npc_restraints.py

import IMP.npc
import IMP.pmi.representation

class XYRadialPositionRestraint(object):
    """Create XYRadial Position Restraint
    """
    def __init__(self,
                 representation = None,
                 protein = None,
                 lower_bound = 0.0,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 term = 'C',
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("XYRadialPositionRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 lower_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("XYRadialPositionLowerRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("XYRadialPositionUpperRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 lower_bound = 0.0,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 term = 'C',
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("ZAxialPositionRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 lower_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("ZAxialPositionLowerRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("ZAxialPositionUpperRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 lower_bound = 0.0,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 term = 'C',
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("YAxialPositionRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 lower_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("YAxialPositionLowerRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 upper_bound = 0.0,
                 consider_radius = False,
                 sigma = 1.0,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("YAxialPositionUpperRestraint: must pass hier or representation")

        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)
        #terminal_residue = IMP.pmi.tools.get_terminal_residue(representation, representation.hier_dict[protein], terminus="C")
        residues = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 tor_R = 540.0,
                 tor_r = 127.5,
                 tor_th = 45.0,
                 sigma = 0.2,
                 resolution = 1,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("MembraneSurfaceLocationRestraint: must pass hier or representation")

        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.pmi.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.pmi.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 = None,
                 protein1 = None,
                 protein2 = None,
                 tor_R = 540.0,
                 tor_r = 127.5,
                 tor_th = 45.0,
                 sigma = 0.2,
                 resolution = 1,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("MembraneSurfaceLocationConditionalRestraint: must pass hier or representation")

        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.pmi.tools.select_by_tuple(representation, protein1, resolution=resolution)
        for residue in residues1:
            #print (residue, type(residue))
            msl.add_particle1(residue)
        residues2 = IMP.pmi.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.pmi.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 = None,
                 protein = None,
                 tor_R = 540.0,
                 tor_r = 127.5,
                 tor_th = 45.0,
                 sigma = 0.2,
                 resolution = 1,
                 hier = None):
        """Constructor
        @param representation representation
        """

        # PMI1/2 selection
        if representation is None and hier is not None:
            self.m = hier.get_model()
        elif hier is None and representation is not None:
            self.m = representation.prot.get_model()
        else:
            raise Exception("MembraneExclusionRestraint: must pass hier or representation")

        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.pmi.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.pmi.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)