def randomSample():
root = 'golden.dat'
if not os.path.exists(root): os.mkdir(root)
def mol2mol_init(ele):
mol = [[i, 0.0, 0.0, 0.0] for i in ele]
return mol
size = 200
folder_id = 0
file_count = 0
confs = calculator.grid._iter_conf()
confs = list(confs)
if len(confs) > 2000:
confs = sample(list(confs), 2000)
for idx, coors in calculator.gen_PDB(confs):
#for id, coors in calculator.gen_atomic_coors(0,10):
#print(idx, coors)
if file_count % size == 0:
folder = os.path.join(root, "EFT_%04d" % (folder_id))
if not os.path.exists(folder): os.mkdir(folder)
folder_id += 1
pdb = open("%s/eft.%s.pdb" % (folder, idx), "w")
pdb.write(coors)
pdb.close()
file_count += 1
def addHydrogensAndBonds(proteinpdbal):
""" takes atom list, writes pdb
runs tleap to add hydrogens and bonds
I order the atoms in the individual residues, because tleap uses oreder that does not work with scream
"""
f = tempfile.NamedTemporaryFile(mode='w', prefix='tmpAmber', dir='.')
f.close()
filename = f.name
al = proteinpdbal
for a in al:
if a.aTag != 'ATOM ':
print 'Warning: addHydrogensAndBonds: will run TLEAP with HETATM entries, so not sure what will happen'
break
pdb.write(filename + '.pdb', al, withConect=False)
with open(filename + '.tleap', 'w') as f:
f.write('source leaprc.ff99SB \n')
f.write('logFile %s.log \n' % filename)
f.write('pdb = loadpdb %s.pdb \n' % filename)
f.write('saveamberparm pdb %s.prmtop %s.inpcrd \n' %
(filename, filename))
f.write('quit \n')
subprocess.call(['tleap', '-f', filename + '.tleap'])
# check if wrong atoms have been added
lines = open(filename + '.log').readlines()
for line in lines:
if line[0:5] == 'FATAL':
sys.exit(
'Error: fatal error in tleap (probably there are some unknown or extra atoms in the pdb)'
)
elif line[0:7] == ' Added':
a = line.split()[-2].split('<')[-1]
if a != 'OXT':
print 'Warning: addHydrogensAndBonds: tleap added more heavy atoms than just OXT: %s in %s ' % (
a, ' '.join(line.split()[4:]))
# read the amber files
al2 = readTopoCord(filename + '.prmtop', filename + '.inpcrd')
rl = residues.makeList(al)
rl2 = residues.makeList(al2)
if len(rl) != len(rl2):
sys.exit(
'Error: addHydrogensAndBonds: the file from tleap has different number of residues %d than the original file %d'
% (len(rl2), len(rl)))
for i, r in enumerate(rl):
rl2[i].chain = r.chain
rl2[i].rNo = r.rNo
rl2[i].updateAtoms()
rl2[i].sort()
al2 = residues.makeAtomList(rl2)
for a in al2:
a.aTag = 'ATOM '
# clean up
os.remove(filename + '.prmtop')
os.remove(filename + '.inpcrd')
os.remove(filename + '.tleap')
os.remove(filename + '.pdb')
os.remove(filename + '.log')
os.remove('leap.log')
return al2
def phase1(self):
ti1=time.clock()
print "Optimizing water positions"
self.optimize()
print "Optimizing organic positions"
self.optimize2()
ti2=time.clock()
print ti2-ti1
print "Preprocessing organic molecules."
self.phase2()
for pdb in self.pdbs:
pdb.write(self.stamp,1)
def phase1(self):
ti1 = time.clock()
print "Optimizing water positions"
self.optimize()
print "Optimizing organic positions"
self.optimize2()
ti2 = time.clock()
print ti2 - ti1
print "Preprocessing organic molecules."
self.phase2()
for pdb in self.pdbs:
pdb.write(self.stamp, 1)
def phase1(self,myid=0):
ti1=time.clock()
print "Optimizing water positions"
self.optimize()
#print "Optimizing organic positions"
#self.optimize2()
"""
sym=symgen.symgen()
print "Preprocessing water molecules."
for w in self.waters:
w['chain']='W'
symm=sym.varpass(w)
flagger=0
for j in symm:
for i in j:
if(len(w.pdb.findneighbor(i,w['res num']))>0):
#print "SYMMETRY"
flagger+=1
t0 = "ATOM 957 O HOH B 1 36.504 -10.582 -2.929 1.00 13.36 A O"
t1 = w['res num']
t2 = w.pdb
temp = Atom(t0, t1, t2)
temp['x'] = i[0]
temp['y'] = i[1]
temp['z'] = i[2]
temp['res num']=w['res num']
#temp['B']=float("%.2d"%flagger)
temp['chain']='S'
w.pdb.append(temp)
"""
ti2=time.clock()
print ti2-ti1
print "Preprocessing organic molecules."
self.phase2()
for pdb in self.pdbs:
pdb.write(self.stamp,999,int(myid))
os.chdir('../../../results/%d'%int(myid))
filenames= os.listdir(os.getcwd())
zf = zipfile.ZipFile('results.zip', 'w', zipfile.ZIP_DEFLATED)
for f in filenames:
zf.write(f)
os.system('rm -rf %s'%f)
zf.close()
return
def typeBondShell(al):
'''runs on shell
this assignes bond order to atom list using openbabel
first pdb is created
then it is read by python openbabel (pybel)
then it is written into bgf
then only the bond orders from the new bgf are used
'''
import os
from pyvasek import mol2
pdb.write('tempMol.pdb', al)
os.system('babel ---errorlevel 2 -ipdb tempMol.pdb -omol2 tempMol.mol2')
al2 = mol2.read('tempMol.mol2')
#
atoms.sortBondsLists(al)
atoms.sortBondsLists(al2)
for i in range(len(al)):
a1 = al[i]
a2 = al2[i]
a1.order = a2.order[:]
def phase1(self):
ti1 = time.clock()
print "Optimizing water positions"
self.optimize()
#print "Optimizing organic positions"
#self.optimize2()
"""
sym=symgen.symgen()
print "Preprocessing water molecules."
for w in self.waters:
w['chain']='W'
symm=sym.varpass(w)
flagger=0
for j in symm:
for i in j:
if(len(w.pdb.findneighbor(i,w['res num']))>0):
#print "SYMMETRY"
flagger+=1
t0 = "ATOM 957 O HOH B 1 36.504 -10.582 -2.929 1.00 13.36 A O"
t1 = w['res num']
t2 = w.pdb
temp = Atom(t0, t1, t2)
temp['x'] = i[0]
temp['y'] = i[1]
temp['z'] = i[2]
temp['res num']=w['res num']
#temp['B']=float("%.2d"%flagger)
temp['chain']='S'
w.pdb.append(temp)
"""
ti2 = time.clock()
print ti2 - ti1
print "Preprocessing organic molecules."
self.phase2()
for pdb in self.pdbs:
pdb.write(self.stamp, 1)
def phase1(self):
ti1=time.clock()
print "Optimizing water positions"
self.optimize()
#print "Optimizing organic positions"
#self.optimize2()
"""
sym=symgen.symgen()
print "Preprocessing water molecules."
for w in self.waters:
w['chain']='W'
symm=sym.varpass(w)
flagger=0
for j in symm:
for i in j:
if(len(w.pdb.findneighbor(i,w['res num']))>0):
#print "SYMMETRY"
flagger+=1
t0 = "ATOM 957 O HOH B 1 36.504 -10.582 -2.929 1.00 13.36 A O"
t1 = w['res num']
t2 = w.pdb
temp = Atom(t0, t1, t2)
temp['x'] = i[0]
temp['y'] = i[1]
temp['z'] = i[2]
temp['res num']=w['res num']
#temp['B']=float("%.2d"%flagger)
temp['chain']='S'
w.pdb.append(temp)
"""
ti2=time.clock()
print ti2-ti1
print "Preprocessing organic molecules."
self.phase2()
for pdb in self.pdbs:
pdb.write(self.stamp,1)