rst7', comment='rst7 written by pawel')
Rf = zeros((numops, 3, 3))
Tf = zeros((numops, 3))
op = 0
for line in symops.splitlines():
line = line.split('\'')[-1].split()
for i in range(3):
for j in range(3):
Rf[op][i][j] = line[i * 3 + j + 1]
try:
Tf[op][i] = float(line[((i * 2) - 1 + 11)]) / float(line[(
(i * 2) + 11)])
except ZeroDivisionError:
Tf[op][i] = 0.0
op += 1
pdbf = raf.pdb(pdbfile)
box = pdbf.Get_Box()
u, invu = raf.CompXfrm(box)
print "================================"
Tc = zeros(shape(Tf))
for i in range(numops):
Tc[i] = dot(invu, Tf[i]).astype(float32)
#~ print Tc
print "================================"
Rc = zeros(shape(Rf))
for i in range(numops):
Rc[i] = dot(dot(invu, Rf[i]), u)
#~ print Rc
print "================================"
#! /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
numops=len(symops.splitlines())
Rf=zeros((numops,3,3))
Tf=zeros((numops,3))
op=0
for line in symops.splitlines():
line=line.split('\'')[-1].split()
for i in range(3):
for j in range(3):
Rf[op][i][j]=line[i*3+j+1]
try:
Tf[op][i]=float(line[((i*2)-1+11)])/float(line[((i*2)+11)])
except ZeroDivisionError:
Tf[op][i]=0.0
op+=1
pdbf=raf.pdb(pdbfile)
box=pdbf.Get_Box()
print box, type(box)
u,invu=raf.CompXfrm(box)
print "================================"
Tc=zeros(shape(Tf))
for i in range(numops):
Tc[i]=dot(invu,Tf[i]).astype(float32)
#~ print Tc
print "================================"
Rc=zeros(shape(Rf))
for i in range(numops):
Rc[i]=dot(dot(invu,Rf[i]),u)
def NAsu(pdbfile_name):
pdbfile = RAF.pdb(pdbfile_name)
smtry, tr = pdbfile.Get_SMTRY()
n_asu = len(smtry)
return n_asu
#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):
#~ if line.strip():
#~ fails.append( line.strip().split('/')[0] )
fails=['1a21', '1a8v', '1ba7', '1c03', '1dvm', '1ezs', '1f3u', '1fc3',
'1fh5', '1jxo', '1ofp', '1oy3', '1q32', '1q4o', '1r19', '1r1z',
'1r52', '1rzi', '1t0j', '1tee', '1tks', '1tw9', '1tzo', '1vh0',
'1vr4', '1w3b', '1wp7', '1wp8', '1x13']
dirs=[ name for name in os.listdir('.') if os.path.isdir(name) and name[0]=='1' ]
bad=[]
good=[]
for dir in dirs:
if dir in fails:
print dir
trst=raf.rst7('%s/%s.rst7' %(dir,dir))
box=trst.Get_Box()
bad.append( raf.Get_volume(box) )
else:
print dir
trst=raf.rst7('%s/%s.rst7' %(dir,dir))
box=trst.Get_Box()
good.append( raf.Get_volume(box) )
print "BAD: mean %1.0f\n" %(np.mean(bad))
for v in bad:
print "%d\n" %v
print "\n"
print "GOOD: mean %1.0f\n" %(np.mean(good))
#! /usr/bin/python
import ReadAmberFiles as raf
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("pdbfile", help="name of pdb file")
args = parser.parse_args()
pdb = raf.pdb(args.pdbfile)
box = pdb.Get_Box()
print(" %7.3f %7.3f %7.3f %7.3f %7.3f %7.3f " % (box[0], box[1], box[2], box[3], box[4], box[5]))
# 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
fails = [
'1a21', '1a8v', '1ba7', '1c03', '1dvm', '1ezs', '1f3u', '1fc3', '1fh5',
'1jxo', '1ofp', '1oy3', '1q32', '1q4o', '1r19', '1r1z', '1r52', '1rzi',
'1t0j', '1tee', '1tks', '1tw9', '1tzo', '1vh0', '1vr4', '1w3b', '1wp7',
'1wp8', '1x13'
]
dirs = [
name for name in os.listdir('.') if os.path.isdir(name) and name[0] == '1'
]
bad = []
good = []
for dir in dirs:
if dir in fails:
print dir
trst = raf.rst7('%s/%s.rst7' % (dir, dir))
box = trst.Get_Box()
bad.append(raf.Get_volume(box))
else:
print dir
trst = raf.rst7('%s/%s.rst7' % (dir, dir))
box = trst.Get_Box()
good.append(raf.Get_volume(box))
print "BAD: mean %1.0f\n" % (np.mean(bad))
for v in bad:
print "%d\n" % v
print "\n"
print "GOOD: mean %1.0f\n" % (np.mean(good))
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]")
def get_U_invU(asu_rst7_file_name):
rst7 = Rst7.open(asu_rst7_file_name)
UCbox = rst7.box
U, invU = raf.CompXfrm(UCbox)
return U, invU, UCbox
