def main():
if len(sys.argv) != 7: # if no input
print "ERORR:"
print "syntex: dx-combine_grids.py gist-Eww-dens.dx 1 gist-gO.dx 1 0.0 temp"
print "v[i] = w1*v1[i] + w2*v2[i] + c3"
return
infile1 = sys.argv[1]
weight1 = float(sys.argv[2])
infile2 = sys.argv[3]
weight2 = float(sys.argv[4])
const3 = float(sys.argv[5])
outfile = sys.argv[6]
xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1 = dxlib.read_in_dx_file(
infile1)
xn2, yn2, zn2, dx2, dy2, dz2, origin2, values2 = dxlib.read_in_dx_file(
infile2)
new_values = dxlib.combine_values(outfile + '.dat', xn1, yn1, zn1, dx1,
dy1, dz1, origin1, values1, weight1, xn2,
yn2, zn2, dx2, dy2, dz2, origin2,
values2, weight2, const3)
dxlib.write_out_dx_file(outfile + '.dx', xn1, yn1, zn1, dx1, dy1, dz1,
origin1, new_values)
def main():
if len(sys.argv) != 4: # if no input
print "ERORR:"
print "this script caluculates the difference grid and the second norm over the grid. "
print "syntex: dx-compare_2norm.py gist-Eww-dens.dx gist-gO.dx diff_grid"
return
infile1 = sys.argv[1]
infile2 = sys.argv[2]
outfile = sys.argv[3]
weight1 = 1
weight2 = -1
const3 = 0
xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1 = dxlib.read_in_dx_file(
infile1)
xn2, yn2, zn2, dx2, dy2, dz2, origin2, values2 = dxlib.read_in_dx_file(
infile2)
# caluclate the differents grid
new_values = dxlib.combine_values(outfile + '.dat', xn1, yn1, zn1, dx1,
dy1, dz1, origin1, values1, weight1, xn2,
yn2, zn2, dx2, dy2, dz2, origin2,
values2, weight2, const3)
dxlib.write_out_dx_file(outfile + '.dx', xn1, yn1, zn1, dx1, dy1, dz1,
origin1, new_values)
norm = square_root_sum_of_squares(new_values)
print "norm = ", norm
def main():
if len(sys.argv) != 4: # if no input
print "ERORR:"
print "syntex: dx-gist_precalculate_sphere.py infile sphradius outfileprefix"
return
infile1 = sys.argv[1]
sphradius = float(sys.argv[2])
outfile = sys.argv[3]
print infile1
print sphradius
print outfile
#exit()
xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1 = dxlib.read_in_dx_file(
infile1)
write_pdb_threshold(outfile + 'old.pdb', xn1, yn1, zn1, values1, origin1,
dx1, dy1, dz1)
new_xn, new_yn, new_zn, new_origin, nvalues = pre_compute(
outfile + '.dat', xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1,
sphradius)
dxlib.write_out_dx_file(outfile + '.dx', new_xn, new_yn, new_zn, dx1, dy1,
dz1, new_origin, nvalues)
write_pdb_threshold(outfile + 'new.pdb', new_xn, new_yn, new_zn, nvalues,
new_origin, dx1, dy1, dz1)
def main():
if len(sys.argv) != 6: # if no input
print "ERORR:"
print "syntex: dx-gist_precalculate_sphere.py infile sphradius divider pad_radius outfileprefix"
return
infile1 = sys.argv[1]
sphradius = float(sys.argv[2])
divider = float(sys.argv[3])
pad_radius = float(sys.argv[4])
outfile = sys.argv[5]
if (pad_radius < sphradius):
print "warning pap_radius (%f) is less than sphradius (%f).\n" % (
pad_radius, sphradius)
print "This might cause boundary problems.\n"
print infile1
print sphradius
print outfile
#exit()
xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1 = dxlib.read_in_dx_file(
infile1)
#write_pdb_threshold(outfile+'old.pdb',xn1,yn1,zn1,values1,origin1,dx1,dy1,dz1)
new_xn, new_yn, new_zn, new_origin, nvalues = pre_compute(
outfile + '.dat', xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1,
sphradius, divider, pad_radius)
dxlib.write_out_dx_file(outfile + '.dx', new_xn, new_yn, new_zn, dx1, dy1,
dz1, new_origin, nvalues)
def main():
if len(sys.argv) != 6: # if no input
print "ERORR:"
print "syntex: dx-gist_make_centers.py dx-input-file sign cutoff distint pdb-output-file"
print "sign can be 1 or -1: if one should always be used for densities,"
print " for energies, weight of one means pdb contains cordenates where "
print " waters do not want to be(anti-waters)."
print " for energies, weight of negative one means pdb contains cordenates "
print " where waters do want to be (negative energies)."
print "cutoff can only be a positive floating point number. "
print " this point is used to deterint clusters of points"
print "distint howmeny grid points away considered conected. should be 1 (0.5 angstroms) or 2(1.0 A), 3 (1.5 A)"
print "dx-input-file input file in dx formate produed by gist, may be disities or energies"
print "pdb-output-file is an output file in pdb formate contains the weighted mean poition of clusters"
return
infile1 = sys.argv[1]
sign = float(sys.argv[2])
threshold = float(sys.argv[3])
dist = int(sys.argv[4])
outfile = sys.argv[5]
xn,yn,zn,dx,dy,dz,origin,values = dxlib.read_in_dx_file(infile1)
gridscale = dx # assumes that they are all the same spaceing
make_centers(outfile,values,gridscale,xn,yn,zn,origin, sign, threshold, dist)
def main():
if len(sys.argv) != 3: # if no input
print "ERORR:"
print "syntex: dx-gist_rescore.py dx-file sphere_file"
print "dx-input-file input file in dx formate produed by gist, may be disities or energies"
print "sphere file that defines the binding site (low dielectric sphere recomended) "
return
infiledx = sys.argv[1]
infilesph = sys.argv[2]
prefixdx = extract_fileprefix_from_path(infiledx)
prefixsph = extract_fileprefix_from_path(infilesph)
outfile = "site_energetics_dx-"+prefixdx+"sph-"+prefixsph
print infiledx
print infilesph
xn,yn,zn,dx,dy,dz,origin,values = dxlib.read_in_dx_file(infiledx)
gridscale = dx # assumes that they are all the same spaceing
print gridscale ,xn,yn,zn,dx,dy,dz,origin
sphs = sph_lib.read_sph(infilesph,'A','A')
file1 = open(outfile+'gist_values.txt','w')
new_values, atom_energies = calc_score(outfile+'.txt',values,gridscale,xn,yn,zn,origin, sphs, file1, True)
dxlib.write_out_dx_file(outfile+'.dx',xn,yn,zn,dx,dy,dz,origin,new_values)
convert_sph_to_pdb_and_write(sphs,atom_energies,outfile+'.pdb')
file1.close()
def main():
if len(sys.argv) != 5: # if no input
print "ERORR:"
print "syntex: dx-divide_grids.py gist-Eww-dens.dx gist-gO.dx 0.0329 temp"
print "v[i] = v1[i] / (w2*v2[i]) "
return
infile1 = sys.argv[1]
infile2 = sys.argv[2]
weight2 = float(sys.argv[3])
outfile = sys.argv[4]
xn1,yn1,zn1,dx1,dy1,dz1,origin1,values1 = dx.read_in_dx_file(infile1)
xn2,yn2,zn2,dx2,dy2,dz2,origin2,values2 = dx.read_in_dx_file(infile2)
new_values = dx.divide_energy_density(outfile+'.dat',xn1,yn1,zn1,dx1,dy1,dz1,origin1,values1,xn2,yn2,zn2,dx2,dy2,dz2,origin2,values2,weight2)
dx.write_out_dx_file(outfile+'.dx',xn1,yn1,zn1,dx1,dy1,dz1,origin1,new_values)
def main():
if len(sys.argv) != 5: # if no input
print "ERORR:"
print "syntex: dx-combine_grids.py gist-Eww-dens.dx gist-gO.dx 10.0 temp"
print "v[i] = {v1[i], if v2[i]>t or 0, if v2[i]<t"
print "v1 is energey, v2 is the density, t is the threshold that must be exceded."
return
infile1 = sys.argv[1] # gist energy
infile2 = sys.argv[2] # density
threshold = float(sys.argv[3]) # density threshold
outfile = sys.argv[4]
xn1,yn1,zn1,dx1,dy1,dz1,origin1,values1 = dxlib.read_in_dx_file(infile1)
xn2,yn2,zn2,dx2,dy2,dz2,origin2,values2 = dxlib.read_in_dx_file(infile2)
new_values = dxlib.combine_values_density_threshold(outfile+'.dat',xn1,yn1,zn1,dx1,dy1,dz1,origin1,values1,xn2,yn2,zn2,dx2,dy2,dz2,origin2,values2,threshold)
dxlib.write_out_dx_file(outfile+'.dx',xn1,yn1,zn1,dx1,dy1,dz1,origin1,new_values)
def main():
if len(sys.argv) != 5: # if no input
print "ERORR:"
print "syntex: dx-gist_rescore.py dx-file mol2"
print "dx-input-file input file in dx formate produed by gist, may be disities or energies"
print "mol2 containing docked poses. "
print "Hchoice [0(use standard radius), 1 (use 0.8 for nonpolar H, instead of 1.540), or 2 (ignore H)]"
print "radius_pad : if a value of 8.0 is given then 8 angstroms is added to all atom radii"
return
infiledx = sys.argv[1]
infilemol2 = sys.argv[2]
Hchoice = int(sys.argv[3])
pad = float(sys.argv[4])
outfile = "out"
print infiledx
print infilemol2
DOCKpath = os.getenv('DOCKBASE')
print(DOCKpath)
vdwdict = intialize_vdw_parm(DOCKpath +
'/proteins/defaults/vdw.parms.amb.mindock')
#vdwdict = intialize_vdw_parm('/nfs/home/tbalius/zzz.github/DOCK/proteins/defaults/vdw.parms.amb.mindock')
xn, yn, zn, dx, dy, dz, origin, values = dxlib.read_in_dx_file(infiledx)
gridscale = dx # assumes that they are all the same spaceing
mols = mol2.read_Mol2_file(infilemol2)
file1 = open(outfile + 'gist_values.txt', 'w')
N = len(mols)
count = 0
for mol in mols:
new_values = calc_score(outfile, values, gridscale, xn, yn, zn, origin,
mol, vdwdict, file1, (N < 3), Hchoice, pad)
if N < 3: # only print gist grids if there are a few poses in the mol2 file
print "writting gist grid for overlap with ligand . . ."
dxlib.write_out_dx_file(outfile + str(count) + "new_gist.dx", xn,
yn, zn, dx, dy, dz, origin, new_values)
count = count + 1
#exit()
file1.close()
def main():
if len(sys.argv) != 4: # if no input
print "ERORR:"
print "syntex: dx-gist_extreme.py dx-input-file cutoff pdb-output-file"
print "cutoff can only be a positive floating point number. "
print " this point is used to deterint clusters of points"
print "dx-input-file input file in dx formate produed by gist, may be disities or energies"
print "pdb-output-file is an output file in pdb formate contains the weighted mean poition of clusters"
return
infile1 = sys.argv[1]
threshold = float(sys.argv[2])
outfile = sys.argv[3]
xn, yn, zn, dx, dy, dz, origin, values = dxlib.read_in_dx_file(infile1)
gridscale = dx # assumes that they are all the same spaceing
get_extreme(outfile, values, gridscale, xn, yn, zn, origin, threshold)
def main():
if len(sys.argv) != 4: # if no input
print "ERORR:"
print "syntex: dx-gist_make_courser.py gist-Eww-dens.dx 1 temp"
#print "syntex: dx-combine_grids.py gist-Eww-dens.dx 3 temp"
print " "
return
infile1 = sys.argv[1]
number = int(sys.argv[2])
outfile = sys.argv[3]
xn,yn,zn,dx,dy,dz,origin,values = dxlib.read_in_dx_file(infile1)
gridscale = dx # assumes that they are all the same spaceing
xnew,ynew,znew,origin_new,gridscale_new,values_new = dxlib.make_courser(outfile+'.dat',values,gridscale,xn,yn,zn,origin,number)
dxlib.write_out_dx_file(outfile+'.dx',xnew,ynew,znew,gridscale_new,gridscale_new,gridscale_new,origin_new,values_new)
def main():
if len(sys.argv) != 4: # if no input
print "ERORR:"
print "syntex: dx-remove_extrema.py gistvalues.dx 5.0 gistvalues_cap"
print "vnew[i] = {-t1, if v[i] <= -t1 "
print " t1, if v[i] >= t1 "
print " v[i] otherwise "
return
infile1 = sys.argv[1] # gist energy
t1 = float(sys.argv[2]) # energy threshold
outfile = sys.argv[3]
xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1 = dxlib.read_in_dx_file(
infile1)
new_values = []
countn = 0
countp = 0
for val in values1:
if (val < -1.0 * t1):
val = -1.0 * t1
countn = countn + 1
elif (val > 1.0 * t1):
val = 1.0 * t1
countp = countp + 1
#else:
new_values.append(val)
print "%d number of point are caped in positive direction" % countp
print "%d number of point are caped in negative direction" % countn
#new_values = combine_values_density_threshold(outfile+'.dat',xn1,yn1,zn1,dx1,dy1,dz1,origin1,values1,xn2,yn2,zn2,dx2,dy2,dz2,origin2,values2,threshold)
dxlib.write_out_dx_file(outfile + '.dx', xn1, yn1, zn1, dx1, dy1, dz1,
origin1, new_values)
def main():
if len(sys.argv) != 7: # if no input
print "ERORR:"
print "syntex: dx-histogram.py gistvalues.dx min max num output [vyes,vno]"
return
infile1 = sys.argv[1] # gist energy
minv = float(sys.argv[2]) # energy threshold
maxv = float(sys.argv[3])
num = int(sys.argv[4])
output = sys.argv[5]
verbose = sys.argv[6]
#threshold = sys.argv[7]
threshold = 3.0
if verbose == "vyes":
boolverbose = True
elif verbose == "vno":
boolverbose = False
else:
print "error: must be vyes,vno"
xn1, yn1, zn1, dx1, dy1, dz1, origin1, values1 = dxlib.read_in_dx_file(
infile1)
histogram = []
histogram_t = [] # trunc histogram
histogram_nz = [] # histogram without zero values counted
midbins = []
step = (maxv - minv) / float(num)
print "infile = %s" % infile1
print "minv = %f\nmaxv = %f\n num = %d\n step = %f\n" % (minv, maxv, num,
step)
midbin = minv + step / 2.0
for i in range(0, num):
histogram.append(0)
histogram_t.append(0)
histogram_nz.append(0)
if midbin > maxv:
print "error"
exit()
midbins.append(midbin)
midbin = midbin + step
countn = 0
countp = 0
min_ov = 1000 # minimum observed value
max_ov = -1000 # maximum observed value
ip3 = int(round((+3.0 - minv) / (maxv - minv) *
(num - 1))) # value of index for value of +3.0
in3 = int(round((-3.0 - minv) / (maxv - minv) *
(num - 1))) # value of index for value of -3.0
for val in values1:
if (val < minv):
countn = countn + 1
continue
if (val > maxv):
countp = countp + 1
continue
i = int(round((val - minv) / (maxv - minv) * (num - 1)))
if boolverbose:
print "%f->%d->%f" % (val, i, midbins[i])
histogram[i] = histogram[i] + 1
if val != 0.0:
histogram_nz[i] = histogram_nz[i] + 1
if val <= threshold and val >= -1.0 * threshold:
histogram_t[i] = histogram_t[i] + 1
elif (val > threshold):
histogram_t[ip3] = histogram_t[ip3] + 1
elif (val < -1.0 * threshold):
histogram_t[in3] = histogram_t[in3] + 1
fh = open(output, 'w')
for i in range(0, num):
print "%f, %d,%d,%d" % (midbins[i], histogram[i], histogram_nz[i],
histogram_t[i])
fh.write("%f,%d,%d,%d\n" %
(midbins[i], histogram[i], histogram_nz[i], histogram_t[i]))
print "number less than min: %d\nnumber grater than max: %d" % (countn,
countp)