crosslinking.py

"""@namespace IMP.pmi.restraints.crosslinking
Restraints for handling crosslinking data.
"""

from __future__ import print_function
import IMP
import IMP.core
import IMP.algebra
import IMP.atom
import IMP.isd
import IMP.container
import IMP.pmi.tools
import IMP.pmi.output
import IMP.pmi.io.crosslink
from math import log
from collections import defaultdict
import itertools
import operator

class CrossLinkingMassSpectrometryRestraint(object):
    """Setup cross-link distance restraints from mass spectrometry data.
    The noise in the data and the structural uncertainty of cross-linked amino-acids
    is inferred using Bayes theory of probability
    \note Wraps an IMP::isd::CrossLinkMSRestraint
    """
    def __init__(self, representation=None,
                 root_hier=None,
                 CrossLinkDataBase=None,
                 length=10.0,
                 resolution=None,
                 slope=0.02,
                 label="None",
                 filelabel="None",
                 attributes_for_label=None):
        """Constructor.
        @param representation DEPRECATED The IMP.pmi.representation.Representation
                object that contain the molecular system
        @param root_hier The canonical hierarchy containing all the states
        @param CrossLinkDataBase The IMP.pmi.io.crosslink.CrossLinkDataBase
                object that contains the cross-link dataset
        @param length maximal cross-linker length (including the residue sidechains)
        @param resolution what representation resolution should the cross-link
                restraint be applied to.
        @param slope  The slope of a distance-linear scoring function that
               funnels the score when the particles are
               too far away. Suggested value 0.02.
        @param label the extra text to label the restraint so that it is
                searchable in the output
        @param filelabel automatically generated file containing missing/included/excluded
                cross-links will be labeled using this text
        @param attributes_for_label
        """

        use_pmi2 = True
        if representation is not None:
            use_pmi2 = False
            if type(representation) != list:
                representations = [representation]
            else:
                representations = representation
            self.m = representations[0].prot.get_model()
        elif root_hier is not None:
            self.m = root_hier.get_model()
        else:
            raise Exception("You must pass either representation or root_hier")

        if CrossLinkDataBase is None:
            raise Exception("You must pass a CrossLinkDataBase")
        if not isinstance(CrossLinkDataBase,IMP.pmi.io.crosslink.CrossLinkDataBase):
            raise TypeError("CrossLinkingMassSpectrometryRestraint: CrossLinkDataBase should be an IMP.pmi.io.crosslink.CrossLinkDataBase object")
        self.CrossLinkDataBase = CrossLinkDataBase

        if resolution==0 or resolution is None:
            raise Exception("You must pass a resolution and it can't be zero")

        indb = open("included." + filelabel + ".xl.db", "w")
        exdb = open("excluded." + filelabel + ".xl.db", "w")
        midb = open("missing." + filelabel + ".xl.db", "w")


        self.rs = IMP.RestraintSet(self.m, 'likelihood')
        self.rspsi = IMP.RestraintSet(self.m, 'prior_psi')
        self.rssig = IMP.RestraintSet(self.m, 'prior_sigmas')
        self.rslin = IMP.RestraintSet(self.m, 'linear_dummy_restraints')

        # dummy linear restraint used for Chimera display
        self.linear = IMP.core.Linear(0, 0.0)
        self.linear.set_slope(0.0)
        dps2 = IMP.core.DistancePairScore(self.linear)

        self.label = label
        self.psi_is_sampled = True
        self.sigma_is_sampled = True
        self.psi_dictionary={}
        self.sigma_dictionary={}
        self.xl_list=[]
        self.outputlevel = "low"

        restraints = []

        # if PMI2, first add all the molecule copies as clones to the database
        if use_pmi2:
            copies_to_add = defaultdict(int)
            print('gathering copies')
            for xlid in self.CrossLinkDataBase.xlid_iterator():
                for xl in self.CrossLinkDataBase[xlid]:
                    r1 = xl[self.CrossLinkDataBase.residue1_key]
                    c1 = xl[self.CrossLinkDataBase.protein1_key]
                    r2 = xl[self.CrossLinkDataBase.residue2_key]
                    c2 = xl[self.CrossLinkDataBase.protein2_key]
                    for c,r in ((c1,r1),(c2,r2)):
                        if c in copies_to_add:
                            continue
                        sel = IMP.atom.Selection(root_hier,
                                                 state_index=0,
                                                 molecule=c,
                                                 residue_index=r,
                                                 resolution=resolution).get_selected_particles()
                        if len(sel)>0:
                            copies_to_add[c] = len(sel)-1
            print(copies_to_add)
            for molname in copies_to_add:
                if copies_to_add[molname]==0:
                    continue
                fo1 = IMP.pmi.io.crosslink.FilterOperator(self.CrossLinkDataBase.protein1_key,operator.eq,molname)
                self.CrossLinkDataBase.set_value(self.CrossLinkDataBase.protein1_key,molname+'.0',fo1)
                fo2 = IMP.pmi.io.crosslink.FilterOperator(self.CrossLinkDataBase.protein2_key,operator.eq,molname)
                self.CrossLinkDataBase.set_value(self.CrossLinkDataBase.protein2_key,molname+'.0',fo2)
                for ncopy in range(copies_to_add[molname]):
                    self.CrossLinkDataBase.clone_protein('%s.0'%molname,'%s.%i'%(molname,ncopy+1))
            print('done pmi2 prelims')

        for xlid in self.CrossLinkDataBase.xlid_iterator():
            new_contribution=True
            for xl in self.CrossLinkDataBase[xlid]:

                r1 = xl[self.CrossLinkDataBase.residue1_key]
                c1 = xl[self.CrossLinkDataBase.protein1_key]
                r2 = xl[self.CrossLinkDataBase.residue2_key]
                c2 = xl[self.CrossLinkDataBase.protein2_key]

                if use_pmi2:
                    iterlist = range(len(IMP.atom.get_by_type(root_hier,IMP.atom.STATE_TYPE)))
                else:
                    iterlist = representations
                for nstate, r in enumerate(iterlist):
                    # loop over every state
                    xl[self.CrossLinkDataBase.state_key]=nstate
                    xl[self.CrossLinkDataBase.data_set_name_key]=self.label

                    if use_pmi2:
                        name1 = c1
                        name2 = c2
                        copy1 = 0
                        copy2 = 0
                        if '.' in c1:
                            name1,copy1 = c1.split('.')
                        if '.' in c2:
                            name2,copy2 = c2.split('.')
                        ps1 = IMP.atom.Selection(root_hier,
                                                 state_index=nstate,
                                                 molecule=name1,
                                                 copy_index=int(copy1),
                                                 residue_index=r1,
                                                 resolution=resolution).get_selected_particles()
                        ps2 = IMP.atom.Selection(root_hier,
                                                 state_index=nstate,
                                                 molecule=name2,
                                                 copy_index=int(copy2),
                                                 residue_index=r2,
                                                 resolution=resolution).get_selected_particles()

                        ps1 = [IMP.atom.Hierarchy(p) for p in ps1]
                        ps2 = [IMP.atom.Hierarchy(p) for p in ps2]
                    else:
                        ps1 = IMP.pmi.tools.select(
                             r,
                             resolution=resolution,
                             name=c1,
                             name_is_ambiguous=False,
                             residue=r1)
                        ps2 = IMP.pmi.tools.select(
                             r,
                             resolution=resolution,
                             name=c2,
                             name_is_ambiguous=False,
                             residue=r2)

                    if len(ps1) > 1:
                        raise ValueError("residue %d of chain %s selects multiple particles %s" % (r1, c1, str(ps1)))
                    elif len(ps1) == 0:
                        print("CrossLinkingMassSpectrometryRestraint: WARNING> residue %d of chain %s is not there" % (r1, c1))
                        midb.write(str(xl) + "\n")
                        continue

                    if len(ps2) > 1:
                        raise ValueError("residue %d of chain %s selects multiple particles %s" % (r2, c2, str(ps2)))
                    elif len(ps2) == 0:
                        print("CrossLinkingMassSpectrometryRestraint: WARNING> residue %d of chain %s is not there" % (r2, c2))
                        midb.write(str(xl) + "\n")
                        continue

                    p1 = ps1[0]
                    p2 = ps2[0]

                    if p1 == p2 and r1 == r2:
                        print("CrossLinkingMassSpectrometryRestraint: WARNING> same particle and same residue, skipping cross-link")
                        continue

                    if new_contribution:
                        print("generating a new crosslink restraint")
                        new_contribution=False
                        dr = IMP.isd.CrossLinkMSRestraint(
                            self.m,
                            length,
                            slope)
                        restraints.append(dr)


                    if self.CrossLinkDataBase.sigma1_key not in xl.keys():
                        sigma1name="SIGMA"
                        xl[self.CrossLinkDataBase.sigma1_key]=sigma1name
                    else:
                        sigma1name=xl[self.CrossLinkDataBase.sigma1_key]
                    sigma1=self.create_sigma(sigma1name)

                    if self.CrossLinkDataBase.sigma2_key not in xl.keys():
                        sigma2name="SIGMA"
                        xl[self.CrossLinkDataBase.sigma2_key]=sigma2name
                    else:
                        sigma2name=xl[self.CrossLinkDataBase.sigma2_key]
                    sigma2=self.create_sigma(sigma2name)

                    if self.CrossLinkDataBase.psi_key not in xl.keys():
                        psiname="PSI"
                        xl[self.CrossLinkDataBase.psi_key]=psiname
                    else:
                        psiname=xl[self.CrossLinkDataBase.psi_key]

                    psi=self.create_psi(psiname)


                    p1i = p1.get_particle_index()
                    xl["Particle1"]=p1
                    p2i = p2.get_particle_index()
                    xl["Particle2"]=p2
                    s1i = sigma1.get_particle().get_index()
                    xl["Particle_sigma1"]=sigma1
                    s2i = sigma2.get_particle().get_index()
                    xl["Particle_sigma2"]=sigma2
                    psii = psi.get_particle().get_index()
                    xl["Particle_psi"]=psi

                    dr.add_contribution((p1i, p2i), (s1i, s2i), psii)
                    xl["Restraint"]=dr

                    print("--------------")
                    print("CrossLinkingMassSpectrometryRestraint: generating cross-link restraint between")
                    print("CrossLinkingMassSpectrometryRestraint: residue %d of chain %s and residue %d of chain %s" % (r1, c1, r2, c2))
                    print("CrossLinkingMassSpectrometryRestraint: with sigma1 %s sigma2 %s psi %s" % (sigma1name, sigma2name, psiname))
                    print("CrossLinkingMassSpectrometryRestraint: between particles %s and %s" % (p1.get_name(), p2.get_name()))
                    print("==========================================\n")

                    # check if the two residues belong to the same rigid body
                    if(IMP.core.RigidMember.get_is_setup(p1) and
                        IMP.core.RigidMember.get_is_setup(p2) and
                        IMP.core.RigidMember(p1).get_rigid_body() ==
                        IMP.core.RigidMember(p2).get_rigid_body()):
                        xl["IntraRigidBody"]=True
                    else:
                        xl["IntraRigidBody"]=False

                    xl_label=self.CrossLinkDataBase.get_short_cross_link_string(xl)
                    xl["ShortLabel"]=xl_label
                    dr.set_name(xl_label)

                    if p1i != p2i:
                        pr = IMP.core.PairRestraint(self.m, dps2, (p1i, p2i))
                        pr.set_name(xl_label)
                        self.rslin.add_restraint(pr)

                    self.xl_list.append(xl)

                    indb.write(str(xl) + "\n")

        if len(self.xl_list) == 0:
            raise SystemError("CrossLinkingMassSpectrometryRestraint: no crosslink was constructed")

        lw = IMP.isd.LogWrapper(restraints,1.0)
        self.rs.add_restraint(lw)

    def add_to_model(self):
        """ Add the restraint to the model so that it is evaluated """
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rspsi)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rssig)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rslin)

    def get_hierarchies(self):
        """ get the hierarchy """
        return self.prot

    def get_restraint_sets(self):
        """ get the restraint set """
        return self.rs

    def get_restraint(self):
        """ get the restraint set  (redundant with get_restraint_sets)"""
        return self.rs

    def get_restraint_for_rmf(self):
        """ get the dummy restraints to be displayed in the rmf file """
        return self.rslin

    def get_restraints(self):
        """ get the restraints in a list """
        rlist = []
        for r in self.rs.get_restraints():
            rlist.append(IMP.core.PairRestraint.get_from(r))
        return rlist

    def get_particle_pairs(self):
        """ Get a list of tuples containing the particle pairs """
        ppairs = []
        for i in range(len(self.pairs)):
            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            ppairs.append((p0, p1))
        return ppairs

    def set_output_level(self, level="low"):
        """ Set the output level of the output """
        self.outputlevel = level

    def set_psi_is_sampled(self, is_sampled=True):
        """ Switch on/off the sampling of psi particles """
        self.psi_is_sampled = is_sampled

    def set_sigma_is_sampled(self, is_sampled=True):
        """ Switch on/off the sampling of sigma particles """
        self.sigma_is_sampled = is_sampled


    def create_sigma(self, name):
        """ This is called internally. Creates a nuisance
        on the structural uncertainty """
        if name in self.sigma_dictionary:
            return self.sigma_dictionary[name][0]

        sigmainit = 2.0
        sigmaminnuis = 0.0000001
        sigmamaxnuis = 1000.0
        sigmamin = 0.01
        sigmamax = 100.0
        sigmatrans = 0.5
        sigma = IMP.pmi.tools.SetupNuisance(self.m, sigmainit,
                                                 sigmaminnuis, sigmamaxnuis, self.sigma_is_sampled).get_particle()
        self.sigma_dictionary[name] = (
            sigma,
            sigmatrans,
            self.sigma_is_sampled)
        self.rssig.add_restraint(
            IMP.isd.UniformPrior(
                self.m,
                sigma,
                1000000000.0,
                sigmamax,
                sigmamin))
        return sigma

    def create_psi(self, name):
        """ This is called internally. Creates a nuisance
        on the data uncertainty """
        if name in self.psi_dictionary:
            return self.psi_dictionary[name][0]

        psiinit=0.25
        psiminnuis = 0.0000001
        psimaxnuis = 0.4999999
        psimin = 0.01
        psimax = 0.49
        psitrans = 0.1
        psi = IMP.pmi.tools.SetupNuisance(self.m, psiinit,
                                               psiminnuis, psimaxnuis,
                                               self.psi_is_sampled).get_particle()
        self.psi_dictionary[name] = (
            psi,
            psitrans,
            self.psi_is_sampled)

        self.rspsi.add_restraint(
            IMP.isd.UniformPrior(
                self.m,
                psi,
                1000000000.0,
                psimax,
                psimin))

        self.rspsi.add_restraint(IMP.isd.JeffreysRestraint(self.m, psi))
        return psi

    def set_label(self, s):
        """ Set the restraint output label """
        self.label=s

    def get_output(self):
        """ Get the output of the restraint to be used by the IMP.pmi.output object"""
        self.m.update()

        output = {}
        score = self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["CrossLinkingMassSpectrometryRestraint_Data_Score_" + self.label] = str(score)
        output["CrossLinkingMassSpectrometryRestraint_PriorSig_Score_" +
               self.label] = self.rssig.unprotected_evaluate(None)
        output["CrossLinkingMassSpectrometryRestraint_PriorPsi_Score_" +
                   self.label] = self.rspsi.unprotected_evaluate(None)
        output["CrossLinkingMassSpectrometryRestraint_Linear_Score_" +
               self.label] = self.rslin.unprotected_evaluate(None)
        for xl in self.xl_list:

            xl_label=xl["ShortLabel"]
            ln = xl["Restraint"]
            p0 = xl["Particle1"]
            p1 = xl["Particle2"]
            output["CrossLinkingMassSpectrometryRestraint_Score_" +
                   xl_label] = str(-log(ln.unprotected_evaluate(None)))

            d0 = IMP.core.XYZ(p0)
            d1 = IMP.core.XYZ(p1)
            output["CrossLinkingMassSpectrometryRestraint_Distance_" +
                   xl_label] = str(IMP.core.get_distance(d0, d1))


        for psiname in self.psi_dictionary:
            output["CrossLinkingMassSpectrometryRestraint_Psi_" +
                    str(psiname) + "_" + self.label] = str(self.psi_dictionary[psiname][0].get_scale())

        for sigmaname in self.sigma_dictionary:
            output["CrossLinkingMassSpectrometryRestraint_Sigma_" +
                   str(sigmaname) + "_" + self.label] = str(self.sigma_dictionary[sigmaname][0].get_scale())


        return output

    def get_particles_to_sample(self):
        """ Get the particles to be sampled by the IMP.pmi.sampler object """
        ps = {}
        if self.sigma_is_sampled:
            for sigmaname in self.sigma_dictionary:
                ps["Nuisances_CrossLinkingMassSpectrometryRestraint_Sigma_" + str(sigmaname) + "_" + self.label] =\
                    ([self.sigma_dictionary[sigmaname][0]],
                     self.sigma_dictionary[sigmaname][1])

        if self.psi_is_sampled:
            for psiname in self.psi_dictionary:
                ps["Nuisances_CrossLinkingMassSpectrometryRestraint_Psi_" +
                    str(psiname) + "_" + self.label] =\
                   ([self.psi_dictionary[psiname][0]], self.psi_dictionary[psiname][1])

        return ps


class AtomicCrossLinkMSRestraint(object):
    """Setup cross-link distance restraints at atomic level
    The "atomic" aspect is that it models the particle uncertainty with a Gaussian
    The noise in the data and the structural uncertainty of cross-linked amino-acids
    is inferred using Bayes' theory of probability
    \note Wraps an IMP::isd::AtomicCrossLinkMSRestraint
    """
    def __init__(self,
                 root_hier,
                 xldb,
                 atom_type="NZ",
                 length=10.0,
                 slope=0.01,
                 nstates=None,
                 label='',
                 nuisances_are_optimized=True,
                 sigma_init=5.0,
                 psi_init = 0.01,
                 one_psi=True,
                 filelabel=None):
        """Constructor.
        Automatically creates one "sigma" per crosslinked residue and one "psis" per pair.
        Other nuisance options are available.
        \note Will return an error if the data+extra_sel don't specify two particles per XL pair.
        @param root_hier  The root hierarchy on which you'll do selection
        @param xldb       CrossLinkDataBase object
        @param atom_type  Can either be "NZ" or "CA"
        @param length     The XL linker length
        @param slope      Linear term to add to the restraint function to help when far away
        @param nstates    The number of states to model. Defaults to the number of states in root.
        @param label      The output label for the restraint
        @param nuisances_are_optimized Whether to optimize nuisances
        @param sigma_init The initial value for all the sigmas
        @param psi_init   The initial value for all the psis
        @param one_psi    Use a single psi for all restraints (if False, creates one per XL)
        @param filelabel automatically generated file containing missing/included/excluded
                cross-links will be labeled using this text
        """

        # basic params
        self.root = root_hier
        self.mdl = self.root.get_model()
        self.xldb = xldb
        self.weight = 1.0
        self.label = label
        self.length = length
        self.sigma_is_sampled = nuisances_are_optimized
        self.psi_is_sampled = nuisances_are_optimized

        if atom_type not in("NZ","CA"):
            raise Exception("AtomicXLRestraint: atom_type must be NZ or CA")
        self.atom_type = atom_type
        self.nstates = nstates
        if nstates is None:
            self.nstates = len(IMP.atom.get_by_type(self.root,IMP.atom.STATE_TYPE))
        elif nstates!=len(IMP.atom.get_by_type(self.root,IMP.atom.STATE_TYPE)):
            print("Warning: nstates is not the same as the number of states in root")

        self.rs = IMP.RestraintSet(self.mdl, 'likelihood')
        self.rs_psi = IMP.RestraintSet(self.mdl, 'prior_psi')
        self.rs_sig = IMP.RestraintSet(self.mdl, 'prior_sigmas')
        self.rs_lin = IMP.RestraintSet(self.mdl, 'linear_dummy_restraints')


        self.psi_dictionary = {}
        self.sigma_dictionary = {}

        self.particles=defaultdict(set)
        self.one_psi = one_psi
        self.bonded_pairs = []
        if self.one_psi:
            print('creating a single psi for all XLs')
        else:
            print('creating one psi for each XL')

        # output logging file
        if filelabel is not None:
            indb = open("included." + filelabel + ".xl.db", "w")
            exdb = open("excluded." + filelabel + ".xl.db", "w")
            midb = open("missing." + filelabel + ".xl.db", "w")



        ### Setup nuisances
        '''
        # read ahead to get the number of XL's per residue
        num_xls_per_res=defaultdict(int)
        for unique_id in data:
           for nstate in range(self.nstates):
               for xl in data[unique_id]:
                   num_xls_per_res[str(xl.r1)]+=1
                   num_xls_per_res[str(xl.r2)]+=1

        # Will setup two sigmas based on promiscuity of the residue
        sig_threshold=4
        self.sig_low = setup_nuisance(self.mdl,self.rs_nuis,init_val=sigma_init,min_val=1.0,
                                      max_val=100.0,is_opt=self.nuis_opt)
        self.sig_high = setup_nuisance(self.mdl,self.rs_nuis,init_val=sigma_init,min_val=1.0,
                                       max_val=100.0,is_opt=self.nuis_opt)
        '''
        self._create_sigma('sigma',sigma_init)
        if one_psi:
            self._create_psi('psi',psi_init)
        else:
            for xlid in self.xldb.xlid_iterator():
                self._create_psi(xlid,psi_init)

        ### create all the XLs
        xlrs=[]
        for xlid in self.xldb.xlid_iterator():
            # create restraint for this data point
            if one_psi:
                psip = self.psi_dictionary['psi'][0].get_particle_index()
            else:
                psip = self.psi_dictionary[unique_id][0].get_particle_index()
            r = IMP.isd.AtomicCrossLinkMSRestraint(self.mdl,
                                                   self.length,
                                                   psip,
                                                   slope,
                                                   True)
            num_contributions=0

            # add a contribution for each XL ambiguity option within each state
            for nstate in self.nstates:
                for xl in self.xldb[xlid]:
                    r1 = xl[self.xldb.residue1_key]
                    c1 = xl[self.xldb.protein1_key].strip()
                    r2 = xl[self.xldb.residue2_key]
                    c2 = xl[self.xldb.protein2_key].strip()

                    # perform selection. these may contain multiples if Copies are used
                    ps1 = IMP.atom.Selection(self.root,
                                             state_index=nstate,
                                             atom_type = IMP.atom.AtomType(self.atom_type),
                                             molecule=c1,
                                             residue_index=r1).get_selected_particles()
                    ps2 = IMP.atom.Selection(self.root,
                                             state_index=nstate,
                                             atom_type = IMP.atom.AtomType(self.atom_type),
                                             molecule=c2,
                                             residue_index=r2).get_selected_particles()
                    if len(ps1) == 0:
                        print("AtomicXLRestraint: WARNING> residue %d of chain %s is not there" % (r1, c1))
                        if filelabel is not None:
                            midb.write(str(xl) + "\n")
                        continue

                    if len(ps2) == 0:
                        print("AtomicXLRestraint: WARNING> residue %d of chain %s is not there" % (r2, c2))
                        if filelabel is not None:
                            midb.write(str(xl) + "\n")
                        continue


                    # figure out sig1 and sig2 based on num XLs
                    '''
                    num1=num_xls_per_res[str(xl.r1)]
                    num2=num_xls_per_res[str(xl.r2)]
                    if num1<sig_threshold:
                        sig1=self.sig_low
                    else:
                        sig1=self.sig_high
                    if num2<sig_threshold:
                        sig2=self.sig_low
                    else:
                        sig2=self.sig_high
                    '''
                    sig1 = self.sigma_dictionary['sigma'][0]
                    sig2 = self.sigma_dictionary['sigma'][0]

                    # add each copy contribution to restraint
                    for p1,p2 in itertools.product(ps1,ps2):
                        if p1==p2:
                            continue
                        self.particles[nstate]|=set((p1,p2))
                        r.add_contribution([p1.get_index(),p2.get_index()],
                                           [sig1.get_particle_index(),sig2.get_particle_index()])
                        num_contributions+=1

            if num_contributions>0:
                print('XL:',xlid,'num contributions:',num_contributions)
                xlrs.append(r)
        if len(xlrs)==0:
            raise Exception("You didn't create any XL restraints")
        print('created',len(xlrs),'XL restraints')
        self.rs=IMP.isd.LogWrapper(xlrs,self.weight)

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

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

    def add_to_model(self):
        IMP.pmi.tools.add_restraint_to_model(self.mdl, self.rs)
        IMP.pmi.tools.add_restraint_to_model(self.mdl, self.rs_sig)
        IMP.pmi.tools.add_restraint_to_model(self.mdl, self.rs_psi)

    def get_hierarchy(self):
        return self.prot

    def get_restraint_set(self):
        return self.rs

    def _create_sigma(self, name,sigmainit):
        """ This is called internally. Creates a nuisance
        on the structural uncertainty """
        if name in self.sigma_dictionary:
            return self.sigma_dictionary[name][0]

        sigmaminnuis = 0.0000001
        sigmamaxnuis = 1000.0
        sigmamin = 0.01
        sigmamax = 100.0
        sigmatrans = 0.5
        sigma = IMP.pmi.tools.SetupNuisance(self.mdl,
                                            sigmainit,
                                            sigmaminnuis,
                                            sigmamaxnuis,
                                            self.sigma_is_sampled).get_particle()
        self.sigma_dictionary[name] = (
            sigma,
            sigmatrans,
            self.sigma_is_sampled)
        self.rs_sig.add_restraint(
            IMP.isd.UniformPrior(
                self.mdl,
                sigma,
                1000000000.0,
                sigmamax,
                sigmamin))
        return sigma

    def _create_psi(self, name,psiinit):
        """ This is called internally. Creates a nuisance
        on the data uncertainty """
        if name in self.psi_dictionary:
            return self.psi_dictionary[name][0]

        psiminnuis = 0.0000001
        psimaxnuis = 0.4999999
        psimin = 0.01
        psimax = 0.49
        psitrans = 0.1
        psi = IMP.pmi.tools.SetupNuisance(self.mdl,
                                          psiinit,
                                          psiminnuis,
                                          psimaxnuis,
                                          self.psi_is_sampled).get_particle()
        self.psi_dictionary[name] = (
            psi,
            psitrans,
            self.psi_is_sampled)

        self.rs_psi.add_restraint(
            IMP.isd.UniformPrior(
                self.mdl,
                psi,
                1000000000.0,
                psimax,
                psimin))

        self.rs_psi.add_restraint(IMP.isd.JeffreysRestraint(self.mdl, psi))
        return psi

    def create_restraints_for_rmf(self):
        """ create dummy harmonic restraints for each XL but don't add to model
        Makes it easy to see each contribution to each XL in RMF
        """
        class MyGetRestraint(object):
            def __init__(self,rs):
                self.rs=rs
            def get_restraint_for_rmf(self):
                return self.rs

        dummy_mdl=IMP.Model()
        hps = IMP.core.HarmonicDistancePairScore(self.length,1.0)
        dummy_rs=[]
        for nxl in range(self.get_number_of_restraints()):
            xl=IMP.isd.AtomicCrossLinkMSRestraint.get_from(self.rs.get_restraint(nxl))
            rs = IMP.RestraintSet(dummy_mdl, 'atomic_xl_'+str(nxl))
            for ncontr in range(xl.get_number_of_contributions()):
                ps=xl.get_contribution(ncontr)
                dr = IMP.core.PairRestraint(hps,[self.mdl.get_particle(p) for p in ps],
                                            'xl%i_contr%i'%(nxl,ncontr))
                rs.add_restraint(dr)
                dummy_rs.append(MyGetRestraint(rs))
        return dummy_rs


    def get_particles_to_sample(self):
        """ Get the particles to be sampled by the IMP.pmi.sampler object """
        ps = {}
        if self.sigma_is_sampled:
            for sigmaname in self.sigma_dictionary:
                ps["Nuisances_AtomicCrossLinkingMSRestraint_Sigma_" + str(sigmaname) + "_" + self.label] = \
                    ([self.sigma_dictionary[sigmaname][0]],
                     self.sigma_dictionary[sigmaname][1])
        if self.psi_is_sampled:
            for psiname in self.psi_dictionary:
                ps["Nuisances_CrossLinkingMassSpectrometryRestraint_Psi_" +
                    str(psiname) + "_" + self.label] =\
                   ([self.psi_dictionary[psiname][0]], self.psi_dictionary[psiname][1])
        return ps

    def get_bonded_pairs(self):
        return self.bonded_pairs

    def get_number_of_restraints(self):
        return self.rs.get_number_of_restraints()

    def __repr__(self):
        return 'XL restraint with '+str(len(self.rs.get_restraint(0).get_number_of_restraints())) \
            + ' data points'

    def load_nuisances_from_stat_file(self,in_fn,nframe):
        """Read a stat file and load all the sigmas.
        This is potentially quite stupid.
        It's also a hack since the sigmas should be stored in the RMF file.
        Also, requires one sigma and one psi for ALL XLs.
        """
        import subprocess
        sig_val = float(subprocess.check_output(["process_output.py","-f",in_fn,
                                                 "-s","AtomicXLRestraint_sigma"]).split('\n>')[1+nframe])
        psi_val = float(subprocess.check_output(["process_output.py","-f",in_fn,
                                                 "-s","AtomicXLRestraint_psi"]).split('\n>')[1+nframe])
        for nxl in range(self.rs.get_number_of_restraints()):
            xl=IMP.isd.AtomicCrossLinkMSRestraint.get_from(self.rs.get_restraint(nxl))
            psip = xl.get_psi()
            IMP.isd.Scale(self.mdl,psip).set_scale(psi_val)
            for contr in range(xl.get_number_of_contributions()):
                sig1,sig2=xl.get_contribution_sigmas(contr)
                IMP.isd.Scale(self.mdl,sig1).set_scale(sig_val)

        print('loaded nuisances from file')

    def plot_violations(self,out_prefix,
                        max_prob_for_violation=0.1,
                        min_dist_for_violation=1e9,
                        coarsen=False,
                        limit_to_chains=None,
                        exclude_chains=''):
        """Create CMM files, one for each state, of all crosslinks.
        will draw in GREEN if non-violated in all states (or if only one state)
        will draw in PURPLE if non-violated only in a subset of states (draws nothing elsewhere)
        will draw in RED in ALL states if all violated
        (if only one state, you'll only see green and red)

        @param out_prefix             Output xlink files prefix
        @param max_prob_for_violation It's a violation if the probability is below this
        @param min_dist_for_violation It's a violation if the min dist is above this
        @param coarsen                Use CA positions
        @param limit_to_chains        Try to visualize just these chains
        @param exclude_to_chains        Try to NOT visualize these chains
        """
        print('going to calculate violations and plot CMM files')
        all_stats = self.get_best_stats()
        all_dists = [s["low_dist"] for s in all_stats]

        # prepare one output file per state
        out_fns=[]
        out_nvs=[]
        state_info=[]
        cmds = defaultdict(set)
        for nstate in range(self.nstates):
            outf=open(out_prefix+str(nstate)+'.cmm','w')
            outf.write('<marker_set name="xlinks_state%i"> \n' % nstate)
            out_fns.append(outf)
            out_nvs.append(0)
            print('will limit to',limit_to_chains)
            print('will exclude',exclude_chains)
            state_info.append(self.get_best_stats(nstate,
                                                  limit_to_chains,
                                                  exclude_chains))

        for nxl in range(self.rs.get_number_of_restraints()):
            # for this XL, check which states passed
            npass=[]
            nviol=[]
            for nstate in range(self.nstates):
                prob = state_info[nstate][nxl]["prob"]
                low_dist = state_info[nstate][nxl]["low_dist"]
                if prob<max_prob_for_violation or low_dist>min_dist_for_violation:
                    nviol.append(nstate)
                else:
                    npass.append(nstate)

            # special coloring when all pass or all fail
            all_pass=False
            all_viol=False
            if len(npass)==self.nstates:
                all_pass=True
            elif len(nviol)==self.nstates:
                all_viol=True

            # finally, color based on above info
            print(nxl,'state dists:',[state_info[nstate][nxl]["low_dist"] for nstate in range(self.nstates)],
                  'viol states:',nviol,'all viol?',all_viol)
            for nstate in range(self.nstates):
                if all_pass:
                    r=0.365; g=0.933; b=0.365;
                    continue
                elif all_viol:
                    r=0.980; g=0.302; b=0.247;
                    continue
                else:
                    if nstate in nviol:
                        continue
                    else:
                        #r=0.9; g=0.34; b=0.9;
                        r=0.365; g=0.933; b=0.365;
                # now only showing if UNIQUELY PASSING in this state
                pp = state_info[nstate][nxl]["low_pp"]
                c1=IMP.core.XYZ(self.mdl,pp[0]).get_coordinates()
                c2=IMP.core.XYZ(self.mdl,pp[1]).get_coordinates()

                r1 = IMP.atom.get_residue(IMP.atom.Atom(self.mdl,pp[0])).get_index()
                ch1 = IMP.atom.get_chain_id(IMP.atom.Atom(self.mdl,pp[0]))
                r2 = IMP.atom.get_residue(IMP.atom.Atom(self.mdl,pp[0])).get_index()
                ch2 = IMP.atom.get_chain_id(IMP.atom.Atom(self.mdl,pp[0]))

                cmds[nstate].add((ch1,r1))
                cmds[nstate].add((ch2,r2))

                outf = out_fns[nstate]
                nv = out_nvs[nstate]
                outf.write('<marker id= "%d" x="%.3f" y="%.3f" z="%.3f" radius="0.8" '
                           'r="%.2f" g="%.2f" b="%.2f"/> \n' % (nv,c1[0],c1[1],c1[2],r,g,b))
                outf.write('<marker id= "%d" x="%.3f" y="%.3f" z="%.3f" radius="0.8"  '
                           'r="%.2f" g="%.2f" b="%.2f"/> \n' % (nv+1,c2[0],c2[1],c2[2],r,g,b))
                outf.write('<link id1= "%d" id2="%d" radius="0.8" '
                           'r="%.2f" g="%.2f" b="%.2f"/> \n' % (nv,nv+1,r,g,b))
                out_nvs[nstate]+=2

        for nstate in range(self.nstates):
            out_fns[nstate].write('</marker_set>\n')
            out_fns[nstate].close()
            cmd = ''
            for ch,r in cmds[nstate]:
                cmd+='#%i:%i.%s '%(nstate,r,ch)
            print(cmd)

        return all_dists
    def _get_contribution_info(self,xl,ncontr,use_CA=False):
        """Return the particles at that contribution. If requested will return CA's instead"""
        idx1=xl.get_contribution(ncontr)[0]
        idx2=xl.get_contribution(ncontr)[1]
        if use_CA:
            idx1 = IMP.atom.Selection(IMP.atom.get_residue(IMP.atom.Atom(self.mdl,idx1)),
                                      atom_type=IMP.atom.AtomType("CA")).get_selected_particle_indexes()[0]
            idx2 = IMP.atom.Selection(IMP.atom.get_residue(IMP.atom.Atom(self.mdl,idx2)),
                                      atom_type=IMP.atom.AtomType("CA")).get_selected_particle_indexes()[0]
        dist = IMP.algebra.get_distance(IMP.core.XYZ(self.mdl,idx1).get_coordinates(),
                                        IMP.core.XYZ(self.mdl,idx2).get_coordinates())
        return idx1,idx2,dist

    def get_best_stats(self,limit_to_state=None,limit_to_chains=None,exclude_chains='',use_CA=False):
        ''' return the probability, best distance, two coords, and possibly the psi for each xl
        @param limit_to_state Only examine contributions from one state
        @param limit_to_chains Returns the particles for certain "easy to visualize" chains
        @param exclude_chains  Even if you limit, don't let one end be in this list.
                               Only works if you also limit chains
        @param use_CA          Limit to CA particles
        '''
        ret = []
        for nxl in range(self.rs.get_number_of_restraints()):
            this_info = {}
            xl=IMP.isd.AtomicCrossLinkMSRestraint.get_from(self.rs.get_restraint(nxl))
            low_dist=1e6
            low_contr = None
            low_pp = None
            state_contrs=[]
            low_pp_lim = None
            low_dist_lim = 1e6
            for contr in range(xl.get_number_of_contributions()):
                pp = xl.get_contribution(contr)
                if use_CA:
                    idx1 = IMP.atom.Selection(IMP.atom.get_residue(IMP.atom.Atom(self.mdl,pp[0])),
                                              atom_type=IMP.atom.AtomType("CA")).get_selected_particle_indexes()[0]
                    idx2 = IMP.atom.Selection(IMP.atom.get_residue(IMP.atom.Atom(self.mdl,pp[1])),
                                              atom_type=IMP.atom.AtomType("CA")).get_selected_particle_indexes()[0]
                    pp = [idx1,idx2]
                if limit_to_state is not None:
                    nstate = IMP.atom.get_state_index(IMP.atom.Atom(self.mdl,pp[0]))
                    if nstate!=limit_to_state:
                        continue
                    state_contrs.append(contr)
                dist = IMP.core.get_distance(IMP.core.XYZ(self.mdl,pp[0]),
                                             IMP.core.XYZ(self.mdl,pp[1]))
                if limit_to_chains is not None:
                    c1 = IMP.atom.get_chain_id(IMP.atom.Atom(self.mdl,pp[0]))
                    c2 = IMP.atom.get_chain_id(IMP.atom.Atom(self.mdl,pp[1]))
                    if (c1 in limit_to_chains or c2 in limit_to_chains) and (
                            c1 not in exclude_chains and c2 not in exclude_chains):
                        if dist<low_dist_lim:
                            low_dist_lim = dist
                            low_pp_lim = pp
                if dist<low_dist:
                    low_dist = dist
                    low_contr = contr
                    low_pp = pp
            if limit_to_state is not None:
                this_info["prob"] = xl.evaluate_for_contributions(state_contrs,None)
            else:
                this_info["prob"] = xl.unprotected_evaluate(None)
            if limit_to_chains is not None:
                this_info["low_pp"] = low_pp_lim
            else:
                this_info["low_pp"] = low_pp

            this_info["low_dist"] = low_dist
            if not self.one_psi:
                pval = IMP.isd.Scale(self.mdl,xl.get_psi()).get_scale()
                this_info["psi"] = pval
            ret.append(this_info)
        return ret

    def print_stats(self):
        #print("XL restraint statistics\n<num> <prob> <bestdist> <sig1> <sig2> <is_viol>")
        stats = self.get_best_stats()
        for nxl,s in enumerate(stats):
            #print('%i %.4f %.4f %.4f %.4f %i'%(nxl,prob,low_dist,sig1,sig2,is_viol))
            print(s["low_dist"])


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

        ### HACK to make it easier to see the few sigmas
        #output["AtomicXLRestraint_sigma"] = self.sigma.get_scale()
        output["AtomicXLRestraint_sigma"] = self.rs_sig.unprotected_evaluate(None)
        output["AtomicXLRestraint_psi"] = self.rs_psi.unprotected_evaluate(None)
        #if self.one_psi:
        #    output["AtomicXLRestraint_psi"] = self.psi.get_scale()
        ######

        # count distances above length
        bad_count=0
        stats = self.get_best_stats()
        for nxl,s in enumerate(stats):
            if s['low_dist']>20.0:
                bad_count+=1
            output["AtomicXLRestraint_%i_%s"%(nxl,"Prob")]=str(s['prob'])
            output["AtomicXLRestraint_%i_%s"%(nxl,"BestDist")]=str(s['low_dist'])
            if not self.one_psi:
                output["AtomicXLRestraint_%i_%s"%(nxl,"psi")]=str(s['psi'])
        output["AtomicXLRestraint_NumViol"] = str(bad_count)
        return output


@IMP.deprecated_object("2.5", "Use IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint instead.")
class ConnectivityCrossLinkMS(object):
    """This restraint allows ambiguous crosslinking between multiple copies
    it is a variant of the SimplifiedCrossLinkMS
    """
    def __init__(
        self,
        representation,
        restraints_file,
        expdistance,
        strength=None,
            resolution=None):

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'data')
        self.weight = 1.0
        self.label = "None"
        self.pairs = []

        self.outputlevel = "low"
        self.expdistance = expdistance
        self.strength = strength

        fl = IMP.pmi.tools.open_file_or_inline_text(restraints_file)

        for line in fl:

            tokens = line.split()
            # skip character
            if (tokens[0] == "#"):
                continue
            r1 = int(tokens[2])
            c1 = tokens[0]
            r2 = int(tokens[3])
            c2 = tokens[1]

            ps1 = IMP.pmi.tools.select(
                representation,
                resolution=resolution,
                name=c1,
                name_is_ambiguous=True,
                residue=r1)
            hrc1 = [representation.hier_db.particle_to_name[p] for p in ps1]
            if len(ps1) == 0:
                print("ConnectivityCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r1, c1))
                continue

            ps2 = IMP.pmi.tools.select(
                representation,
                resolution=resolution,
                name=c2,
                name_is_ambiguous=True,
                residue=r2)
            hrc2 = [representation.hier_db.particle_to_name[p] for p in ps2]
            if len(ps2) == 0:
                print("ConnectivityCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r2, c2))
                continue

            s1 = IMP.atom.Selection(ps1)
            s2 = IMP.atom.Selection(ps2)

            # calculate the radii to estimate the slope of the restraint
            if self.strength is None:
                rad1 = 0
                rad2 = 0
                for p in ps1:
                    rad1 += IMP.pmi.Uncertainty(p).get_uncertainty()

                for p in ps2:
                    rad2 += IMP.pmi.Uncertainty(p).get_uncertainty()

                rad1 = rad1 / len(ps1)
                rad2 = rad2 / len(ps2)

                self.strength = 1 / (rad1 ** 2 + rad2 ** 2)

            sels = [s1, s2]
            cr = IMP.atom.create_connectivity_restraint(
                sels,
                self.expdistance,
                self.strength)

            self.rs.add_restraint(cr)
            self.pairs.append((ps1, hrc1, c1, r1, ps2, hrc2, c2, r2, cr))

    def plot_restraint(
        self,
        uncertainty1,
        uncertainty2,
        maxdist=50,
            npoints=10):

        p1 = IMP.Particle(self.m)
        p2 = IMP.Particle(self.m)
        d1 = IMP.core.XYZR.setup_particle(p1)
        d2 = IMP.core.XYZR.setup_particle(p2)
        d1.set_radius(uncertainty1)
        d2.set_radius(uncertainty2)
        s1 = IMP.atom.Selection(p1)
        s2 = IMP.atom.Selection(p2)
        sels = [s1, s2]
        strength = 1 / (uncertainty1 ** 2 + uncertainty2 ** 2)
        cr = IMP.atom.create_connectivity_restraint(
            sels,
            self.expdistance,
            strength)
        dists = []
        scores = []
        for i in range(npoints):
            d2.set_coordinates(
                IMP.algebra.Vector3D(maxdist / npoints * float(i), 0, 0))
            dists.append(IMP.core.get_distance(d1, d2))
            scores.append(cr.unprotected_evaluate(None))
        IMP.pmi.output.plot_xy_data(dists, scores)

    def set_label(self, label):
        self.label = label
        self.rs.set_name(label)
        for r in self.rs.get_restraints():
            r.set_name(label)

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

    def get_restraint_sets(self):
        return self.rs

    def get_restraint(self):
        return self.rs

    def set_output_level(self, level="low"):
            # this might be "low" or "high"
        self.outputlevel = level

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

    def get_output(self):
        # content of the crosslink database pairs
        # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
        self.m.update()

        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["ConnectivityCrossLinkMS_Score_" + self.label] = str(score)
        for n, p in enumerate(self.pairs):

            ps1 = p[0]
            hrc1 = p[1]
            c1 = p[2]
            r1 = p[3]
            ps2 = p[4]
            hrc2 = p[5]
            c2 = p[6]
            r2 = p[7]
            cr = p[8]
            for n1, p1 in enumerate(ps1):
                name1 = hrc1[n1]

                for n2, p2 in enumerate(ps2):
                    name2 = hrc2[n2]
                    d1 = IMP.core.XYZR(p1)
                    d2 = IMP.core.XYZR(p2)
                    label = str(r1) + ":" + name1 + "_" + str(r2) + ":" + name2
                    output["ConnectivityCrossLinkMS_Distance_" +
                           label] = str(IMP.core.get_distance(d1, d2))

            label = str(r1) + ":" + c1 + "_" + str(r2) + ":" + c2
            output["ConnectivityCrossLinkMS_Score_" +
                   label] = str(self.weight * cr.unprotected_evaluate(None))

        return output

@IMP.deprecated_object("2.5", "Use IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint instead.")
class SimplifiedCrossLinkMS(object):
    def __init__(
        self,
        representation,
        restraints_file,
        expdistance,
        strength,
        resolution=None,
        columnmapping=None,
        truncated=True,
            spheredistancepairscore=True):
        # columnindexes is a list of column indexes for protein1, protein2, residue1, residue2
        # by default column 0 = protein1; column 1 = protein2; column 2 =
        # residue1; column 3 = residue2

        if columnmapping is None:
            columnmapping = {}
            columnmapping["Protein1"] = 0
            columnmapping["Protein2"] = 1
            columnmapping["Residue1"] = 2
            columnmapping["Residue2"] = 3

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'data')
        self.weight = 1.0
        self.label = "None"
        self.pairs = []
        self.already_added_pairs = {}

        self.outputlevel = "low"
        self.expdistance = expdistance
        self.strength = strength
        self.truncated = truncated
        self.spheredistancepairscore = spheredistancepairscore

        # fill the cross-linker pmfs
        # to accelerate the init the list listofxlinkertypes might contain only
        # yht needed crosslinks
        protein1 = columnmapping["Protein1"]
        protein2 = columnmapping["Protein2"]
        residue1 = columnmapping["Residue1"]
        residue2 = columnmapping["Residue2"]

        fl = IMP.pmi.tools.open_file_or_inline_text(restraints_file)

        for line in fl:

            tokens = line.split()
            # skip character
            if (tokens[0] == "#"):
                continue
            r1 = int(tokens[residue1])
            c1 = tokens[protein1]
            r2 = int(tokens[residue2])
            c2 = tokens[protein2]

            ps1 = IMP.pmi.tools.select(
                representation,
                resolution=resolution,
                name=c1,
                name_is_ambiguous=False,
                residue=r1)
            ps2 = IMP.pmi.tools.select(
                representation,
                resolution=resolution,
                name=c2,
                name_is_ambiguous=False,
                residue=r2)

            if len(ps1) > 1:
                raise ValueError(
                   "residue %d of chain %s selects multiple particles; "
                   "particles are: %s"
                   % (r1, c1, "".join(p.get_name() for p in ps1)))
            elif len(ps1) == 0:
                print("SimplifiedCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r1, c1))
                continue

            if len(ps2) > 1:
                raise ValueError(
                   "residue %d of chain %s selects multiple particles; "
                   "particles are: %s"
                   % (r2, c2, "".join(p.get_name() for p in ps2)))
            elif len(ps2) == 0:
                print("SimplifiedCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r2, c2))
                continue

            p1 = ps1[0]
            p2 = ps2[0]

            if (p1, p2) in self.already_added_pairs:
                dr = self.already_added_pairs[(p1, p2)]
                weight = dr.get_weight()
                dr.set_weight(weight + 1.0)
                print("SimplifiedCrossLinkMS> crosslink %d %s %d %s was already found, adding 1.0 to the weight, weight is now %d" % (r1, c1, r2, c2, weight + 1.0))
                continue

            else:

                if self.truncated:
                    limit = self.strength * (self.expdistance + 15) ** 2 + 10.0
                    hub = IMP.core.TruncatedHarmonicUpperBound(
                        self.expdistance,
                        self.strength,
                        self.expdistance +
                        15.,
                        limit)
                else:
                    hub = IMP.core.HarmonicUpperBound(
                        self.expdistance,
                        self.strength)
                if self.spheredistancepairscore:
                    df = IMP.core.SphereDistancePairScore(hub)
                else:
                    df = IMP.core.DistancePairScore(hub)
                dr = IMP.core.PairRestraint(df, (p1, p2))
                dr.set_name(c1 + ":" + str(r1) + "-" + c2 + ":" + str(r2))

                self.rs.add_restraint(dr)
                self.pairs.append((p1, p2, dr, r1, c1, r2, c2))
                self.already_added_pairs[(p1, p2)] = dr
                self.already_added_pairs[(p2, p1)] = dr

    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_sets(self):
        return self.rs

    def get_restraint(self):
        return self.rs

    def get_restraints(self):
        rlist = []
        for r in self.rs.get_restraints():
            rlist.append(IMP.core.PairRestraint.get_from(r))
        return rlist

    def get_particle_pairs(self):
        ppairs = []
        for i in range(len(self.pairs)):
            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            ppairs.append((p0, p1))
        return ppairs

    def set_output_level(self, level="low"):
            # this might be "low" or "high"
        self.outputlevel = level

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

    def plot_restraint(self, radius1, radius2, maxdist=50, npoints=10):

        p1 = IMP.Particle(self.m)
        p2 = IMP.Particle(self.m)
        d1 = IMP.core.XYZR.setup_particle(p1)
        d2 = IMP.core.XYZR.setup_particle(p2)
        d1.set_radius(radius1)
        d2.set_radius(radius2)
        if self.truncated:
            limit = self.strength * (self.expdistance + 15) ** 2 + 10.0
            hub = IMP.core.TruncatedHarmonicUpperBound(
                self.expdistance,
                self.strength,
                self.expdistance +
                15.,
                limit)
        else:
            hub = IMP.core.HarmonicUpperBound(
                self.expdistance,
                self.strength)
        df = IMP.core.SphereDistancePairScore(hub)
        dr = IMP.core.PairRestraint(df, (p1, p2))
        dists = []
        scores = []
        for i in range(npoints):
            d2.set_coordinates(
                IMP.algebra.Vector3D(maxdist / npoints * float(i), 0, 0))
            dists.append(IMP.core.get_distance(d1, d2))
            scores.append(dr.unprotected_evaluate(None))
        IMP.pmi.output.plot_xy_data(dists, scores)

    def get_output(self):
        # content of the crosslink database pairs
        # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
        self.m.update()

        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["SimplifiedCrossLinkMS_Score_" + self.label] = str(score)
        for i in range(len(self.pairs)):

            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            crosslinker = 'standard'
            ln = self.pairs[i][2]
            resid1 = self.pairs[i][3]
            chain1 = self.pairs[i][4]
            resid2 = self.pairs[i][5]
            chain2 = self.pairs[i][6]

            label = str(resid1) + ":" + chain1 + "_" + \
                str(resid2) + ":" + chain2
            output["SimplifiedCrossLinkMS_Score_" + crosslinker + "_" +
                   label] = str(self.weight * ln.unprotected_evaluate(None))

            if self.spheredistancepairscore:
                d0 = IMP.core.XYZR(p0)
                d1 = IMP.core.XYZR(p1)
            else:
                d0 = IMP.core.XYZ(p0)
                d1 = IMP.core.XYZ(p1)
            output["SimplifiedCrossLinkMS_Distance_" +
                   label] = str(IMP.core.get_distance(d0, d1))

        return output

#

@IMP.deprecated_object("2.5", "Use IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint instead.")
class SigmoidalCrossLinkMS(object):
    def __init__(
        self, representation, restraints_file, inflection, slope, amplitude,
        linear_slope, resolution=None, columnmapping=None, csvfile=False,
            filters=None, filelabel="None"):
        # columnindexes is a list of column indexes for protein1, protein2, residue1, residue2
        # by default column 0 = protein1; column 1 = protein2; column 2 = residue1; column 3 = residue2
        # the filters applies to the csvfile, the format is
        # filters=[("Field1",">|<|=|>=|<=",value),("Field2","is","String"),("Field2","in","String")]

        if columnmapping is None:
            columnmapping = {}
            columnmapping["Protein1"] = 0
            columnmapping["Protein2"] = 1
            columnmapping["Residue1"] = 2
            columnmapping["Residue2"] = 3

        if csvfile:
            # in case the file is a csv file
            # columnmapping will contain the field names
            # that compare in the first line of the csv file
            db = tools.get_db_from_csv(restraints_file)
        else:
            db = IMP.pmi.tools.open_file_or_inline_text(restraints_file)

        self.m = representation.prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'data')
        self.weight = 1.0

        self.label = "None"
        self.pairs = []
        self.already_added_pairs = {}
        self.inflection = inflection
        self.slope = slope
        self.amplitude = amplitude
        self.linear_slope = linear_slope

        self.outputlevel = "low"

        # fill the cross-linker pmfs
        # to accelerate the init the list listofxlinkertypes might contain only
        # yht needed crosslinks
        protein1 = columnmapping["Protein1"]
        protein2 = columnmapping["Protein2"]
        residue1 = columnmapping["Residue1"]
        residue2 = columnmapping["Residue2"]

        indb = open("included." + filelabel + ".xl.db", "w")
        exdb = open("excluded." + filelabel + ".xl.db", "w")
        midb = open("missing." + filelabel + ".xl.db", "w")

        for entry in db:
            if not csvfile:
                tokens = entry.split()
                # skip character
                if (tokens[0] == "#"):
                    continue
                r1 = int(tokens[residue1])
                c1 = tokens[protein1]
                r2 = int(tokens[residue2])
                c2 = tokens[protein2]
            else:
                if filters is not None:
                    if eval(tools.cross_link_db_filter_parser(filters)) == False:
                        exdb.write(str(entry) + "\n")
                        continue
                indb.write(str(entry) + "\n")
                r1 = int(entry[residue1])
                c1 = entry[protein1]
                r2 = int(entry[residue2])
                c2 = entry[protein2]

            ps1 = IMP.pmi.tools.select(
                representation,
                resolution=resolution,
                name=c1,
                name_is_ambiguous=False,
                residue=r1)
            ps2 = IMP.pmi.tools.select(
                representation,
                resolution=resolution,
                name=c2,
                name_is_ambiguous=False,
                residue=r2)

            if len(ps1) > 1:
                raise ValueError("residue %d of chain %s selects multiple particles %s" % (r1, c1, str(ps1)))
            elif len(ps1) == 0:
                print("SigmoidalCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r1, c1))
                midb.write(str(entry) + "\n")
                continue

            if len(ps2) > 1:
                raise ValueError("residue %d of chain %s selects multiple particles %s" % (r2, c2, str(ps2)))
            elif len(ps2) == 0:
                print("SigmoidalCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r2, c2))
                midb.write(str(entry) + "\n")
                continue

            p1 = ps1[0]
            p2 = ps2[0]

            if (p1, p2) in self.already_added_pairs:
                dr = self.already_added_pairs[(p1, p2)]
                weight = dr.get_weight()
                dr.increment_amplitude(amplitude)
                print("SigmoidalCrossLinkMS> crosslink %d %s %d %s was already found, adding %d to the amplitude, amplitude is now %d" % (r1, c1, r2, c2, amplitude, dr.get_amplitude()))
                dr.set_name(c1 + ":" + str(r1) + "-" + c2 + ":" + str(r2)
                            + "-ampl:" + str(dr.get_amplitude()))
                continue

            else:

                dr = IMP.pmi.SigmoidRestraintSphere(
                    self.m,
                    p1,
                    p2,
                    self.inflection,
                    self.slope,
                    self.amplitude,
                    self.linear_slope)
                dr.set_name(c1 + ":" + str(r1) + "-" + c2 + ":" + str(r2)
                            + "-ampl:" + str(dr.get_amplitude()))

                self.rs.add_restraint(dr)

                self.pairs.append((p1, p2, dr, r1, c1, r2, c2))
                self.already_added_pairs[(p1, p2)] = dr
                self.already_added_pairs[(p2, p1)] = dr

    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_sets(self):
        return self.rs

    def get_restraint(self):
        return self.rs

    def get_restraints(self):
        rlist = []
        for r in self.rs.get_restraints():
            rlist.append(IMP.core.PairRestraint.get_from(r))
        return rlist

    def get_particle_pairs(self):
        ppairs = []
        for i in range(len(self.pairs)):
            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            ppairs.append((p0, p1))
        return ppairs

    def set_output_level(self, level="low"):
            # this might be "low" or "high"
        self.outputlevel = level

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

    def plot_restraint(self, radius1, radius2, maxdist=50, npoints=10):
        p1 = IMP.Particle(self.m)
        p2 = IMP.Particle(self.m)
        d1 = IMP.core.XYZR.setup_particle(p1)
        d2 = IMP.core.XYZR.setup_particle(p2)
        d1.set_radius(radius1)
        d2.set_radius(radius2)
        dr = IMP.pmi.SigmoidRestraintSphere(
            self.m,
            p1,
            p2,
            self.inflection,
            self.slope,
            self.amplitude,
            self.linear_slope)
        dists = []
        scores = []
        for i in range(npoints):
            d2.set_coordinates(
                IMP.algebra.Vector3D(maxdist / npoints * float(i), 0, 0))
            dists.append(IMP.core.get_distance(d1, d2))
            scores.append(dr.unprotected_evaluate(None))
        IMP.pmi.output.plot_xy_data(dists, scores)

    def get_output(self):
        # content of the crosslink database pairs
        # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
        self.m.update()

        output = {}
        score = self.weight * self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["SigmoidalCrossLinkMS_Score_" + self.label] = str(score)
        for i in range(len(self.pairs)):

            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            crosslinker = 'standard'
            ln = self.pairs[i][2]
            resid1 = self.pairs[i][3]
            chain1 = self.pairs[i][4]
            resid2 = self.pairs[i][5]
            chain2 = self.pairs[i][6]

            label = str(resid1) + ":" + chain1 + "_" + \
                str(resid2) + ":" + chain2
            output["SigmoidalCrossLinkMS_Score_" + crosslinker + "_" +
                   label + "_" + self.label] = str(self.weight * ln.unprotected_evaluate(None))
            d0 = IMP.core.XYZR(p0)
            d1 = IMP.core.XYZR(p1)
            output["SigmoidalCrossLinkMS_Distance_" +
                   label + "_" + self.label] = str(IMP.core.get_distance(d0, d1))

        return output

@IMP.deprecated_object("2.5", "Use IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint instead.")
class ISDCrossLinkMS(IMP.pmi.restraints._NuisancesBase):
    def __init__(self, representation,
                 restraints_file,
                 length,
                 jackknifing=None,
                 # jackknifing (Float [0,1]) default=None; percentage of data to be
                 # removed randomly
                 resolution=None,
                 # resolution (Non-negative Integer) default=None; percentage of data
                 # to be removed randomly
                 slope=0.0,
                 inner_slope=0.0,
                 columnmapping=None,
                 rename_dict=None,
                 offset_dict=None,
                 csvfile=False,
                 ids_map=None,
                 radius_map=None,
                 filters=None,
                 label="None",
                 filelabel="None",
                 automatic_sigma_classification=False,
                 attributes_for_label=None):

        # columnindexes is a list of column indexes for protein1, protein2, residue1, residue2,idscore, XL unique id
        # by default column 0 = protein1; column 1 = protein2; column 2 = residue1; column 3 = residue2;
        # column 4 = idscores
        # attributes_for_label: anything in the csv database that must be added to the label
        # slope is the slope defined on the linear function
        # inner_slope is the slope defined on the restraint directly
        # suggestion: do not use both!

        if type(representation) != list:
            representations = [representation]
        else:
            representations = representation

        if columnmapping is None:
            columnmapping = {}
            columnmapping["Protein1"] = 0
            columnmapping["Protein2"] = 1
            columnmapping["Residue1"] = 2
            columnmapping["Residue2"] = 3
            columnmapping["IDScore"] = 4
            columnmapping["XLUniqueID"] = 5

        if csvfile:
            # in case the file is a csv file
            # columnmapping will contain the field names
            # that compare in the first line of the csv file
            db = IMP.pmi.tools.get_db_from_csv(restraints_file)
        else:
            db = IMP.pmi.tools.open_file_or_inline_text(restraints_file)

        indb = open("included." + filelabel + ".xl.db", "w")
        exdb = open("excluded." + filelabel + ".xl.db", "w")
        midb = open("missing." + filelabel + ".xl.db", "w")

        self.m = representations[0].prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'data')
        self.rspsi = IMP.RestraintSet(self.m, 'prior_psi')
        self.rssig = IMP.RestraintSet(self.m, 'prior_sigmas')
        self.rslin = IMP.RestraintSet(self.m, 'prior_linear')
        self.rslen = IMP.RestraintSet(self.m, 'prior_length')

        self.label = label
        self.pairs = []
        self.sigma_dictionary = {}
        self.psi_dictionary = {}
        self.psi_is_sampled = True
        self.sigma_is_sampled = True

        # isd_map is a dictionary/map that is used to determine the psi
        # parameter from identity scores (such as ID-Score, or FDR)
        if ids_map is None:
            self.ids_map = IMP.pmi.tools.map()
            self.ids_map.set_map_element(20.0, 0.05)
            self.ids_map.set_map_element(65.0, 0.01)
        else:
            self.ids_map = ids_map

        if radius_map is None:
            self.radius_map = IMP.pmi.tools.map()
            if automatic_sigma_classification:
                self.radius_map.set_map_element(10, 10)
            self.radius_map.set_map_element(1, 1)
        else:
            self.radius_map = radius_map

        self.outputlevel = "low"

        # small linear contribution for long range
        self.linear = IMP.core.Linear(0, 0.0)
        self.linear.set_slope(slope)
        dps2 = IMP.core.DistancePairScore(self.linear)

        protein1 = columnmapping["Protein1"]
        protein2 = columnmapping["Protein2"]
        residue1 = columnmapping["Residue1"]
        residue2 = columnmapping["Residue2"]
        idscore = columnmapping["IDScore"]
        try:
            xluniqueid = columnmapping["XLUniqueID"]
        except:
            xluniqueid = None

        restraints = []

        # we need this dictionary to create ambiguity (i.e., multistate)
        # if one id is already present in the dictionary, add the term to the
        # corresponding already generated restraint

        uniqueid_restraints_map = {}

        for nxl, entry in enumerate(db):

            if not jackknifing is None:

                # to be implemented
                # the problem is that in the replica exchange
                # you have to broadcast the same restraints to every
                # replica

                raise NotImplementedError("jackknifing not yet implemented")

            if not csvfile:
                tokens = entry.split()
                if len(tokens)==0:
                    continue

                # skip character
                if (tokens[0] == "#"):
                    continue
                try:
                    r1 = int(tokens[residue1])
                    c1 = tokens[protein1]
                    r2 = int(tokens[residue2])
                    c2 = tokens[protein2]

                    if offset_dict is not None:
                        if c1 in offset_dict: r1+=offset_dict[c1]
                        if c2 in offset_dict: r2+=offset_dict[c2]

                    if rename_dict is not None:
                        if c1 in rename_dict: c1=rename_dict[c1]
                        if c2 in rename_dict: c2=rename_dict[c2]

                    if idscore is None:
                        ids = 1.0
                    else:
                        ids = float(tokens[idscore])
                    if xluniqueid is None:
                        xlid = str(nxl)
                    else:
                        xlid = tokens[xluniqueid]
                except:
                    print("this line was not accessible " + str(entry))
                    if residue1 not in entry: print(str(residue1)+" keyword not in database")
                    if residue2 not in entry: print(str(residue2)+" keyword not in database")
                    if protein1 not in entry: print(str(protein1)+" keyword not in database")
                    if protein2 not in entry: print(str(protein2)+" keyword not in database")
                    if idscore not in entry: print(str(idscore)+" keyword not in database")
                    if xluniqueid not in entry: print(str(xluniqueid)+" keyword not in database")
                    continue

            else:
                if filters is not None:
                    if eval(IMP.pmi.tools.cross_link_db_filter_parser(filters)) == False:
                        exdb.write(str(entry) + "\n")
                        continue

                try:
                    r1 = int(entry[residue1])
                    c1 = entry[protein1]
                    r2 = int(entry[residue2])
                    c2 = entry[protein2]

                    if offset_dict is not None:
                        if c1 in offset_dict: r1+=offset_dict[c1]
                        if c2 in offset_dict: r2+=offset_dict[c2]

                    if rename_dict is not None:
                        if c1 in rename_dict: c1=rename_dict[c1]
                        if c2 in rename_dict: c2=rename_dict[c2]

                    if idscore is None:
                        ids = 1.0
                    else:
                        try:
                            ids = float(entry[idscore])
                        except ValueError:
                            ids = entry[idscore]
                    if xluniqueid is None:
                        xlid = str(nxl)
                    else:
                        xlid = entry[xluniqueid]

                except:
                    print("this line was not accessible " + str(entry))
                    if residue1 not in entry: print(str(residue1)+" keyword not in database")
                    if residue2 not in entry: print(str(residue2)+" keyword not in database")
                    if protein1 not in entry: print(str(protein1)+" keyword not in database")
                    if protein2 not in entry: print(str(protein2)+" keyword not in database")
                    if idscore not in entry: print(str(idscore)+" keyword not in database")
                    if xluniqueid not in entry: print(str(xluniqueid)+" keyword not in database")
                    continue

            for nstate, r in enumerate(representations):
                # loop over every state

                ps1 = IMP.pmi.tools.select(
                    r,
                    resolution=resolution,
                    name=c1,
                    name_is_ambiguous=False,
                    residue=r1)
                ps2 = IMP.pmi.tools.select(
                    r,
                    resolution=resolution,
                    name=c2,
                    name_is_ambiguous=False,
                    residue=r2)

                if len(ps1) > 1:
                    raise ValueError("residue %d of chain %s selects multiple particles %s" % (r1, c1, str(ps1)))
                elif len(ps1) == 0:
                    print("ISDCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r1, c1))
                    midb.write(str(entry) + "\n")
                    continue

                if len(ps2) > 1:
                    raise ValueError("residue %d of chain %s selects multiple particles %s" % (r2, c2, str(ps2)))
                elif len(ps2) == 0:
                    print("ISDCrossLinkMS: WARNING> residue %d of chain %s is not there" % (r2, c2))
                    midb.write(str(entry) + "\n")
                    continue

                p1 = ps1[0]
                p2 = ps2[0]

                if (p1 == p2) and (r1 == r2) :
                    print("ISDCrossLinkMS Restraint: WARNING> on the identical bead particles and the identical residues, thus skipping this cross-link.")
                    continue

                if xlid in uniqueid_restraints_map:
                    print("Appending a crosslink restraint into the uniqueID %s" % str(xlid))
                    dr = uniqueid_restraints_map[xlid]
                else:
                    print("Generating a NEW crosslink restraint with a uniqueID %s" % str(xlid))
                    dr = IMP.isd.CrossLinkMSRestraint(
                        self.m,
                        length,
                        inner_slope)
                    restraints.append(dr)
                    uniqueid_restraints_map[xlid] = dr

                mappedr1 = self.radius_map.get_map_element(
                    IMP.pmi.Uncertainty(p1).get_uncertainty())
                sigma1 = self.get_sigma(mappedr1)[0]
                mappedr2 = self.radius_map.get_map_element(
                    IMP.pmi.Uncertainty(p2).get_uncertainty())
                sigma2 = self.get_sigma(mappedr2)[0]

                psival = self.ids_map.get_map_element(ids)
                psi = self.get_psi(psival)[0]


                p1i = p1.get_particle_index()
                p2i = p2.get_particle_index()
                s1i = sigma1.get_particle().get_index()
                s2i = sigma2.get_particle().get_index()

                #print nstate, p1i, p2i, p1.get_name(), p2.get_name()

                psii = psi.get_particle().get_index()

                dr.add_contribution((p1i, p2i), (s1i, s2i), psii)
                print("--------------")
                print("ISDCrossLinkMS: generating cross-link restraint between")
                print("ISDCrossLinkMS: residue %d of chain %s and residue %d of chain %s" % (r1, c1, r2, c2))
                print("ISDCrossLinkMS: with sigma1 %f sigma2 %f psi %s" % (mappedr1, mappedr2, psival))
                print("ISDCrossLinkMS: between particles %s and %s" % (p1.get_name(), p2.get_name()))
                print("==========================================\n")
                indb.write(str(entry) + "\n")

                # check if the two residues belong to the same rigid body
                if(IMP.core.RigidMember.get_is_setup(p1) and
                   IMP.core.RigidMember.get_is_setup(p2) and
                   IMP.core.RigidMember(p1).get_rigid_body() ==
                   IMP.core.RigidMember(p2).get_rigid_body()):
                    xlattribute = "intrarb"
                else:
                    xlattribute = "interrb"

                if csvfile:
                    if not attributes_for_label is None:
                        for a in attributes_for_label:
                            xlattribute = xlattribute + "_" + str(entry[a])

                xlattribute = xlattribute + "-State:" + str(nstate)

                dr.set_name(
                    xlattribute + "-" + c1 + ":" + str(r1) + "-" + c2 + ":" + str(r2) + "_" + self.label)

                if p1i != p2i:
                    pr = IMP.core.PairRestraint(self.m, dps2, (p1i, p2i))
                    pr.set_name(
                        xlattribute + "-" + c1 + ":" + str(r1) + "-" + c2 + ":" + str(r2) + "_" + self.label)
                    self.rslin.add_restraint(pr)


                self.pairs.append(
                    (p1,
                     p2,
                     dr,
                     r1,
                     c1,
                     r2,
                     c2,
                     xlattribute,
                     mappedr1,
                     mappedr2,
                     psival,
                     xlid,
                     nstate,
                     ids))

        lw = IMP.isd.LogWrapper(restraints,1.0)
        self.rs.add_restraint(lw)


    def set_slope_linear_term(self, slope):
        self.linear.set_slope(slope)

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

    def add_to_model(self):
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rspsi)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rssig)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rslen)
        IMP.pmi.tools.add_restraint_to_model(self.m, self.rslin)

    def get_hierarchies(self):
        return self.prot

    def get_restraint_sets(self):
        return self.rs

    def get_restraint(self):
        return self.rs

    def get_restraint_for_rmf(self):
        return self.rslin

    def get_restraints(self):
        rlist = []
        for r in self.rs.get_restraints():
            rlist.append(IMP.core.PairRestraint.get_from(r))
        return rlist

    def get_particle_pairs(self):
        ppairs = []
        for i in range(len(self.pairs)):
            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            ppairs.append((p0, p1))
        return ppairs

    def set_output_level(self, level="low"):
            # this might be "low" or "high"
        self.outputlevel = level

    def set_psi_is_sampled(self, is_sampled=True):
        self.psi_is_sampled = is_sampled

    def set_sigma_is_sampled(self, is_sampled=True):
        self.sigma_is_sampled = is_sampled

    def get_label(self,pairs_index):
        resid1 = self.pairs[pairs_index][3]
        chain1 = self.pairs[pairs_index][4]
        resid2 = self.pairs[pairs_index][5]
        chain2 = self.pairs[pairs_index][6]
        attribute = self.pairs[pairs_index][7]
        rad1 = self.pairs[pairs_index][8]
        rad2 = self.pairs[pairs_index][9]
        psi = self.pairs[pairs_index][10]
        xlid= self.pairs[pairs_index][11]
        label = attribute + "-" + \
            str(resid1) + ":" + chain1 + "_" + str(resid2) + ":" + \
            chain2 + "-" + str(rad1) + "-" + str(rad2) + "-" + str(psi)
        return label

    def write_db(self,filename):
        cldb=IMP.pmi.output.CrossLinkIdentifierDatabase()

        for pairs_index in range(len(self.pairs)):

            resid1 = self.pairs[pairs_index][3]
            chain1 = self.pairs[pairs_index][4]
            resid2 = self.pairs[pairs_index][5]
            chain2 = self.pairs[pairs_index][6]
            attribute = self.pairs[pairs_index][7]
            rad1 = self.pairs[pairs_index][8]
            rad2 = self.pairs[pairs_index][9]
            psi = self.pairs[pairs_index][10]
            xlid= self.pairs[pairs_index][11]
            nstate=self.pairs[pairs_index][12]
            ids=self.pairs[pairs_index][13]

            label=self.get_label(pairs_index)
            cldb.set_unique_id(label,xlid)
            cldb.set_protein1(label,chain1)
            cldb.set_protein2(label,chain2)
            cldb.set_residue1(label,resid1)
            cldb.set_residue2(label,resid2)
            cldb.set_idscore(label,ids)
            cldb.set_state(label,nstate)
            cldb.set_sigma1(label,rad1)
            cldb.set_sigma2(label,rad2)
            cldb.set_psi(label,psi)
            cldb.write(filename)


    def get_output(self):
        # content of the crosslink database pairs
        # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
        self.m.update()

        output = {}
        score = self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["ISDCrossLinkMS_Data_Score_" + self.label] = str(score)
        output["ISDCrossLinkMS_PriorSig_Score_" +
               self.label] = self.rssig.unprotected_evaluate(None)
        output["ISDCrossLinkMS_PriorPsi_Score_" +
                   self.label] = self.rspsi.unprotected_evaluate(None)
        output["ISDCrossLinkMS_Linear_Score_" +
               self.label] = self.rslin.unprotected_evaluate(None)
        for i in range(len(self.pairs)):

            label=self.get_label(i)
            ln = self.pairs[i][2]
            p0 = self.pairs[i][0]
            p1 = self.pairs[i][1]
            output["ISDCrossLinkMS_Score_" +
                   label + "_" + self.label] = str(-log(ln.unprotected_evaluate(None)))

            d0 = IMP.core.XYZ(p0)
            d1 = IMP.core.XYZ(p1)
            output["ISDCrossLinkMS_Distance_" +
                   label + "_" + self.label] = str(IMP.core.get_distance(d0, d1))


        for psiindex in self.psi_dictionary:
            output["ISDCrossLinkMS_Psi_" +
                    str(psiindex) + "_" + self.label] = str(self.psi_dictionary[psiindex][0].get_scale())

        for resolution in self.sigma_dictionary:
            output["ISDCrossLinkMS_Sigma_" +
                   str(resolution) + "_" + self.label] = str(self.sigma_dictionary[resolution][0].get_scale())


        return output

    def get_particles_to_sample(self):
        ps = {}
        for resolution in self.sigma_dictionary:
            if self.sigma_dictionary[resolution][2] and self.sigma_is_sampled:
                ps["Nuisances_ISDCrossLinkMS_Sigma_" + str(resolution) + "_" + self.label] =\
                    ([self.sigma_dictionary[resolution][0]],
                     self.sigma_dictionary[resolution][1])
        if self.psi_is_sampled:
            for psiindex in self.psi_dictionary:
                if self.psi_dictionary[psiindex][2]:
                    ps["Nuisances_ISDCrossLinkMS_Psi_" +
                        str(psiindex) + "_" + self.label] = ([self.psi_dictionary[psiindex][0]], self.psi_dictionary[psiindex][1])
        return ps

#
class CysteineCrossLinkRestraint(object):
    def __init__(self, representations, filename, cbeta=False,
                 betatuple=(0.03, 0.1),
                 disttuple=(0.0, 25.0, 1000),
                 omegatuple=(1.0, 1000.0, 50),
                 sigmatuple=(0.3, 0.3, 1),
                 betaissampled=True,
                 sigmaissampled=False,
                 weightissampled=True,
                 epsilonissampled=True
                 ):
    # the file must have residue1 chain1 residue2 chain2 fractionvalue epsilonname
    # epsilonname is a name for the epsilon particle that must be used for that particular
    # residue pair, eg, "Epsilon-Intra-Solvent", or
    # "Epsilon-Solvent-Membrane", etc.

        self.representations = representations
        self.m = self.representations[0].prot.get_model()
        self.rs = IMP.RestraintSet(self.m, 'Cysteine_Crosslink')
        self.cbeta = cbeta
        self.epsilonmaxtrans = 0.01
        self.sigmamaxtrans = 0.1
        self.betamaxtrans = 0.01
        self.weightmaxtrans = 0.1
        self.label = "None"
        self.outputlevel = "low"
        self.betaissampled = betaissampled
        self.sigmaissampled = sigmaissampled
        self.weightissampled = weightissampled
        self.epsilonissampled = epsilonissampled

        betalower = betatuple[0]
        betaupper = betatuple[1]
        beta = 0.04
        sigma = 10.0
        betangrid = 30
        crossdataprior = 1

        # beta
        self.beta = IMP.pmi.tools.SetupNuisance(
            self.m,
            beta,
            betalower,
            betaupper,
            betaissampled).get_particle(
        )
        # sigma
        self.sigma = IMP.pmi.tools.SetupNuisance(
            self.m,
            sigma,
            sigmatuple[0],
            sigmatuple[1],
            sigmaissampled).get_particle()
        # population particle
        self.weight = IMP.pmi.tools.SetupWeight(
            self.m,
            weightissampled).get_particle(
        )

        # read the file
        fl = IMP.pmi.tools.open_file_or_inline_text(filename)
        # determine the upperlimit for epsilon
        # and also how many epsilon are needed
        self.epsilons = {}
        data = []
        for line in fl:
            t = line.split()
            if t[0][0] == "#":
                continue
            if t[5] in self.epsilons:
                if 1.0 - float(t[4]) <= self.epsilons[t[5]].get_upper():
                    self.epsilons[t[5]].set_upper(1.0 - float(t[4]))
            else:
                self.epsilons[t[5]] = IMP.pmi.tools.SetupNuisance(self.m,
                                                                  0.01, 0.01, 1.0 - float(t[4]), epsilonissampled).get_particle()
            up = self.epsilons[t[5]].get_upper()
            low = self.epsilons[t[5]].get_lower()
            if up < low:
                self.epsilons[t[5]].set_upper(low)

            data.append((int(t[0]), t[1], int(t[2]), t[3], float(t[4]), t[5]))

        # create CrossLinkData
        if not self.cbeta:
            crossdata = IMP.pmi.tools.get_cross_link_data(
                "cysteine", "cysteine_CA_FES.txt.standard",
                disttuple, omegatuple, sigmatuple, disttuple[1], disttuple[1], 1)
        else:
            crossdata = IMP.pmi.tools.get_cross_link_data(
                "cysteine", "cysteine_CB_FES.txt.standard",
                disttuple, omegatuple, sigmatuple, disttuple[1], disttuple[1], 1)

        # create grids needed by CysteineCrossLinkData
        fmod_grid = IMP.pmi.tools.get_grid(0.0, 1.0, 300, True)
        omega2_grid = IMP.pmi.tools.get_log_grid(0.001, 10000.0, 100)
        beta_grid = IMP.pmi.tools.get_log_grid(betalower, betaupper, betangrid)

        for d in data:
            print("--------------")
            print("CysteineCrossLink: attempting to create a restraint " + str(d))
            resid1 = d[0]
            chain1 = d[1]
            resid2 = d[2]
            chain2 = d[3]
            fexp = d[4]
            epslabel = d[5]

            # CysteineCrossLinkData

            ccldata = IMP.isd.CysteineCrossLinkData(
                fexp,
                fmod_grid,
                omega2_grid,
                beta_grid)

            ccl = IMP.isd.CysteineCrossLinkRestraint(
                self.m,
                self.beta,
                self.sigma,
                self.epsilons[epslabel],
                self.weight,
                crossdata,
                ccldata)

            failed = False
            for i, representation in enumerate(self.representations):

                if not self.cbeta:
                    p1 = None
                    p2 = None

                    p1 = IMP.pmi.tools.select(representation,
                                              resolution=1, name=chain1,
                                              name_is_ambiguous=False, residue=resid1)[0]

                    if p1 is None:
                        failed = True

                    p2 = IMP.pmi.tools.select(representation,
                                              resolution=1, name=chain2,
                                              name_is_ambiguous=False, residue=resid2)[0]

                    if p2 is None:
                        failed = True

                else:
                    # use cbetas
                    p1 = []
                    p2 = []
                    for t in range(-1, 2):
                        p = IMP.pmi.tools.select(representation,
                                                 resolution=1, name=chain1,
                                                 name_is_ambiguous=False, residue=resid1 + t)

                        if len(p) == 1:
                            p1 += p
                        else:
                            failed = True
                            print("\033[93m CysteineCrossLink: missing representation for residue %d of chain %s \033[0m" % (resid1 + t, chain1))

                        p = IMP.pmi.tools.select(representation,
                                                 resolution=1, name=chain2,
                                                 name_is_ambiguous=False, residue=resid2 + t)

                        if len(p) == 1:
                            p2 += p
                        else:
                            failed = True
                            print("\033[93m CysteineCrossLink: missing representation for residue %d of chain %s \033[0m" % (resid2 + t, chain2))

                if not self.cbeta:
                    if (p1 is not None and p2 is not None):
                        ccl.add_contribution(p1, p2)
                        d1 = IMP.core.XYZ(p1)
                        d2 = IMP.core.XYZ(p2)

                        print("Distance_" + str(resid1) + "_" + chain1 + ":" + str(resid2) + "_" + chain2, IMP.core.get_distance(d1, d2))

                else:
                    if (len(p1) == 3 and len(p2) == 3):
                        p11n = p1[0].get_name()
                        p12n = p1[1].get_name()
                        p13n = p1[2].get_name()
                        p21n = p2[0].get_name()
                        p22n = p2[1].get_name()
                        p23n = p2[2].get_name()

                        print("CysteineCrossLink: generating CB cysteine cross-link restraint between")
                        print("CysteineCrossLink: residue %d of chain %s and residue %d of chain %s" % (resid1, chain1, resid2, chain2))
                        print("CysteineCrossLink: between particles %s %s %s and %s %s %s" % (p11n, p12n, p13n, p21n, p22n, p23n))

                        ccl.add_contribution(p1, p2)

            if not failed:
                self.rs.add_restraint(ccl)
                ccl.set_name("CysteineCrossLink_" + str(resid1)
                             + "_" + chain1 + ":" + str(resid2) + "_" + chain2)

    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_particles_to_sample(self):
        ps = {}
        if self.epsilonissampled:
            for eps in self.epsilons.keys():
                ps["Nuisances_CysteineCrossLinkRestraint_epsilon_" + eps + "_" +
                    self.label] = ([self.epsilons[eps]], self.epsilonmaxtrans)
        if self.betaissampled:
            ps["Nuisances_CysteineCrossLinkRestraint_beta_" +
                self.label] = ([self.beta], self.betamaxtrans)
        if self.weightissampled:
            ps["Weights_CysteineCrossLinkRestraint_" +
                self.label] = ([self.weight], self.weightmaxtrans)
        if self.sigmaissampled:
            ps["Nuisances_CysteineCrossLinkRestraint_" +
                self.label] = ([self.sigma], self.sigmamaxtrans)
        return ps

    def set_output_level(self, level="low"):
                # this might be "low" or "high"
        self.outputlevel = level

    def get_restraint(self):
        return self.rs

    def get_sigma(self):
        return self.sigma

    def get_output(self):
        self.m.update()
        output = {}
        score = self.rs.unprotected_evaluate(None)
        output["_TotalScore"] = str(score)
        output["CysteineCrossLinkRestraint_Score_" + self.label] = str(score)
        output["CysteineCrossLinkRestraint_sigma_" +
               self.label] = str(self.sigma.get_scale())
        for eps in self.epsilons.keys():
            output["CysteineCrossLinkRestraint_epsilon_" + eps + "_" +
                   self.label] = str(self.epsilons[eps].get_scale())
        output["CysteineCrossLinkRestraint_beta_" +
               self.label] = str(self.beta.get_scale())
        for n in range(self.weight.get_number_of_states()):
            output["CysteineCrossLinkRestraint_weights_" +
                   str(n) + "_" + self.label] = str(self.weight.get_weight(n))

        if self.outputlevel == "high":
            for rst in self.rs.get_restraints():
                output["CysteineCrossLinkRestraint_Total_Frequency_" +
                       IMP.isd.CysteineCrossLinkRestraint.get_from(rst).get_name() +
                       "_" + self.label] = IMP.isd.CysteineCrossLinkRestraint.get_from(rst).get_model_frequency()
                output["CysteineCrossLinkRestraint_Standard_Error_" +
                       IMP.isd.CysteineCrossLinkRestraint.get_from(
                           rst).get_name(
                       ) + "_"
                       + self.label] = IMP.isd.CysteineCrossLinkRestraint.get_from(rst).get_standard_error()
                if len(self.representations) > 1:
                    for i in range(len(self.prots)):
                        output["CysteineCrossLinkRestraint_Frequency_Contribution_" +
                               IMP.isd.CysteineCrossLinkRestraint.get_from(rst).get_name() +
                               "_State_" + str(i) + "_" + self.label] = IMP.isd.CysteineCrossLinkRestraint.get_from(rst).get_frequencies()[i]

        return output