コード例 #1
0
def get_molecule_status(name, autoflip=False):
    mol = gjfwriter.NamedMolecule(name, autoflip=autoflip)
    name_error = mol.get_name_error()
    error_report = ErrorReport.objects.filter(molecule=name).exists() or None
    new = not DataPoint.objects.filter(
        exact_name=mol.get_exact_name()).exists()
    return mol, name_error, error_report, new
コード例 #2
0
ファイル: views.py プロジェクト: crcollins/chemtools-webapp
def write_svg(request, molecule):
    mol_form = MoleculeForm(request.REQUEST)
    mol_form.is_valid()
    mol_settings = dict(mol_form.cleaned_data)

    out = gjfwriter.NamedMolecule(molecule, **mol_settings)
    response = HttpResponse(out.get_svg(), content_type="image/svg+xml")
    response['Content-Disposition'] = 'filename=%s.svg' % molecule
    return response
コード例 #3
0
def save_names(names):
    for name in names:
        struct = gjfwriter.NamedMolecule(
            name,
            keywords="opt B3LYP/6-31g(d,p)",
            nprocshared=12,
            memory=30,
        )
        with open(name + ".gjf", 'w') as f:
            f.write(struct.get_gjf())
コード例 #4
0
ファイル: views.py プロジェクト: crcollins/chemtools-webapp
def write_mol2(request, molecule):
    mol_form = MoleculeForm(request.REQUEST)
    mol_form.is_valid()
    add = "" if request.REQUEST.get("view") else "attachment; "

    mol_settings = dict(mol_form.cleaned_data)
    out = gjfwriter.NamedMolecule(molecule, **mol_settings)
    response = HttpResponse(out.get_mol2(), content_type="text/plain")
    response['Content-Disposition'] = add + 'filename=%s.mol2' % molecule
    return response
コード例 #5
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def run_name(name):
    from chemtools import gjfwriter
    mol = gjfwriter.NamedMolecule(name).structure
    links, tree = breadth_first_search(mol)

    cycles, link_nodes = get_cycles(links, tree)
    pruned_cycles = prune_cycles(cycles, link_nodes)
    fused = get_fused_cycles(pruned_cycles)
    sorted_cycles = sort_fused_cycles(fused)
    temp = identify_cycle_types(mol, sorted_cycles)

    noncycles = get_noncycles(mol, pruned_cycles)
    pruned_noncycles = prune_noncycles(noncycles)
    temp2 = identify_noncycle_types(pruned_noncycles)
    return set(temp + temp2)
コード例 #6
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def run_standard_jobs(credential, string, mol_settings, job_settings):
    results = {
        "worked": [],
        "failed": [],
        "error": None,
    }
    # This is to catch invalid users early on
    try:
        results["cluster"] = credential.cluster.name
        if not credential.user.is_staff:
            results["error"] = "You must be a staff user to submit a job."
            return results
    except Exception as e:
        results["error"] = "Invalid credential"
        results["cluster"] = None
        return results

    names = []
    gjfs = []
    for mol in name_expansion(string):
        try:
            out = gjfwriter.NamedMolecule(mol, **mol_settings)
            # This instantiation needs to be done here because of the errors
            # in a structure are calculated lazily.
            gjf = out.get_gjf()
            names.append(mol)
            gjfs.append(gjf)
        except Exception as e:
            logger.warn("Failed gjf write -- %s -- %s" % (mol, e))
            results["failed"].append((mol, str(e)))
            continue

    if names:
        settings = {
            k: v
            for k, v in job_settings.items() + mol_settings.items()
        }
        temp = run_jobs(credential, names, gjfs, **settings)
        results["worked"] = temp["worked"]
        results["failed"].extend(temp["failed"])
        results["error"] = temp["error"]
    return results
コード例 #7
0
 def wrapper(request, molecule, *args, **kwargs):
     if request.REQUEST.get("autoflip"):
         mol = gjfwriter.NamedMolecule(molecule, autoflip=True)
         return redirect(wrapper, mol.name)
     return f(request, molecule, *args, **kwargs)