def long_chain_limit(request, upload_form):
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for f in upload_form.cleaned_data["files"]:
parser = dataparser.DataParser(f)
homolumo, gap = parser.get_graphs()
name, _ = os.path.splitext(f.name)
if len(upload_form.cleaned_data["files"]) > 1:
zfile.writestr(name + "/output.txt", parser.format_output())
zfile.writestr(name + "/homolumo.eps", homolumo.getvalue())
zfile.writestr(name + "/gap.eps", gap.getvalue())
else:
zfile.writestr("output.txt", parser.format_output())
zfile.writestr("homolumo.eps", homolumo.getvalue())
zfile.writestr("gap.eps", gap.getvalue())
if len(upload_form.cleaned_data["files"]) > 1:
name = "output"
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=%s.zip" % name
return response
def parse_file_list(files):
for f in files:
if f.name.endswith(".zip"):
with zipfile.ZipFile(f, "r") as zfile:
names = [x for x in zfile.namelist() if not x.endswith("/")]
for name in names:
newfile = StringIO(zfile.open(name).read(), name=name)
yield newfile
elif f.name.endswith(".tar.bz2") or f.name.endswith(".tar.gz"):
end = f.name.split(".")[-1]
with tarfile.open(fileobj=f, mode='r:' + end) as tfile:
for name in tfile.getnames():
if tfile.getmember(name).isfile():
newfile = StringIO(tfile.extractfile(name).read(),
name=name)
yield newfile
else:
yield f
def draw(xvals, yvals, vert, horz):
offset = 0.25
scale = 10
mins = numpy.array([min(xvals), min(yvals)])
maxs = numpy.array([max(xvals), max(yvals)])
dimensions = maxs - mins + 2 * offset
mins = mins - offset
dimensions *= scale
WIDTH = int(dimensions[1])
HEIGHT = int(dimensions[0])
f = StringIO()
surface = cairo.SVGSurface(f, WIDTH, HEIGHT)
ctx = cairo.Context(surface)
ctx.scale(scale, scale)
ctx.rotate(math.pi / 2)
# hack to fix the translation from the rotation
ctx.translate(0, -dimensions[1] / scale)
ctx.translate(-mins[0], -mins[1])
ctx.set_line_width(0.1)
for i, (x, y) in enumerate(zip(xvals, yvals)):
if i in vert:
color = (0, 255, 0)
elif i in horz:
color = (255, 0, 0)
else:
color = (0, 0, 255)
ctx.set_source_rgb(*color)
ctx.arc(x, y, 0.25, 0, 2 * math.pi)
ctx.fill()
surface.write_to_png(f)
# THIS IS REQUIRED BECAUSE OF ISSUES WITH CAIRO.
del surface
del ctx
#############
string = "data:image/png;base64,"
string += base64.b64encode(f.getvalue())
return string
def setUp(self):
self.client = Client()
user = get_user_model().objects.create_user(**USER)
user.save()
self.user = user
self.template = models.JobTemplate(
name="test-template-delete",
creator=self.user,
)
self.template.template = File(StringIO("template", name="test-template-delete"))
self.template.save()
def long_chain_limit(request, upload_form):
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for f in upload_form.cleaned_data["files"]:
parser = dataparser.DataParser(f)
homolumo, gap = parser.get_graphs()
name, _ = os.path.splitext(f.name)
if len(upload_form.cleaned_data["files"]) > 1:
zfile.writestr(name + "/output.txt", parser.format_output())
zfile.writestr(name + "/homolumo.eps", homolumo.getvalue())
zfile.writestr(name + "/gap.eps", gap.getvalue())
else:
zfile.writestr("output.txt", parser.format_output())
zfile.writestr("homolumo.eps", homolumo.getvalue())
zfile.writestr("gap.eps", gap.getvalue())
if len(upload_form.cleaned_data["files"]) > 1:
name = "output"
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=%s.zip" % name
return response
def get_ssh_connection(self):
if self.use_password:
return get_ssh_connection(self.cluster.hostname,
self.username,
password=self.password,
port=self.cluster.port)
else:
user = type(self.user).objects.get(id=self.user.id)
private = StringIO(user.private_key)
return get_ssh_connection(self.cluster.hostname,
self.username,
key=private,
port=self.cluster.port)
def save_model(model, errors):
logger.info("Saving Model")
with StringIO(name="decay_predictors.pkl") as f:
cPickle.dump(model, f, protocol=-1)
f.seek(0)
pred = Predictor(
homo_error=errors[0],
lumo_error=errors[1],
gap_error=errors[2],
pickle=File(f),
)
pred.save()
def compute_axes_percents(f):
data = f.read()
coords = get_coordinates(StringIO(data))
atom_idxs, elements, orb_values, occupied_orbs = get_numbers(StringIO(data))
body = '\n'.join("%s %f %f %f" % (ele, x, y, z) for ele, (x, y, z) in zip(elements, coords))
bonds = calculate_bonds(body)
mol = from_xyz(StringIO(body + "\n\n" + bonds))
vert_idxs, horz_idxs = get_group_indices(mol)
vert_idxs = set(vert_idxs)
horz_idxs = set(horz_idxs)
center_idxs = [i for i in xrange(len(coords)) if i not in vert_idxs and i not in horz_idxs]
homo_idx = get_homo_index(occupied_orbs)
homo_values = [x[homo_idx] for x in orb_values]
lumo_values = [x[homo_idx + 1] for x in orb_values]
homo_res = calculate_groups(homo_values, atom_idxs, vert_idxs, horz_idxs)
lumo_res = calculate_groups(lumo_values, atom_idxs, vert_idxs, horz_idxs)
# X and Y coordinates are flipped in Gaussian files
image = draw([x[1] for x in coords], [x[0] for x in coords], vert_idxs, horz_idxs)
return ("H**O", ) + homo_res, ("LUMO", ) + lumo_res, image
def convert_logs(logsets):
converted = []
for key in logsets:
nvals = []
homovals = []
lumovals = []
gapvals = []
for num, log in logsets[key]:
parser = fileparser.Log(log)
nvals.append(num)
homovals.append(parser["H**O"])
lumovals.append(parser["LUMO"])
gapvals.append(parser["ExcitationEnergy1"])
f = StringIO(name=key)
f.write(', '.join(nvals) + '\n')
f.write(', '.join(homovals) + '\n')
f.write(', '.join(lumovals) + '\n')
f.write(', '.join(gapvals) + '\n')
f.seek(0)
converted.append(f)
return converted
def get_sftp_connection(self):
if self.use_password:
return get_sftp_connection(self.cluster.hostname,
self.username,
password=self.password,
port=self.cluster.port)
else:
try:
del self.user._profile_cache
except:
pass
private = StringIO(self.user.private_key)
return get_sftp_connection(self.cluster.hostname,
self.username,
key=private,
port=self.cluster.port)
def parse_log(request, upload_form):
split_iter = upload_form.cleaned_data['split_iter']
parser = fileparser.LogSet(split_iter=split_iter)
for f in upload_form.cleaned_data["files"]:
parser.parse_file(f)
output = parser.format_output()
f2 = StringIO(output)
if upload_form.cleaned_data['store'] and request.user.is_staff:
number_added = load_data.main(f2)
string = "%d datapoint(s) added to database." % number_added
logger.info(string)
output += "\n\n\n" + string
response = HttpResponse(output, content_type="text/plain")
return response
def convert_logs(logsets):
converted = []
for key in logsets:
nvals = []
homovals = []
lumovals = []
gapvals = []
for num, log in logsets[key]:
parser = fileparser.Log(log)
nvals.append(num)
homovals.append(parser["H**O"])
lumovals.append(parser["LUMO"])
gapvals.append(parser["ExcitationEnergy1"])
f = StringIO(name=key)
f.write(', '.join(nvals) + '\n')
f.write(', '.join(homovals) + '\n')
f.write(', '.join(lumovals) + '\n')
f.write(', '.join(gapvals) + '\n')
f.seek(0)
converted.append(f)
return converted
def draw(self,
scale,
svg=False,
hydrogens=True,
colors=True,
fancy_bonds=True):
'''Draws a basic image of the molecule.'''
offset = 0.25
mins, maxs = self.bounding_box()
dimensions = (maxs - mins) + 2 * offset
dimensions *= scale
mins = mins - offset
WIDTH = int(dimensions[1])
HEIGHT = int(dimensions[0])
f = StringIO()
surface = cairo.SVGSurface(f, WIDTH, HEIGHT)
ctx = cairo.Context(surface)
ctx.scale(scale, scale)
ctx.rotate(math.pi / 2)
# hack to fix the translation from the rotation
ctx.translate(0, -dimensions[1] / scale)
ctx.translate(-mins[0], -mins[1])
ctx.set_line_width(0.1)
def draw_bond(ctx, coords1, coords2, unit, factors):
for x in factors:
ctx.move_to(*(x * unit + coords1))
ctx.line_to(*(x * unit + coords2))
ctx.stroke()
ctx.set_source_rgb(*COLORS2['1'])
for bond in self.bonds:
if not hydrogens and any(x.element == 'H' for x in bond.atoms):
continue
if colors:
ctx.set_source_rgb(*COLORS2[bond.type])
coords1 = numpy.array(bond.atoms[0].xyz_tuple[:2])
coords2 = numpy.array(bond.atoms[1].xyz_tuple[:2])
temp = (coords2 - coords1)
mag = numpy.linalg.norm(temp)
unit = numpy.array([-temp[1] / mag, temp[0] / mag])
if fancy_bonds:
if bond.type == '2':
draw_bond(ctx, coords1, coords2, unit, [0.1, -0.1])
elif bond.type == '3':
draw_bond(ctx, coords1, coords2, unit, [0.2, 0.0, -0.2])
elif bond.type == 'Ar':
ctx.save()
ctx.set_dash([0.3, 0.15])
draw_bond(ctx, coords1, coords2, unit, [0.1, -0.1])
ctx.restore()
else:
draw_bond(ctx, coords1, coords2, unit, [0.0])
else:
draw_bond(ctx, coords1, coords2, unit, [0.0])
for atom in self.atoms:
if not hydrogens and atom.element == 'H':
continue
ctx.set_source_rgb(*COLORS2[atom.element])
point = atom.xyz_tuple
ctx.arc(point[0], point[1], 0.25, 0, 2 * math.pi)
ctx.fill()
if svg:
surface.finish()
else:
surface.write_to_png(f)
return f
def clean_template(self):
template = self.cleaned_data.get("template")
name = self.cleaned_data.get("name")
return File(StringIO(template, name=name))
def reset_gjf(request, upload_form):
job_form = JobForm.get_form(request, "{{ name }}")
errors = []
strings = []
names = []
for f in upload_form.cleaned_data["files"]:
try:
parser = fileparser.Log(f)
name, _ = os.path.splitext(f.name)
td = False
if request.REQUEST.get("td_reset"):
name += '_TD'
td = True
strings.append(parser.format_gjf(td=td))
names.append(name)
except Exception as e:
logger.warn("There was an error when trying to reset a gjf: '%s'" %
str(e))
errors.append((f.name, e))
if request.REQUEST.get("gjf_submit"):
if not job_form.is_valid(request.method):
if request.is_ajax():
upload_form_html = render_crispy_form(
upload_form, context=RequestContext(request))
job_form_html = render_crispy_form(
job_form, context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"upload_form_html": upload_form_html,
}
return HttpResponse(json.dumps(a),
content_type="application/json")
c = {
"job_form": job_form,
"upload_form": upload_form,
}
return render(request, "chem/upload_log.html", c)
d = dict(job_form.cleaned_data)
cred = d.pop("credential")
a = cluster.interface.run_jobs(cred, names, strings, **d)
a["failed"].extend(errors)
do_html = request.REQUEST.get("html", False)
if do_html:
html = render_to_string("chem/multi_submit.html", a)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(a), content_type="application/json")
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for name, string in zip(names, strings):
zfile.writestr("%s.gjf" % name, string)
if errors:
temp = ['%s - %s' % (name, error) for (name, error) in errors]
zfile.writestr("errors.txt", '\n'.join(temp))
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=output.zip"
return response
def mock_exec_command(string):
return StringIO(''), StringIO(''), StringIO('')
def mock_exec_command2(string):
print string
return StringIO(''), StringIO(''), StringIO('some cp error')
def from_log(file):
out = fileparser.Log(file)
return from_gjf(StringIO(out.format_gjf()))
def make_io_triplet(stdin='', stdout='', stderr=''):
return StringIO(stdin), StringIO(stdout), StringIO(stderr)
def reset_gjf(request, upload_form):
job_form = JobForm.get_form(request, "{{ name }}")
errors = []
strings = []
names = []
for f in upload_form.cleaned_data["files"]:
try:
parser = fileparser.Log(f)
name, _ = os.path.splitext(f.name)
td = False
if request.REQUEST.get("td_reset"):
name += '_TD'
td = True
strings.append(parser.format_gjf(td=td))
names.append(name)
except Exception as e:
logger.warn("There was an error when trying to reset a gjf: '%s'" % str(e))
errors.append((f.name, e))
if request.REQUEST.get("gjf_submit"):
if not job_form.is_valid(request.method):
if request.is_ajax():
upload_form_html = render_crispy_form(upload_form,
context=RequestContext(request))
job_form_html = render_crispy_form(job_form,
context=RequestContext(request))
a = {
"success": False,
"job_form_html": job_form_html,
"upload_form_html": upload_form_html,
}
return HttpResponse(json.dumps(a),
content_type="application/json")
c = {
"job_form": job_form,
"upload_form": upload_form,
}
return render(request, "chem/upload_log.html", c)
d = dict(job_form.cleaned_data)
cred = d.pop("credential")
a = cluster.interface.run_jobs(cred, names, strings, **d)
a["failed"].extend(errors)
do_html = request.REQUEST.get("html", False)
if do_html:
html = render_to_string("chem/multi_submit.html", a)
temp = {"success": True, "html": html}
return HttpResponse(json.dumps(temp),
content_type="application/json")
else:
return HttpResponse(json.dumps(a),
content_type="application/json")
buff = StringIO()
zfile = zipfile.ZipFile(buff, 'w', zipfile.ZIP_DEFLATED)
for name, string in zip(names, strings):
zfile.writestr("%s.gjf" % name, string)
if errors:
temp = ['%s - %s' % (name, error) for (name, error) in errors]
zfile.writestr("errors.txt", '\n'.join(temp))
zfile.close()
buff.flush()
ret_zip = buff.getvalue()
buff.close()
response = HttpResponse(ret_zip, content_type="application/zip")
response["Content-Disposition"] = "attachment; filename=output.zip"
return response
def from_gjf(file):
data = file.read().replace('\r', '')
parts = data.split("\n\n")
header = parts[0].strip()
assert "#" in header
header_lines = header.split('\n')
if "#" in header_lines[-1]:
has_bonds = "connectivity" in header_lines[-1]
has_redundant = "modredundant" in header_lines[-1]
else:
raise Exception("The header is missing a #")
# title = parts[1].strip()
other = [x for x in parts[3:] if x.strip()]
if len(other) < (has_bonds + has_redundant):
raise Exception(
"Either the bonds data or redundant coords are missing")
letter_first = []
number_first = []
for part in other:
if part.strip()[0] in string.letters:
letter_first.append(part)
elif part.strip()[0] in string.digits:
number_first.append(part)
if has_redundant:
if len(letter_first) > 1:
variables, redundant = letter_first
else:
redundant = letter_first[0]
variables = ''
else:
if len(letter_first) == 1:
variables = letter_first[0]
redundant = ''
elif len(letter_first) < 1:
variables = ''
redundant = ''
else:
raise Exception("Too many letter first groups")
if has_bonds:
temp = number_first[0]
bonds = []
for line in temp.split('\n'):
comp = line.strip().split()
if len(comp) < 3:
continue
main = comp[0]
comp = comp[1:]
for i, x in enumerate(comp[::2]):
bonds.append("%s %s %s" % (main, x, comp[2 * i + 1]))
bonds_string = "\n".join(bonds)
else:
bonds_string = ''
body = parts[2].strip()
start = body.index('\n')
charge, multiplicity = body[0:start].strip().split()
geom = body[start + 1:]
if variables:
geom = replace_geom_vars(geom, variables)
if len(geom[:geom.index("\n")].strip().split()) < 4:
geom = convert_zmatrix_to_cart(geom)
if not has_bonds:
bonds_string = calculate_bonds(geom)
f = StringIO(geom + "\n\n" + bonds_string)
return from_xyz(f)