Instruction:
How would you code a function in Python 3 to
parse a processed. top GROMACS topology file and return a dict containing the current section and molecule names and the CMAP parameters.

Response:
def _parse(self, fname):
        """Parse a processed.top GROMACS topology file

        The function reads in the file line-by-line, and it's a bunch of 'elif' statements,
        writing parameter/atom line to current section/molecule.

        ParamTypes are added to self.xyztypes (AtomType goes to self.atomtypes).
        Params are added to current molecule (Atom goes to mol.atoms.append(atom))

        MoleculeTypes and Molecules are odd, and are added to
            * MoleculeType to :attr:`self.dict_molname_mol[mol.name] = mol`
            * Molecule to :attr:`self.molecules.append(self.dict_molname_mol[mname])`

        :obj:`curr_sec` variable stores to current section being read-in
        :obj:`mol` variable stores the current molecule being read-in
        :obj:`cmap_lines` are a little odd, since CMAP parameters are stored on multiple lines

        :Arguments:
          *fname*
              name of the processed.top file

        :Returns: None
        """
        def _find_section(line):
            return  line.strip('[').strip(']').strip()

        def _add_info(sys_or_mol, section, container):
            # like (mol, 'atomtypes', mol.atomtypes)
            if sys_or_mol.information.get(section, False) is False:
                sys_or_mol.information[section] = container

        mol        = None   # to hold the current mol
        curr_sec   = None
        cmap_lines = []

        with open(fname) as f:
            for i_line, line in enumerate(f):

                # trimming
                if ';' in line:
                    line = line[0:line.index(';')]
                line = line.strip()

                if line == '':
                    continue

                if line[0] == '*':
                    continue

                # the topology must be stand-alone (i.e. no includes)
                if line.startswith('#include'):
                    msg = 'The topology file has "#include" statements.'
                    msg+= ' You must provide a processed topology file that grompp creates.'
                    raise ValueError(msg)

                # find sections
                if line[0] == '[':
                    curr_sec = _find_section(line)
                    self.found_sections.append(curr_sec)
                    continue

                fields = line.split()

                if curr_sec == 'defaults':
                    '''
                    # ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
                    #1               2               yes             0.5     0.8333
                    '''
                    assert len(fields) in  [2, 5]
                    self.defaults['nbfunc']    = int(fields[0])
                    self.defaults['comb-rule'] = int(fields[1])
                    if len(fields) == 5:

                       self.defaults['gen-pairs'] = fields[2]
                       self.defaults['fudgeLJ']   = float(fields[3])
                       self.defaults['fudgeQQ']   = float(fields[4])

                elif curr_sec == 'atomtypes':
                    '''
                    # ;name               at.num    mass         charge    ptype  sigma   epsilon
                    # ;name   bond_type   at.num    mass         charge    ptype  sigma   epsilon
                    # ;name                         mass         charge    ptype  c6      c12

                    '''
                    if len(fields) not in (6,7,8):
                        self.logger.warning('skipping atomtype line with neither 7 or 8 fields: \n {0:s}'.format(line))
                        continue

                    #shift = 0 if len(fields) == 7 else 1
                    shift = len(fields) - 7
                    at = blocks.AtomType('gromacs')
                    at.atype = fields[0]
                    if shift == 1: at.bond_type = fields[1]

                    at.mass  = float(fields[2+shift])
                    at.charge= float(fields[3+shift])

                    particletype = fields[4+shift]
                    assert particletype in ('A', 'S', 'V', 'D')
                    if particletype not in ('A',):
                        self.logger.warning('warning: non-atom particletype: "{0:s}"'.format(line))

                    sig = float(fields[5+shift])
                    eps = float(fields[6+shift])

                    at.gromacs= {'param': {'lje':eps, 'ljl':sig, 'lje14':None, 'ljl14':None} }

                    self.atomtypes.append(at)

                    _add_info(self, curr_sec, self.atomtypes)

                # extend system.molecules
                elif curr_sec == 'moleculetype':
                    assert len(fields) == 2

                    mol = blocks.Molecule()

                    mol.name = fields[0]
                    mol.exclusion_numb = int(fields[1])

                    self.dict_molname_mol[mol.name] = mol

                elif curr_sec == 'atoms':
                    '''
                    #id    at_type     res_nr  residu_name at_name  cg_nr  charge   mass  typeB    chargeB      massB
                    # 1       OC          1       OH          O1       1      -1.32

                    OR

                    [ atoms ]
                    ; id   at type  res nr  residu name at name     cg nr   charge
                    1       OT      1       SOL              OW             1       -0.834

                    '''

                    aserial = int(fields[0])
                    atype   = fields[1]
                    resnumb = int(fields[2])
                    resname = fields[3]
                    aname   = fields[4]
                    cgnr    = int(fields[5])
                    charge  = float(fields[6])
                    rest = fields[7:]

                    atom         = blocks.Atom()
                    atom.name    = aname
                    atom.atomtype= atype
                    atom.number  = aserial
                    atom.resname = resname
                    atom.resnumb = resnumb
                    atom.charge  = charge

                    if rest:
                        mass = float(rest[0])
                        atom.mass = mass

                    mol.atoms.append(atom)

                    _add_info(mol, curr_sec, mol.atoms)

                elif curr_sec in ('pairtypes', 'pairs', 'pairs_nb'):
                    '''
                    section     #at     fu      #param
                    ---------------------------------
                    pairs       2       1       V,W
                    pairs       2       2       fudgeQQ, qi, qj, V, W
                    pairs_nb    2       1       qi, qj, V, W

                    '''

                    ai, aj = fields[:2]
                    fu     = int(fields[2])
                    assert fu in (1,2)

                    pair = blocks.InteractionType('gromacs')
                    if fu == 1:
                        if curr_sec=='pairtypes':
                            pair.atype1 = ai
                            pair.atype2 = aj
                            v, w = list(map(float, fields[3:5]))
                            pair.gromacs = {'param': {'lje':None, 'ljl':None, 'lje14':w, 'ljl14':v}, 'func':fu }

                            self.pairtypes.append(pair)
                            _add_info(self, curr_sec, self.pairtypes)

                        elif curr_sec == 'pairs':
                            ai, aj = list( map(int, [ai,aj]) )
                            pair.atom1 = mol.atoms[ai-1]
                            pair.atom2 = mol.atoms[aj-1]
                            pair.gromacs['func'] = fu

                            mol.pairs.append(pair)
                            _add_info(mol, curr_sec, mol.pairs)

                        else:
                            raise ValueError

                    else:
                        raise NotImplementedError('{0:s} with functiontype {1:d} is not supported'.format(curr_sec,fu))

                elif curr_sec == 'nonbond_params':
                    '''
                    ; typei typej  f.type sigma   epsilon
                    ; f.type=1 means LJ (not buckingham)
                    ; sigma&eps since mixing-rule = 2
                    '''

                    assert len(fields) == 5
                    ai, aj = fields[:2]
                    fu     = int(fields[2])

                    assert fu == 1
                    sig    = float(fields[3])
                    eps    = float(fields[4])

                    nonbond_param = blocks.NonbondedParamType('gromacs')
                    nonbond_param.atype1 = ai
                    nonbond_param.atype2 = aj
                    nonbond_param.gromacs['func'] = fu
                    nonbond_param.gromacs['param'] = {'eps': eps, 'sig': sig}

                    self.nonbond_params.append(nonbond_param)
                    _add_info(self, curr_sec, self.nonbond_params)

                elif curr_sec in ('bondtypes', 'bonds'):
                    '''
                    section     #at     fu      #param
                    ----------------------------------
                    bonds       2       1       2
                    bonds       2       2       2
                    bonds       2       3       3
                    bonds       2       4       2
                    bonds       2       5       ??
                    bonds       2       6       2
                    bonds       2       7       2
                    bonds       2       8       ??
                    bonds       2       9       ??
                    bonds       2       10      4
                    '''

                    ai, aj = fields[:2]
                    fu     = int(fields[2])
                    assert fu in (1,2,3,4,5,6,7,8,9,10)

                    if fu != 1:
                        raise NotImplementedError('function {0:d} is not yet supported'.format(fu))

                    bond = blocks.BondType('gromacs')

                    if fu == 1:
                        if curr_sec == 'bondtypes':
                            bond.atype1 = ai
                            bond.atype2 = aj

                            b0, kb = list(map(float, fields[3:5]))
                            bond.gromacs = {'param':{'kb':kb, 'b0':b0}, 'func':fu}

                            self.bondtypes.append(bond)
                            _add_info(self, curr_sec, self.bondtypes)

                        elif curr_sec == 'bonds':
                            ai, aj = list(map(int, [ai, aj]))
                            bond.atom1 = mol.atoms[ai-1]
                            bond.atom2 = mol.atoms[aj-1]
                            bond.gromacs['func'] = fu

                            if len(fields) > 3:
                                b0, kb = list(map(float, fields[3:5]))
                                bond.gromacs = {'param':{'kb':kb, 'b0':b0}, 'func':fu}

                            mol.bonds.append(bond)
                            _add_info(mol, curr_sec, mol.bonds)

                    else:
                        raise NotImplementedError

                elif curr_sec in ('angletypes', 'angles'):
                    '''
                    section     #at     fu      #param
                    ----------------------------------
                    angles      3       1       2
                    angles      3       2       2
                    angles      3       3       3
                    angles      3       4       4
                    angles      3       5       4
                    angles      3       6       6
                    angles      3       8       ??
                    '''

                    ai, aj , ak = fields[:3]
                    fu          = int(fields[3])
                    assert fu in (1,2,3,4,5,6,8)  # no 7

                    if fu not in (1,2,5):
                        raise NotImplementedError('function {0:d} is not yet supported'.format(fu))

                    ang = blocks.AngleType('gromacs')
                    if fu == 1:
                        if curr_sec == 'angletypes':
                            ang.atype1 = ai
                            ang.atype2 = aj
                            ang.atype3 = ak

                            tetha0, ktetha = list(map(float, fields[4:6]))
                            ang.gromacs = {'param':{'ktetha':ktetha, 'tetha0':tetha0, 'kub':None, 's0':None}, 'func':fu}

                            self.angletypes.append(ang)
                            _add_info(self, curr_sec, self.angletypes)

                        elif curr_sec == 'angles':
                            ai, aj, ak = list(map(int, [ai, aj, ak]))
                            ang.atom1 = mol.atoms[ai-1]
                            ang.atom2 = mol.atoms[aj-1]
                            ang.atom3 = mol.atoms[ak-1]
                            ang.gromacs['func'] = fu

                            mol.angles.append(ang)
                            _add_info(mol, curr_sec, mol.angles)

                        else:
                            raise ValueError

                    elif fu == 2:
                        if curr_sec == 'angletypes':
                            raise NotImplementedError()

                        elif curr_sec == 'angles':
                            ai, aj, ak = list(map(int, [ai, aj, ak]))
                            ang.atom1 = mol.atoms[ai-1]
                            ang.atom2 = mol.atoms[aj-1]
                            ang.atom3 = mol.atoms[ak-1]
                            ang.gromacs['func'] = fu

                            tetha0, ktetha = list(map(float, fields[4:6]))
                            ang.gromacs = {'param':{'ktetha':ktetha, 'tetha0':tetha0, 'kub':None, 's0':None}, 'func':fu}

                            mol.angles.append(ang)
                            _add_info(mol, curr_sec, mol.angles)

                    elif fu == 5:
                        if curr_sec == 'angletypes':
                            ang.atype1 = ai
                            ang.atype2 = aj
                            ang.atype3 = ak
                            tetha0, ktetha, s0, kub = list(map(float, fields[4:8]))

                            ang.gromacs = {'param':{'ktetha':ktetha, 'tetha0':tetha0, 'kub':kub, 's0':s0}, 'func':fu}

                            self.angletypes.append(ang)
                            _add_info(self, curr_sec, self.angletypes)

                        elif curr_sec == 'angles':
                            ai, aj, ak = list(map(int, [ai, aj, ak]))
                            ang.atom1 = mol.atoms[ai-1]
                            ang.atom2 = mol.atoms[aj-1]
                            ang.atom3 = mol.atoms[ak-1]
                            ang.gromacs['func'] = fu

                            mol.angles.append(ang)
                            _add_info(mol, curr_sec, mol.angles)

                        else:
                            raise ValueError

                    else:
                        raise NotImplementedError

                elif curr_sec in  ('dihedraltypes', 'dihedrals'):
                    '''
                    section     #at     fu      #param
                    ----------------------------------
                    dihedrals   4       1       3
                    dihedrals   4       2       2
                    dihedrals   4       3       6
                    dihedrals   4       4       3
                    dihedrals   4       5       4
                    dihedrals   4       8       ??
                    dihedrals   4       9       3
                    '''

                    if curr_sec == 'dihedraltypes' and len(fields) == 6:
                        # in oplsaa - quartz parameters
                        fields.insert(2, 'X')
                        fields.insert(0, 'X')

                    ai, aj, ak, am = fields[:4]
                    fu = int(fields[4])
                    assert fu in (1,2,3,4,5,8,9)

                    if fu not in (1,2,3,4,9):
                        raise NotImplementedError('dihedral function {0:d} is not yet supported'.format(fu))

                    dih = blocks.DihedralType('gromacs')
                    imp = blocks.ImproperType('gromacs')
                    # proper dihedrals
                    if fu in (1,3,9):
                        if curr_sec == 'dihedraltypes':
                            dih.atype1 = ai
                            dih.atype2 = aj
                            dih.atype3 = ak
                            dih.atype4 = am

                            dih.line = i_line + 1

                            if fu == 1:
                                delta, kchi, n = list(map(float, fields[5:8]))
                                dih.gromacs['param'].append({'kchi':kchi, 'n':n, 'delta':delta})
                            elif fu == 3:
                                c0, c1, c2, c3, c4, c5 = list(map(float, fields[5:11]))
                                m = dict(c0=c0, c1=c1, c2=c2, c3=c3, c4=c4, c5=c5)
                                dih.gromacs['param'].append(m)
                            elif fu == 4:
                                delta, kchi, n = list(map(float, fields[5:8]))
                                dih.gromacs['param'].append({'kchi':kchi, 'n':int(n), 'delta':delta})
                            elif fu == 9:
                                delta, kchi, n = list(map(float, fields[5:8]))
                                dih.gromacs['param'].append({'kchi':kchi, 'n':int(n), 'delta':delta})
                            else:
                                raise ValueError

                            dih.gromacs['func'] = fu
                            self.dihedraltypes.append(dih)
                            _add_info(self, curr_sec, self.dihedraltypes)

                        elif curr_sec == 'dihedrals':
                            ai, aj, ak, am = list(map(int, fields[:4]))
                            dih.atom1 = mol.atoms[ai-1]
                            dih.atom2 = mol.atoms[aj-1]
                            dih.atom3 = mol.atoms[ak-1]
                            dih.atom4 = mol.atoms[am-1]
                            dih.gromacs['func'] = fu

                            dih.line = i_line + 1

                            if fu == 1:
                                delta, kchi, n = list(map(float, fields[5:8]))
                                dih.gromacs['param'].append({'kchi':kchi, 'n': int(n), 'delta':delta})
                            elif fu == 3:
                                pass
                            elif fu == 4:
                                pass
                            elif fu == 9:
                                if len(fields[5:8]) == 3:
                                    delta, kchi, n = list(map(float, fields[5:8]))
                                    dih.gromacs['param'].append({'kchi':kchi, 'n':int(n), 'delta':delta})
                            else:
                                raise ValueError

                            mol.dihedrals.append(dih)
                            _add_info(mol, curr_sec, mol.dihedrals)

                        else:
                            raise ValueError
                    # impropers
                    elif fu in (2,4):
                        if curr_sec == 'dihedraltypes':
                            imp.atype1 = ai
                            imp.atype2 = aj
                            imp.atype3 = ak
                            imp.atype4 = am

                            imp.line = i_line + 1

                            if fu == 2:
                                psi0 , kpsi = list(map(float, fields[5:7]))
                                imp.gromacs['param'].append({'kpsi':kpsi, 'psi0': psi0})
                            elif fu == 4:
                                psi0 , kpsi, n = list(map(float, fields[5:8]))
                                imp.gromacs['param'].append({'kpsi':kpsi, 'psi0': psi0, 'n': int(n)})
                            else:
                                raise ValueError

                            imp.gromacs['func'] = fu
                            self.impropertypes.append(imp)
                            _add_info(self, curr_sec, self.impropertypes)

                        elif curr_sec == 'dihedrals':
                            ai, aj, ak, am = list(map(int, fields[:4]))
                            imp.atom1 = mol.atoms[ai-1]
                            imp.atom2 = mol.atoms[aj-1]
                            imp.atom3 = mol.atoms[ak-1]
                            imp.atom4 = mol.atoms[am-1]
                            imp.gromacs['func'] = fu

                            imp.line = i_line + 1

                            if fu == 2:
                                pass
                            elif fu == 4:
                                # in-line override of dihedral parameters
                                if len(fields[5:8]) == 3:
                                    psi0 , kpsi, n = list(map(float, fields[5:8]))
                                    imp.gromacs['param'].append({'kpsi':kpsi, 'psi0': psi0, 'n': int(n)})
                            else:
                                raise ValueError

                            mol.impropers.append(imp)
                            _add_info(mol, curr_sec, mol.impropers)

                        else:
                            raise ValueError

                    else:
                        raise NotImplementedError

                elif curr_sec in ('cmaptypes', 'cmap'):

                    cmap = blocks.CMapType('gromacs')
                    if curr_sec == 'cmaptypes':
                        cmap_lines.append(line)
                        _add_info(self, curr_sec, self.cmaptypes)
                    else:
                        ai, aj, ak, am, an = list(map(int, fields[:5]))
                        fu = int(fields[5])
                        assert fu == 1
                        cmap.atom1 = mol.atoms[ai-1]
                        cmap.atom2 = mol.atoms[aj-1]
                        cmap.atom3 = mol.atoms[ak-1]
                        cmap.atom4 = mol.atoms[am-1]
                        cmap.atom8 = mol.atoms[an-1]
                        cmap.gromacs['func'] = fu

                        mol.cmaps.append(cmap)
                        _add_info(mol, curr_sec, mol.cmaps)

                elif curr_sec == 'settles':
                    '''
                    section     #at     fu      #param
                    ----------------------------------
                    '''

                    assert len(fields) == 4
                    ai = int(fields[0])
                    fu = int(fields[1])
                    assert fu == 1

                    settle = blocks.SettleType('gromacs')
                    settle.atom = mol.atoms[ai-1]
                    settle.dOH = float(fields[2])
                    settle.dHH = float(fields[3])

                    mol.settles.append(settle)
                    _add_info(mol, curr_sec, mol.settles)

                elif curr_sec == "virtual_sites3":
                    '''
                        ; Dummy from            funct   a       b
                        4   1   2   3   1   0.131937768 0.131937768
                    '''
                    assert len(fields) == 7
                    ai = int(fields[0])
                    aj = int(fields[1])
                    ak = int(fields[2])
                    al = int(fields[3])
                    fu = int(fields[4])
                    assert fu == 1
                    a = float(fields[5])
                    b = float(fields[6])

                    vs3 = blocks.VirtualSites3Type('gromacs')
                    vs3.atom1 = ai
                    vs3.atom2 = aj
                    vs3.atom3 = ak
                    vs3.atom4 = al
                    vs3.gromacs['func'] = fu
                    vs3.gromacs['param'] = { 'a': a, 'b':b }
                    mol.virtual_sites3.append(vs3)
                    _add_info(mol, curr_sec, mol.virtual_sites3)

                elif curr_sec in ('exclusions',):
                    ai = int(fields[0])
                    other = list(map(int, fields[1:]))

                    exc = blocks.Exclusion()
                    exc.main_atom  = mol.atoms[ai-1]
                    exc.other_atoms= [mol.atoms[k-1] for k in other]

                    mol.exclusions.append(exc)
                    _add_info(mol, curr_sec, mol.exclusions)

                elif curr_sec in ('constrainttypes', 'constraints'):
                    '''
                    section     #at     fu      #param
                    ----------------------------------
                    constraints 2       1       1
                    constraints 2       2       1
                    '''

                    ai, aj = fields[:2]
                    fu = int(fields[2])
                    assert fu in (1,2)

                    cons = blocks.ConstraintType('gromacs')

                    # TODO: what's different between 1 and 2
                    if fu in [1, 2]:
                        if curr_sec == 'constrainttypes':
                            cons.atype1 = ai
                            cons.atype2 = aj
                            b0 = float(fields[3])
                            cons.gromacs = {'param':{'b0':b0}, 'func': fu}

                            self.constrainttypes.append(cons)
                            _add_info(self, curr_sec, self.constrainttypes)

                        elif curr_sec == 'constraints':
                            ai, aj = list(map(int, fields[:2]))
                            cons.atom1 = mol.atoms[ai-1]
                            cons.atom2 = mol.atoms[aj-1]
                            cons.gromacs['func'] = fu

                            mol.constraints.append(cons)
                            _add_info(mol, curr_sec, mol.constraints)

                        else:
                            raise ValueError
                    else:
                        raise ValueError

                elif curr_sec in ('position_restraints',
                                  'distance_restraints',
                                  'dihedral_restraints',
                                  'orientation_restraints',
                                  'angle_restraints',
                                  'angle_restraints_z'):
                    pass

                elif curr_sec in ('implicit_genborn_params',):
                    '''
                    attype   sar     st      pi      gbr      hct
                    '''
                    pass

                elif curr_sec == 'system':
                    #assert len(fields) == 1
                    self.name = fields[0]

                elif curr_sec == 'molecules':
                    assert len(fields) == 2
                    mname, nmol = fields[0], int(fields[1])

                    # if the number of a molecule is more than 1, add copies to system.molecules
                    for i in range(nmol):
                        self.molecules.append(self.dict_molname_mol[mname])

                else:
                    raise NotImplementedError('Unknown section in topology: {0}'.format(curr_sec))

        # process cmap_lines
        curr_cons = None
        for line in cmap_lines:

            # cmaptype opening line
            if len(line.split()) == 8:
                cons = blocks.CMapType('gromacs')

                atype1, atype2, atype3, atype4, atype8, func, sizeX, sizeY = line.replace("\\","").split()
                func, sizeX, sizeY = int(func), int(sizeX), int(sizeY)
                cons.atype1 = atype1
                cons.atype2 = atype2
                cons.atype3 = atype3
                cons.atype4 = atype4
                cons.atype8 = atype8
                cons.gromacs = {'param':[], 'func': func}

                curr_cons = cons

            # cmap body
            elif len(line.split()) == 10:
                cmap_param = map(float, line.replace("\\","").split())
                cons.gromacs['param'] += cmap_param

            # cmaptype cloning line
            elif len(line.split()) == 6:
                cmap_param = map(float, line.replace("\\","").split())
                cons.gromacs['param'] += cmap_param
                self.cmaptypes.append(curr_cons)
            else:
                raise ValueError


Instruction:
Can you generate a brief explanation for the following Python 3 code
def assemble_topology(self):
        self.logger.debug("starting to assemble topology...")

        top = ''

        self.logger.debug("making atom/pair/bond/angle/dihedral/improper types")
        top += self.toptemplate
        top = top.replace('*DEFAULTS*',       ''.join( self._make_defaults(self.system)) )
        top = top.replace('*ATOMTYPES*',      ''.join( self._make_atomtypes(self.system)) )
        top = top.replace('*NONBOND_PARAM*',  ''.join( self._make_nonbond_param(self.system)) )
        top = top.replace('*PAIRTYPES*',      ''.join( self._make_pairtypes(self.system)) )
        top = top.replace('*BONDTYPES*',      ''.join( self._make_bondtypes(self.system)) )
        top = top.replace('*CONSTRAINTTYPES*',''.join( self._make_constrainttypes(self.system)))
        top = top.replace('*ANGLETYPES*',     ''.join( self._make_angletypes(self.system)))
        top = top.replace('*DIHEDRALTYPES*',  ''.join( self._make_dihedraltypes(self.system)) )
        top = top.replace('*IMPROPERTYPES*',  ''.join( self._make_impropertypes(self.system)) )
        top = top.replace('*CMAPTYPES*',      ''.join( self._make_cmaptypes(self.system)) )

        for i,(molname,m) in enumerate(self.system.dict_molname_mol.items()):

            itp = self.itptemplate
            itp = itp.replace('*MOLECULETYPE*',  ''.join( self._make_moleculetype(m, molname, m.exclusion_numb))  )
            itp = itp.replace('*ATOMS*',         ''.join( self._make_atoms(m))  )
            itp = itp.replace('*BONDS*',         ''.join( self._make_bonds(m))  )
            itp = itp.replace('*PAIRS*',         ''.join( self._make_pairs(m))  )
            itp = itp.replace('*SETTLES*',       ''.join( self._make_settles(m))  )
            itp = itp.replace('*VIRTUAL_SITES3*',''.join( self._make_virtual_sites3(m))  )
            itp = itp.replace('*EXCLUSIONS*',    ''.join( self._make_exclusions(m))  )
            itp = itp.replace('*ANGLES*',        ''.join( self._make_angles(m)) )
            itp = itp.replace('*DIHEDRALS*',     ''.join( self._make_dihedrals(m)) )
            itp = itp.replace('*IMPROPERS*',     ''.join( self._make_impropers(m)) )
            itp = itp.replace('*CMAPS*',         ''.join( self._make_cmaps(m)) )
            if not self.multiple_output:
                top += itp
            else:
                outfile = "mol_{0}.itp".format(molname)
                top += '#include "mol_{0}.itp" \n'.format( molname )
                with open(outfile, "w") as f:
                    f.writelines([itp])

        top += '\n[system]  \nConvertedSystem\n\n'
        top += '[molecules] \n'
        molecules = [("", 0)]

        for m in self.system.molecules:
            if (molecules[-1][0] != m.name):
                molecules.append([m.name, 0])
            if molecules[-1][0] == m.name:
                molecules[-1][1] += 1

        for molname, n in molecules[1:]:
            top += '{0:s}     {1:d}\n'.format(molname, n)
        top += '\n'

        with open(self.outfile, 'w') as f:
            f.writelines([top])

Response: Assemble the topology into a string


Instruction:
Write a Python 3 function for
building a new topology file from a structure.

Response:
def topology(struct=None, protein='protein',
             top='system.top',  dirname='top',
             posres="posres.itp",
             ff="oplsaa", water="tip4p",
             **pdb2gmx_args):
    """Build Gromacs topology files from pdb.

    :Keywords:
       *struct*
           input structure (**required**)
       *protein*
           name of the output files
       *top*
           name of the topology file
       *dirname*
           directory in which the new topology will be stored
       *ff*
           force field (string understood by ``pdb2gmx``); default
           "oplsaa"
       *water*
           water model (string), default "tip4p"
       *pdb2gmxargs*
           other arguments for ``pdb2gmx``

    .. note::
       At the moment this function simply runs ``pdb2gmx`` and uses
       the resulting topology file directly. If you want to create
       more complicated topologies and maybe also use additional itp
       files or make a protein itp file then you will have to do this
       manually.
    """

    structure = realpath(struct)

    new_struct = protein + '.pdb'
    if posres is None:
        posres = protein + '_posres.itp'

    pdb2gmx_args.update({'f': structure, 'o': new_struct, 'p': top, 'i': posres,
                         'ff': ff, 'water': water})

    with in_dir(dirname):
        logger.info("[{dirname!s}] Building topology {top!r} from struct = {struct!r}".format(**vars()))
        # perhaps parse output from pdb2gmx 4.5.x to get the names of the chain itp files?
        gromacs.pdb2gmx(**pdb2gmx_args)
    return { \
            'top': realpath(dirname, top), \
            'struct': realpath(dirname, new_struct), \
            'posres' : realpath(dirname, posres) }


Instruction:
Create a Python 3 function to
make index file with the special groups. This routine adds the group __main__ and the group __environment__ to the end of the index file. __main__ contains what the user defines as the *central* and *most important* parts of the system. __environment__ is everything else. The template mdp file, for instance, uses these two groups for T-coupling. These groups are mainly useful if the default groups "Protein" and "Non-Protein" are not appropriate. By using symbolic names such as __main__ one can keep scripts more general. :Returns: *groups* is a list of dictionaries that describe the index groups. See :func:`gromacs.cbook.parse_ndxlist` for details. :Arguments: *struct* : filename structure (tpr, pdb, gro) *selection* : string is a ``make_ndx`` command such as ``"Protein"`` or ``r DRG`` which determines what is considered the main group for centering etc. It is passed directly to ``make_ndx``. *ndx* : string name of the final index file *oldndx* : string name of index file that should be used as a basis; if None then the ``make_ndx`` default groups are used. This routine is very dumb at the moment; maybe some heuristics will be added later as could be other symbolic groups such as __membrane__.

Response:
def make_main_index(struct, selection='"Protein"', ndx='main.ndx', oldndx=None):
    """Make index file with the special groups.

    This routine adds the group __main__ and the group __environment__
    to the end of the index file. __main__ contains what the user
    defines as the *central* and *most important* parts of the
    system. __environment__ is everything else.

    The template mdp file, for instance, uses these two groups for T-coupling.

    These groups are mainly useful if the default groups "Protein" and "Non-Protein"
    are not appropriate. By using symbolic names such as __main__ one
    can keep scripts more general.

    :Returns:
      *groups* is a list of dictionaries that describe the index groups. See
      :func:`gromacs.cbook.parse_ndxlist` for details.

    :Arguments:
      *struct* : filename
        structure (tpr, pdb, gro)
      *selection* : string
        is a ``make_ndx`` command such as ``"Protein"`` or ``r DRG`` which
        determines what is considered the main group for centering etc. It is
        passed directly to ``make_ndx``.
      *ndx* : string
         name of the final index file
      *oldndx* : string
         name of index file that should be used as a basis; if None
         then the ``make_ndx`` default groups are used.

    This routine is very dumb at the moment; maybe some heuristics will be
    added later as could be other symbolic groups such as __membrane__.
    """

    logger.info("Building the main index file {ndx!r}...".format(**vars()))

    # pass 1: select
    # get a list of groups
    # need the first "" to get make_ndx to spit out the group list.
    _,out,_ = gromacs.make_ndx(f=struct, n=oldndx, o=ndx, stdout=False,
                                      input=("", "q"))
    groups = cbook.parse_ndxlist(out)

    # find the matching groups,
    # there is a nasty bug in GROMACS where make_ndx may have multiple
    # groups, which caused the previous approach to fail big time.
    # this is a work around the make_ndx bug.
    # striping the "" allows compatibility with existing make_ndx selection commands.
    selection = selection.strip("\"")

    selected_groups = [g for g in groups if g['name'].lower() == selection.lower()]

    if len(selected_groups) > 1:
        logging.warn("make_ndx created duplicated groups, performing work around")

    if len(selected_groups) <= 0:
        msg = "no groups found for selection {0}, available groups are {1}".format(selection, groups)
        logging.error(msg)
        raise ValueError(msg)

    # Found at least one matching group, we're OK

    # index of last group
    last = len(groups) - 1
    assert last == groups[-1]['nr']

    group = selected_groups[0]

    # pass 2:
    # 1) last group is __main__
    # 2) __environment__ is everything else (eg SOL, ions, ...)
    _,out,_ = gromacs.make_ndx(f=struct, n=ndx, o=ndx,
                                      stdout=False,
                                             # make copy selected group, this now has index last + 1
                                      input=("{0}".format(group['nr']),
                                             # rename this to __main__
                                             "name {0} __main__".format(last+1),
                                             # make a complement to this group, it get index last + 2
                                             "! \"__main__\"",
                                             # rename this to __environment__
                                             "name {0} __environment__".format(last+2),
                                             # list the groups
                                             "",
                                             # quit
                                             "q"))
    return cbook.parse_ndxlist(out)


Instruction:
Can you create a Python 3 function that
finds vdwradii. dat and add special entries for lipids.

Response:
def get_lipid_vdwradii(outdir=os.path.curdir, libdir=None):
    """Find vdwradii.dat and add special entries for lipids.

    See :data:`gromacs.setup.vdw_lipid_resnames` for lipid
    resnames. Add more if necessary.
    """
    vdwradii_dat = os.path.join(outdir, "vdwradii.dat")

    if libdir is not None:
        filename = os.path.join(libdir, 'vdwradii.dat')  # canonical name
        if not os.path.exists(filename):
            msg = 'No VDW database file found in {filename!r}.'.format(**vars())
            logger.exception(msg)
            raise OSError(msg, errno.ENOENT)
    else:
        try:
            filename = os.path.join(os.environ['GMXLIB'], 'vdwradii.dat')
        except KeyError:
            try:
                filename = os.path.join(os.environ['GMXDATA'], 'top', 'vdwradii.dat')
            except KeyError:
                msg = "Cannot find vdwradii.dat. Set GMXLIB (point to 'top') or GMXDATA ('share/gromacs')."
                logger.exception(msg)
                raise OSError(msg, errno.ENOENT)
    if not os.path.exists(filename):
        msg = "Cannot find {filename!r}; something is wrong with the Gromacs installation.".format(**vars())
        logger.exception(msg, errno.ENOENT)
        raise OSError(msg)

    # make sure to catch 3 and 4 letter resnames
    patterns = vdw_lipid_resnames + list({x[:3] for x in vdw_lipid_resnames})
    # TODO: should do a tempfile...
    with open(vdwradii_dat, 'w') as outfile:
        # write lipid stuff before general
        outfile.write('; Special larger vdw radii for solvating lipid membranes\n')
        for resname in patterns:
            for atom,radius in vdw_lipid_atom_radii.items():
                outfile.write('{resname:4!s} {atom:<5!s} {radius:5.3f}\n'.format(**vars()))
        with open(filename, 'r') as infile:
            for line in infile:
                outfile.write(line)
    logger.debug('Created lipid vdW radii file {vdwradii_dat!r}.'.format(**vars()))
    return realpath(vdwradii_dat)


Instruction:
Create a Python 3 function for
putting protein into box, add water, add counter-ions. Currently this really only supports solutes in water. If you need to embedd a protein in a membrane then you will require more sophisticated approaches. However, you *can* supply a protein already inserted in a bilayer. In this case you will probably want to set *distance* = ``None`` and also enable *with_membrane* = ``True`` (using extra big vdw radii for typical lipids). .. Note:: The defaults are suitable for solvating a globular protein in a fairly tight (increase *distance*!) dodecahedral box. :Arguments: *struct* : filename pdb or gro input structure *top* : filename Gromacs topology *distance* : float When solvating with water, make the box big enough so that at least *distance* nm water are between the solute *struct* and the box boundary. Set *boxtype* to ``None`` in order to use a box size in the input file (gro or pdb). *boxtype* or *bt*: string Any of the box types supported by :class:`~gromacs.tools.Editconf` (triclinic, cubic, dodecahedron, octahedron). Set the box dimensions either with *distance* or the *box* and *angle* keywords. If set to ``None`` it will ignore *distance* and use the box inside the *struct* file. *bt* overrides the value of *boxtype*. *box* List of three box lengths [A,B,C] that are used by :class:`~gromacs.tools.Editconf` in combination with *boxtype* (``bt`` in :program:`editconf`) and *angles*. Setting *box* overrides *distance*. *angles* List of three angles (only necessary for triclinic boxes). *concentration* : float Concentration of the free ions in mol/l. Note that counter ions are added in excess of this concentration. *cation* and *anion* : string Molecule names of the ions. This depends on the chosen force field. *water* : string Name of the water model; one of "spc", "spce", "tip3p", "tip4p". This should be appropriate for the chosen force field. If an alternative solvent is required, simply supply the path to a box with solvent molecules (used by :func:`~gromacs.genbox`'s *cs* argument) and also supply the molecule name via *solvent_name*. *solvent_name* Name of the molecules that make up the solvent (as set in the itp/top). Typically needs to be changed when using non-standard/non-water solvents. ["SOL"] *with_membrane* : bool ``True``: use special ``vdwradii.dat`` with 0.1 nm-increased radii on lipids. Default is ``False``. *ndx* : filename How to name the index file that is produced by this function. *mainselection* : string A string that is fed to :class:`~gromacs.tools.Make_ndx` and which should select the solute. *dirname* : directory name Name of the directory in which all files for the solvation stage are stored. *includes* List of additional directories to add to the mdp include path *kwargs* Additional arguments are passed on to :class:`~gromacs.tools.Editconf` or are interpreted as parameters to be changed in the mdp file.

Response:
def solvate(struct='top/protein.pdb', top='top/system.top',
            distance=0.9, boxtype='dodecahedron',
            concentration=0, cation='NA', anion='CL',
            water='tip4p', solvent_name='SOL', with_membrane=False,
            ndx = 'main.ndx', mainselection = '"Protein"',
            dirname='solvate',
            **kwargs):
    """Put protein into box, add water, add counter-ions.

    Currently this really only supports solutes in water. If you need
    to embedd a protein in a membrane then you will require more
    sophisticated approaches.

    However, you *can* supply a protein already inserted in a
    bilayer. In this case you will probably want to set *distance* =
    ``None`` and also enable *with_membrane* = ``True`` (using extra
    big vdw radii for typical lipids).

    .. Note:: The defaults are suitable for solvating a globular
       protein in a fairly tight (increase *distance*!) dodecahedral
       box.

    :Arguments:
      *struct* : filename
          pdb or gro input structure
      *top* : filename
          Gromacs topology
      *distance* : float
          When solvating with water, make the box big enough so that
          at least *distance* nm water are between the solute *struct*
          and the box boundary.
          Set *boxtype*  to ``None`` in order to use a box size in the input
          file (gro or pdb).
      *boxtype* or *bt*: string
          Any of the box types supported by :class:`~gromacs.tools.Editconf`
          (triclinic, cubic, dodecahedron, octahedron). Set the box dimensions
          either with *distance* or the *box* and *angle* keywords.

          If set to ``None`` it will ignore *distance* and use the box
          inside the *struct* file.

          *bt* overrides the value of *boxtype*.
      *box*
          List of three box lengths [A,B,C] that are used by :class:`~gromacs.tools.Editconf`
          in combination with *boxtype* (``bt`` in :program:`editconf`) and *angles*.
          Setting *box* overrides *distance*.
      *angles*
          List of three angles (only necessary for triclinic boxes).
      *concentration* : float
          Concentration of the free ions in mol/l. Note that counter
          ions are added in excess of this concentration.
      *cation* and *anion* : string
          Molecule names of the ions. This depends on the chosen force field.
      *water* : string
          Name of the water model; one of "spc", "spce", "tip3p",
          "tip4p". This should be appropriate for the chosen force
          field. If an alternative solvent is required, simply supply the path to a box
          with solvent molecules (used by :func:`~gromacs.genbox`'s  *cs* argument)
          and also supply the molecule name via *solvent_name*.
      *solvent_name*
          Name of the molecules that make up the solvent (as set in the itp/top).
          Typically needs to be changed when using non-standard/non-water solvents.
          ["SOL"]
      *with_membrane* : bool
           ``True``: use special ``vdwradii.dat`` with 0.1 nm-increased radii on
           lipids. Default is ``False``.
      *ndx* : filename
          How to name the index file that is produced by this function.
      *mainselection* : string
          A string that is fed to :class:`~gromacs.tools.Make_ndx` and
          which should select the solute.
      *dirname* : directory name
          Name of the directory in which all files for the solvation stage are stored.
      *includes*
          List of additional directories to add to the mdp include path
      *kwargs*
          Additional arguments are passed on to
          :class:`~gromacs.tools.Editconf` or are interpreted as parameters to be
          changed in the mdp file.

    """
    sol = solvate_sol(struct=struct, top=top,
                      distance=distance, boxtype=boxtype,
                      water=water, solvent_name=solvent_name,
                      with_membrane=with_membrane,
                      dirname=dirname, **kwargs)

    ion = solvate_ion(struct=sol['struct'], top=top,
                      concentration=concentration, cation=cation, anion=anion,
                      solvent_name=solvent_name, ndx=ndx,
                      mainselection=mainselection, dirname=dirname,
                      **kwargs)
    return ion


Instruction:
Given the following Python 3 function, write the documentation
def check_mdpargs(d):
    if len(d) > 0:
        wmsg = "Unprocessed mdp option are interpreted as options for grompp:\n"+str(d)
        logger.warn(wmsg)
        warnings.warn(wmsg, category=UsageWarning)
    return len(d) == 0

Response: Check if any arguments remain in dict *d*.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def energy_minimize(dirname='em', mdp=config.templates['em.mdp'],
                    struct='solvate/ionized.gro', top='top/system.top',
                    output='em.pdb', deffnm="em",
                    mdrunner=None, mdrun_args=None,
                    **kwargs):
    """Energy minimize the system.

    This sets up the system (creates run input files) and also runs
    ``mdrun_d``. Thus it can take a while.

    Additional itp files should be in the same directory as the top file.

    Many of the keyword arguments below already have sensible values.

    :Keywords:
       *dirname*
          set up under directory dirname [em]
       *struct*
          input structure (gro, pdb, ...) [solvate/ionized.gro]
       *output*
          output structure (will be put under dirname) [em.pdb]
       *deffnm*
          default name for mdrun-related files [em]
       *top*
          topology file [top/system.top]
       *mdp*
          mdp file (or use the template) [templates/em.mdp]
       *includes*
          additional directories to search for itp files
       *mdrunner*
          :class:`gromacs.run.MDrunner` instance; by default we
          just try :func:`gromacs.mdrun_d` and :func:`gromacs.mdrun` but a
          MDrunner instance gives the user the ability to run mpi jobs
          etc. [None]
       *mdrun_args*
          arguments for *mdrunner* (as a dict), e.g. ``{'nt': 2}``;
          empty by default

          .. versionaddedd:: 0.7.0

       *kwargs*
          remaining key/value pairs that should be changed in the
          template mdp file, eg ``nstxtcout=250, nstfout=250``.

    .. note:: If :func:`~gromacs.mdrun_d` is not found, the function
              falls back to :func:`~gromacs.mdrun` instead.
    """

    structure = realpath(struct)
    topology = realpath(top)
    mdp_template = config.get_template(mdp)
    deffnm = deffnm.strip()

    mdrun_args = {} if mdrun_args is None else mdrun_args

    # write the processed topology to the default output
    kwargs.setdefault('pp', 'processed.top')

    # filter some kwargs that might come through when feeding output
    # from previous stages such as solvate(); necessary because *all*
    # **kwargs must be *either* substitutions in the mdp file *or* valid
    # command line parameters for ``grompp``.
    kwargs.pop('ndx', None)
    # mainselection is not used but only passed through; right now we
    # set it to the default that is being used in all argument lists
    # but that is not pretty. TODO.
    mainselection = kwargs.pop('mainselection', '"Protein"')
    # only interesting when passed from solvate()
    qtot = kwargs.pop('qtot', 0)

    # mdp is now the *output* MDP that will be generated from mdp_template
    mdp = deffnm+'.mdp'
    tpr = deffnm+'.tpr'

    logger.info("[{dirname!s}] Energy minimization of struct={struct!r}, top={top!r}, mdp={mdp!r} ...".format(**vars()))

    cbook.add_mdp_includes(topology, kwargs)

    if qtot != 0:
        # At the moment this is purely user-reported and really only here because
        # it might get fed into the function when using the keyword-expansion pipeline
        # usage paradigm.
        wmsg = "Total charge was reported as qtot = {qtot:g} <> 0; probably a problem.".format(**vars())
        logger.warn(wmsg)
        warnings.warn(wmsg, category=BadParameterWarning)

    with in_dir(dirname):
        unprocessed = cbook.edit_mdp(mdp_template, new_mdp=mdp, **kwargs)
        check_mdpargs(unprocessed)
        gromacs.grompp(f=mdp, o=tpr, c=structure, r=structure, p=topology, **unprocessed)
        mdrun_args.update(v=True, stepout=10, deffnm=deffnm, c=output)
        if mdrunner is None:
            mdrun = run.get_double_or_single_prec_mdrun()
            mdrun(**mdrun_args)
        else:
            if type(mdrunner) is type:
                # class
                # user wants full control and provides simulation.MDrunner **class**
                # NO CHECKING --- in principle user can supply any callback they like
                mdrun = mdrunner(**mdrun_args)
                mdrun.run()
            else:
                # anything with a run() method that takes mdrun arguments...
                try:
                    mdrunner.run(mdrunargs=mdrun_args)
                except AttributeError:
                    logger.error("mdrunner: Provide a gromacs.run.MDrunner class or instance or a callback with a run() method")
                    raise TypeError("mdrunner: Provide a gromacs.run.MDrunner class or instance or a callback with a run() method")

        # em.gro --> gives 'Bad box in file em.gro' warning --- why??
        # --> use em.pdb instead.
        if not os.path.exists(output):
            errmsg = "Energy minimized system NOT produced."
            logger.error(errmsg)
            raise GromacsError(errmsg)
        final_struct = realpath(output)

    logger.info("[{dirname!s}] energy minimized structure {final_struct!r}".format(**vars()))
    return {'struct': final_struct,
            'top': topology,
            'mainselection': mainselection,
            }

Response: Energy minimize the system.


Instruction:
Make a summary of the following Python 3 code
def em_schedule(**kwargs):

    mdrunner = kwargs.pop('mdrunner', None)
    integrators = kwargs.pop('integrators', ['l-bfgs', 'steep'])
    kwargs.pop('integrator', None)  # clean input; we set intgerator from integrators
    nsteps = kwargs.pop('nsteps', [100, 1000])

    outputs = ['em{0:03d}_{1!s}.pdb'.format(i, integrator) for i,integrator in enumerate(integrators)]
    outputs[-1] = kwargs.pop('output', 'em.pdb')

    files = {'struct': kwargs.pop('struct', None)}  # fake output from energy_minimize()

    for i, integrator in enumerate(integrators):
        struct = files['struct']
        logger.info("[em %d] energy minimize with %s for maximum %d steps", i, integrator, nsteps[i])
        kwargs.update({'struct':struct, 'output':outputs[i],
                       'integrator':integrator, 'nsteps': nsteps[i]})
        if not integrator == 'l-bfgs':
            kwargs['mdrunner'] = mdrunner
        else:
            kwargs['mdrunner'] = None
            logger.warning("[em %d]  Not using mdrunner for L-BFGS because it cannot "
                           "do parallel runs.", i)

        files = energy_minimize(**kwargs)

    return files

Response: Run multiple energy minimizations one after each other.


Instruction:
Can you tell what is the following Python 3 function doing
def _setup_MD(dirname,
              deffnm='md', mdp=config.templates['md_OPLSAA.mdp'],
              struct=None,
              top='top/system.top', ndx=None,
              mainselection='"Protein"',
              qscript=config.qscript_template, qname=None, startdir=None, mdrun_opts="", budget=None, walltime=1/3.,
              dt=0.002, runtime=1e3, **mdp_kwargs):
    """Generic function to set up a ``mdrun`` MD simulation.

    See the user functions for usage.
    """

    if struct is None:
        raise ValueError('struct must be set to a input structure')
    structure = realpath(struct)
    topology = realpath(top)
    try:
        index = realpath(ndx)
    except AttributeError:  # (that's what realpath(None) throws...)
        index = None        # None is handled fine below

    qname = mdp_kwargs.pop('sgename', qname)    # compatibility for old scripts
    qscript = mdp_kwargs.pop('sge', qscript)    # compatibility for old scripts
    qscript_template = config.get_template(qscript)
    mdp_template = config.get_template(mdp)

    nsteps = int(float(runtime)/float(dt))

    mdp = deffnm + '.mdp'
    tpr = deffnm + '.tpr'
    mainindex = deffnm + '.ndx'
    final_structure = deffnm + '.gro'   # guess... really depends on templates,could also be DEFFNM.pdb

    # write the processed topology to the default output
    mdp_parameters = {'nsteps':nsteps, 'dt':dt, 'pp': 'processed.top'}
    mdp_parameters.update(mdp_kwargs)

    cbook.add_mdp_includes(topology, mdp_parameters)

    logger.info("[%(dirname)s] input mdp  = %(mdp_template)r", vars())
    with in_dir(dirname):
        if not (mdp_parameters.get('Tcoupl','').lower() == 'no' or mainselection is None):
            logger.info("[{dirname!s}] Automatic adjustment of T-coupling groups".format(**vars()))

            # make index file in almost all cases; with mainselection == None the user
            # takes FULL control and also has to provide the template or index
            groups = make_main_index(structure, selection=mainselection,
                                     oldndx=index, ndx=mainindex)
            natoms = {g['name']: float(g['natoms']) for g in groups}
            tc_group_names = ('__main__', '__environment__')   # defined in make_main_index()
            try:
                x = natoms['__main__']/natoms['__environment__']
            except KeyError:
                x = 0   # force using SYSTEM in code below
                wmsg = "Missing __main__ and/or __environment__ index group.\n" \
                       "This probably means that you have an atypical system. You can " \
                       "set mainselection=None and provide your own mdp and index files " \
                       "in order to set up temperature coupling.\n" \
                       "If no T-coupling is required then set Tcoupl='no'.\n" \
                       "For now we will just couple everything to 'System'."
                logger.warn(wmsg)
                warnings.warn(wmsg, category=AutoCorrectionWarning)
            if x < 0.1:
                # couple everything together
                tau_t = firstof(mdp_parameters.pop('tau_t', 0.1))
                ref_t = firstof(mdp_parameters.pop('ref_t', 300))
                # combine all in one T-coupling group
                mdp_parameters['tc-grps'] = 'System'
                mdp_parameters['tau_t'] = tau_t   # this overrides the commandline!
                mdp_parameters['ref_t'] = ref_t   # this overrides the commandline!
                mdp_parameters['gen-temp'] = mdp_parameters.pop('gen_temp', ref_t)
                wmsg = "Size of __main__ is only %.1f%% of __environment__ so " \
                       "we use 'System' for T-coupling and ref_t = %g K and " \
                       "tau_t = %g 1/ps (can be changed in mdp_parameters).\n" \
                       % (x * 100, ref_t, tau_t)
                logger.warn(wmsg)
                warnings.warn(wmsg, category=AutoCorrectionWarning)
            else:
                # couple protein and bath separately
                n_tc_groups = len(tc_group_names)
                tau_t = asiterable(mdp_parameters.pop('tau_t', 0.1))
                ref_t = asiterable(mdp_parameters.pop('ref_t', 300))

                if len(tau_t) != n_tc_groups:
                    tau_t = n_tc_groups * [tau_t[0]]
                    wmsg = "%d coupling constants should have been supplied for tau_t. "\
                        "Using %f 1/ps for all of them." % (n_tc_groups, tau_t[0])
                    logger.warn(wmsg)
                    warnings.warn(wmsg, category=AutoCorrectionWarning)
                if len(ref_t) != n_tc_groups:
                    ref_t = n_tc_groups * [ref_t[0]]
                    wmsg = "%d temperatures should have been supplied for ref_t. "\
                        "Using %g K for all of them." % (n_tc_groups, ref_t[0])
                    logger.warn(wmsg)
                    warnings.warn(wmsg, category=AutoCorrectionWarning)

                mdp_parameters['tc-grps'] = tc_group_names
                mdp_parameters['tau_t'] = tau_t
                mdp_parameters['ref_t'] = ref_t
                mdp_parameters['gen-temp'] = mdp_parameters.pop('gen_temp', ref_t[0])
            index = realpath(mainindex)
        if mdp_parameters.get('Tcoupl','').lower() == 'no':
            logger.info("Tcoupl == no: disabling all temperature coupling mdp options")
            mdp_parameters['tc-grps'] = ""
            mdp_parameters['tau_t'] = ""
            mdp_parameters['ref_t'] = ""
            mdp_parameters['gen-temp'] = ""
        if mdp_parameters.get('Pcoupl','').lower() == 'no':
            logger.info("Pcoupl == no: disabling all pressure coupling mdp options")
            mdp_parameters['tau_p'] = ""
            mdp_parameters['ref_p'] = ""
            mdp_parameters['compressibility'] = ""

        unprocessed = cbook.edit_mdp(mdp_template, new_mdp=mdp, **mdp_parameters)
        check_mdpargs(unprocessed)
        gromacs.grompp(f=mdp, p=topology, c=structure, n=index, o=tpr, **unprocessed)

        runscripts = qsub.generate_submit_scripts(
            qscript_template, deffnm=deffnm, jobname=qname, budget=budget,
            startdir=startdir, mdrun_opts=mdrun_opts, walltime=walltime)

    logger.info("[%(dirname)s] output mdp = %(mdp)r", vars())
    logger.info("[%(dirname)s] output ndx = %(ndx)r", vars())
    logger.info("[%(dirname)s] output tpr = %(tpr)r", vars())
    logger.info("[%(dirname)s] output runscripts = %(runscripts)r", vars())
    logger.info("[%(dirname)s] All files set up for a run time of %(runtime)g ps "
                "(dt=%(dt)g, nsteps=%(nsteps)g)" % vars())

    kwargs = {'struct': realpath(os.path.join(dirname, final_structure)),      # guess
              'top': topology,
              'ndx': index,            # possibly mainindex
              'qscript': runscripts,
              'mainselection': mainselection,
              'deffnm': deffnm,        # return deffnm (tpr = deffnm.tpr!)
              }
    kwargs.update(mdp_kwargs)  # return extra mdp args so that one can use them for prod run
    return kwargs

Response: This function is used to setup a new MD simulation.


Instruction:
Can you write a function in Python 3 where it
sets up MD with position restraints.

Response:
def MD_restrained(dirname='MD_POSRES', **kwargs):
    """Set up MD with position restraints.

    Additional itp files should be in the same directory as the top file.

    Many of the keyword arguments below already have sensible values. Note that
    setting *mainselection* = ``None`` will disable many of the automated
    choices and is often recommended when using your own mdp file.

    :Keywords:
       *dirname*
          set up under directory dirname [MD_POSRES]
       *struct*
          input structure (gro, pdb, ...) [em/em.pdb]
       *top*
          topology file [top/system.top]
       *mdp*
          mdp file (or use the template) [templates/md.mdp]
       *ndx*
          index file (supply when using a custom mdp)
       *includes*
          additional directories to search for itp files
       *mainselection*
          :program:`make_ndx` selection to select main group ["Protein"]
          (If ``None`` then no canonical index file is generated and
          it is the user's responsibility to set *tc_grps*,
          *tau_t*, and *ref_t* as keyword arguments, or provide the mdp template
          with all parameter pre-set in *mdp* and probably also your own *ndx*
          index file.)
       *deffnm*
          default filename for Gromacs run [md]
       *runtime*
          total length of the simulation in ps [1000]
       *dt*
          integration time step in ps [0.002]
       *qscript*
          script to submit to the queuing system; by default
          uses the template :data:`gromacs.config.qscript_template`, which can
          be manually set to another template from :data:`gromacs.config.templates`;
          can also be a list of template names.
       *qname*
          name to be used for the job in the queuing system [PR_GMX]
       *mdrun_opts*
          option flags for the :program:`mdrun` command in the queuing system
          scripts such as "-stepout 100". [""]
       *kwargs*
          remaining key/value pairs that should be changed in the template mdp
          file, eg ``nstxtcout=250, nstfout=250`` or command line options for
          ``grompp` such as ``maxwarn=1``.

          In particular one can also set **define** and activate
          whichever position restraints have been coded into the itp
          and top file. For instance one could have

             *define* = "-DPOSRES_MainChain -DPOSRES_LIGAND"

          if these preprocessor constructs exist. Note that there
          **must not be any space between "-D" and the value.**

          By default *define* is set to "-DPOSRES".

    :Returns: a dict that can be fed into :func:`gromacs.setup.MD`
              (but check, just in case, especially if you want to
              change the ``define`` parameter in the mdp file)

    .. Note:: The output frequency is drastically reduced for position
              restraint runs by default. Set the corresponding ``nst*``
              variables if you require more output. The `pressure coupling`_
              option *refcoord_scaling* is set to "com" by default (but can
              be changed via *kwargs*) and the pressure coupling
              algorithm itself is set to *Pcoupl* = "Berendsen" to
              run a stable simulation.

    .. _`pressure coupling`: http://manual.gromacs.org/online/mdp_opt.html#pc
    """

    logger.info("[{dirname!s}] Setting up MD with position restraints...".format(**vars()))
    kwargs.setdefault('struct', 'em/em.pdb')
    kwargs.setdefault('qname', 'PR_GMX')
    kwargs.setdefault('define', '-DPOSRES')
    # reduce size of output files
    kwargs.setdefault('nstxout', '50000')   # trr pos
    kwargs.setdefault('nstvout', '50000')   # trr veloc
    kwargs.setdefault('nstfout', '0')       # trr forces
    kwargs.setdefault('nstlog', '500')      # log file
    kwargs.setdefault('nstenergy', '2500')  # edr energy
    kwargs.setdefault('nstxtcout', '5000')  # xtc pos
    # try to get good pressure equilibration
    kwargs.setdefault('refcoord_scaling', 'com')
    kwargs.setdefault('Pcoupl', "Berendsen")

    new_kwargs =  _setup_MD(dirname, **kwargs)

    # clean up output kwargs
    new_kwargs.pop('define', None)          # but make sure that -DPOSRES does not stay...
    new_kwargs.pop('refcoord_scaling', None)
    new_kwargs.pop('Pcoupl', None)
    return new_kwargs


Instruction:
Here you have a function in Python 3, explain what it does
def MD(dirname='MD', **kwargs):

    logger.info("[{dirname!s}] Setting up MD...".format(**vars()))
    kwargs.setdefault('struct', 'MD_POSRES/md.gro')
    kwargs.setdefault('qname', 'MD_GMX')
    return _setup_MD(dirname, **kwargs)

Response: Set up equilibrium MD.


Instruction:
Implement a Python 3 function for
generating the submit scripts for a queuing system.

Response:
def generate_submit_scripts(templates, prefix=None, deffnm='md', jobname='MD', budget=None,
                            mdrun_opts=None, walltime=1.0, jobarray_string=None, startdir=None,
                            npme=None, **kwargs):
    """Write scripts for queuing systems.

    This sets up queuing system run scripts with a simple search and replace in
    templates. See :func:`gromacs.cbook.edit_txt` for details. Shell scripts
    are made executable.

    :Arguments:
      *templates*
          Template file or list of template files. The "files" can also be names
          or symbolic names for templates in the templates directory. See
          :mod:`gromacs.config` for details and rules for writing templates.
      *prefix*
          Prefix for the final run script filename; by default the filename will be
          the same as the template. [None]
      *dirname*
          Directory in which to place the submit scripts. [.]
      *deffnm*
          Default filename prefix for :program:`mdrun` ``-deffnm`` [md]
      *jobname*
          Name of the job in the queuing system. [MD]
      *budget*
          Which budget to book the runtime on [None]
      *startdir*
          Explicit path on the remote system (for run scripts that need to `cd`
          into this directory at the beginning of execution) [None]
      *mdrun_opts*
          String of additional options for :program:`mdrun`.
      *walltime*
          Maximum runtime of the job in hours. [1]
      *npme*
          number of PME nodes
      *jobarray_string*
          Multi-line string that is spliced in for job array functionality
          (see :func:`gromacs.qsub.generate_submit_array`; do not use manually)
      *kwargs*
          all other kwargs are ignored

    :Returns: list of generated run scripts
    """
    if not jobname[0].isalpha():
        jobname = 'MD_'+jobname
        wmsg = "To make the jobname legal it must start with a letter: changed to {0!r}".format(jobname)
        logger.warn(wmsg)
        warnings.warn(wmsg, category=AutoCorrectionWarning)
    if prefix is None:
        prefix = ""
    if mdrun_opts is not None:
        mdrun_opts = '"'+str(mdrun_opts)+'"'  # TODO: could test if quotes already present

    dirname = kwargs.pop('dirname', os.path.curdir)

    wt = Timedelta(hours=walltime)
    walltime = wt.strftime("%h:%M:%S")
    wall_hours = wt.ashours

    def write_script(template):
        submitscript = os.path.join(dirname, prefix + os.path.basename(template))
        logger.info("Setting up queuing system script {submitscript!r}...".format(**vars()))
        # These substitution rules are documented for the user in the module doc string
        qsystem = detect_queuing_system(template)
        if qsystem is not None and (qsystem.name == 'Slurm'):
            cbook.edit_txt(template,
                           [('^ *DEFFNM=','(?<==)(.*)', deffnm),
                            ('^#.*(-J)', '((?<=-J\s))\s*\w+', jobname),
                            ('^#.*(-A|account_no)', '((?<=-A\s)|(?<=account_no\s))\s*\w+', budget),
                            ('^#.*(-t)', '(?<=-t\s)(\d+:\d+:\d+)', walltime),
                            ('^ *WALL_HOURS=', '(?<==)(.*)', wall_hours),
                            ('^ *STARTDIR=', '(?<==)(.*)', startdir),
                            ('^ *NPME=', '(?<==)(.*)', npme),
                            ('^ *MDRUN_OPTS=', '(?<==)("")', mdrun_opts),  # only replace literal ""
                            ('^# JOB_ARRAY_PLACEHOLDER', '^.*$', jobarray_string),
                            ],
                           newname=submitscript)
            ext = os.path.splitext(submitscript)[1]
        else:
            cbook.edit_txt(template,
                           [('^ *DEFFNM=','(?<==)(.*)', deffnm),
                            ('^#.*(-N|job_name)', '((?<=-N\s)|(?<=job_name\s))\s*\w+', jobname),
                            ('^#.*(-A|account_no)', '((?<=-A\s)|(?<=account_no\s))\s*\w+', budget),
                            ('^#.*(-l walltime|wall_clock_limit)', '(?<==)(\d+:\d+:\d+)', walltime),
                            ('^ *WALL_HOURS=', '(?<==)(.*)', wall_hours),
                            ('^ *STARTDIR=', '(?<==)(.*)', startdir),
                            ('^ *NPME=', '(?<==)(.*)', npme),
                            ('^ *MDRUN_OPTS=', '(?<==)("")', mdrun_opts),  # only replace literal ""
                            ('^# JOB_ARRAY_PLACEHOLDER', '^.*$', jobarray_string),
                           ],
                           newname=submitscript)
            ext = os.path.splitext(submitscript)[1]
        if ext in ('.sh', '.csh', '.bash'):
            os.chmod(submitscript, 0o755)
        return submitscript

    return [write_script(template) for template in config.get_templates(templates)]


Instruction:
Write a Python 3 script for
generating a submit script for a single array job.

Response:
def generate_submit_array(templates, directories, **kwargs):
    """Generate a array job.

    For each ``work_dir`` in *directories*, the array job will
     1. cd into ``work_dir``
     2. run the job as detailed in the template
    It will use all the queuing system directives found in the
    template. If more complicated set ups are required, then this
    function cannot be used.

    :Arguments:
       *templates*
          Basic template for a single job; the job array logic is spliced into
          the position of the line ::
              # JOB_ARRAY_PLACEHOLDER
          The appropriate commands for common queuing systems (Sun Gridengine, PBS)
          are hard coded here. The queuing system is detected from the suffix of
          the template.
       *directories*
          List of directories under *dirname*. One task is set up for each
          directory.
       *dirname*
          The array script will be placed in this directory. The *directories*
          **must** be located under *dirname*.
       *kwargs*
          See :func:`gromacs.setup.generate_submit_script` for details.
    """
    dirname = kwargs.setdefault('dirname', os.path.curdir)
    reldirs = [relpath(p, start=dirname) for p in asiterable(directories)]
    missing = [p for p in (os.path.join(dirname, subdir) for subdir in reldirs)
               if not os.path.exists(p)]
    if len(missing) > 0:
        logger.debug("template=%(template)r: dirname=%(dirname)r reldirs=%(reldirs)r", vars())
        logger.error("Some directories are not accessible from the array script: "
                     "%(missing)r", vars())
    def write_script(template):
        qsystem = detect_queuing_system(template)
        if qsystem is None or not qsystem.has_arrays():
            logger.warning("Not known how to make a job array for %(template)r; skipping...", vars())
            return None
        kwargs['jobarray_string'] = qsystem.array(reldirs)
        return generate_submit_scripts(template, **kwargs)[0]   # returns list of length 1

    # must use config.get_templates() because we need to access the file for detecting
    return [write_script(template) for template in config.get_templates(templates)]


Instruction:
Here you have a function in Python 3, explain what it does
def array(self, directories):
        if not self.has_arrays():
            raise NotImplementedError('Not known how make array jobs for '
                                      'queuing system %(name)s' % vars(self))
        hrule = '#'+60*'-'
        lines = [
            '',
            hrule,
            '# job array:',
            self.array_flag(directories),
            hrule,
            '# directories for job tasks',
            'declare -a jobdirs']
        for i,dirname in enumerate(asiterable(directories)):
            idx = i+1   # job array indices are 1-based
            lines.append('jobdirs[{idx:d}]={dirname!r}'.format(**vars()))
        lines.extend([
                '# Switch to the current tasks directory:',
                'wdir="${{jobdirs[${{{array_variable!s}}}]}}"'.format(**vars(self)),
                'cd "$wdir" || { echo "ERROR: failed to enter $wdir."; exit 1; }',
                hrule,
                ''
                ])
        return "\n".join(lines)

Response: Return multiline string for simple array jobs over directories.


Instruction:
Make a summary of the following Python 3 code
def isMine(self, scriptname):
        suffix = os.path.splitext(scriptname)[1].lower()
        if suffix.startswith('.'):
            suffix = suffix[1:]
        return self.suffix == suffix

Response: Primitive queuing system detection ; only looks at suffix at the moment.


Instruction:
How would you implement a function in Python 3 that
returns the atom object corresponding to an anumb number

Response:
def anumb_to_atom(self, anumb):
        '''Returns the atom object corresponding to an atom number'''

        assert isinstance(anumb, int), "anumb must be integer"

        if not self._anumb_to_atom:   # empty dictionary

            if self.atoms:
                for atom in self.atoms:
                    self._anumb_to_atom[atom.number] = atom
                return self._anumb_to_atom[anumb]
            else:
                self.logger("no atoms in the molecule")
                return False

        else:
            if anumb in self._anumb_to_atom:
                return self._anumb_to_atom[anumb]
            else:
                self.logger("no such atom number ({0:d}) in the molecule".format(anumb))
                return False


Instruction:
Given the following Python 3 function, write the documentation
def renumber_atoms(self):
        if self.atoms:

            # reset the mapping
            self._anumb_to_atom = {}

            for i,atom in enumerate(self.atoms):
                atom.number = i+1   # starting from 1

        else:
            self.logger("the number of atoms is zero - no renumbering")

Response: Reset the molecule s atoms : attr : number to be 1 - indexed


Instruction:
Implement a Python 3 function for
computing the total number of unmasked regular pixels in a masks.

Response:
def total_regular_pixels_from_mask(mask):
    """Compute the total number of unmasked regular pixels in a masks."""

    total_regular_pixels = 0

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):
            if not mask[y, x]:
                total_regular_pixels += 1

    return total_regular_pixels


Instruction:
Can you generate a brief explanation for the following Python 3 code
def total_sparse_pixels_from_mask(mask, unmasked_sparse_grid_pixel_centres):

    total_sparse_pixels = 0

    for unmasked_sparse_pixel_index in range(unmasked_sparse_grid_pixel_centres.shape[0]):

        y = unmasked_sparse_grid_pixel_centres[unmasked_sparse_pixel_index, 0]
        x = unmasked_sparse_grid_pixel_centres[unmasked_sparse_pixel_index, 1]

        if not mask[y,x]:
            total_sparse_pixels += 1

    return total_sparse_pixels

Response: This function calculates the total number of pixels which are within the regular - masks of the unmasked pixelization grid and the unmasked pixelization grid s pixel centers.


Instruction:
How would you explain what the following Python 3 function does
def mask_circular_from_shape_pixel_scale_and_radius(shape, pixel_scale, radius_arcsec, centre=(0.0, 0.0)):

    mask = np.full(shape, True)

    centres_arcsec = mask_centres_from_shape_pixel_scale_and_centre(shape=mask.shape, pixel_scale=pixel_scale, centre=centre)

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):

            y_arcsec = (y - centres_arcsec[0]) * pixel_scale
            x_arcsec = (x - centres_arcsec[1]) * pixel_scale

            r_arcsec = np.sqrt(x_arcsec ** 2 + y_arcsec ** 2)

            if r_arcsec <= radius_arcsec:
                mask[y, x] = False

    return mask

Response: Compute a circular mask from an input masks radius and regular shape.


Instruction:
Write a Python 3 function that can
compute an annular mask from an input inner and outer masks radius and regular shape.

Response:
def mask_circular_annular_from_shape_pixel_scale_and_radii(shape, pixel_scale, inner_radius_arcsec, outer_radius_arcsec,
                                                           centre=(0.0, 0.0)):
    """Compute an annular masks from an input inner and outer masks radius and regular shape."""

    mask = np.full(shape, True)

    centres_arcsec = mask_centres_from_shape_pixel_scale_and_centre(shape=mask.shape, pixel_scale=pixel_scale, centre=centre)

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):

            y_arcsec = (y - centres_arcsec[0]) * pixel_scale
            x_arcsec = (x - centres_arcsec[1]) * pixel_scale

            r_arcsec = np.sqrt(x_arcsec ** 2 + y_arcsec ** 2)

            if outer_radius_arcsec >= r_arcsec >= inner_radius_arcsec:
                mask[y, x] = False

    return mask


Instruction:
Make a summary of the following Python 3 code
def mask_elliptical_from_shape_pixel_scale_and_radius(shape, pixel_scale, major_axis_radius_arcsec, axis_ratio, phi,
                                                      centre=(0.0, 0.0)):
    """Compute a circular masks from an input masks radius and regular shape."""

    mask = np.full(shape, True)

    centres_arcsec = mask_centres_from_shape_pixel_scale_and_centre(shape=mask.shape, pixel_scale=pixel_scale,
                                                                  centre=centre)

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):

            y_arcsec = (y - centres_arcsec[0]) * pixel_scale
            x_arcsec = (x - centres_arcsec[1]) * pixel_scale

            r_arcsec_elliptical = elliptical_radius_from_y_x_phi_and_axis_ratio(y_arcsec, x_arcsec, phi, axis_ratio)

            if r_arcsec_elliptical <= major_axis_radius_arcsec:
                mask[y, x] = False

    return mask

Response: Compute a circular mask from an input masks radius and regular shape.


Instruction:
Implement a Python 3 function for
computing a circular mask from an input masks radius and regular shape.

Response:
def mask_elliptical_annular_from_shape_pixel_scale_and_radius(shape, pixel_scale,
                                                              inner_major_axis_radius_arcsec, inner_axis_ratio, inner_phi,
                                                              outer_major_axis_radius_arcsec, outer_axis_ratio, outer_phi,
                                                      centre=(0.0, 0.0)):
    """Compute a circular masks from an input masks radius and regular shape."""

    mask = np.full(shape, True)

    centres_arcsec = mask_centres_from_shape_pixel_scale_and_centre(shape=mask.shape, pixel_scale=pixel_scale,
                                                                  centre=centre)

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):

            y_arcsec = (y - centres_arcsec[0]) * pixel_scale
            x_arcsec = (x - centres_arcsec[1]) * pixel_scale

            inner_r_arcsec_elliptical = elliptical_radius_from_y_x_phi_and_axis_ratio(y_arcsec, x_arcsec,
                                                                                inner_phi, inner_axis_ratio)

            outer_r_arcsec_elliptical = elliptical_radius_from_y_x_phi_and_axis_ratio(y_arcsec, x_arcsec,
                                                                                outer_phi, outer_axis_ratio)

            if inner_r_arcsec_elliptical >= inner_major_axis_radius_arcsec and \
                outer_r_arcsec_elliptical <= outer_major_axis_radius_arcsec:
                mask[y, x] = False

    return mask


Instruction:
Write a Python 3 script to
compute a blurring mask from an input masks and psf shape.

Response:
def mask_blurring_from_mask_and_psf_shape(mask, psf_shape):
    """Compute a blurring masks from an input masks and psf shape.

    The blurring masks corresponds to all pixels which are outside of the masks but will have a fraction of their \
    light blur into the masked region due to PSF convolution."""

    blurring_mask = np.full(mask.shape, True)

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):
            if not mask[y, x]:
                for y1 in range((-psf_shape[0] + 1) // 2, (psf_shape[0] + 1) // 2):
                    for x1 in range((-psf_shape[1] + 1) // 2, (psf_shape[1] + 1) // 2):
                        if 0 <= x + x1 <= mask.shape[1] - 1 and 0 <= y + y1 <= mask.shape[0] - 1:
                            if mask[y + y1, x + x1]:
                                blurring_mask[y + y1, x + x1] = False
                        else:
                            raise exc.MaskException(
                                "setup_blurring_mask extends beyond the sub_grid_size of the masks - pad the "
                                "datas array before masking")

    return blurring_mask


Instruction:
Make a summary of the following Python 3 code
def masked_grid_1d_index_to_2d_pixel_index_from_mask(mask):

    total_regular_pixels = total_regular_pixels_from_mask(mask)
    grid_to_pixel = np.zeros(shape=(total_regular_pixels, 2))
    pixel_count = 0

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):
            if not mask[y, x]:
                grid_to_pixel[pixel_count, :] = y, x
                pixel_count += 1

    return grid_to_pixel

Response: Compute a 1D array that maps every unmasked pixel to its corresponding 2d pixel using its ( y x ) pixel indexes.


Instruction:
Write a Python 3 script to
compute a 1D array that maps every unmasked pixel to its corresponding 2d pixel using its ( y x ) pixel indexes.

Response:
def masked_sub_grid_1d_index_to_2d_sub_pixel_index_from_mask(mask, sub_grid_size):
    """Compute a 1D array that maps every unmasked pixel to its corresponding 2d pixel using its (y,x) pixel indexes.

    For howtolens if pixel [2,5] corresponds to the second pixel on the 1D array, grid_to_pixel[1] = [2,5]"""

    total_sub_pixels = total_sub_pixels_from_mask_and_sub_grid_size(mask=mask, sub_grid_size=sub_grid_size)
    sub_grid_to_sub_pixel = np.zeros(shape=(total_sub_pixels, 2))
    sub_pixel_count = 0

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):
            if not mask[y, x]:
                for y1 in range(sub_grid_size):
                    for x1 in range(sub_grid_size):
                        sub_grid_to_sub_pixel[sub_pixel_count, :] = (y*sub_grid_size)+y1, (x*sub_grid_size)+x1
                        sub_pixel_count += 1

    return sub_grid_to_sub_pixel


Instruction:
Make a summary of the following Python 3 code
def total_edge_pixels_from_mask(mask):

    border_pixel_total = 0

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):
            if not mask[y, x]:
                if mask[y + 1, x] or mask[y - 1, x] or mask[y, x + 1] or mask[y, x - 1] or \
                        mask[y + 1, x + 1] or mask[y + 1, x - 1] or mask[y - 1, x + 1] or mask[y - 1, x - 1]:
                    border_pixel_total += 1

    return border_pixel_total

Response: Compute the total number of borders - pixels in a masks.


Instruction:
Can you implement a function in Python 3 that
computes a 1D array listing all edge pixels in the masks.

Response:
def edge_pixels_from_mask(mask):
    """Compute a 1D array listing all edge pixel indexes in the masks. An edge pixel is a pixel which is not fully \
    surrounding by False masks values i.e. it is on an edge."""

    edge_pixel_total = total_edge_pixels_from_mask(mask)

    edge_pixels = np.zeros(edge_pixel_total)
    edge_index = 0
    regular_index = 0

    for y in range(mask.shape[0]):
        for x in range(mask.shape[1]):
            if not mask[y, x]:
                if mask[y + 1, x] or mask[y - 1, x] or mask[y, x + 1] or mask[y, x - 1] or \
                        mask[y + 1, x + 1] or mask[y + 1, x - 1] or mask[y - 1, x + 1] or mask[y - 1, x - 1]:
                    edge_pixels[edge_index] = regular_index
                    edge_index += 1

                regular_index += 1

    return edge_pixels


Instruction:
Explain what the following Python 3 code does
def total_border_pixels_from_mask_and_edge_pixels(mask, edge_pixels, masked_grid_index_to_pixel):

    border_pixel_total = 0

    for i in range(edge_pixels.shape[0]):

        if check_if_border_pixel(mask, edge_pixels[i], masked_grid_index_to_pixel):
            border_pixel_total += 1

    return border_pixel_total

Response: Compute the total number of borders - pixels in a masks.


Instruction:
Write a Python 3 function that can
compute a 1D array listing all borders pixels in a masked pixel.

Response:
def border_pixels_from_mask(mask):
    """Compute a 1D array listing all borders pixel indexes in the masks. A borders pixel is a pixel which:

     1) is not fully surrounding by False masks values.
     2) Can reach the edge of the array without hitting a masked pixel in one of four directions (upwards, downwards,
     left, right).

     The borders pixels are thus pixels which are on the exterior edge of the masks. For example, the inner ring of edge \
     pixels in an annular masks are edge pixels but not borders pixels."""

    edge_pixels = edge_pixels_from_mask(mask)
    masked_grid_index_to_pixel = masked_grid_1d_index_to_2d_pixel_index_from_mask(mask)

    border_pixel_total = total_border_pixels_from_mask_and_edge_pixels(mask, edge_pixels, masked_grid_index_to_pixel)

    border_pixels = np.zeros(border_pixel_total)

    border_pixel_index = 0

    for edge_pixel_index in range(edge_pixels.shape[0]):

        if check_if_border_pixel(mask, edge_pixels[edge_pixel_index], masked_grid_index_to_pixel):
            border_pixels[border_pixel_index] = edge_pixels[edge_pixel_index]
            border_pixel_index += 1

    return border_pixels


Instruction:
Can you write a function in Python 3 where it
bins up an array to coarser resolution by using the sum value of the new pixel.

Response:
def bin_up_mask_2d(mask_2d, bin_up_factor):
    """Bin up an array to coarser resolution, by binning up groups of pixels and using their sum value to determine \
     the value of the new pixel.

    If an array of shape (8,8) is input and the bin up size is 2, this would return a new array of size (4,4) where \
    every pixel was the sum of each collection of 2x2 pixels on the (8,8) array.

    If binning up the array leads to an edge being cut (e.g. a (9,9) array binned up by 2), an array is first \
    extracted around the centre of that array.

    Parameters
    ----------
    mask_2d : ndarray
        The 2D array that is resized.
    new_shape : (int, int)
        The (y,x) new pixel dimension of the trimmed array.
    origin : (int, int)
        The oigin of the resized array, e.g. the central pixel around which the array is extracted.

    Returns
    -------
    ndarray
        The resized 2D array from the input 2D array.

    Examples
    --------
    array_2d = np.ones((5,5))
    resize_array = resize_array_2d(array_2d=array_2d, new_shape=(2,2), origin=(2, 2))
    """

    padded_array_2d = array_util.pad_2d_array_for_binning_up_with_bin_up_factor(
        array_2d=mask_2d, bin_up_factor=bin_up_factor, pad_value=True)

    binned_array_2d = np.zeros(shape=(padded_array_2d.shape[0] // bin_up_factor,
                                      padded_array_2d.shape[1] // bin_up_factor))

    for y in range(binned_array_2d.shape[0]):
        for x in range(binned_array_2d.shape[1]):
            value = True
            for y1 in range(bin_up_factor):
                for x1 in range(bin_up_factor):
                    padded_y = y*bin_up_factor + y1
                    padded_x = x*bin_up_factor + x1
                    if padded_array_2d[padded_y, padded_x] == False:
                        value = False

            binned_array_2d[y,x] = value

    return binned_array_2d


Instruction:
Implement a Python 3 function for
plotting the model datas_ of an analysis using the lens fit.

Response:
def plot_fit_subplot_lens_plane_only(
        fit, should_plot_mask=True, extract_array_from_mask=False, zoom_around_mask=False, positions=None,
        should_plot_image_plane_pix=False,
        units='arcsec', figsize=None, aspect='square',
        cmap='jet', norm='linear', norm_min=None, norm_max=None, linthresh=0.05, linscale=0.01,
        cb_ticksize=10, cb_fraction=0.047, cb_pad=0.01, cb_tick_values=None, cb_tick_labels=None,
        titlesize=10, xlabelsize=10, ylabelsize=10, xyticksize=10,
        mask_pointsize=10, position_pointsize=10, grid_pointsize=1,
        output_path=None, output_filename='lens_fit', output_format='show'):
    """Plot the model datas_ of an analysis, using the *Fitter* class object.

    The visualization and output type can be fully customized.

    Parameters
    -----------
    fit : autolens.lens.fitting.Fitter
        Class containing fit between the model datas_ and observed lens datas_ (including residual_map, chi_squared_map etc.)
    output_path : str
        The path where the datas_ is output if the output_type is a file format (e.g. png, fits)
    output_filename : str
        The name of the file that is output, if the output_type is a file format (e.g. png, fits)
    output_format : str
        How the datas_ is output. File formats (e.g. png, fits) output the datas_ to harddisk. 'show' displays the datas_ \
        in the python interpreter window.
    """

    rows, columns, figsize_tool = plotter_util.get_subplot_rows_columns_figsize(number_subplots=6)

    mask = lens_plotter_util.get_mask(fit=fit, should_plot_mask=should_plot_mask)

    if figsize is None:
        figsize = figsize_tool

    plt.figure(figsize=figsize)
    plt.subplot(rows, columns, 1)

    kpc_per_arcsec = fit.tracer.image_plane.kpc_per_arcsec

    image_plane_pix_grid = lens_plotter_util.get_image_plane_pix_grid(should_plot_image_plane_pix, fit)

    lens_plotter_util.plot_image(
        fit=fit, mask=mask, extract_array_from_mask=extract_array_from_mask, zoom_around_mask=zoom_around_mask,
        positions=positions, image_plane_pix_grid=image_plane_pix_grid, as_subplot=True,
        units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
        cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
        cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
        cb_tick_values=cb_tick_values, cb_tick_labels=cb_tick_labels,
        titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
        grid_pointsize=grid_pointsize, position_pointsize=position_pointsize, mask_pointsize=mask_pointsize,
        output_path=output_path, output_filename='', output_format=output_format)

    plt.subplot(rows, columns, 2)

    lens_plotter_util.plot_noise_map(
        fit=fit, mask=mask, extract_array_from_mask=extract_array_from_mask, zoom_around_mask=zoom_around_mask,
        positions=positions, as_subplot=True,
        units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
        cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
        cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
        cb_tick_values=cb_tick_values, cb_tick_labels=cb_tick_labels,
        titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
        position_pointsize=position_pointsize, mask_pointsize=mask_pointsize,
        output_path=output_path, output_filename='', output_format=output_format)

    plt.subplot(rows, columns, 3)

    lens_plotter_util.plot_signal_to_noise_map(
        fit=fit, mask=mask, extract_array_from_mask=extract_array_from_mask, zoom_around_mask=zoom_around_mask,
        positions=positions, as_subplot=True,
        units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
        cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
        cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
        cb_tick_values=cb_tick_values, cb_tick_labels=cb_tick_labels,
        titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
        position_pointsize=position_pointsize, mask_pointsize=mask_pointsize,
        output_path=output_path, output_filename='', output_format=output_format)

    plt.subplot(rows, columns, 4)

    lens_plotter_util.plot_model_data(
        fit=fit, mask=mask, extract_array_from_mask=extract_array_from_mask, zoom_around_mask=zoom_around_mask, as_subplot=True,
        units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
        cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
        cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
        cb_tick_values=cb_tick_values, cb_tick_labels=cb_tick_labels,
        titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
        output_path=output_path, output_filename='', output_format=output_format)

    plt.subplot(rows, columns, 5)

    lens_plotter_util.plot_residual_map(
        fit=fit, mask=mask, extract_array_from_mask=extract_array_from_mask, zoom_around_mask=zoom_around_mask, as_subplot=True,
        units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
        cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
        cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
        cb_tick_values=cb_tick_values, cb_tick_labels=cb_tick_labels,
        titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
        output_path=output_path, output_filename='', output_format=output_format)

    plt.subplot(rows, columns, 6)

    lens_plotter_util.plot_chi_squared_map(
        fit=fit, mask=mask, extract_array_from_mask=extract_array_from_mask, zoom_around_mask=zoom_around_mask, as_subplot=True,
        units=units, kpc_per_arcsec=kpc_per_arcsec, figsize=figsize, aspect=aspect,
        cmap=cmap, norm=norm, norm_min=norm_min, norm_max=norm_max, linthresh=linthresh, linscale=linscale,
        cb_ticksize=cb_ticksize, cb_fraction=cb_fraction, cb_pad=cb_pad,
        cb_tick_values=cb_tick_values, cb_tick_labels=cb_tick_labels,
        titlesize=titlesize, xlabelsize=xlabelsize, ylabelsize=ylabelsize, xyticksize=xyticksize,
        output_path=output_path, output_filename='', output_format=output_format)

    plotter_util.output_subplot_array(output_path=output_path, output_filename=output_filename,
                                      output_format=output_format)

    plt.close()