예제 #1
0
 def parse(cls, filename, structure=False):
     self = cls(filename)
     if structure:
         obj = Structure()
         for _ in range(self.natom):
             # fake
             obj.add_atom(Atom(), resname='XXX', resnum=0)
         obj.box = self.box
         obj.coordinates = self.coordinates[0]
         obj._coordinates = self.coordinates
         return obj
     else:
         return self
예제 #2
0
파일: asciicrd.py 프로젝트: ChayaSt/ParmEd
 def parse(cls, filename, structure=False):
     self = cls(filename)
     if structure:
         obj = Structure()
         for _ in range(self.natom):
             # fake
             obj.add_atom(Atom(), resname='XXX', resnum=0)
         obj.box = self.box
         obj.coordinates = self.coordinates[0]
         obj._coordinates = self.coordinates
         return obj
     else:
         return self
예제 #3
0
    def parse(filename):
        """ Parses a Gromacs GRO file

        Parameters
        ----------
        filename : str or file-like
            Name of the file or the GRO file object

        Returns
        -------
        struct : :class:`Structure`
            The Structure instance instantiated with *just* residues and atoms
            populated (with coordinates)
        """
        struct = Structure()
        if isinstance(filename, string_types):
            fileobj = genopen(filename, 'r')
            own_handle = True
        else:
            fileobj = filename
            own_handle = False
        try:
            # Ignore the title line
            fileobj.readline()
            try:
                natom = int(fileobj.readline().strip())
            except ValueError:
                raise GromacsError('Could not parse %s as GRO file' % filename)
            digits = None
            for i, line in enumerate(fileobj):
                if i == natom: break
                try:
                    resnum = int(line[:5])
                    resname = line[5:10].strip()
                    atomname = line[10:15].strip()
                    elem = element_by_name(atomname)
                    atomic_number = AtomicNum[elem]
                    mass = Mass[elem]
                    atnum = int(line[15:20])
                    if atomic_number == 0:
                        atom = ExtraPoint(name=atomname, number=atnum)
                    else:
                        atom = Atom(atomic_number=atomic_number, name=atomname,
                                    number=atnum, mass=mass)
                    if digits is None:
                        pdeci = line.index('.', 20)
                        ndeci = line.index('.', pdeci+1)
                        digits = ndeci - pdeci
                    atom.xx, atom.xy, atom.xz = (
                            float(line[20+i*digits:20+(i+1)*digits])*10
                                for i in range(3)
                    )
                    i = 4
                    wbeg = (pdeci-4)+(5+ndeci)*(i-1)
                    wend = (pdeci-4)+(5+ndeci)*i
                    if line[wbeg:wend].strip():
                        atom.vx, atom.vy, atom.vz = (
                                float(line[(pdeci-3)+(6+ndeci)*i:
                                           (pdeci-3)+(6+ndeci)*(i+1)])*10
                                for i in range(3, 6)
                        )
                except (ValueError, IndexError):
                    raise GromacsError('Could not parse the atom record of '
                                       'GRO file %s' % filename)
                struct.add_atom(atom, resname, resnum)
            # Get the box from the last line if it's present
            if line.strip():
                try:
                    box = [float(x) for x in line.split()]
                except ValueError:
                    raise GromacsError('Could not understand box line of GRO '
                                       'file %s' % filename)
                if len(box) == 3:
                    struct.box = [box[0]*10, box[1]*10, box[2]*10,
                                  90.0, 90.0, 90.0]
                elif len(box) == 9:
                    # Assume we have vectors
                    leng, ang = box_vectors_to_lengths_and_angles(
                                [box[0], box[3], box[4]]*u.nanometers,
                                [box[5], box[1], box[6]]*u.nanometers,
                                [box[7], box[8], box[2]]*u.nanometers)
                    a, b, c = leng.value_in_unit(u.angstroms)
                    alpha, beta, gamma = ang.value_in_unit(u.degrees)
                    struct.box = [a, b, c, alpha, beta, gamma]
        finally:
            if own_handle:
                fileobj.close()

        return struct
예제 #4
0
파일: topsystem.py 프로젝트: drroe/ParmEd
def load_topology(topology, system=None):
    """
    Creates a :class:`parmed.structure.Structure` instance from an OpenMM
    Topology, optionally filling in parameters from a System

    Parameters
    ----------
    topology : :class:`simtk.openmm.app.Topology`
        The Topology instance with the list of atoms and bonds for this system
    system : :class:`simtk.openmm.System` or str, optional
        If provided, parameters from this System will be applied to the
        Structure. If a string is given, it will be interpreted as the file name
        of an XML-serialized System, and it will be deserialized into a System
        before used to supply parameters

    Returns
    -------
    struct : :class:`Structure <parmed.structure.Structure>`
        The structure from the provided topology

    Raises
    ------
    OpenMMWarning if parameters are found that cannot be interpreted or
    processed by ParmEd

    TypeError if there are any mismatches between the provided topology and
    system (e.g., they have different numbers of atoms)

    IOError if system is a string and it is not an existing file

    Notes
    -----
    Due to its flexibility with CustomForces, it is entirely possible that the
    functional form of the potential will be unknown to ParmEd. This function
    will try to use the energy expression to identify supported potential types
    that are implemented as CustomForce objects. In particular, quadratic
    improper torsions, when recognized, will be extracted.

    Other CustomForces, including the CustomNonbondedForce used to implement
    NBFIX (off-diagonal L-J modifications) and the 12-6-4 potential, will not be
    processed and will result in an unknown functional form
    """
    struct = Structure()
    atommap = dict()
    for c in topology.chains():
        chain = c.id
        for r in c.residues():
            residue = r.name
            resid = r.index
            for a in r.atoms():
                if a.element is None:
                    atom = ExtraPoint(name=a.name)
                else:
                    atom = Atom(atomic_number=a.element.atomic_number,
                                name=a.name, mass=a.element.mass)
                struct.add_atom(atom, residue, resid, chain)
                atommap[a] = atom
    for a1, a2 in topology.bonds():
        struct.bonds.append(Bond(atommap[a1], atommap[a2]))

    vectors = topology.getPeriodicBoxVectors()
    if vectors is not None:
        leng, ang = box_vectors_to_lengths_and_angles(*vectors)
        leng = leng.value_in_unit(u.angstroms)
        ang = ang.value_in_unit(u.degrees)
        struct.box = [leng[0], leng[1], leng[2], ang[0], ang[1], ang[2]]

    if struct.box is not None:
        struct.box = create_array(struct.box)

    if system is None:
        return struct

    if isinstance(system, string_types):
        with open(system, 'r') as f:
            system = mm.XmlSerializer.deserialize(f.read())

    # We have a system, try to extract parameters from it
    if len(struct.atoms) != system.getNumParticles():
        raise TypeError('Topology and System have different numbers of atoms '
                '(%d vs. %d)' % (len(struct.atoms), system.getNumParticles()))

    processed_forces = set()
    ignored_forces = (mm.CMMotionRemover, mm.AndersenThermostat,
                      mm.MonteCarloBarostat, mm.MonteCarloAnisotropicBarostat,
                      mm.MonteCarloMembraneBarostat, mm.CustomExternalForce,
                      mm.GBSAOBCForce, mm.CustomGBForce)

    if system.usesPeriodicBoundaryConditions():
        vectors = system.getDefaultPeriodicBoxVectors()
        leng, ang = box_vectors_to_lengths_and_angles(*vectors)
        leng = leng.value_in_unit(u.angstroms)
        ang = ang.value_in_unit(u.degrees)
        struct.box = create_array(
                [leng[0], leng[1], leng[2], ang[0], ang[1], ang[2]]
        )
    else:
        struct.box = None

    for force in system.getForces():
        if isinstance(force, mm.HarmonicBondForce):
            if mm.HarmonicBondForce in processed_forces:
                # Try to process this HarmonicBondForce as a Urey-Bradley term
                _process_urey_bradley(struct, force)
            else:
                _process_bond(struct, force)
        elif isinstance(force, mm.HarmonicAngleForce):
            _process_angle(struct, force)
        elif isinstance(force, mm.PeriodicTorsionForce):
            _process_dihedral(struct, force)
        elif isinstance(force, mm.RBTorsionForce):
            _process_rbtorsion(struct, force)
        elif isinstance(force, mm.CustomTorsionForce):
            if not _process_improper(struct, force):
                struct.unknown_functional = True
                warnings.warn('Unknown functional form of CustomTorsionForce',
                              OpenMMWarning)
        elif isinstance(force, mm.CMAPTorsionForce):
            _process_cmap(struct, force)
        elif isinstance(force, mm.NonbondedForce):
            _process_nonbonded(struct, force)
        elif isinstance(force, ignored_forces):
            continue
        else:
            struct.unknown_functional = True
            warnings.warn('Unsupported Force type %s' % type(force).__name__,
                          OpenMMWarning)
        processed_forces.add(type(force))

    return struct
예제 #5
0
    def parse(filename, skip_bonds=False):
        """ Parses a Gromacs GRO file

        Parameters
        ----------
        filename : str or file-like
            Name of the file or the GRO file object
        skip_bonds : bool, optional
            If True, skip trying to assign bonds. This can save substantial time
            when parsing large files with non-standard residue names. However,
            no bonds are assigned. This is OK if, for instance, the GRO file is
            being parsed simply for its coordinates. This will also reduce the
            accuracy of assigned atomic numbers for typical ions. Default is
            False.

        Returns
        -------
        struct : :class:`Structure`
            The Structure instance instantiated with *just* residues and atoms
            populated (with coordinates)
        """
        struct = Structure()
        if isinstance(filename, string_types):
            fileobj = genopen(filename, 'r')
            own_handle = True
        else:
            fileobj = filename
            own_handle = False
        try:
            # Ignore the title line
            fileobj.readline()
            try:
                natom = int(fileobj.readline().strip())
            except ValueError:
                raise GromacsError('Could not parse %s as GRO file' % filename)
            line_parser = _AtomLineParser()
            for i, line in enumerate(fileobj):
                if i == natom: break
                try:
                    atom, resname, resnum = line_parser.read(line)
                except (ValueError, IndexError):
                    raise GromacsError('Could not parse the atom record of '
                                       'GRO file %s' % filename)
                struct.add_atom(atom, resname, resnum)
            else:
                # If no box exists, the break did not hit, so line still
                # contains the last atom (which cannot be interpreted as a box).
                # This wipes out line (IFF fileobj reached the line)
                line = fileobj.readline()
                if i+1 != natom:
                    raise GromacsError('Truncated GRO file. Found %d of %d '
                                       'atoms' % (i+1, natom))
            # Get the box from the last line if it's present
            if line.strip():
                try:
                    box = [float(x) for x in line.split()]
                except ValueError:
                    raise GromacsError('Could not understand box line of GRO '
                                       'file %s' % filename)
                if len(box) == 3:
                    struct.box = [box[0]*10, box[1]*10, box[2]*10,
                                  90.0, 90.0, 90.0]
                elif len(box) == 9:
                    # Assume we have vectors
                    leng, ang = box_vectors_to_lengths_and_angles(
                                [box[0], box[3], box[4]]*u.nanometers,
                                [box[5], box[1], box[6]]*u.nanometers,
                                [box[7], box[8], box[2]]*u.nanometers)
                    a, b, c = leng.value_in_unit(u.angstroms)
                    alpha, beta, gamma = ang.value_in_unit(u.degrees)
                    struct.box = [a, b, c, alpha, beta, gamma]
        finally:
            if own_handle:
                fileobj.close()

        # Assign bonds (and improved element guesses)
        if not skip_bonds:
            struct.assign_bonds()

        return struct
예제 #6
0
파일: mol2.py 프로젝트: drroe/ParmEd
    def parse(filename, structure=False):
        """ Parses a mol2 file (or mol3) file

        Parameters
        ----------
        filename : str or file-like
            Name of the file to parse or file-like object to parse from
        structure : bool, optional
            If True, the return value is a :class:`Structure` instance. If
            False, it is either a :class:`ResidueTemplate` or
            :class:`ResidueTemplateContainter` instance, depending on whether
            there is one or more than one residue defined in it. Default is
            False

        Returns
        -------
        molecule : :class:`Structure`, :class:`ResidueTemplate`, or
                   :class:`ResidueTemplateContainer`
            The molecule defined by this mol2 file

        Raises
        ------
        Mol2Error
            If the file format is not recognized or non-numeric values are
            present where integers or floating point numbers are expected. Also
            raises Mol2Error if you try to parse a mol2 file that has multiple
            @<MOLECULE> entries with ``structure=True``.
        """
        if isinstance(filename, string_types):
            f = genopen(filename, 'r')
            own_handle = True
        else:
            f = filename
            own_handle = False
        rescont = ResidueTemplateContainer()
        struct = Structure()
        restemp = ResidueTemplate()
        mol_info = []
        multires_structure = False
        try:
            section = None
            last_residue = None
            headtail = 'head'
            molecule_number = 0
            for line in f:
                if line.startswith('#'): continue
                if not line.strip() and section is None: continue
                if line.startswith('@<TRIPOS>'):
                    section = line[9:].strip()
                    if section == 'MOLECULE' and (restemp.atoms or rescont):
                        if structure:
                            raise Mol2Error('Cannot convert MOL2 with multiple '
                                            '@<MOLECULE>s to a Structure')
                        # Set the residue name from the MOL2 title if the
                        # molecule had only 1 residue and it was given a name in
                        # the title
                        if not multires_structure and mol_info[0]:
                            restemp.name = mol_info[0]
                        multires_structure = False
                        rescont.append(restemp)
                        restemp = ResidueTemplate()
                        struct = Structure()
                        last_residue = None
                        molecule_number += 1
                        mol_info = []
                    continue
                if section is None:
                    raise Mol2Error('Bad mol2 file format')
                if section == 'MOLECULE':
                    # Section formatted as follows:
                    #   mol_name
                    #   num_atoms [num_bonds [num_substr [num_feat [num_sets]]]]
                    #   mol_type
                    #   charge_type
                    #   [status_bits]
                    #   [mol_comment]
                    # TODO: Do something with the name.
                    if len(mol_info) == 0:
                        mol_info.append(line.strip())
                    elif len(mol_info) == 1:
                        mol_info.append([int(x) for x in line.split()])
                    elif len(mol_info) == 2:
                        mol_info.append(line.strip())
                    elif len(mol_info) == 3:
                        mol_info.append(line.strip())
                    # Ignore the rest
                    continue
                if section == 'ATOM':
                    # Section formatted as follows:
                    #   atom_id -- serial number of atom
                    #   atom_name -- name of the atom
                    #   x -- X-coordinate of the atom
                    #   y -- Y-coordinate of the atom
                    #   z -- Z-coordinate of the atom
                    #   atom_type -- type of the atom
                    #   subst_id -- Residue serial number
                    #   subst_name -- Residue name
                    #   charge -- partial atomic charge
                    #   status_bit -- ignored
                    words = line.split()
                    id = int(words[0])
                    name = words[1]
                    x = float(words[2])
                    y = float(words[3])
                    z = float(words[4])
                    typ = words[5]
                    try:
                        resid = int(words[6])
                    except IndexError:
                        resid = 0
                    try:
                        resname = words[7]
                    except IndexError:
                        resname = 'UNK'
                    if 'NO_CHARGES' not in mol_info:
                        try:
                            charge = float(words[8])
                        except IndexError:
                            charge = 0
                    else:
                        charge = 0
                    if last_residue is None:
                        last_residue = (resid, resname)
                        restemp.name = resname
                    atom = Atom(name=name, type=typ, number=id, charge=charge)
                    atom.xx, atom.xy, atom.xz = x, y, z
                    struct.add_atom(atom, resname, resid)
                    if last_residue != (resid, resname):
                        rescont.append(restemp)
                        restemp = ResidueTemplate()
                        restemp.name = resname
                        last_residue = (resid, resname)
                        multires_structure = True
                    restemp.add_atom(copy.copy(atom))
                    continue
                if section == 'BOND':
                    # Section formatted as follows:
                    #   bond_id -- serial number of bond (ignored)
                    #   origin_atom_id -- serial number of first atom in bond
                    #   target_atom_id -- serial number of other atom in bond
                    #   bond_type -- string describing bond type (ignored)
                    #   status_bits -- ignored
                    words = line.split()
                    int(words[0]) # Bond serial number... redundant and ignored
                    a1 = int(words[1])
                    a2 = int(words[2])
                    atom1 = struct.atoms.find_original_index(a1)
                    atom2 = struct.atoms.find_original_index(a2)
                    struct.bonds.append(Bond(atom1, atom2))
                    # Now add it to our residue container
                    # See if it's a head/tail connection
                    if atom1.residue is not atom2.residue:
                        if atom1.residue.idx == len(rescont):
                            res1 = restemp
                        elif atom1.residue.idx < len(rescont):
                            res1 = rescont[atom1.residue.idx]
                        else:
                            raise Mol2Error('Bad bonding pattern detected')
                        if atom2.residue.idx == len(rescont):
                            res2 = restemp
                        elif atom1.residue.idx < len(rescont):
                            res2 = rescont[atom2.residue.idx]
                        else:
                            raise Mol2Error('Bad bonding pattern detected')
                        assert res1 is not res2, 'BAD identical residues'
                        idx1 = atom1.idx - atom1.residue[0].idx
                        idx2 = atom2.idx - atom2.residue[0].idx
                        if atom1.residue.idx < atom2.residue.idx:
                            res1.tail = res1[idx1]
                            res2.head = res2[idx2]
                        else:
                            res1.head = res1[idx1]
                            res2.tail = res2[idx2]
                    elif not multires_structure:
                        restemp.add_bond(a1-1, a2-1)
                    else:
                        # Same residue, add the bond
                        offset = atom1.residue[0].idx
                        if atom1.residue.idx == len(rescont):
                            res = restemp
                        else:
                            res = rescont[atom1.residue.idx]
                        res.add_bond(atom1.idx-offset, atom2.idx-offset)
                    continue
                if section == 'CRYSIN':
                    # Section formatted as follows:
                    #   a -- length of first unit cell vector
                    #   b -- length of second unit cell vector
                    #   c -- length of third unit cell vector
                    #   alpha -- angle b/w b and c
                    #   beta -- angle b/w a and c
                    #   gamma -- angle b/w a and b
                    #   space group -- number of space group (ignored)
                    #   space group setting -- ignored
                    words = line.split()
                    box = [float(x) for x in words[:6]]
                    if len(box) != 6:
                        raise ValueError('%d box dimensions found; needed 6' %
                                         len(box))
                    struct.box = copy.copy(box)
                    rescont.box = copy.copy(box)
                    continue
                if section == 'SUBSTRUCTURE':
                    # Section formatted as follows:
                    #   subst_id -- residue number
                    #   subst_name -- residue name
                    #   root_atom -- first atom of residue
                    #   subst_type -- ignored (usually 'RESIDUE')
                    #   dict_type -- type of substructure (ignored)
                    #   chain -- chain ID of residue
                    #   sub_type -- type of the chain
                    #   inter_bonds -- # of inter-substructure bonds
                    #   status -- ignored
                    #   comment -- ignored
                    words = line.split()
                    if not words: continue
                    id = int(words[0])
                    resname = words[1]
                    try:
                        chain = words[5]
                    except IndexError:
                        chain = ''
                    # Set the chain ID
                    for res in struct.residues:
                        if res.number == id and res.name == resname:
                            res.chain = chain
                    continue
                # MOL3 sections
                if section == 'HEADTAIL':
                    atname, residx = line.split()
                    residx = int(residx)
                    if residx in (0, 1) or residx - 1 == len(rescont):
                        res = restemp
                    elif residx - 1 < len(rescont):
                        res = rescont[residx-1]
                    else:
                        raise Mol2Error('Residue out of range in head/tail')
                    for atom in res:
                        if atom.name == atname:
                            if headtail == 'head':
                                res.head = atom
                                headtail = 'tail'
                            else:
                                res.tail = atom
                                headtail = 'head'
                            break
                    else:
                        if headtail == 'head':
                            headtail = 'tail'
                        else:
                            headtail = 'head'
                    continue
                if section == 'RESIDUECONNECT':
                    words = line.split()
                    residx = int(words[0])
                    if residx - 1 == len(rescont):
                        res = restemp
                    elif residx - 1 < len(rescont):
                        res = rescont[residx-1]
                    else:
                        raise Mol2Error('Residue out of range in '
                                        'residueconnect')
                    for a in words[3:]:
                        if a == '0': continue
                        for atom in res:
                            if atom.name == a:
                                atom.connections.append(atom)
                                break
                        else:
                            raise Mol2Error('Residue connection atom %s not '
                                            'found in residue %d' % (a, residx))
            if structure:
                return struct
            elif len(rescont) > 0:
                if not multires_structure and mol_info[0]:
                    restemp.name = mol_info[0]
                rescont.append(restemp)
                return rescont
            else:
                return restemp
        except ValueError as e:
            raise Mol2Error('String conversion trouble: %s' % e)
        finally:
            if own_handle: f.close()
예제 #7
0
파일: mol2.py 프로젝트: pengfeili1/ParmEd
    def parse(filename, structure=False):
        """ Parses a mol2 file (or mol3) file

        Parameters
        ----------
        filename : str or file-like
            Name of the file to parse or file-like object to parse from
        structure : bool, optional
            If True, the return value is a :class:`Structure` instance. If
            False, it is either a :class:`ResidueTemplate` or
            :class:`ResidueTemplateContainter` instance, depending on whether
            there is one or more than one residue defined in it. Default is
            False

        Returns
        -------
        molecule : :class:`Structure`, :class:`ResidueTemplate`, or
                   :class:`ResidueTemplateContainer`
            The molecule defined by this mol2 file

        Raises
        ------
        Mol2Error
            If the file format is not recognized or non-numeric values are
            present where integers or floating point numbers are expected. Also
            raises Mol2Error if you try to parse a mol2 file that has multiple
            @<MOLECULE> entries with ``structure=True``.
        """
        if isinstance(filename, string_types):
            f = genopen(filename, 'r')
            own_handle = True
        else:
            f = filename
            own_handle = False
        rescont = ResidueTemplateContainer()
        struct = Structure()
        restemp = ResidueTemplate()
        mol_info = []
        multires_structure = False
        try:
            section = None
            last_residue = None
            headtail = 'head'
            molecule_number = 0
            for line in f:
                if line.startswith('#'): continue
                if not line.strip() and section is None: continue
                if line.startswith('@<TRIPOS>'):
                    section = line[9:].strip()
                    if section == 'MOLECULE' and (restemp.atoms or rescont):
                        if structure:
                            raise Mol2Error('Cannot convert MOL2 with multiple '
                                            '@<MOLECULE>s to a Structure')
                        # Set the residue name from the MOL2 title if the
                        # molecule had only 1 residue and it was given a name in
                        # the title
                        if not multires_structure and mol_info[0]:
                            restemp.name = mol_info[0]
                        multires_structure = False
                        rescont.append(restemp)
                        restemp = ResidueTemplate()
                        struct = Structure()
                        last_residue = None
                        molecule_number += 1
                        mol_info = []
                    continue
                if section is None:
                    raise Mol2Error('Bad mol2 file format')
                if section == 'MOLECULE':
                    # Section formatted as follows:
                    #   mol_name
                    #   num_atoms [num_bonds [num_substr [num_feat [num_sets]]]]
                    #   mol_type
                    #   charge_type
                    #   [status_bits]
                    #   [mol_comment]
                    # TODO: Do something with the name.
                    if len(mol_info) == 0:
                        mol_info.append(line.strip())
                    elif len(mol_info) == 1:
                        mol_info.append([int(x) for x in line.split()])
                    elif len(mol_info) == 2:
                        mol_info.append(line.strip())
                    elif len(mol_info) == 3:
                        mol_info.append(line.strip())
                    # Ignore the rest
                    continue
                if section == 'ATOM':
                    # Section formatted as follows:
                    #   atom_id -- serial number of atom
                    #   atom_name -- name of the atom
                    #   x -- X-coordinate of the atom
                    #   y -- Y-coordinate of the atom
                    #   z -- Z-coordinate of the atom
                    #   atom_type -- type of the atom
                    #   subst_id -- Residue serial number
                    #   subst_name -- Residue name
                    #   charge -- partial atomic charge
                    #   status_bit -- ignored
                    words = line.split()
                    id = int(words[0])
                    name = words[1]
                    x = float(words[2])
                    y = float(words[3])
                    z = float(words[4])
                    typ = words[5]
                    try:
                        resid = int(words[6])
                    except IndexError:
                        resid = 0
                    try:
                        resname = words[7]
                    except IndexError:
                        resname = 'UNK'
                    if 'NO_CHARGES' not in mol_info:
                        try:
                            charge = float(words[8])
                        except IndexError:
                            charge = 0
                    else:
                        charge = 0
                    if last_residue is None:
                        last_residue = (resid, resname)
                        restemp.name = resname
                    atom = Atom(name=name, type=typ, number=id, charge=charge)
                    atom.xx, atom.xy, atom.xz = x, y, z
                    struct.add_atom(atom, resname, resid)
                    if last_residue != (resid, resname):
                        rescont.append(restemp)
                        restemp = ResidueTemplate()
                        restemp.name = resname
                        last_residue = (resid, resname)
                        multires_structure = True
                    try:
                        restemp.add_atom(copy.copy(atom))
                    except ValueError:
                        # Allow mol2 files being parsed as a Structure to have
                        # duplicate atom names
                        if not structure:
                            raise
                    continue
                if section == 'BOND':
                    # Section formatted as follows:
                    #   bond_id -- serial number of bond (ignored)
                    #   origin_atom_id -- serial number of first atom in bond
                    #   target_atom_id -- serial number of other atom in bond
                    #   bond_type -- string describing bond type (ignored)
                    #   status_bits -- ignored
                    words = line.split()
                    int(words[0]) # Bond serial number... redundant and ignored
                    a1 = int(words[1])
                    a2 = int(words[2])
                    atom1 = struct.atoms.find_original_index(a1)
                    atom2 = struct.atoms.find_original_index(a2)
                    struct.bonds.append(Bond(atom1, atom2))
                    # Now add it to our residue container
                    # See if it's a head/tail connection
                    if atom1.residue is not atom2.residue:
                        if atom1.residue.idx == len(rescont):
                            res1 = restemp
                        elif atom1.residue.idx < len(rescont):
                            res1 = rescont[atom1.residue.idx]
                        assert atom.residue.idx <= len(rescont), 'Bad bond!'
                        if atom2.residue.idx == len(rescont):
                            res2 = restemp
                        elif atom2.residue.idx < len(rescont):
                            res2 = rescont[atom2.residue.idx]
                        assert atom.residue.idx <= len(rescont), 'Bad bond!'
                        assert res1 is not res2, 'BAD identical residues'
                        idx1 = atom1.idx - atom1.residue[0].idx
                        idx2 = atom2.idx - atom2.residue[0].idx
                        if atom1.residue.idx < atom2.residue.idx:
                            res1.tail = res1[idx1]
                            res2.head = res2[idx2]
                        else:
                            res1.head = res1[idx1]
                            res2.tail = res2[idx2]
                    elif not multires_structure:
                        if not structure:
                            restemp.add_bond(a1-1, a2-1)
                    else:
                        # Same residue, add the bond
                        offset = atom1.residue[0].idx
                        if atom1.residue.idx == len(rescont):
                            res = restemp
                        else:
                            res = rescont[atom1.residue.idx]
                        res.add_bond(atom1.idx-offset, atom2.idx-offset)
                    continue
                if section == 'CRYSIN':
                    # Section formatted as follows:
                    #   a -- length of first unit cell vector
                    #   b -- length of second unit cell vector
                    #   c -- length of third unit cell vector
                    #   alpha -- angle b/w b and c
                    #   beta -- angle b/w a and c
                    #   gamma -- angle b/w a and b
                    #   space group -- number of space group (ignored)
                    #   space group setting -- ignored
                    words = line.split()
                    box = [float(w) for w in words[:6]]
                    if len(box) != 6:
                        raise ValueError('%d box dimensions found; needed 6' %
                                         len(box))
                    struct.box = copy.copy(box)
                    rescont.box = copy.copy(box)
                    continue
                if section == 'SUBSTRUCTURE':
                    # Section formatted as follows:
                    #   subst_id -- residue number
                    #   subst_name -- residue name
                    #   root_atom -- first atom of residue
                    #   subst_type -- ignored (usually 'RESIDUE')
                    #   dict_type -- type of substructure (ignored)
                    #   chain -- chain ID of residue
                    #   sub_type -- type of the chain
                    #   inter_bonds -- # of inter-substructure bonds
                    #   status -- ignored
                    #   comment -- ignored
                    words = line.split()
                    if not words: continue
                    id = int(words[0])
                    resname = words[1]
                    try:
                        chain = words[5]
                    except IndexError:
                        chain = ''
                    # Set the chain ID
                    for res in struct.residues:
                        if res.number == id and res.name == resname:
                            res.chain = chain
                    continue
                # MOL3 sections
                if section == 'HEADTAIL':
                    atname, residx = line.split()
                    residx = int(residx)
                    if residx in (0, 1) or residx - 1 == len(rescont):
                        res = restemp
                    elif residx - 1 < len(rescont):
                        res = rescont[residx-1]
                    else:
                        raise Mol2Error('Residue out of range in head/tail')
                    for atom in res:
                        if atom.name == atname:
                            if headtail == 'head':
                                res.head = atom
                                headtail = 'tail'
                            else:
                                res.tail = atom
                                headtail = 'head'
                            break
                    else:
                        if headtail == 'head':
                            headtail = 'tail'
                        else:
                            headtail = 'head'
                    continue
                if section == 'RESIDUECONNECT':
                    words = line.split()
                    residx = int(words[0])
                    if residx - 1 == len(rescont):
                        res = restemp
                    elif residx - 1 < len(rescont):
                        res = rescont[residx-1]
                    else:
                        raise Mol2Error('Residue out of range in '
                                        'residueconnect')
                    for a in words[3:]:
                        if a == '0': continue
                        for atom in res:
                            if atom.name == a:
                                res.connections.append(atom)
                                break
                        else:
                            raise Mol2Error('Residue connection atom %s not '
                                            'found in residue %d' % (a, residx))
            if structure:
                return struct
            elif len(rescont) > 0:
                if not multires_structure and mol_info[0]:
                    restemp.name = mol_info[0]
                rescont.append(restemp)
                return rescont
            else:
                return restemp
        except ValueError as e:
            raise Mol2Error('String conversion trouble: %s' % e)
        finally:
            if own_handle: f.close()
예제 #8
0
파일: pqr.py 프로젝트: jchodera/ParmEd
    def parse(filename):
        """ Read a PQR file and return a populated `Structure` class

        Parameters
        ----------
        filename : str or file-like
            Name of the PQR file to read, or a file-like object that can iterate
            over the lines of a PQR. Compressed file names can be specified and
            are determined by file-name extension (e.g., file.pqr.gz,
            file.pqr.bz2)

        Returns
        -------
        structure : :class:`Structure`
            The Structure object initialized with all of the information from
            the PDB file.  No bonds or other topological features are added by
            default.
        """
        if isinstance(filename, string_types):
            own_handle = True
            fileobj = genopen(filename, "r")
        else:
            own_handle = False
            fileobj = filename

        struct = Structure()
        # Add metadata fields
        modelno = 1  # For PDB files with multiple MODELs
        atomno = 0
        coordinates = []
        all_coordinates = []

        # Support hexadecimal numbering like that printed by VMD
        try:
            for line in fileobj:
                words = line.split()
                if words[0] in ("ATOM", "HETATM"):
                    atomno += 1
                    if len(words) == 10:
                        _, num, nam, res, resn, x, y, z, chg, rad = words
                        chn = ""
                    elif len(words) >= 11:
                        _, num, nam, res, chn, resn, x, y, z, chg, rad = (words[i] for i in range(11))
                        # If the radius is not a float (but rather a letter,
                        # like the element or something), then the chain might
                        # be missing. In this case, shift all tokens "back" one
                        # and empty the chn string
                        try:
                            float(rad)
                        except ValueError:
                            resn, x, y, z, chg, rad = chn, resn, x, y, z, chg
                    else:
                        raise ValueError("Illegal PQR record format: expected " "10 or 11 tokens on the atom line")
                    x, y, z = float(x), float(y), float(z)
                    chg, rad = float(chg), float(rad)
                    resn, num = int(resn), int(num)
                    elem = element_by_name(nam)  # Yuck
                    atomic_number = AtomicNum[elem]
                    mass = Mass[elem]
                    if nam in ("EP", "LP"):  # lone pair
                        atom = ExtraPoint(
                            atomic_number=atomic_number, name=nam, charge=chg, mass=mass, number=num, solvent_radius=rad
                        )
                    else:
                        atom = Atom(
                            atomic_number=atomic_number, name=nam, charge=chg, mass=mass, number=num, solvent_radius=rad
                        )
                    atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
                    if modelno == 1:
                        struct.add_atom(atom, res, resn, chn)
                    else:
                        try:
                            orig_atom = struct.atoms[atomno - 1]
                        except IndexError:
                            raise PDBError("Extra atom in MODEL %d" % modelno)
                        if orig_atom.residue.name != res.strip() or orig_atom.name != nam.strip():
                            raise PDBError(
                                "Atom %d differs in MODEL %d [%s %s "
                                "vs. %s %s]" % (atomno, modelno, orig_atom.residue.name, orig_atom.name, res, nam)
                            )
                    coordinates.extend([atom.xx, atom.xy, atom.xz])
                elif words[0] == "ENDMDL":
                    # End the current model
                    if len(struct.atoms) == 0:
                        raise PDBError("MODEL ended before any atoms read in")
                    modelno += 1
                    if len(struct.atoms) * 3 != len(coordinates):
                        raise PDBError("Inconsistent atom numbers in some PDB models")
                    all_coordinates.append(coordinates)
                    atomno = 0
                    coordinates = []
                elif words[0] == "MODEL":
                    if modelno == 1 and len(struct.atoms) == 0:
                        continue
                    if len(coordinates) > 0:
                        if len(struct.atoms) * 3 != len(coordinates):
                            raise PDBError("Inconsistent atom numbers in " "some PDB models")
                        warnings.warn("MODEL not explicitly ended", PDBWarning)
                        all_coordinates.append(coordinates)
                        coordinates = []
                    modelno += 1
                    atomno = 0
                elif words[0] == "CRYST1":
                    a, b, c = (float(w) for w in words[1:4])
                    try:
                        A, B, C = (float(w) for w in words[4:7])
                    except ValueError:
                        A = B = C = 90.0
                    struct.box = [a, b, c, A, B, C]
        finally:
            if own_handle:
                fileobj.close()

        struct.unchange()
        if coordinates:
            if len(coordinates) != 3 * len(struct.atoms):
                raise PDBError("bad number of atoms in some PQR models")
            all_coordinates.append(coordinates)
        struct._coordinates = np.array(all_coordinates).reshape((-1, len(struct.atoms), 3))
        return struct
예제 #9
0
파일: pqr.py 프로젝트: pengfeili1/ParmEd
    def parse(filename):
        """ Read a PQR file and return a populated `Structure` class

        Parameters
        ----------
        filename : str or file-like
            Name of the PQR file to read, or a file-like object that can iterate
            over the lines of a PQR. Compressed file names can be specified and
            are determined by file-name extension (e.g., file.pqr.gz,
            file.pqr.bz2)

        Returns
        -------
        structure : :class:`Structure`
            The Structure object initialized with all of the information from
            the PDB file.  No bonds or other topological features are added by
            default.
        """
        if isinstance(filename, string_types):
            own_handle = True
            fileobj = genopen(filename, 'r')
        else:
            own_handle = False
            fileobj = filename

        struct = Structure()
        # Add metadata fields
        modelno = 1  # For PDB files with multiple MODELs
        atomno = 0
        coordinates = []
        all_coordinates = []

        # Support hexadecimal numbering like that printed by VMD
        try:
            for line in fileobj:
                words = line.split()
                if words[0] in ('ATOM', 'HETATM'):
                    atomno += 1
                    if len(words) == 10:
                        _, num, nam, res, resn, x, y, z, chg, rad = words
                        chn = ''
                    elif len(words) >= 11:
                        _, num, nam, res, chn, resn, x, y, z, chg, rad = (
                            words[i] for i in range(11))
                        # If the radius is not a float (but rather a letter,
                        # like the element or something), then the chain might
                        # be missing. In this case, shift all tokens "back" one
                        # and empty the chn string
                        try:
                            float(rad)
                        except ValueError:
                            resn, x, y, z, chg, rad = chn, resn, x, y, z, chg
                    else:
                        raise ValueError('Illegal PQR record format: expected '
                                         '10 or 11 tokens on the atom line')
                    x, y, z = float(x), float(y), float(z)
                    chg, rad = float(chg), float(rad)
                    resn, num = int(resn), int(num)
                    elem = element_by_name(nam)  # Yuck
                    atomic_number = AtomicNum[elem]
                    mass = Mass[elem]
                    if nam in ('EP', 'LP'):  # lone pair
                        atom = ExtraPoint(atomic_number=atomic_number,
                                          name=nam,
                                          charge=chg,
                                          mass=mass,
                                          number=num,
                                          solvent_radius=rad)
                    else:
                        atom = Atom(atomic_number=atomic_number,
                                    name=nam,
                                    charge=chg,
                                    mass=mass,
                                    number=num,
                                    solvent_radius=rad)
                    atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
                    if modelno == 1:
                        struct.add_atom(atom, res, resn, chn)
                    else:
                        try:
                            orig_atom = struct.atoms[atomno - 1]
                        except IndexError:
                            raise PDBError('Extra atom in MODEL %d' % modelno)
                        if (orig_atom.residue.name != res.strip()
                                or orig_atom.name != nam.strip()):
                            raise PDBError(
                                'Atom %d differs in MODEL %d [%s %s '
                                'vs. %s %s]' %
                                (atomno, modelno, orig_atom.residue.name,
                                 orig_atom.name, res, nam))
                    coordinates.extend([atom.xx, atom.xy, atom.xz])
                elif words[0] == 'ENDMDL':
                    # End the current model
                    if len(struct.atoms) == 0:
                        raise PDBError('MODEL ended before any atoms read in')
                    modelno += 1
                    if len(struct.atoms) * 3 != len(coordinates):
                        raise PDBError(
                            'Inconsistent atom numbers in some PDB models')
                    all_coordinates.append(coordinates)
                    atomno = 0
                    coordinates = []
                elif words[0] == 'MODEL':
                    if modelno == 1 and len(struct.atoms) == 0: continue
                    if len(coordinates) > 0:
                        if len(struct.atoms) * 3 != len(coordinates):
                            raise PDBError('Inconsistent atom numbers in '
                                           'some PDB models')
                        warnings.warn('MODEL not explicitly ended', PDBWarning)
                        all_coordinates.append(coordinates)
                        coordinates = []
                    modelno += 1
                    atomno = 0
                elif words[0] == 'CRYST1':
                    a, b, c = (float(w) for w in words[1:4])
                    try:
                        A, B, C = (float(w) for w in words[4:7])
                    except ValueError:
                        A = B = C = 90.0
                    struct.box = [a, b, c, A, B, C]
        finally:
            if own_handle: fileobj.close()

        struct.unchange()
        if coordinates:
            if len(coordinates) != 3 * len(struct.atoms):
                raise PDBError('bad number of atoms in some PQR models')
            all_coordinates.append(coordinates)
        struct._coordinates = np.array(all_coordinates).reshape(
            (-1, len(struct.atoms), 3))
        return struct
예제 #10
0
def load_topology(topology, system=None, xyz=None, box=None):
    """
    Creates a :class:`parmed.structure.Structure` instance from an OpenMM
    Topology, optionally filling in parameters from a System

    Parameters
    ----------
    topology : :class:`simtk.openmm.app.Topology`
        The Topology instance with the list of atoms and bonds for this system
    system : :class:`simtk.openmm.System` or str, optional
        If provided, parameters from this System will be applied to the
        Structure. If a string is given, it will be interpreted as the file name
        of an XML-serialized System, and it will be deserialized into a System
        before used to supply parameters
    xyz : str or array of float
        Name of a file containing coordinate information or an array of
        coordinates. If file has unit cell information, it also uses that
        information unless ``box`` (below) is also specified
    box : array of 6 floats
        Unit cell dimensions

    Returns
    -------
    struct : :class:`Structure <parmed.structure.Structure>`
        The structure from the provided topology

    Raises
    ------
    OpenMMWarning if parameters are found that cannot be interpreted or
    processed by ParmEd

    TypeError if there are any mismatches between the provided topology and
    system (e.g., they have different numbers of atoms)

    IOError if system is a string and it is not an existing file

    Notes
    -----
    Due to its flexibility with CustomForces, it is entirely possible that the
    functional form of the potential will be unknown to ParmEd. This function
    will try to use the energy expression to identify supported potential types
    that are implemented as CustomForce objects. In particular, quadratic
    improper torsions, when recognized, will be extracted.

    Other CustomForces, including the CustomNonbondedForce used to implement
    NBFIX (off-diagonal L-J modifications) and the 12-6-4 potential, will not be
    processed and will result in an unknown functional form
    """
    import simtk.openmm as mm
    struct = Structure()
    atommap = dict()
    for c in topology.chains():
        chain = c.id
        for r in c.residues():
            residue = r.name
            resid = r.index
            for a in r.atoms():
                if a.element is None:
                    atom = ExtraPoint(name=a.name)
                else:
                    atom = Atom(atomic_number=a.element.atomic_number,
                                name=a.name,
                                mass=a.element.mass)
                struct.add_atom(atom, residue, resid, chain)
                atommap[a] = atom
    for a1, a2 in topology.bonds():
        struct.bonds.append(Bond(atommap[a1], atommap[a2]))

    vectors = topology.getPeriodicBoxVectors()
    if vectors is not None:
        leng, ang = box_vectors_to_lengths_and_angles(*vectors)
        leng = leng.value_in_unit(u.angstroms)
        ang = ang.value_in_unit(u.degrees)
        struct.box = [leng[0], leng[1], leng[2], ang[0], ang[1], ang[2]]

    loaded_box = False

    if xyz is not None:
        if isinstance(xyz, string_types):
            xyz = load_file(xyz, skip_bonds=True)
            struct.coordinates = xyz.coordinates
            if struct.box is not None:
                if xyz.box is not None:
                    loaded_box = True
                    struct.box = xyz.box
        else:
            struct.coordinates = xyz

    if box is not None:
        loaded_box = True
        struct.box = box

    if struct.box is not None:
        struct.box = np.asarray(struct.box)

    if system is None:
        return struct

    if isinstance(system, string_types):
        system = load_file(system)

    if not isinstance(system, mm.System):
        raise TypeError('system must be an OpenMM System object or serialized '
                        'XML of an OpenMM System object')

    # We have a system, try to extract parameters from it
    if len(struct.atoms) != system.getNumParticles():
        raise TypeError('Topology and System have different numbers of atoms '
                        '(%d vs. %d)' %
                        (len(struct.atoms), system.getNumParticles()))

    processed_forces = set()
    ignored_forces = (mm.CMMotionRemover, mm.AndersenThermostat,
                      mm.MonteCarloBarostat, mm.MonteCarloAnisotropicBarostat,
                      mm.MonteCarloMembraneBarostat, mm.CustomExternalForce,
                      mm.GBSAOBCForce, mm.CustomGBForce)

    if system.usesPeriodicBoundaryConditions():
        if not loaded_box:
            vectors = system.getDefaultPeriodicBoxVectors()
            leng, ang = box_vectors_to_lengths_and_angles(*vectors)
            leng = leng.value_in_unit(u.angstroms)
            ang = ang.value_in_unit(u.degrees)
            struct.box = np.asarray(
                [leng[0], leng[1], leng[2], ang[0], ang[1], ang[2]])
    else:
        struct.box = None

    for force in system.getForces():
        if isinstance(force, mm.HarmonicBondForce):
            if mm.HarmonicBondForce in processed_forces:
                # Try to process this HarmonicBondForce as a Urey-Bradley term
                _process_urey_bradley(struct, force)
            else:
                _process_bond(struct, force)
        elif isinstance(force, mm.HarmonicAngleForce):
            _process_angle(struct, force)
        elif isinstance(force, mm.PeriodicTorsionForce):
            _process_dihedral(struct, force)
        elif isinstance(force, mm.RBTorsionForce):
            _process_rbtorsion(struct, force)
        elif isinstance(force, mm.CustomTorsionForce):
            if not _process_improper(struct, force):
                struct.unknown_functional = True
                warnings.warn('Unknown functional form of CustomTorsionForce',
                              OpenMMWarning)
        elif isinstance(force, mm.CMAPTorsionForce):
            _process_cmap(struct, force)
        elif isinstance(force, mm.NonbondedForce):
            _process_nonbonded(struct, force)
        elif isinstance(force, ignored_forces):
            continue
        else:
            struct.unknown_functional = True
            warnings.warn('Unsupported Force type %s' % type(force).__name__,
                          OpenMMWarning)
        processed_forces.add(type(force))

    return struct
예제 #11
0
    def parse(filename):
        """ Parses a Gromacs GRO file

        Parameters
        ----------
        filename : str or file-like
            Name of the file or the GRO file object

        Returns
        -------
        struct : :class:`Structure`
            The Structure instance instantiated with *just* residues and atoms
            populated (with coordinates)
        """
        struct = Structure()
        if isinstance(filename, string_types):
            fileobj = genopen(filename, 'r')
            own_handle = True
        else:
            fileobj = filename
            own_handle = False
        try:
            # Ignore the title line
            fileobj.readline()
            try:
                natom = int(fileobj.readline().strip())
            except ValueError:
                raise GromacsError('Could not parse %s as GRO file' % filename)
            digits = None
            line_parser = _AtomLineParser()
            for i, line in enumerate(fileobj):
                if i == natom: break
                try:
                    atom, resname, resnum = line_parser.read(line)
                except (ValueError, IndexError):
                    raise GromacsError('Could not parse the atom record of '
                                       'GRO file %s' % filename)
                struct.add_atom(atom, resname, resnum)
            else:
                # If no box exists, the break did not hit, so line still
                # contains the last atom (which cannot be interpreted as a box).
                # This wipes out line (IFF fileobj reached the line)
                line = fileobj.readline()
                if i+1 != natom:
                    raise GromacsError('Truncated GRO file. Found %d of %d '
                                       'atoms' % (i+1, natom))
            # Get the box from the last line if it's present
            if line.strip():
                try:
                    box = [float(x) for x in line.split()]
                except ValueError:
                    raise GromacsError('Could not understand box line of GRO '
                                       'file %s' % filename)
                if len(box) == 3:
                    struct.box = [box[0]*10, box[1]*10, box[2]*10,
                                  90.0, 90.0, 90.0]
                elif len(box) == 9:
                    # Assume we have vectors
                    leng, ang = box_vectors_to_lengths_and_angles(
                                [box[0], box[3], box[4]]*u.nanometers,
                                [box[5], box[1], box[6]]*u.nanometers,
                                [box[7], box[8], box[2]]*u.nanometers)
                    a, b, c = leng.value_in_unit(u.angstroms)
                    alpha, beta, gamma = ang.value_in_unit(u.degrees)
                    struct.box = [a, b, c, alpha, beta, gamma]
        finally:
            if own_handle:
                fileobj.close()

        return struct