DockSymmCircle.py

# -*- coding: utf-8 -*-
# Copyright (c) 2012 EPFL (Ecole Polytechnique federale de Lausanne)
# Laboratory for Biomolecular Modeling, School of Life Sciences
#
# POW is free software ;
# you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation ;
# either version 2 of the License, or (at your option) any later version.
# POW is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY ;
# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with POW ;
# if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
#
# Author : Matteo Degiacomi, matteothomas.degiacomi@epfl.ch
# Web site : http://lbm.epfl.ch


from Default import Parser as R
from Default import Space as S
from Default import Postprocess as PP
from Default import BaseFitness as BF

import numpy as np
import os, sys
from scipy.cluster.vq import *
from copy import deepcopy

from Protein import Protein
import Multimer as M
import flexibility

from mpi4py import MPI
comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()

import ClusterAndDraw as CnD
import wx

class Parser(R):
    def __init__(self):
        R.__init__(self)

        #fitness function flags
        self.add('constraint','constraint','str',"NA")
        self.add('target','target','array float',np.array([]))
        self.add('detectClash','detect_clash','str',"on")
        self.add('mixingWeight','mix_weight','float', 0.2)

        #flags for search space and data structure
        self.add('degree','degree','int',-1)
        self.add('radius','radius','float',"NA")

        #postprocessing flags
        self.add('cluster_threshold','cluster_threshold','float',"NA")
        self.add('output_folder','output_folder','str',"result")

        #define style (rigid, flexible)
        self.add('style','style','str',"rigid")

        #flexible assembly flags
        self.add('projection','proj_file','str',"NA")
        self.add('align','align','str',"no")
        self.add('ratio','ratio','float',0.9)
        self.add('trajectory','trajectory','str',"NA")
        self.add('trajSelection','trajselection','array str',np.array(["NA"]))
        self.add('topology','topology','str',"NA")
        self.add('frameDistancePenalty','frame_distance','float',10.0)
        #rigid assembly flags
        self.add('monomer','pdb_file_name','str',"NA")

        #receptor flags
        self.add('receptor','receptor','str',"NA")
        self.add('boundaryMaxReceptor','high_input_rec','array float',"NA")
        self.add('boundaryMinReceptor','low_input_rec','array float',"NA")
        self.add('z_padding','pad','int',5.0)


    def check_variables(self):

        #needed, set flag of clash detection
        if self.detect_clash == 'on' :
            self.detect_clash=True
        elif self.detect_clash== 'off':
            self.detect_clash=False
        else:
            print 'ERROR: detectClash should either be "on" or "off"!'
            sys.exit(1)

        #check if fitness function's energy vs geometry mixing weight is sane
        if self.mix_weight>1 or self.mix_weight<0:
            print 'ERROR: mixingWeight should be a float within 0 and 1!'
            sys.exit(1)

        #check if number of monomers is provided
        if self.degree==-1 :
            print 'ERROR: number of monomer not provided!'
            sys.exit(1)

        #check if number of target measures are provided
        if len(self.target) == 0 :
            print 'ERROR: target measures not specified!'
            sys.exit(1)

        #verify existence of constraint file (in search path)
        if self.constraint=="NA":
            print "ERROR: constraint file not provided"
            sys.exit(1)
        if os.path.isfile(self.constraint)!=1:
            print "ERROR: constraint file %s not found"%self.constraint
            sys.exit(1)

        #add path of constraint file to search space
        a,b=os.path.split(self.constraint)
        self.constraint=b
        sys.path.append(a)

        #test if constraint file exists, and function constaint_check is available
        try:
            exec 'import %s as constraint'%(self.constraint.split('.')[0])
        except:
            print "ERROR: load of user defined constraint function failed!"
            print "ERROR: awww, there may be a syntax error in there..."
            sys.exit(1)
        try:
            constraint.constraint_check
        except AttributeError:
            print 'ERROR: constraint_check function not found in file %s'%self.constraint
            sys.exit(1)


        #check assembly style flag
        if self.style!="rigid" and self.style!="flexible":
            print 'ERROR: style should either be "rigid" or "flexible"!'
            sys.exit(1)

        ###RIGID ASSEMBLY FLAGS###
        if self.pdb_file_name=="NA" and self.style=="rigid":
            print "ERROR: in rigid style (default), a monomer should be provided!"
            sys.exit(1)
        elif self.pdb_file_name!="NA" and self.style!="rigid":
            print "ERROR: %s style requested"%self.style
            print "ERROR: usage of monomer flag requires rigid style!"
            sys.exit(1)
        elif os.path.isfile(self.pdb_file_name)!=1 and self.style=="rigid":
            print "ERROR: pdb file %s not found"%self.pdb_file_name
            sys.exit(1)


        ###FLEXIBLE ASSEMBLY FLAGS###
        #verify existence of topology
        if self.topology!="NA":
            if self.style=="flexible":
                tmp=os.path.abspath(self.topology)
                self.topology=tmp
            else:
                print "ERROR: %s style requested"%self.style
                print "ERROR: usage of topology flag requires flexible style!"
                sys.exit(1)
        if os.path.isfile(self.topology)!=1 and self.style=="flexible":
            print "ERROR: topology %s not found"%self.topology
            sys.exit(1)

        #verify existence of traj
        if self.trajectory!="NA":
            if self.style=="flexible":
                tmp=os.path.abspath(self.trajectory)
                self.trajectory=tmp
            else:
                print "ERROR: %s style requested"%self.style
                print "ERROR: usage of trajectory flag requires flexible style!"
                sys.exit(1)
        if os.path.isfile(self.trajectory)!=1 and self.style=="flexible":
            print "ERROR: trajectory %s not found"%self.trajectory
            sys.exit(1)

        #verify existence of projections file
        if self.proj_file!="NA":
            if self.style=="flexible":
                tmp=os.path.abspath(self.proj_file)
                self.proj_file=tmp
            else:
                print "ERROR: %s style requested"%self.style
                print "ERROR: usage of projection flag requires flexible style!"
                sys.exit(1)
        if self.proj_file!="NA" and os.path.isfile(self.proj_file)!=1 and self.style=="flexible":
            print "ERROR: projections file %s not found"%self.proj_file
            sys.exit(1)

        #verify format trajectory selection (if needed)
        if self.trajselection[0]!="NA" and self.style!="flexible":
            print "ERROR: %s style requested"%self.style
            print "ERROR: usage of trajSelection flag requires flexible style!"
            sys.exit(1)
        if self.style=="flexible" and self.trajselection[0]=="NA":
            tmp="protein"
        else:
            tmp =' '.join(self.trajselection[0:len(self.trajselection)])
        self.trajselection=tmp


        #RECEPTOR FLAGS
        if self.receptor!="NA":

            #verify existence of receptor
            tmp=os.path.abspath(self.receptor)
            self.receptor=tmp
            if os.path.isfile(self.receptor)!=1:
                print "ERROR: receptor file %s not found"%self.receptor
                sys.exit(1)

            #check receptor boundaries consistency
            if len(self.high_input_rec)!=len(self.low_input_rec):
                print "ERROR: boundaryMinReceptor and boundaryMaxReceptor should have the same length!"
                sys.exit(1)

            #if len(self.high_input_rec)!=len(self.boundary_type_rec) and self.boundary_type_rec!="NA":
            #    print "ERROR: boundaryTypeReceptor length inconsistent with low and high boundary length!"
            #    print 'ERROR: %s dimensions given, but %s needed!'%(len(self.boundary_type),len(self.low_input))
            #    sys.exit(1)

            if self.high_input_rec!="NA" and (self.low_input_rec>self.high_input_rec).any():
                print 'ERROR: a receptor lower boundary condition is greated than a higher one!'
                print self.low_input_rec
                print self.high_input_rec
                sys.exit(1)

class Data:


    def __init__(self,params):

        self.index=[]
        self.index_receptor=[]
        self.eigenspace_size=""

        if params.style=="flexible":
            print ">> flexible docking requested, launching PCA..."
            #check align flag
            if params.align!="yes" and params.align!="no":
                print "ERROR: align flag should be set either to \"yes\" or \"no\"!"
                sys.exit(1)

            #load trajectory
            try:
                self.traj=flexibility.loader(params.trajectory, params.topology, params.align, params.trajselection)
            except ImportError, e:
                print "ERROR: Trajectory loading failed, aborting!"
                sys.exit(1)

            #if projection on eigenvectors has been already performed, use the user provided file
            if params.proj_file!="NA":
                if os.path.isfile(params.proj_file)!=1 :
                    print "ERROR: projections file not found!"
                    sys.exit(1)
                else:
                    print ">> loading frames projections file..."
                    p_file = open(params.proj_file, 'r+')
                    p_list=[]
                    line = p_file.readline()
                    while line:
                        w = line.split()
                        p_list.append(w)
                        line = p_file.readline()
                    self.proj=np.array(p_list).transpose().astype(float)
                    p_file.close()
                    if self.traj.shape[1]!=self.proj.shape[1]:
                        print "ERROR: trajectory has %s frames, projection has %s, aborting!"%(self.traj.shape[1],self.proj.shape[1])
                        sys.exit(1)
            #else, peform PCA on trajectory
            else:
                try:
                    self.proj,e=flexibility.pca(params.trajectory,params.topology, params.ratio)
                except ImportError, e:
                    print "ERROR: PCA failed, aborting!"
                    sys.exit(1)


            #compute projections centroid
            try:
                self.centroid=flexibility.clusterize(self.proj)

            except ImportError, e:
                print "ERROR: Clustering failed, aborting!"
                sys.exit(1)

            #suppose that data assigned to cluster can be fitted with a gaussian.
            #interval will be set at 95% of obtained distribution
            p=[]
            for i in xrange(0,len(self.proj),1):
                p.append(np.std(self.proj[i])*2)

            self.eigenspace_size=np.array(p)
            print ">> Flexibility interval in 95% confidence..."
            print "   "+str(self.eigenspace_size)

            #PCA automatically generates a reference pdb file called "protein.pdb"
            #check its existence and load its name in local params object!
            params.pdb_file_name="protein.pdb"
            if os.path.isfile(params.pdb_file_name)!=1 :
                print "ERROR: pdb file %s not found"%params.pdb_file_name
                sys.exit(1)

        #load monomeric structure (both for rigid )
        self.structure = Protein()
        try:
            self.structure.import_pdb(params.pdb_file_name)
        except IOError:
            sys.exit(1)

        #load receptor structure, if provided, and center it to the origin
        self.receptor_structure=[]
        if params.receptor!="NA":
            print ">> loading receptor, and centering it to origin..."
            self.receptor_structure = Protein()
            try:
                self.receptor_structure.import_pdb(params.receptor)
            except IOError,e:
                print e
                print "Man, a loading error!"
                sys.exit(1)

            coords=self.receptor_structure.get_xyz()
            self.receptor_structure.set_xyz(coords-np.mean(coords,axis=0))


        #if clash avoidance is requested, compute indexes of relevant atom
        #this call currently just selects the CA atoms
        if params.detect_clash:
            #self.index=self.get_index(["CA","CB"])
            #self.index=self.get_index(["CA"])
            self.get_index(["CA"])


    def get_index(self,atoms=["CA","CB"]):

        #generate a dummy multimer
        multimer = M.Multimer(self.structure)
        multimer.create_multimer(3,10,np.array([0.0,0.0,0.0]))

        #extract the indexes where atoms of interest are located
        for aname in atoms:
            [m,p_index]=multimer.atomselect(1,"*","*",aname,True)
            for i in p_index:
                self.index.append(i)

            if self.receptor_structure!=[]:
                [m,p_index]=self.receptor_structure.atomselect("*","*",aname,True)
                for i in p_index:
                    self.index_receptor.append(i)
        #return self.index
        
        # extract the indexes of CA for the postprocessing session
        


class Space(S):
    # n dim. space: 3 monomer rotations, 1 monomer radial translation, 1 multimer z translation, 3 receptor rotations, n monomer eigenvectors
    def __init__(self,params,data):
        S.__init__(self)

        #add receptor dimensions if needed
        rec_dim=0
        if params.receptor!="NA":
            rec_dim=4

        self.low=np.zeros(4+rec_dim+len(data.eigenspace_size))
        self.high=np.zeros(4+rec_dim+len(data.eigenspace_size))
        self.cell_size=np.zeros(4+rec_dim+len(data.eigenspace_size))
        self.boundary_type=np.zeros(4+rec_dim+len(data.eigenspace_size))

        if len(params.high_input)!=len(params.low_input):
            print "ERROR: seems that low and high boundaries have different length..."
            sys.exit(1)

        #assign monomer low boundaries
        if params.low_input!="NA" :
            if len(params.low_input)==3 or len(params.low_input)==4:
                for i in xrange(0,len(params.low_input),1):
                    self.low[i]=params.low_input[i]
            else:
                print "ERROR: boundaryMin should contain within 3 or 4 values"
                sys.exit(1)
        else:
            print "WARNING: boundaryMin undefined, using default values for monomer rotation"

        #assign monomer high boundaries
        if params.high_input!="NA" :
            if len(params.high_input)==3 or len(params.high_input)==4:
                for i in xrange(0,len(params.high_input),1):
                    self.high[i]=params.high_input[i]
            else:
                print "ERROR: boundaryMax should contain 3 or 4 values"
                sys.exit(1)
        else:
            print "WARNING: boundaryMin undefined, using default values for monomer rotation"
            self.high[0]=360.0
            self.high[1]=180.0
            self.high[2]=360.0

        #if needed assign radius boundaries
        if params.radius!="NA":
            if params.high_input=="NA":
                self.low[3]=params.radius
                self.high[3]=params.radius
            else:
                print "ERROR: radius keyword used when also using boundary condition list!"
                sys.exit(1)
        if params.radius=="NA" and params.high_input=="NA":
            print "ERROR: translation undefined boundary or radius keywords needed!"
            sys.exit(1)


        #if needed, add receptor dimensions
        if params.receptor!="NA":

                #multimer z-axis translation
            if params.high_input_rec=="NA":
                d=data.structure.get_xyz()
                self.low[4]=d[2].min()+params.pad
                self.high[4]=d[2].max()+params.pad
            else:
                self.low[4]=params.low_input_rec[0]
                self.high[4]=params.high_input_rec[0]

                #receptor x,y,z axis rotations
                if len(params.high_input_rec)!=4:
                    print "WARNING: Receptor rotations undefined in boundaryMinReceptor, using default values"
                    self.low[5]=0.0
                    self.low[6]=0.0
                    self.low[7]=-360/(2*params.degree)
                    self.high[5]=0
                    self.high[6]=0
                    self.high[7]=360/(2*params.degree)
                else:
                    self.low[5]=params.low_input_rec[1]
                    self.high[5]=params.high_input_rec[1]
                    self.low[6]=params.low_input_rec[2]
                    self.high[6]=params.high_input_rec[2]
                    self.low[7]=params.low_input_rec[3]
                    self.high[7]=params.high_input_rec[3]


        #add eigenvector fluctuations in search space
        #for i in xrange(0,len(data.eigenspace_size),1):
        #    self.low[4+rec_dim+i]=-data.eigenspace_size[i]
        #    self.high[4+rec_dim+i]=data.eigenspace_size[i]

        #print "PROJ SHAPE: %s %s"%(data.proj.shape[0],data.proj.shape[1])
        #for i in xrange(0,len(data.eigenspace_size),1):
        #    self.low[4+rec_dim+i]=-data.eigenspace_size[i]
        #    self.high[4+rec_dim+i]=data.eigenspace_size[i]

	    #print "PROJ SHAPE: %s %s"%(data.proj.shape[0],data.proj.shape[1])
        for i in xrange(0,len(data.eigenspace_size),1):
            self.low[4+rec_dim+i]=data.proj[i,:].min()
            self.high[4+rec_dim+i]=data.proj[i,:].max()
        #final check for all boundary conditions consistency (cause we're paranoid)
        if (self.low>self.high).any():
            print 'ERROR: a lower boundary condition is greater than a higher one'
            sys.exit(1)

        #define cell size
        self.cell_size=self.high-self.low

        #set boundary type
        if params.boundary_type[0]=="NA":
            for i in xrange(0,len(self.low),1):
                self.boundary_type[i]=0
        elif params.boundary_type[0]!="NA" and len(params.boundary_type)!=len(self.low):
            print 'ERROR: boundaries type inconsistent with system dimensions'
            print 'ERROR: %s dimensions given, but %s needed!'%(len(params.boundary_type),len(self.low))
            sys.exit(1)
        else:
            for i in xrange(0,len(self.low),1):
                self.boundary_type[i]=params.boundary_type[i]


class Fitness(BF):

    def __init__(self,data,params):
        BF.__init__(self)

        self.params=params
        self.style=params.style
        self.clash=params.detect_clash
        self.target=params.target

        self.constraint=params.constraint.split('.')[0]
        #test if constraint file exists, and function constaint_check is available
        try:
            exec 'import %s as constraint'%(self.constraint)
        except ImportError, e:
            print "ERROR: load of user defined constraint function failed!"
            sys.exit(1)

        try:
            constraint.constraint_check
        except AttributeError:
            print 'ERROR: constraint_check function not found'
            sys.exit(1)

        #data to manipulate
        self.data=data
        self.degree=params.degree

        #receptor space size
        self.rec_dim=0
        if params.receptor!="NA":
            self.rec_dim=4

        #energy vs geometry mixing weight
        self.c1=params.mix_weight


    def evaluate(self,num,pos):


        #import user provided constraint file and class needed to construct multimer
        exec 'import %s as constraint'%(self.constraint)
        import Multimer as M

        frame_penalty=0.0

        if self.style=="flexible":
        #pick monomeric structure from database
            deform_coeffs=pos[(4+self.rec_dim):len(pos)]
            #pos_eig=self.data.proj[:,self.data.centroid]+deform_coeffs
            code,min_dist=vq(self.data.proj.transpose(),np.array([deform_coeffs]))
            #code,min_dist=vq(self.data.proj.transpose(),np.array([pos_eig]))
            target_frame=min_dist.argmin()
            coords=self.data.traj[:,target_frame]
            coords_reshaped=coords.reshape(len(coords)/3,3)
            self.data.structure.set_xyz(coords_reshaped)

        #penalize solutions too far from the sampled space
        #if min_dist.min()>self.params.frame_distance:
        #    frame_penalty=min_dist.min()-self.params.frame_distance
        #print "penalty %s : %s"%(num,frame_penalty)

        #assemble multimer
        self.multimer = M.Multimer(self.data.structure)
        self.multimer.create_multimer(self.degree,pos[3],pos[0:3])

        measure=[]
        if self.data.receptor_structure!=[]:
            #shift multimer on z axis
            self.multimer.z_to_origin()
            self.multimer.z_shift(pos[4])

            #rotate receptor (backing up original position, and putting it back when measure is done)
            coords=self.data.receptor_structure.get_xyz()
            self.data.receptor_structure.rotation(pos[5],pos[6],pos[7])
            measure = constraint.constraint_check(self.multimer,self.data.receptor_structure)
            self.data.receptor_structure.set_xyz(coords)
        else:
            try:
                measure = constraint.constraint_check(self.multimer)
            except:
                print "ERROR: syntax error in constraint file!"
                raise

        if len(measure) != len(self.target) :
            print 'ERROR: constraint file produced %s measures, but %s target measures are provided!'%(len(measure),len(self.target))
            sys.exit(1)

        #measure distance within target values and obtained values
        diff=self.target-np.array(measure)
        distance=np.sqrt(np.dot(diff,diff))

        #detect clashes
        if self.clash:
            energy=self.interface_vdw()
            return self.c1*energy+(1-self.c1)*distance+frame_penalty
        else:
            return distance+frame_penalty


    def interface_vdw(self):

        epsilon=1.0
        sigma=4.7
        cutoff=12.0

        energy=0

        #CLASH WITH NEIGHBORING MONOMER
        #extract coords of monomers 1 and 2 of multimeric structure according to desired atoms

        m1=self.multimer.get_multimer_uxyz()[0][self.data.index]
        m2=self.multimer.get_multimer_uxyz()[1][self.data.index]

        #extract distances of every atom from all the others
        d=[]
        for i in xrange(0,len(m1),1):
            d.append(np.sqrt(np.sum((m2-m1[i])**2,axis=1)))

        dist=np.array(d)

        #detect interfacing atoms (atom couples at less than a certain cutoff distance
        couples=np.array(np.where(dist<cutoff)) #detect couples of clashing residues

        for i in xrange(0,len(couples[0]),1):
            d=dist[couples[0,i],couples[1,i]]
            energy+=4*epsilon*((sigma/d)**9-(sigma/d)**6)

        #CLASH WITH RECEPTOR (if needed)
        if self.data.receptor_structure!=[]:
            m1=self.data.receptor_structure.get_xyz()[self.data.index_receptor]

            #extract distances of every atom from all the others
            d=[]
            for i in xrange(0,len(m1),1):
                d.append(np.sqrt(np.sum((m2-m1[i])**2,axis=1)))

            dist=np.array(d)

            #detect interfacing atoms (atom couples at less than a certain cutoff distance
            couples=np.array(np.where(dist<cutoff)) #detect couples of clashing residues

            for i in xrange(0,len(couples[0]),1):
                d=dist[couples[0,i],couples[1,i]]
                energy+=4*epsilon*((sigma/d)**9-(sigma/d)**6)

        return energy



class Postprocess(PP):

    def __init__(self,data,params):
        self.data=data
        self.params=params

        self.rec_dim=0
        if params.receptor!="NA":
            self.rec_dim=4

        #load constraint file
        self.constraint=params.constraint.split('.')[0]
        try:
            exec 'import %s as constraint'%(self.constraint)
        except ImportError, e:
            print "ERROR: load of user defined constraint function failed!"
            sys.exit(1)

        try:
            constraint.constraint_check
        except NameError:
            print 'ERROR: constraint_check function not found'

    #clustering according to rmsd of solutions in search space


    def run(self):
        
        
        multimer = M.Multimer(self.data.structure)
        multimer.create_multimer(2,10,np.array([0.0,0.0,0.0]))
        [m,self.index]=multimer.atomselect(1,"*","*","CA",True) # -> extracting indexes of CA

        #load the monomeric structure positions (needed for resetting atom position after displacement)
        s = Protein()
        s.import_pdb(self.params.pdb_file_name)
        coords=s.get_xyz()
        self.coords = deepcopy(coords)
        
        Matrix_creator = CnD.Matrix_creator(self.params, self.data, self)
        Matrix_creator.computeMatrix()
        
        comm.Barrier()
        self.OUTPUT_DIRECTORY=self.params.output_folder
        if rank == 0:
            
            if os.path.isdir(self.OUTPUT_DIRECTORY)!=1:
                os.mkdir(self.OUTPUT_DIRECTORY)
            
            #self.OUTPUT_DIRECTORY=self.params.output_folder
            app = wx.App(False)
            frame = CnD.MainFrame(None, "Clustering interface",self.OUTPUT_DIRECTORY ,self.params, self.data, self)
            frame.distancePanel.computeCluster()
            
            if self.params.cluster_threshold == "NA":
                frame.Show()
                app.MainLoop()
            else:
                frame.distancePanel.convertCoordsAndExport(self.params.cluster_threshold)

    #this function superseed the standard euclidean distance implemented in Default.py
    def computeDistance (self, data1, data2):            
        
        # create the first multimer
        if self.params.style=="flexible":
            #pick monomeric structure from database
            deform_coeffs=data1[(4+self.rec_dim):-1]
            #pos_eig=self.data.proj[:,self.data.centroid]+deform_coeffs
            #code,min_dist=vq(self.data.proj.transpose(),np.array([pos_eig]))
            code,min_dist=vq(self.data.proj.transpose(),np.array([deform_coeffs]))
            target_frame=min_dist.argmin()
            coords=self.data.traj[:,target_frame]
            coords_reshaped=coords.reshape(len(coords)/3,3)
            self.data.structure.set_xyz(coords_reshaped)                         
        else:
            self.data.structure.set_xyz(self.coords)

        #pos = np.array(C[cnt-1])[0:(4+self.rec_dim)].astype(float)
        multimer1 = M.Multimer(self.data.structure)
        multimer1.create_multimer(self.params.degree,data1[3],np.array([data1[0],data1[1],data1[2]]))
        m1=multimer1.get_multimer_uxyz()[0][self.index] # getting all the coordinates of m1

        #create the second multimer
        # create the first multimer
        if self.params.style=="flexible":
            #pick monomeric structure from database
            deform_coeffs=data2[(4+self.rec_dim):-1]
            #pos_eig=self.data.proj[:,self.data.centroid]+deform_coeffs
            #code,min_dist=vq(self.data.proj.transpose(),np.array([pos_eig]))
            code,min_dist=vq(self.data.proj.transpose(),np.array([deform_coeffs]))
            target_frame=min_dist.argmin()
            coords=self.data.traj[:,target_frame]
            coords_reshaped=coords.reshape(len(coords)/3,3)
            self.data.structure.set_xyz(coords_reshaped)                         
        else:
            self.data.structure.set_xyz(self.coords)
            
        multimer2 = M.Multimer(self.data.structure)
        multimer2.create_multimer(self.params.degree,data2[3],np.array([data2[0],data2[1],data2[2]]))
        m2=multimer2.get_multimer_uxyz()[0][self.index]

        # calculate distance between the 2
        rmsd=self.align(m1,m2) # --> comes from Default.Postprocess.align()
        
        return rmsd
                
                
    def make_output(self, coordinateArray, average_RMSD_ARRAY):
        
        self.coordinateArray = coordinateArray
                    
        iterant = 0 # this iterator is used (in a bad way :( ) to select the right average RMSD value when iterating over the centroids

        clusters_file=open("%s/solutions.dat"%self.OUTPUT_DIRECTORY,"w")

        # writing the tcl file:
        tcl_file = open("%s/assembly.vmd"%self.OUTPUT_DIRECTORY,"w")

        # import the constraint file:
        self.constraint = self.params.constraint.split('.')[0]

        #test if constraint file exists, and function constaint_check is available
        try:
            exec 'import %s as constraint'%(self.constraint)
        except ImportError, e:
            print "ERROR: load of user defined constraint function failed!"
            sys.exit(1)

        try: constraint.constraint_check
        except NameError:
            print 'ERROR: constraint_check function not found'

        s = Protein()
        s.import_pdb(self.params.pdb_file_name)
        coords=s.get_xyz()
        
        for n in xrange(0,coordinateArray.shape[0],1):
            
            print "creating PDB for structure index: "+str(n)
            # create the first multimer
            if self.params.style=="flexible":
                #pick monomeric structure from database
                deform_coeffs=coordinateArray[n][(4+self.rec_dim):-1]
                #pos_eig=self.data.proj[:,self.data.centroid]+deform_coeffs
                #code,min_dist=vq(self.data.proj.transpose(),np.array([pos_eig]))
                code,min_dist=vq(self.data.proj.transpose(),np.array([deform_coeffs]))
                target_frame=min_dist.argmin()
                coords=self.data.traj[:,target_frame]
                coords_reshaped=coords.reshape(len(coords)/3,3)
                self.data.structure.set_xyz(coords_reshaped)                         
            else:
                self.data.structure.set_xyz(coords)
    
            #pos = np.array(C[cnt-1])[0:(4+self.rec_dim)].astype(float)
            multimer1 = M.Multimer(self.data.structure)
            multimer1.create_multimer(self.params.degree, coordinateArray[n][3], np.array([coordinateArray[n][0],coordinateArray[n][1],coordinateArray[n][2]]))

            # print the pdb file
            multimer1.write_PDB("%s/assembly%s.pdb"%(self.OUTPUT_DIRECTORY,iterant))

            # create the constraint:
            measure = constraint.constraint_check(multimer1)

            # WRITING SOLUTION.DAT
            l = []
            f = []

            # insert coordinates in the solution.dat file
            f.append("assembly "+str(iterant)+" |")
            for item in self.coordinateArray[n][: len(self.coordinateArray[n])-1]:
                l.append(item)
                f.append("%8.3f ")
                #write constraint values
            f.append("| ")
            for item in measure:
                l.append(item)
                f.append("%8.3f ")
            #write fitness
            f.append("| %8.3f")
            l.append(self.coordinateArray[n][-1])
            # write average RMSD OF CLUSTER:
            f.append("| %8.3f\n")
            # check here if the structure belongs to a cluster
            l.append(average_RMSD_ARRAY[iterant])

            formatting=''.join(f)

            clusters_file.write(formatting%tuple(l))

            # --------------------------- WRITING TCL FILE
            if iterant == 0:
                tcl_file.write("mol new assembly"+str(iterant)+".pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all \n")

            else:
                tcl_file.write("mol addfile assembly"+str(iterant)+".pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all \n")

            iterant += 1     
            
        tcl_file.write("mol delrep 0 top \n\
mol representation NewCartoon 0.300000 10.000000 4.100000 0 \n\
mol color Chain \n\
mol selection {all} \n\
mol material Opaque \n\
mol addrep top \n\
mol selupdate 0 top 0 \n\
mol colupdate 0 top 0 \n\
mol scaleminmax top 0 0.000000 0.000000 \n\
mol smoothrep top 0 0 \n\
mol drawframes top 0 {now}")

        clusters_file.close()
        tcl_file.close()