def makecyclicalkane(n):
assert n >= 3
r = CClen/2.0 / math.sin(math.pi/n)
coords = []
for i in range(n):
angle = math.pi * 2.0 * i / n
coords.append([r * math.cos(angle),
r * math.sin(angle),
random()*0.1])
mol = molecule.Molecule()
C = atom.Atom(6, get_c_type(n))
H = atom.Atom(1,5)
for i in range(n):
mol.addatom(C, coords[i])
for i in range(n):
mol.addatom(H, mol.coords[i]
+ numpy.array([random()*0.5,random()*0.5, random()*0.5]))
mol.addatom(H, mol.coords[i]
+ numpy.array([random()*0.5,random()*0.5, random()*0.5]))
for i in range(n):
mol.buildconnect(i, (i+1)%n)
mol.buildconnect(i, n+i*2)
mol.buildconnect(i, n+i*2+1)
#CCS2.shakeH(mol.coords, CCS2.getshakeHdata(mol))
# newmol, newene = Tinker.minimizemol(mol, "mm2")
write.writexyz(mol, sys.stdout)
def removepbc(xyzfname, pbc):
for mol in mtxyz.Mtxyz(file(xyzfname)):
coords = mol.coords
origin = coords[0]
for i in range(1, len(coords)):
coords[i] = nearestmirror(coords[i], origin, pbc)
write.writexyz(mol)
def _writemoltotempfile(mol, dir=None):
if dir is None:
dir = os.getcwd()
ofile = tempfile.NamedTemporaryFile(dir=dir)
write.writexyz(mol, ofile)
ofile.flush()
return ofile
def gjf2xyz(gjffname, ofile):
if gjffname == '-':
ifile = sys.stdin
else:
ifile = file(gjffname)
write.writexyz(read.readgjf(ifile), ofile)
ofile.close()
def settype(xyzfile, typefile):
mol = read.readxyz(xyzfile)
types = tuple(_gettypes(typefile))
assert len(mol) == len(types), "%s - %s" % (len(mol), len(types))
for idx, atype in enumerate(types):
mol.settype(idx, atype)
write.writexyz(mol, sys.stdout)
def mirrormol():
if len(sys.argv) != 2:
sys.stderr.write('Usage: %s <xyzfname>\n' % os.path.basename(sys.argv[0]))
sys.exit(1)
mol = read.readxyz(file(sys.argv[1]))
mol.coords = -mol.coords
write.writexyz(mol)
def test_1(self):
mol = read.readxyz(StringIO(test_in))
mol = loads(dumps(mol))
ofile = StringIO()
write.writexyz(mol, ofile)
for line1, line2 in zip(ofile.getvalue().splitlines(),
test_in.splitlines()):
self.assertEqual(line1, line2)
def mtxyz2txyz(ifile, ofilenamepattern):
i = 1
while 1:
try:
ofname = ofilenamepattern % i
mol = read.readxyz(ifile)
write.writexyz(mol, file(ofname, 'w'))
except:
break
i += 1
def dmddat2mtxyz(dmddatfile, molfile, ofile, select_frames=None):
aDmddat = dmddat.Dmddat(dmddatfile)
mol = read.readxyz(molfile)
if select_frames is None:
select_frames = range(aDmddat.framenum)
for frame_idx in select_frames:
aDmddat.seek_frame(frame_idx)
frame = aDmddat.next().coords
for i in range(len(frame)):
mol.coords[i] = molecule.CoordType(frame[i])
write.writexyz(mol, ofile, comment = 'frame: %i' % (frame_idx+1))
def shake1(mol, dats, ofile):
for i in range(100):
newmol = new_struct(mol)
err_dats = get_status(newmol, dats)
for j in range(500):
if not err_dats:
write.writexyz(newmol, ofile)
return True
print i, j, len(err_dats)
random.shuffle(err_dats)
newmol, err_dats = shake2(newmol, dats, err_dats)
print "failed."
return False
def newton_mol(self, mol, forcefield,
converge = 0.01, prefix=None):
"""newton_mol(mol, forcefield, converge = 0.01, prefix=None) -> (Molecule, Float)
optimized the mol with newton, and return the optimized energy
"""
forcefield = getparam(forcefield)
if curdir:
if prefix is None:
ifname = 'tinker.xyz'
else:
ifname = prefix + '.xyz'
ofile = file(ifname, 'w')
else:
ofile = tempfile.NamedTemporaryFile(suffix='.xyz')
ifname = ofile.name
write.writexyz(mol, ofile)
ofile.flush()
ofname = ifname + '_2'
ifile = subprocess.Popen(['newton', ifname, forcefield, 'A', 'A', str(converge)],
stdout=subprocess.PIPE).communicate()[0]
result = None
lines = ifile.splitlines()
if self.log_iter:
self.do_log_iter(lines)
for line in lines:
if line.startswith(' Final Function'):
result = float(line.split()[-1])
break
if result is None:
sys.stdout.writelines(lines)
raise RuntimeError, ifname
try:
newmol = read.readxyz(file(ofname))
except:
print ifname, ofname
raise
ofile.close()
os.remove(ofname)
if curdir:
os.remove(ifname)
return newmol, result
def __call__(self, ifile, ofile, idxs):
mol = read.readxyz(ifile)
ns = []
for i in range(len(mol)):
if mol.atoms[i].no == 7:
ns.append(i)
for i in idxs:
assert i < len(ns)
self.add_one_methyl(mol, ns[i])
write.writexyz(mol, ofile)
def optimize_minimize_mol(cmdname, mol, forcefield,
converge = 0.01, prefix=None):
"""optimizemol(mol, forcefield, converge = 0.01) -> (Molecule, Float)
optimized the mol, and return the optimized energy
"""
progpath = os.path.join(TINKERDIR, cmdname)
forcefield = getparam(forcefield)
if curdir:
if prefix is None:
ifname = 'tinker.xyz'
else:
ifname = prefix + '.xyz'
ofile = file(ifname, 'w')
else:
ofile = tempfile.NamedTemporaryFile(suffix='.xyz')
ifname = ofile.name
write.writexyz(mol, ofile)
ofile.flush()
ofname = ifname + '_2'
lines = subprocess.Popen([progpath, ifname, forcefield, str(converge)],
stdout=subprocess.PIPE).communicate()[0].splitlines()
result = None
for line in lines:
if line.find('Function') != -1:
result = float(line.split()[-1])
break
if result is None:
sys.stdout.writelines(lines)
raise RuntimeError, ifname
try:
newmol = read.readxyz(file(ofname))
except:
print ifname, ofname
raise
ofile.close()
os.remove(ofname)
if curdir:
os.remove(ifname)
return newmol, result
def rotate_to(idx_ifile, mol_ifile, ofile):
mol = read.readxyz(mol_ifile)
idxs = []
coords = []
for line in idx_ifile:
if not line.strip() or line.strip()[0] == '#':
continue
words = line.split()
assert len(words) == 4
idx = int(words[0]) - 1
assert 0 <= idx < len(mol)
idxs.append(idx)
coords.append([float(x) for x in words[1:]])
coords = numpy.array(coords)
res = _rmsd.rmsd2(coords, mol.coords.take(idxs, axis=0))
mat = numpy.array(res[1])
mol.coords = numpy.dot(mat[:3,:3], mol.coords.transpose()).transpose() + mat[:3,3]
write.writexyz(mol, ofile)
def scalexyz(ifname, scaleratio):
mol = read.readxyz(file(ifname))
mol.coords = [coord * scaleratio for coord in mol.coords]
write.writexyz(mol)
def writemol(self, mol, ene):
write.writexyz(mol, self.tmp_mtxyz_file, '%.4f' % ene)