/restraints/npc.py

"""@namespace IMP.pmi1.restraints.npc
Specialized restraints for modeling the Nuclear Pore Complex.

These restraints have been used to model the Nuclear Pore Complex (NPC)
but may be useful for other applications too. They model the NPC as lying
in the xy plane, centered at the origin. (Transport through the pore
corresponds to movement along the z axis.) The surface of the nuclear
membrane is represented as the surface of a half torus, also lying in
the xy plane and centered at the origin. Individual proteins
(or parts of proteins, such as the N- or C- termini) are then localized to
different regions of the complex (e.g. near the membrane or pore, or on
the nuclear or cytoplasmic side) by simple restraints on their Cartesian
coordinates.
"""

import IMP.npc
import IMP.pmi1.tools


class XYRadialPositionRestraint(object):
    """Create XYRadial Position Restraint
    """
    def __init__(self,
                 representation,
                 protein,
                 lower_bound = 0.0,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 term = 'C'):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'XYRadialPositionRestraint')
        self.weight=1.0
        self.label = "None"

        xyr = IMP.npc.XYRadialPositionRestraint(self.m, lower_bound, upper_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        if (term == 'C'):
            terminal = residues[-1]
            #print (terminal, type(terminal))
            xyr.add_particle(terminal)
        elif (term == 'N'):
            terminal = residues[0]
            #print (terminal, type(terminal))
            xyr.add_particle(terminal)
        else:
            for residue in residues:
                #print (residue, type(residue))
                xyr.add_particle(residue)

        self.dataset = None
        if representation:
            for p, state in representation._protocol_output:
                p.add_xyradial_restraint(state, residues, lower_bound,
                                         upper_bound, sigma, self)

        self.rs.add_restraint(xyr)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["XYRadialPositionRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)

class XYRadialPositionLowerRestraint(object):
    """Create XYRadial Position Lower restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 lower_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'XYRadialPositionLowerRestraint')
        self.weight=1.0
        self.label = "None"

        xyr = IMP.npc.XYRadialPositionLowerRestraint(self.m, lower_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        cterminal = residues[-1]        #nterminal = residues[0]
        #print (cterminal, type(cterminal))

        xyr.add_particle(cterminal)
        self.rs.add_restraint(xyr)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["XYRadialPositionLowerRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)

class XYRadialPositionUpperRestraint(object):
    """Create XYRadial Position Upper restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'XYRadialPositionUpperRestraint')
        self.weight=1.0
        self.label = "None"

        xyr = IMP.npc.XYRadialPositionUpperRestraint(self.m, upper_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        cterminal = residues[-1]        #nterminal = residues[0]
        #print (cterminal, type(cterminal))

        xyr.add_particle(cterminal)
        self.rs.add_restraint(xyr)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["XYRadialPositionUpperRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)


class ZAxialPositionRestraint(object):
    """Create Z-Axial Position restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 lower_bound = 0.0,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 term = 'C'):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'ZAxialPositionRestraint')
        self.weight=1.0
        self.label = "None"

        zax = IMP.npc.ZAxialPositionRestraint(self.m, lower_bound, upper_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        if term == 'C':
            residues = residues[-1:]
        elif term == 'N':
            residues = residues[:1]
        for residue in residues:
            zax.add_particle(residue)

        self.dataset = None
        if representation:
            for p, state in representation._protocol_output:
                p.add_zaxial_restraint(state, residues, lower_bound,
                                       upper_bound, sigma, self)

        self.rs.add_restraint(zax)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["ZAxialPositionRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)

class ZAxialPositionLowerRestraint(object):
    """Create Z-Axial Position Lower restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 lower_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'ZAxialPositionLowerRestraint')
        self.weight=1.0
        self.label = "None"

        zax = IMP.npc.ZAxialPositionLowerRestraint(self.m, lower_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        cterminal = residues[-1]        #nterminal = residues[0]
        #print (cterminal, type(cterminal))

        zax.add_particle(cterminal)
        self.rs.add_restraint(zax)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["ZAxialPositionLowerRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)

class ZAxialPositionUpperRestraint(object):
    """Create Z-Axial Position Upper restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'ZAxialPositionUpperRestraint')
        self.weight=1.0
        self.label = "None"

        zax = IMP.npc.ZAxialPositionUpperRestraint(self.m, upper_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        cterminal = residues[-1]        #nterminal = residues[0]
        #print (cterminal, type(cterminal))

        zax.add_particle(cterminal)
        self.rs.add_restraint(zax)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["ZAxialPositionUpperRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)


class YAxialPositionRestraint(object):
    """Create Y-Axial Position restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 lower_bound = 0.0,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 term = 'C'):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'YAxialPositionRestraint')
        self.weight=1.0
        self.label = "None"

        yax = IMP.npc.YAxialPositionRestraint(self.m, lower_bound, upper_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        if (term == 'C'):
            terminal = residues[-1]
            #print (terminal, type(terminal))
            yax.add_particle(terminal)
        elif (term == 'N'):
            terminal = residues[0]
            #print (terminal, type(terminal))
            yax.add_particle(terminal)
        else:
            for residue in residues:
                #print (residue, type(residue))
                yax.add_particle(residue)

        self.dataset = None
        if representation:
            for p, state in representation._protocol_output:
                p.add_yaxial_restraint(state, residues, lower_bound,
                                       upper_bound, sigma, self)

        self.rs.add_restraint(yax)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["YAxialPositionRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)

class YAxialPositionLowerRestraint(object):
    """Create Y-Axial Position Lower restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 lower_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'YAxialPositionLowerRestraint')
        self.weight=1.0
        self.label = "None"

        yax = IMP.npc.YAxialPositionLowerRestraint(self.m, lower_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        cterminal = residues[-1]        #nterminal = residues[0]
        #print (cterminal, type(cterminal))

        yax.add_particle(cterminal)
        self.rs.add_restraint(yax)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["YAxialPositionLowerRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)

class YAxialPositionUpperRestraint(object):
    """Create Y-Axial Position Upper restraints
    """
    def __init__(self,
                 representation,
                 protein,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'YAxialPositionUpperRestraint')
        self.weight=1.0
        self.label = "None"

        yax = IMP.npc.YAxialPositionUpperRestraint(self.m, upper_bound, consider_radius, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=1)
        cterminal = residues[-1]        #nterminal = residues[0]
        #print (cterminal, type(cterminal))

        yax.add_particle(cterminal)
        self.rs.add_restraint(yax)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["YAxialPositionUpperRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)


class MembraneSurfaceLocationRestraint(object):
    """Create Membrane Surface Location Restraint
    """
    def __init__(self,
                 representation,
                 protein,
                 tor_R = 540.0,
                 tor_r = 127.5,
                 tor_th = 45.0,
                 sigma = 0.2,
                 resolution = 1):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'MembraneSurfaceLocationRestraint')
        self.weight=1.0
        self.label = "None"

        msl = IMP.npc.MembraneSurfaceLocationRestraint(self.m, tor_R, tor_r, tor_th, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=resolution)
        for residue in residues:
            #print (residue, type(residue))
            msl.add_particle(residue)

        self.dataset = None
        if representation:
            for p, state in representation._protocol_output:
                p.add_membrane_surface_location_restraint(
                        state, residues, tor_R, tor_r, tor_th, sigma, self)

        self.rs.add_restraint(msl)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["MembraneSurfaceLocationRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)


class MembraneSurfaceLocationConditionalRestraint(object):
    """Create Membrane Surface Location CONDITIONAL Restraint
       for Nup120 ALPS Motifs - Mutually Exclusive from (135,152,'Nup120') and (197,216,'Nup120').
       It returns a minimum penalty score from two potential ALPS motifs.
    """
    def __init__(self,
                 representation,
                 protein1,
                 protein2,
                 tor_R = 540.0,
                 tor_r = 127.5,
                 tor_th = 45.0,
                 sigma = 0.2,
                 resolution = 1):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'MembraneSurfaceLocationConditionalRestraint')
        self.weight=1.0
        self.label = "None"

        msl = IMP.npc.MembraneSurfaceLocationConditionalRestraint(self.m, tor_R, tor_r, tor_th, sigma)
        residues1 = IMP.pmi1.tools.select_by_tuple(representation, protein1, resolution=resolution)
        for residue in residues1:
            #print (residue, type(residue))
            msl.add_particle1(residue)
        residues2 = IMP.pmi1.tools.select_by_tuple(representation, protein2, resolution=resolution)
        for residue in residues2:
            #print (residue, type(residue))
            msl.add_particle2(residue)

        # Approximate as two membrane restraints
        self.dataset = None
        if representation:
            for p, state in representation._protocol_output:
                for residues in residues1, residues2:
                    p.add_membrane_surface_location_restraint(
                            state, residues, tor_R, tor_r, tor_th, sigma, self)

        self.rs.add_restraint(msl)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["MembraneSurfaceLocationConditionalRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)


class MembraneExclusionRestraint(object):
    """Create Membrane Exclusion Restraint
    """
    def __init__(self,
                 representation,
                 protein,
                 tor_R = 540.0,
                 tor_r = 127.5,
                 tor_th = 45.0,
                 sigma = 0.2,
                 resolution = 1):
        """Constructor
        @param representation representation
        """

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'MembraneExclusionRestraint')
        self.weight=1.0
        self.label = "None"

        mex = IMP.npc.MembraneExclusionRestraint(self.m, tor_R, tor_r, tor_th, sigma)
        residues = IMP.pmi1.tools.select_by_tuple(representation, protein, resolution=resolution)
        for residue in residues:
            #print (residue, type(residue))
            mex.add_particle(residue)

        self.dataset = None
        if representation:
            for p, state in representation._protocol_output:
                p.add_membrane_exclusion_restraint(
                        state, residues, tor_R, tor_r, tor_th, sigma, self)

        self.rs.add_restraint(mex)

    def set_label(self, label):
        self.label = label

    def add_to_model(self):
        IMP.pmi1.tools.add_restraint_to_model(self.m, self.rs)

    def get_restraint(self):
        return self.rs

    def set_weight(self, weight):
        self.weight = weight
        self.rs.set_weight(self.weight)

    def get_output(self):
        self.m.update()
        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["MembraneExclusionRestraint_" + self.label] = str(score)
        return output

    def evaluate(self):
        return self.weight * self.rs.unprotected_evaluate(None)