topology.py

from __future__ import print_function
import IMP
import RMF
import IMP.atom
import IMP.rmf
import IMP.pmi
import IMP.pmi.analysis
import IMP.pmi.output
from collections import defaultdict
import numpy as np

class TopologyPlot(object):
    """A class to read RMF files and make a network contact map"""
    def __init__(self,model,selections,cutoff,frequency_cutoff,
                      colors=None,fixed=None,pos=None,proteomic_edges=None,quantitative_proteomic_data=None):
        """Set up a new graphXL object
        @param model          The IMP model
        @param selection_dict A dictionary containing component names.
                              Keys are labels
                              values are either moleculename or start,stop,moleculename
        @param cutoff        The distance cutoff
        @param frequency_cutoff The frequency cutoff
        @param colors        A dictionary of colors (HEX code,values) for subunits (keywords)
        @param fixed         A list of subunits that are kept fixed
        @param pos           A dictionary with positions (tuple, values) of subunits (keywords)
        @param proteomic_edges A list edges to represent proteomic data
        @param quantitative_proteomic_data A dictionary of edges to represent
                             quantitative proteomic data such as PE Scores, or genetic interactions
        """
        import itertools\

        self.mdl = model
        self.selections = selections
        self.contact_counts={}
        self.edges=defaultdict(int)
        for (name1,name2) in itertools.combinations(self.selections.keys(),2):
            self.edges[tuple(sorted((name1,name2)))]=0
        self.cutoff = cutoff
        self.frequency_cutoff=frequency_cutoff
        self.gcpf = IMP.core.GridClosePairsFinder()
        self.gcpf.set_distance(self.cutoff)
        self.names = list(self.selections.keys())
        self.colors=colors
        self.fixed=fixed
        self.pos=pos
        self.proteomic_edges=proteomic_edges
        self.quantitative_proteomic_data=quantitative_proteomic_data
        self.num_rmf=0

    def add_rmf(self,rmf_fn,nframe):
        """Add selections from an RMF file"""
        print('reading from RMF file',rmf_fn)
        rh = RMF.open_rmf_file_read_only(rmf_fn)
        prots = IMP.rmf.create_hierarchies(rh, self.mdl)
        hier = prots[0]
        IMP.rmf.load_frame(rh, RMF.FrameID(0))
        ps_per_component=defaultdict(list)
        if self.num_rmf==0:
            self.size_per_component=defaultdict(int)
        self.mdl.update()

        #gathers particles for all components
        part_dict = IMP.pmi.analysis.get_particles_at_resolution_one(hier)
        all_particles_by_resolution = []
        for name in part_dict:
            all_particles_by_resolution += part_dict[name]

        for component_name in self.selections:
            for seg in self.selections[component_name]:
                if type(seg) == str:
                    s = IMP.atom.Selection(hier,molecule=seg)
                elif type(seg) == tuple:
                    s = IMP.atom.Selection(hier,molecule=seg[2],
                        residue_indexes=range(seg[0], seg[1] + 1))
                else:
                    raise Exception('could not understand selection tuple '+str(seg))
                parts = list(set(s.get_selected_particles()) & set(all_particles_by_resolution))
                ps_per_component[component_name] += IMP.get_indexes(parts)
                if self.num_rmf==0:
                    self.size_per_component[component_name] += sum(len(IMP.pmi.tools.get_residue_indexes(p)) for p in parts)

        for n1,name1 in enumerate(self.names):
            for name2 in self.names[n1+1:]:
                ncontacts = len(self.gcpf.get_close_pairs(self.mdl,
                                                     ps_per_component[name1],
                                                     ps_per_component[name2]))
                if ncontacts>0:
                    self.edges[tuple(sorted((name1,name2)))]+=1.0

        self.num_rmf+=1

    def make_plot(self,groups,out_fn,quantitative_proteomic_data=False):
        '''
        plot the interaction matrix
        @param groups is the list of groups of domains, eg,
                      [["protA_1-10","prot1A_11-100"],["protB"]....]
                      it will plot a space between different groups
        @param out_fn name of the plot file
        @param quantitative_proteomic_data plot the quantitative proteomic data
        '''
        import numpy as np
        import matplotlib.pyplot as plt
        from matplotlib import cm

        ax=plt.gca()
        ax.set_aspect('equal', 'box')
        ax.xaxis.set_major_locator(plt.NullLocator())
        ax.yaxis.set_major_locator(plt.NullLocator())

        largespace=0.6
        smallspace=0.5
        squaredistance=1.0
        squaresize=0.99
        domain_xlocations={}
        domain_ylocations={}

        xoffset=squaredistance
        yoffset=squaredistance
        xlabels=[]
        ylabels=[]
        for group in groups:
            xoffset+=largespace
            yoffset+=largespace
            for subgroup in group:
                xoffset+=smallspace
                yoffset+=smallspace
                for domain in subgroup:
                    domain_xlocations[domain]=xoffset
                    domain_ylocations[domain]=yoffset
                    #rect = plt.Rectangle([xoffset- squaresize / 2, yoffset - squaresize / 2], squaresize, squaresize,
                    #                     facecolor=(1,1,1), edgecolor=(0.1,0.1,0.1))

                    #ax.add_patch(rect)
                    #ax.text(xoffset , yoffset ,domain,horizontalalignment='left',verticalalignment='center',rotation=-45.0)
                    xoffset+=squaredistance
                    yoffset+=squaredistance

        for edge,count in self.edges.items():

            if quantitative_proteomic_data:
                #normalize
                maxqpd=max(self.quantitative_proteomic_data.values())
                minqpd=min(self.quantitative_proteomic_data.values())
                if edge in self.quantitative_proteomic_data:
                    value=self.quantitative_proteomic_data[edge]
                elif (edge[1],edge[0]) in self.quantitative_proteomic_data:
                    value=self.quantitative_proteomic_data[(edge[1],edge[0])]
                else:
                    value=0.0
                print(minqpd,maxqpd)
                density=(1.0-(value-minqpd)/(maxqpd-minqpd))
            else:
                density=(1.0-float(count)/self.num_rmf)
            color=(density,density,1.0)
            x=domain_xlocations[edge[0]]
            y=domain_ylocations[edge[1]]
            if x>y: xtmp=y; ytmp=x; x=xtmp; y=ytmp
            rect = plt.Rectangle([x - squaresize / 2, y - squaresize / 2], squaresize, squaresize,
                             facecolor=color, edgecolor='Gray', linewidth=0.1)
            ax.add_patch(rect)
            rect = plt.Rectangle([y - squaresize / 2, x - squaresize / 2], squaresize, squaresize,
                             facecolor=color, edgecolor='Gray', linewidth=0.1)
            ax.add_patch(rect)

        ax.autoscale_view()
        plt.savefig(out_fn)
        plt.show()
        exit()

    def make_graph(self,out_fn):
        edges=[]
        weights=[]
        print('num edges',len(self.edges))
        for edge,count in self.edges.items():
            # filter if frequency of contacts is greater than frequency_cutoff
            if float(count)/self.num_rmf>self.frequency_cutoff:
                print(count,edge)
                edges.append(edge)
                weights.append(count)
        for nw,w in enumerate(weights):
            weights[nw]=float(weights[nw])/max(weights)
        IMP.pmi.output.draw_graph(edges,#node_size=1000,
                                  node_size=dict(self.size_per_component),
                                  node_color=self.colors,
                                  fixed=self.fixed,
                                  pos=self.pos,
                                  edge_thickness=1, #weights,
                                  edge_alpha=0.3,
                                  edge_color='gray',
                                  out_filename=out_fn,
                                  validation_edges=self.proteomic_edges)



def draw_component_composition(DegreesOfFreedom, max=1000, draw_pdb_names=False,show=True):
    """A function to plot the representation on the sequence
    @param DegreesOfFreedom input a IMP.pmi.dof.DegreesOfFreedom instance"""
    import matplotlib as mpl
    mpl.use('Agg')
    from matplotlib import pyplot
    from operator import itemgetter
    import IMP.pmi.tools

    #first build the movers dictionary
    movers_mols_res=IMP.pmi.tools.OrderedDict()
    for mv in DegreesOfFreedom.movers_particles_map:
        hs=DegreesOfFreedom.movers_particles_map[mv]
        res=[]

        for h in hs:
            if IMP.atom.Residue.get_is_setup(h):
                res=[IMP.atom.Residue(h).get_index()]
            elif IMP.atom.Fragment.get_is_setup(h):
                res=IMP.atom.Fragment(h).get_residue_indexes()
            if res:
                is_molecule=False
                hp=h
                while not is_molecule:
                    hp=hp.get_parent()
                    is_molecule=IMP.atom.Molecule.get_is_setup(hp)
                name=IMP.atom.Molecule(hp).get_name()+"."+str(IMP.atom.Copy(hp).get_copy_index())
                if not mv in movers_mols_res:
                    movers_mols_res[mv]=IMP.pmi.tools.OrderedDict()
                    movers_mols_res[mv][name]=IMP.pmi.tools.Segments(res)
                else:
                    if not name in movers_mols_res[mv]:
                        movers_mols_res[mv][name]=IMP.pmi.tools.Segments(res)
                    else:
                        movers_mols_res[mv][name].add(res)
    # then get all movers by type
    fb_movers=[]
    rb_movers=[]
    srb_movers=[]
    for mv in movers_mols_res:
        mvtype=None
        if type(mv) is IMP.core.RigidBodyMover:
            rb_movers.append(mv)
        if type(mv) is IMP.core.BallMover:
            fb_movers.append(mv)
        if type(mv) is IMP.pmi.TransformMover:
            srb_movers.append(mv)

    # now remove residue assigned to BallMovers from RigidBodies
    for mv in fb_movers:
        for mol in movers_mols_res[mv]:
            for i in movers_mols_res[mv][mol].get_flatten():
                for mv_rb in rb_movers:
                    try:
                        movers_mols_res[mv_rb][mol].remove(i)
                    except:
                        continue

    elements={}
    c=IMP.pmi.tools.Colors()
    colors=c.get_list_distant_colors()
    colors=["blue", "red", "green", "pink", "cyan", "purple",
            "magenta", "orange", "grey", "brown", "gold",
            "khaki", "olive drab", "deep blue sky"]
    rgb_colors=[(240,163,255),(0,117,220),
            (153,63,0),(76,0,92),(25,25,25),
            (0,92,49),(43,206,72),(255,204,153),
            (128,128,128),(148,255,181),(143,124,0),
            (157,204,0),(194,0,136),(0,51,128),(255,164,5),
            (255,168,187),(66,102,0),(255,0,16),(94,241,242),
            (0,153,143),(224,255,102),(116,10,255),(153,0,0),
            (255,255,128),(255,255,0),(255,80,5)]
    colors=[(float(c0)/255,float(c1)/255,float(c2)/255) for (c0,c1,c2) in rgb_colors]
    mvrb_color={}
    for mv in movers_mols_res:
        mvtype=None
        if type(mv) is IMP.core.RigidBodyMover:
            mvtype="RB"
            if not mv in  mvrb_color:
                color=colors[len(mvrb_color.keys())]
                mvrb_color[mv]=color
            for mol in movers_mols_res[mv]:
                if not mol in elements: elements[mol]=[]
                for seg in movers_mols_res[mv][mol].segs:
                    try:
                        elements[mol].append((seg[0],seg[-1]," ","pdb",mvrb_color[mv]))
                    except:
                        continue
        if type(mv) is IMP.core.BallMover:
            mvtype="FB"
            for mol in movers_mols_res[mv]:
                if not mol in elements: elements[mol]=[]
                for seg in movers_mols_res[mv][mol].segs:
                    elements[mol].append((seg[0],seg[-1]," ","bead"))
        if type(mv) is IMP.pmi.TransformMover:
            mvtype="SRB"

    # sort everything
    for mol in elements:
        elements[mol].sort(key=lambda tup: tup[0])
        elements[mol].append((elements[mol][-1][1],elements[mol][-1][1], " ", "end"))

    for name in elements:
        k = name
        tmplist = sorted(elements[name], key=itemgetter(0))
        try:
            endres = tmplist[-1][1]
        except:
            print("draw_component_composition: missing information for component %s" % name)
            return
        fig = pyplot.figure(figsize=(26.0 * float(endres) / max + 2, 2))
        ax = fig.add_axes([0.05, 0.475, 0.9, 0.15])

        # Set the colormap and norm to correspond to the data for which
        # the colorbar will be used.
        cmap = mpl.cm.cool
        norm = mpl.colors.Normalize(vmin=5, vmax=10)
        bounds = [1]
        colors = []

        for n, l in enumerate(tmplist):
            firstres = l[0]
            lastres = l[1]
            if l[3] != "end":
                if bounds[-1] != l[0]:
                    colors.append("white")
                    bounds.append(l[0])
                    if l[3] == "pdb":
                        colors.append("#99CCFF")
                    if l[3] == "bead":
                        colors.append("white")
                    if l[3] == "helix":
                        colors.append("#33CCCC")
                    if l[3] != "end":
                        bounds.append(l[1] + 1)
                else:
                    if l[3] == "pdb":
                        colors.append(l[4])
                    if l[3] == "bead":
                        colors.append("white")
                    if l[3] == "helix":
                        colors.append("#33CCCC")
                    if l[3] != "end":
                        bounds.append(l[1] + 1)
            else:
                if bounds[-1] - 1 == l[0]:
                    bounds.pop()
                    bounds.append(l[0])
                else:
                    colors.append("white")
                    bounds.append(l[0])

        bounds.append(bounds[-1])
        colors.append("white")
        cmap = mpl.colors.ListedColormap(colors)
        cmap.set_over('0.25')
        cmap.set_under('0.75')

        norm = mpl.colors.BoundaryNorm(bounds, cmap.N)
        cb2 = mpl.colorbar.ColorbarBase(ax, cmap=cmap,
                                        norm=norm,
                                        # to use 'extend', you must
                                        # specify two extra boundaries:
                                        boundaries=bounds,
                                        ticks=bounds,  # optional
                                        spacing='proportional',
                                        orientation='horizontal')

        extra_artists = []
        npdb = 0

        if draw_pdb_names:
            for l in tmplist:
                if l[3] == "pdb":
                    npdb += 1
                    mid = 1.0 / endres * float(l[0])
                    # t =ax.text(mid, float(npdb-1)/2.0+1.5, l[2], ha="left", va="center", rotation=0,
                    # size=10)
                    # t=ax.annotate(l[0],2)
                    t = ax.annotate(
                        l[2], xy=(mid, 1),  xycoords='axes fraction',
                        xytext=(mid + 0.025, float(npdb - 1) / 2.0 + 1.5), textcoords='axes fraction',
                        arrowprops=dict(arrowstyle="->",
                                        connectionstyle="angle,angleA=0,angleB=90,rad=10"),
                    )
                    extra_artists.append(t)

        # set the title of the bar
        title = ax.text(-0.005, 0.5, k, ha="right", va="center", rotation=90,
                        size=20)

        extra_artists.append(title)
        # changing the xticks labels
        labels = len(bounds) * [" "]
        ax.set_xticklabels(labels)
        mid = 1.0 / endres * float(bounds[0])
        t = ax.annotate(bounds[0], xy=(mid, 0),  xycoords='axes fraction',
                        xytext=(mid - 0.01, -0.5), textcoords='axes fraction',)
        extra_artists.append(t)
        offsets = [0, -0.5, -1.0]
        nclashes = 0
        for n in range(1, len(bounds)):
            if bounds[n] == bounds[n - 1]:
                continue
            mid = 1.0 / endres * float(bounds[n])
            if (float(bounds[n]) - float(bounds[n - 1])) / max <= 0.01:
                nclashes += 1
                offset = offsets[nclashes % 3]
            else:
                nclashes = 0
                offset = offsets[0]
            if offset > -0.75:
                t = ax.annotate(
                    bounds[n], xy=(mid, 0),  xycoords='axes fraction',
                    xytext=(mid, -0.5 + offset), textcoords='axes fraction')
            else:
                t = ax.annotate(
                    bounds[n], xy=(mid, 0),  xycoords='axes fraction',
                    xytext=(mid, -0.5 + offset), textcoords='axes fraction', arrowprops=dict(arrowstyle="-"))
            extra_artists.append(t)

        cb2.add_lines(bounds, ["black"] * len(bounds), [1] * len(bounds))
        # cb2.set_label(k)

        pyplot.savefig(
            k + "structure.pdf")
            #transparent="True")
            #dpi=150,
            #bbox_extra_artists=(extra_artists),
            #bbox_inches='tight')
        if show:
            pyplot.show()