def read_enestruc(datfile):
header,structures = read_struc(datfile)
structures = list(structures)
energies = []
for l1,l2 in structures:
for ll in l1:
if ll.startswith("## Energy:"):
ee = ll[10:].strip()
if ee.startswith("nan"):
e = 99999999999999
else:
e = float(ee)
energies.append(e)
energies4 = energies[:4]
energy = sum(energies4)/len(energies4)
return header, energy, energies, structures
raise Exception(
"Please supply an even number of PDB files (unbound, bound)")
unboundfiles = []
boundfiles = []
for n in range(2, len(sys.argv), 2):
unboundfiles.append(sys.argv[n])
boundfiles.append(sys.argv[n + 1])
if len(boundfiles) == 1 and opt_allresidues == False:
raise Exception("Cannot determine the interface for a single PDB")
bounds = [rmsdlib.read_pdb(f) for f in boundfiles]
unbounds = [rmsdlib.read_pdb(f) for f in unboundfiles]
struc_header, structures = read_struc(sys.argv[1])
pivots = []
for hnr, h in enumerate(struc_header):
if not h.startswith("#pivot"): continue
hh = h.split()
assert len(hh) == 5 and hh[1] == str(hnr + 1), h
pivot = numpy.array([float(v) for v in hh[2:5]])
pivots.append(pivot)
initargs = [sys.argv[1]] + unboundfiles
if modefile: initargs += ["--modes", modefile]
if imodefile: initargs += ["--imodes", imodefile]
for nr, ensfile in ensfiles:
initargs += ["--ens", nr, ensfile]
collectlib.collect_init(initargs)
allboundatoms = []
boundatoms = []
for p in bounds:
b = []
for c in p.coordinates():
allboundatoms.append(c)
b.append(c)
boundatoms.append(numpy.array(b))
allboundatoms = numpy.array(allboundatoms)
nstruc = 0
f1 = sys.stdout
if output is not None:
f1 = open(output, 'w')
h, strucs = read_struc(sys.argv[1])
while 1:
sys.stdout.flush()
if name is not None:
newargs = initargs + [
'--imodes', 'flexm-' + str(nstruc + 1) + name + '.dat'
]
if not os.path.exists('flexm-' + str(nstruc + 1) + name + '.dat'):
break
collectlib.collect_iattract(newargs)
result = collectlib.collect_next()
if result: break
nstruc += 1
l1, l2 = strucs.next()
sys.exit()
if score:
for n in range(nrsplit):
fnam = "%s-%d" % (sys.argv[1], n + 1)
for l in open(fnam).readlines():
assert not l.startswith("#") #must be .score file, not .dat file!!
print l,
sys.exit()
allstructures = {}
maxstruc = 0
stnr = 0
for n in range(nrsplit):
fnam = "%s-%d" % (sys.argv[1], n + 1)
header0, structures = read_struc(fnam)
if n == 0:
for h in header0:
print h
currstruc = None
currstruc_false = False
for s in structures:
stnr += 1
l1, l2 = s
print "#" + str(stnr)
skipline = -1
for lnr, l in enumerate(l1):
if l.startswith("### SPLIT "):
try:
currstruc = int(l[len("### SPLIT"):])
except:
def write_clustfile(clust, clustfile):
cf = open(clustfile, "w")
for cnr, c in enumerate(clust):
print >> cf, "Cluster %d ->" % (cnr + 1),
for cc in c:
print >> cf, cc,
print >> cf, ""
rootclusters = read_clustfile(clustfile)
tmpfd, tmpnam = tempfile.mkstemp(text=True)
tmpf = os.fdopen(tmpfd, "w")
try:
header, structures = read_struc(datfile)
structures = list(structures)
for h in header:
print >> tmpf, h
snr = 0
for c in rootclusters:
for cc in c:
snr += 1
print >> tmpf, "#%d" % snr
s1, s2 = structures[cc - 1]
for l in s2:
print >> tmpf, l
tmpf.close()
assert snr == sum([len(c) for c in rootclusters
]), (snr, sum([len(c) for c in rootclusters]))
CLUST_MARGIN = 2 #2 is the theoretical worse case; change to 9999 to disable all effects of clustering
#CLUST_MARGIN = 9999
chicutoff = float(sys.argv[1])
chicutoffmin = chicutoff - 1.0
max_rmsd = float(sys.argv[2])
maxstruc = int(sys.argv[3])
max_msd = max_rmsd**2
maxclusterlevel = CLUSTERING.index(max_rmsd)
coor_structures = sys.argv[4]
coor_clusters = sys.argv[5]
chi_structures = sys.argv[6]
chi_clusters_filename = sys.argv[7]
dat_structures = sys.argv[8]
dat_clusters_filename = sys.argv[9]
header_structures, dof_structures = read_struc(dat_structures)
header_clusters, dof_clusters = read_struc(dat_clusters_filename)
dof_structures = list(dof_structures)
dof_clusters = list(dof_clusters)
coor_structures = np.load(coor_structures)
coor_clusters = np.load(coor_clusters)
chi_structures = np.load(chi_structures)
chi_clusters = np.load(chi_clusters_filename)
for a in coor_clusters, coor_structures:
assert len(a.shape) == 2 and a.shape[1] % 3 == 0, a.shape
arr = [coor_structures, coor_clusters]
nstruc = []
for anr, a in enumerate(arr):
ncoor = a.shape[1] / 3
arr[anr] = a.reshape(a.shape[0], ncoor, 3)
#replaces ligand N in .dat file 1 with ligand N in .dat file 2. .dat file 2 must contain a single structure
import sys
from math import *
from _read_struc import read_struc
import itertools
ligand = int(sys.argv[1])
header, structures2 = read_struc(sys.argv[3])
structures2 = list(structures2)
assert len(structures2) == 1, sys.argv[3]
other = structures2[0]
assert ligand <= len(other[1])
header, structures = read_struc(sys.argv[2])
stnr = 0
for h in header:
print h
for s in structures:
assert len(s[1]) == len(other[1])
stnr += 1
print "#" + str(stnr)
for l in s[0]:
print l
for vnr, v in enumerate(s[1]):
if vnr + 1 == ligand:
print other[1][vnr]
else:
print s[1][vnr]
start = 0
if options.fix_receptor: start = 1
dori = options.ori
dtrans = options.trans
dmode = options.mode
clone = options.clone
keepfirst = options.keepfirst
random.seed(options.seed)
import sys
from _read_struc import read_struc
import random
from math import *
header, structures = read_struc(args[0])
for h in header:
print h
stnr = 0
for s in structures:
clonenr = 0
while 1:
stnr += 1
l1, l2 = s
l1, l2 = list(l1), list(l2) #copy
for lnr in range(start, len(l2)):
l = l2[lnr]
values = [float(v) for v in l.split()]
is_morph, is_ens = False, False
if lnr + 1 in morph: is_morph = True
