Ejemplo n.º 1
0
def simulate(file="simulation.pdb.bz2", dir=None, step_size=2.0, snapshot=10, total=1000, model=1, force=True):
    """Pseudo-Brownian dynamics simulation of the frame order motions.

    @keyword file:      The PDB file for storing the frame order pseudo-Brownian dynamics simulation.  The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
    @type file:         str
    @keyword dir:       The directory name to place the file into.
    @type dir:          str or None
    @keyword step_size: The rotation will be of a random direction but with this fixed angle.  The value is in degrees.
    @type step_size:    float
    @keyword snapshot:  The number of steps in the simulation when snapshots will be taken.
    @type snapshot:     int
    @keyword total:     The total number of snapshots to take before stopping the simulation.
    @type total:        int
    @keyword model:     Only one model from an analysed ensemble of structures can be used for the pseudo-Brownian simulation, as the simulation and corresponding PDB file consists of one model per simulation.
    @type model:        int
    @keyword force:     A flag which, if set to True, will overwrite the any pre-existing file.
    @type force:        bool
    """

    # Printout.
    print("Pseudo-Brownian dynamics simulation of the frame order motions.")

    # Checks.
    check_pipe()
    check_model()
    check_domain()
    check_parameters()
    check_pivot()

    # Skip the rigid model.
    if cdp.model == MODEL_RIGID:
        print("Skipping the rigid model.")
        return

    # Open the output file.
    file = open_write_file(file_name=file, dir=dir, force=force)

    # The parameter values.
    values = assemble_param_vector()
    params = {}
    i = 0
    for name in cdp.params:
        params[name] = values[i]
        i += 1

    # The structure.
    structure = deepcopy(cdp.structure)
    if structure.num_models() > 1:
        structure.collapse_ensemble(model_num=model)

    # The pivot points.
    num_states = 1
    if cdp.model == MODEL_DOUBLE_ROTOR:
        num_states = 2
    pivot = zeros((num_states, 3), float64)
    for i in range(num_states):
        pivot[i] = generate_pivot(order=i+1, pdb_limit=True)

    # Shift to the average position.
    average_position(structure=structure, models=[None])

    # The motional eigenframe.
    frame = generate_axis_system()

    # Create the distribution.
    brownian(file=file, model=cdp.model, structure=structure, parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(), step_size=step_size, snapshot=snapshot, total=total)

    # Close the file.
    file.close()
Ejemplo n.º 2
0
def distribute(file="distribution.pdb.bz2", dir=None, atom_id=None, total=1000, max_rotations=100000, model=1, force=True):
    """Create a uniform distribution of structures for the frame order motions.

    @keyword file:          The PDB file for storing the frame order motional distribution.  The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
    @type file:             str
    @keyword dir:           The directory name to place the file into.
    @type dir:              str or None
    @keyword atom_id:       The atom identification string to allow the distribution to be a subset of all atoms.
    @type atom_id:          None or str
    @keyword total:         The total number of states/model/structures in the distribution.
    @type total:            int
    @keyword max_rotations: The maximum number of rotations to generate the distribution from.  This prevents an execution for an infinite amount of time when a frame order amplitude parameter is close to zero so that the subset of all rotations within the distribution is close to zero.
    @type max_rotations:    int
    @keyword model:         Only one model from an analysed ensemble of structures can be used for the distribution, as the corresponding PDB file consists of one model per state.
    @type model:            int
    @keyword force:         A flag which, if set to True, will overwrite the any pre-existing file.
    @type force:            bool
    """

    # Printout.
    print("Uniform distribution of structures representing the frame order motions.")

    # Check the total.
    if total > 9999:
        raise RelaxError("A maximum of 9999 models is allowed in the PDB format.")

    # Checks.
    check_pipe()
    check_model()
    check_domain()
    check_parameters()
    check_pivot()

    # Skip the rigid model.
    if cdp.model == MODEL_RIGID:
        print("Skipping the rigid model.")
        return

    # Open the output file.
    file = open_write_file(file_name=file, dir=dir, force=force)

    # The parameter values.
    values = assemble_param_vector()
    params = {}
    i = 0
    for name in cdp.params:
        params[name] = values[i]
        i += 1

    # The structure.
    structure = deepcopy(cdp.structure)
    if structure.num_models() > 1:
        structure.collapse_ensemble(model_num=model)

    # The pivot points.
    num_states = 1
    if cdp.model == MODEL_DOUBLE_ROTOR:
        num_states = 2
    pivot = zeros((num_states, 3), float64)
    for i in range(num_states):
        pivot[i] = generate_pivot(order=i+1, pdb_limit=True)

    # Shift to the average position.
    average_position(structure=structure, models=[None])

    # The motional eigenframe.
    frame = generate_axis_system()

    # Only work with a subset.
    if atom_id:
        # The inverted selection.
        selection = structure.selection(atom_id=atom_id, inv=True)

        # Delete the data.
        structure.delete(selection=selection, verbosity=0)

    # Create the distribution.
    uniform_distribution(file=file, model=cdp.model, structure=structure, parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(), total=total, max_rotations=max_rotations)

    # Close the file.
    file.close()
Ejemplo n.º 3
0
def simulate(file="simulation.pdb.bz2",
             dir=None,
             step_size=2.0,
             snapshot=10,
             total=1000,
             model=1,
             force=True):
    """Pseudo-Brownian dynamics simulation of the frame order motions.

    @keyword file:      The PDB file for storing the frame order pseudo-Brownian dynamics simulation.  The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
    @type file:         str
    @keyword dir:       The directory name to place the file into.
    @type dir:          str or None
    @keyword step_size: The rotation will be of a random direction but with this fixed angle.  The value is in degrees.
    @type step_size:    float
    @keyword snapshot:  The number of steps in the simulation when snapshots will be taken.
    @type snapshot:     int
    @keyword total:     The total number of snapshots to take before stopping the simulation.
    @type total:        int
    @keyword model:     Only one model from an analysed ensemble of structures can be used for the pseudo-Brownian simulation, as the simulation and corresponding PDB file consists of one model per simulation.
    @type model:        int
    @keyword force:     A flag which, if set to True, will overwrite the any pre-existing file.
    @type force:        bool
    """

    # Printout.
    print("Pseudo-Brownian dynamics simulation of the frame order motions.")

    # Checks.
    check_pipe()
    check_model()
    check_domain()
    check_parameters()
    check_pivot()

    # Skip the rigid model.
    if cdp.model == MODEL_RIGID:
        print("Skipping the rigid model.")
        return

    # Open the output file.
    file = open_write_file(file_name=file, dir=dir, force=force)

    # The parameter values.
    values = assemble_param_vector()
    params = {}
    i = 0
    for name in cdp.params:
        params[name] = values[i]
        i += 1

    # The structure.
    structure = deepcopy(cdp.structure)
    if structure.num_models() > 1:
        structure.collapse_ensemble(model_num=model)

    # The pivot points.
    num_states = 1
    if cdp.model == MODEL_DOUBLE_ROTOR:
        num_states = 2
    pivot = zeros((num_states, 3), float64)
    for i in range(num_states):
        pivot[i] = generate_pivot(order=i + 1, pdb_limit=True)

    # Shift to the average position.
    average_position(structure=structure, models=[None])

    # The motional eigenframe.
    frame = generate_axis_system()

    # Create the distribution.
    brownian(file=file,
             model=cdp.model,
             structure=structure,
             parameters=params,
             eigenframe=frame,
             pivot=pivot,
             atom_id=domain_moving(),
             step_size=step_size,
             snapshot=snapshot,
             total=total)

    # Close the file.
    file.close()
Ejemplo n.º 4
0
def distribute(file="distribution.pdb.bz2",
               dir=None,
               atom_id=None,
               total=1000,
               max_rotations=100000,
               model=1,
               force=True):
    """Create a uniform distribution of structures for the frame order motions.

    @keyword file:          The PDB file for storing the frame order motional distribution.  The compression is determined automatically by the file extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
    @type file:             str
    @keyword dir:           The directory name to place the file into.
    @type dir:              str or None
    @keyword atom_id:       The atom identification string to allow the distribution to be a subset of all atoms.
    @type atom_id:          None or str
    @keyword total:         The total number of states/model/structures in the distribution.
    @type total:            int
    @keyword max_rotations: The maximum number of rotations to generate the distribution from.  This prevents an execution for an infinite amount of time when a frame order amplitude parameter is close to zero so that the subset of all rotations within the distribution is close to zero.
    @type max_rotations:    int
    @keyword model:         Only one model from an analysed ensemble of structures can be used for the distribution, as the corresponding PDB file consists of one model per state.
    @type model:            int
    @keyword force:         A flag which, if set to True, will overwrite the any pre-existing file.
    @type force:            bool
    """

    # Printout.
    print(
        "Uniform distribution of structures representing the frame order motions."
    )

    # Check the total.
    if total > 9999:
        raise RelaxError(
            "A maximum of 9999 models is allowed in the PDB format.")

    # Checks.
    check_pipe()
    check_model()
    check_domain()
    check_parameters()
    check_pivot()

    # Skip the rigid model.
    if cdp.model == MODEL_RIGID:
        print("Skipping the rigid model.")
        return

    # Open the output file.
    file = open_write_file(file_name=file, dir=dir, force=force)

    # The parameter values.
    values = assemble_param_vector()
    params = {}
    i = 0
    for name in cdp.params:
        params[name] = values[i]
        i += 1

    # The structure.
    structure = deepcopy(cdp.structure)
    if structure.num_models() > 1:
        structure.collapse_ensemble(model_num=model)

    # The pivot points.
    num_states = 1
    if cdp.model == MODEL_DOUBLE_ROTOR:
        num_states = 2
    pivot = zeros((num_states, 3), float64)
    for i in range(num_states):
        pivot[i] = generate_pivot(order=i + 1, pdb_limit=True)

    # Shift to the average position.
    average_position(structure=structure, models=[None])

    # The motional eigenframe.
    frame = generate_axis_system()

    # Only work with a subset.
    if atom_id:
        # The inverted selection.
        selection = structure.selection(atom_id=atom_id, inv=True)

        # Delete the data.
        structure.delete(selection=selection, verbosity=0)

    # Create the distribution.
    uniform_distribution(file=file,
                         model=cdp.model,
                         structure=structure,
                         parameters=params,
                         eigenframe=frame,
                         pivot=pivot,
                         atom_id=domain_moving(),
                         total=total,
                         max_rotations=max_rotations)

    # Close the file.
    file.close()
Ejemplo n.º 5
0
Archivo: uf.py Proyecto: tlinnet/relax
def decompose(root="decomposed", dir=None, atom_id=None, model=1, force=True):
    """Structural representation of the individual frame order motional components.

    @keyword root:          The file root for the PDB files created.  Each motional component will be represented by a different PDB file appended with '_mode1.pdb', '_mode2.pdb', '_mode3.pdb', etc.
    @type root:             str
    @keyword dir:           The directory name to place the file into.
    @type dir:              str or None
    @keyword atom_id:       The atom identification string to allow the decomposition to be applied to subset of all atoms.
    @type atom_id:          None or str
    @keyword model:         Only one model from an analysed ensemble of structures can be used for the decomposition, as the corresponding PDB file consists of one model per state.
    @type model:            int
    @keyword force:         A flag which, if set to True, will overwrite the any pre-existing file.
    @type force:            bool
    """

    # Printout.
    print(
        "PDB representation of the individual components of the frame order motions."
    )

    # Checks.
    check_pipe()
    check_model()
    check_domain()
    check_parameters()
    check_pivot()

    # Skip any unsupported models.
    unsupported = [MODEL_RIGID, MODEL_DOUBLE_ROTOR]
    if cdp.model in unsupported:
        print("Skipping the unsupported '%s' model." % cdp.model)
        return

    # Initialise the angle vector (cone opening angle 1, cone opening angle 2, torsion angle).
    angles = zeros(3, float64)

    # Cone opening.
    if cdp.model in MODEL_LIST_ISO_CONE:
        angles[0] = angles[1] = cdp.cone_theta
    elif cdp.model in MODEL_LIST_PSEUDO_ELLIPSE:
        angles[0] = cdp.cone_theta_y
        angles[1] = cdp.cone_theta_x

    # Non-zero torsion angle.
    if cdp.model in MODEL_LIST_FREE_ROTORS:
        angles[2] = pi
    elif cdp.model in MODEL_LIST_RESTRICTED_TORSION:
        angles[2] = cdp.cone_sigma_max

    # The motional eigenframe.
    frame = generate_axis_system()

    # Mode ordering from largest to smallest.
    indices = argsort(angles)
    angles = angles[indices[::-1]]
    frame = transpose(transpose(frame)[indices[::-1]])

    # The pivot point.
    pivot = generate_pivot(order=1, pdb_limit=True)

    # Loop over each mode.
    for i in range(3):
        # Skip modes with no motion.
        if angles[i] < 1e-7:
            continue

        # Open the output file.
        file_name = "%s_mode%i.pdb" % (root, i + 1)
        file = open_write_file(file_name=file_name, dir=dir, force=force)

        # The structure.
        structure = deepcopy(cdp.structure)
        if structure.num_models() > 1:
            structure.collapse_ensemble(model_num=model)

        # Shift to the average position.
        average_position(structure=structure, models=[None])

        # Create the representation.
        mode_distribution(file=file,
                          structure=structure,
                          axis=frame[:, i],
                          angle=angles[i],
                          pivot=pivot,
                          atom_id=domain_moving())

        # Close the file.
        file.close()
Ejemplo n.º 6
0
def create_geometric_rep(format='PDB', file=None, dir=None, compress_type=0, size=30.0, inc=36, force=False):
    """Create a PDB file containing a geometric object representing the frame order dynamics.

    @keyword format:        The format for outputting the geometric representation.  Currently only the 'PDB' format is supported.
    @type format:           str
    @keyword file:          The name of the file of the PDB representation of the frame order dynamics to create.
    @type file:             str
    @keyword dir:           The name of the directory to place the PDB file into.
    @type dir:              str
    @keyword compress_type: The compression type.  The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
    @type compress_type:    int
    @keyword size:          The size of the geometric object in Angstroms.
    @type size:             float
    @keyword inc:           The number of increments for the filling of the cone objects.
    @type inc:              int
    @keyword force:         Flag which if set to True will cause any pre-existing file to be overwritten.
    @type force:            bool
    """

    # Printout.
    subsection(file=sys.stdout, text="Creating a PDB file containing a geometric object representing the frame order dynamics.")

    # Checks.
    check_parameters(escalate=2)

    # Initialise.
    titles = []
    structures = []
    representation = []
    sims = []
    file_root = []

    # Symmetry for inverted representations?
    sym = True
    if cdp.model in [MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR]:
        sym = False

    # The standard representation.
    titles.append("Representation A")
    structures.append(Internal())
    if sym:
        representation.append('A')
        file_root.append("%s_A" % file)
    else:
        representation.append(None)
        file_root.append(file)
    sims.append(False)

    # The inverted representation.
    if sym:
        titles.append("Representation A")
        structures.append(Internal())
        representation.append('B')
        file_root.append("%s_B" % file)
        sims.append(False)

    # The standard MC simulation representation.
    if hasattr(cdp, 'sim_number'):
        titles.append("MC simulation representation A")
        structures.append(Internal())
        if sym:
            representation.append('A')
            file_root.append("%s_sim_A" % file)
        else:
            representation.append(None)
            file_root.append("%s_sim" % file)
        sims.append(True)

    # The inverted MC simulation representation.
    if hasattr(cdp, 'sim_number') and sym:
        titles.append("MC simulation representation B")
        structures.append(Internal())
        representation.append('B')
        file_root.append("%s_sim_B" % file)
        sims.append(True)

    # Loop over each structure and add the contents.
    for i in range(len(structures)):
        # Printout.
        subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])

        # Create a model for each Monte Carlo simulation.
        if sims[i]:
            for sim_i in range(cdp.sim_number):
                structures[i].add_model(model=sim_i+1)

        # Add the pivots.
        add_pivots(structure=structures[i], sims=sims[i])

        # Add all rotor objects.
        add_rotors(structure=structures[i], representation=representation[i], size=size, sims=sims[i])

        # Add the axis systems.
        add_axes(structure=structures[i], representation=representation[i], size=size, sims=sims[i])

        # Add the cone objects.
        if cdp.model not in [MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR]:
            add_cones(structure=structures[i], representation=representation[i], size=size, inc=inc, sims=sims[i])

        # Add atoms for creating titles.
        add_titles(structure=structures[i], representation=representation[i], displacement=size+10, sims=sims[i])

        # Create the PDB file.
        if format == 'PDB':
            pdb_file = open_write_file(file_root[i]+'.pdb', dir, compress_type=compress_type, force=force)
            structures[i].write_pdb(pdb_file)
            pdb_file.close()
Ejemplo n.º 7
0
def create_geometric_rep(format='PDB',
                         file=None,
                         dir=None,
                         compress_type=0,
                         size=30.0,
                         inc=36,
                         force=False):
    """Create a PDB file containing a geometric object representing the frame order dynamics.

    @keyword format:        The format for outputting the geometric representation.  Currently only the 'PDB' format is supported.
    @type format:           str
    @keyword file:          The name of the file of the PDB representation of the frame order dynamics to create.
    @type file:             str
    @keyword dir:           The name of the directory to place the PDB file into.
    @type dir:              str
    @keyword compress_type: The compression type.  The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
    @type compress_type:    int
    @keyword size:          The size of the geometric object in Angstroms.
    @type size:             float
    @keyword inc:           The number of increments for the filling of the cone objects.
    @type inc:              int
    @keyword force:         Flag which if set to True will cause any pre-existing file to be overwritten.
    @type force:            bool
    """

    # Printout.
    subsection(
        file=sys.stdout,
        text=
        "Creating a PDB file containing a geometric object representing the frame order dynamics."
    )

    # Checks.
    check_parameters(escalate=2)

    # Initialise.
    titles = []
    structures = []
    representation = []
    sims = []
    file_root = []

    # Symmetry for inverted representations?
    sym = True
    if cdp.model in [MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR]:
        sym = False

    # The standard representation.
    titles.append("Representation A")
    structures.append(Internal())
    if sym:
        representation.append('A')
        file_root.append("%s_A" % file)
    else:
        representation.append(None)
        file_root.append(file)
    sims.append(False)

    # The inverted representation.
    if sym:
        titles.append("Representation A")
        structures.append(Internal())
        representation.append('B')
        file_root.append("%s_B" % file)
        sims.append(False)

    # The standard MC simulation representation.
    if hasattr(cdp, 'sim_number'):
        titles.append("MC simulation representation A")
        structures.append(Internal())
        if sym:
            representation.append('A')
            file_root.append("%s_sim_A" % file)
        else:
            representation.append(None)
            file_root.append("%s_sim" % file)
        sims.append(True)

    # The inverted MC simulation representation.
    if hasattr(cdp, 'sim_number') and sym:
        titles.append("MC simulation representation B")
        structures.append(Internal())
        representation.append('B')
        file_root.append("%s_sim_B" % file)
        sims.append(True)

    # Loop over each structure and add the contents.
    for i in range(len(structures)):
        # Printout.
        subsubsection(file=sys.stdout, text="Creating the %s." % titles[i])

        # Create a model for each Monte Carlo simulation.
        if sims[i]:
            for sim_i in range(cdp.sim_number):
                structures[i].add_model(model=sim_i + 1)

        # Add the pivots.
        add_pivots(structure=structures[i], sims=sims[i])

        # Add all rotor objects.
        add_rotors(structure=structures[i],
                   representation=representation[i],
                   size=size,
                   sims=sims[i])

        # Add the axis systems.
        add_axes(structure=structures[i],
                 representation=representation[i],
                 size=size,
                 sims=sims[i])

        # Add the cone objects.
        if cdp.model not in [
                MODEL_ROTOR, MODEL_FREE_ROTOR, MODEL_DOUBLE_ROTOR
        ]:
            add_cones(structure=structures[i],
                      representation=representation[i],
                      size=size,
                      inc=inc,
                      sims=sims[i])

        # Add atoms for creating titles.
        add_titles(structure=structures[i],
                   representation=representation[i],
                   displacement=size + 10,
                   sims=sims[i])

        # Create the PDB file.
        if format == 'PDB':
            pdb_file = open_write_file(file_root[i] + '.pdb',
                                       dir,
                                       compress_type=compress_type,
                                       force=force)
            structures[i].write_pdb(pdb_file)
            pdb_file.close()