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How to use opposite method in Sure

Best Python code snippet using sure_python

twist_discrete.py

Source:twist_discrete.py

1# -*- coding: utf-8 -*-2"""3Created on Fri Oct 14 23:01:08 201645@author: tunaz6"""789import sys1011import re12import numpy13import math1415from scipy import interpolate1617from mpl_toolkits.mplot3d import Axes3D18import matplotlib.pyplot as plt192021class Tee(object):22    def __init__(self, *files):23        self.files = files24    def write(self, obj):25        for f in self.files:26            f.write(obj)27            f.flush() # If you want the output to be visible immediately28    def flush(self) :29        for f in self.files:30            f.flush()31            32            33if len(sys.argv) == 1 or len(sys.argv) == 2 or len(sys.argv) > 3  :34    print "Usage: python twist_region.py pdbfilename.pdb direction"35    sys.exit(0)363738lines_File = [lines1.rstrip('\n') for lines1 in open(sys.argv[1], 'r')]   394041try:42    direction = int(sys.argv[2]) # give direction as input43    '''44    direction= 0 means forward direction, 45    direction = 1 means backword direction 46    '''47    if direction != 0 and direction != 1 :48        print "please input either 0 or 1. 0 = forward, 1 = backword"49        sys.exit(0)50except ValueError:  51        print "please input either 0 or 1. 0 = forward, 1 = backword"52        sys.exit(0)          5354#sys.stdout = open("output_all.pdb", "w")55out_filename = 'twist_angles.txt'56outf = open(out_filename, 'w')5758sys.stdout = open('output_pdb.pdb','w')59#outf2 = open(out_filename2, 'w')60#lines_File = [lines1.rstrip('\n') for lines1 in open('1aky.pdb')]    61#lines_File = [lines1.rstrip('\n') for lines1 in open('1aop.pdb')]  62#lines_File = [lines1.rstrip('\n') for lines1 in open('2p8y.pdb')] #index problem63#lines_File = [lines1.rstrip('\n') for lines1 in open('1s04.pdb')] #complex structure (multple same chain duplicate index)64#lines_File = [lines1.rstrip('\n') for lines1 in open('1atz.pdb')] 65#lines_File = [lines1.rstrip('\n') for lines1 in open('2qtr.pdb')] 66#lines_File = [lines1.rstrip('\n') for lines1 in open('1d5t.pdb')] 67#lines_File = [lines1.rstrip('\n') for lines1 in open('1elu.pdb')]68#lines_File = [lines1.rstrip('\n') for lines1 in open('1a12.pdb')]69#lines_File = [lines1.rstrip('\n') for lines1 in open('1b3a.pdb')]7071#direction = 0 # direction= 0 means forward direction, direction = 1 means backword direction so change here        72            73def draw_interpolation(input_array):74    #print "input  ", input_array75    #print "length  ", len(input_array)76    if  len(input_array) > 2 :77        data = numpy.array(input_array)78        data = data.astype(float)79        80       # print data #ok81           82        data = data[0:100].transpose()83        #print "hi", data #ok84        #now we get all the knots and info about the interpolated spline85		#spacing = int(len(input_array)/.3)86        tck, u= interpolate.splprep(data,k=2)   87        #new = interpolate.splev(numpy.linspace(0,1,50), tck)88        #new = interpolate.splev(numpy.linspace(0,1,int(len(input_array)/.8)), tck) #unit length given 0.189        #new = interpolate.splev(numpy.linspace(0,1,int(len(input_array)/.5)), tck) #we used it for ACM_BCB90        new = interpolate.splev(numpy.linspace(0, 1, int(len(input_array) /.05)), tck)9192        #now lets plot it!93        94        #fig = plt.figure()95        #ax = Axes3D(fig)96        #ax.plot(data[0], data[1], data[2], label='originalpoints', lw =2, c='Dodgerblue')97        #ax.plot(new[0], new[1], new[2], label='fit', lw =2, c='red')98        #ax.legend()99        #plt.savefig('junk.png')100        #plt.show() 101        return new[0], new[1], new[2]             102103104#print (lines_File1)105106direction_opposite = 1 #hydrogen bond 107108count_beta_sheet = 0109count_beta_strand = 0110counter = 0111counter_index = []112problem = 0113a=[]114beta_sheet = []115atom = []116splitted_line = []117count_atom = 0118for sheet_line in lines_File: #find each line in all lines119     if sheet_line.startswith('SHEET'):     #find those lines start with "SHEET"120         #count_atom = count_atom+1121         #print (sheet_line)       #print the lines started with "SHEET"        122         #beta_sheet.append ( re.sub("\s\s+" , " ",sheet_line).split()) #ok for all except 1123         beta_sheet.append([sheet_line[0:6], sheet_line[7:10], sheet_line[11:14], sheet_line[14:16],sheet_line[17:20], sheet_line[21], sheet_line[22:27], sheet_line[28:31], sheet_line[32], sheet_line[33:37], sheet_line[37], sheet_line[38:40],sheet_line[41:45],sheet_line[45:48], sheet_line[49], sheet_line[50:55], sheet_line[56:60], sheet_line[60:63], sheet_line[64], sheet_line[65:69], sheet_line[69]])124     if sheet_line.startswith('ATOM'):  #find those lines start with "ATOM"125         count_atom = count_atom+1126         #print (sheet_line)       #print the lines started with "ATOM"127         atom.append( [sheet_line[:6], sheet_line[6:11], sheet_line[12:16], sheet_line[17:20], sheet_line[21], sheet_line[22:26], sheet_line[30:38], sheet_line[38:46], sheet_line[46:54]])128         #atom.append( [sheet_line[0:6], sheet_line[6:11], sheet_line[12:16], sheet_line[16:17],sheet_line[17:20], sheet_line[21:22], sheet_line[22:26], sheet_line[26:27], sheet_line[30:38], sheet_line[38:46], sheet_line[46:54], sheet_line[46:54], sheet_line[54:60], sheet_line[60:66], sheet_line[76:78], sheet_line[78:80]])129         #atom.append ( re.sub("\s\s+" , " ",sheet_line).split())130#print (int(atom[1836][5].strip()))131#print (atom[1836])132133strand_vector=[]134center_vector = []135CA_vector_between_strand = []136amino_acid = []137138139#common hydrogen bond140strand_vector_opposite=[]141center_vector_opposite = []142CA_vector_between_strand_opposite = []143amino_acid_opposite = []144145146poi = 0147track = 1148149poi_opposite = 0 #hydrogen bond150151152for sheet_index in range (0,len(beta_sheet)): # handle if there is less than 3 atoms in a strand153    if int(beta_sheet[sheet_index][1]) == int(beta_sheet[sheet_index][3]):154        counter = counter + 1155156#print ("number of beta sheet ",counter) #ok157out_char = "number of beta sheet " + str(counter) + '\n\n'158outf.write(out_char)            159for sheet_index in range (0,len(beta_sheet)): # handle if there is less than 3 atoms in a strand160    if abs((int(beta_sheet[sheet_index][9]))  - int(beta_sheet[sheet_index][6])) >= 2 :161        if int(beta_sheet[sheet_index][1]) == int(beta_sheet[sheet_index][3]):162            #counter = counter + 1163            if track == 0 :164                counter_index.append(int(beta_sheet[sheet_index][1]) - problem)165                track = 1166            else:   167                counter_index.append(int(beta_sheet[sheet_index][1]))168                track = 1169    else:170        #print "hi " #ok171        if  (int(beta_sheet[sheet_index][3]) > 2):           172             problem = problem + 1173             #print problem  #ok174             track = 0175            176            177#for i in range (0,len(counter_index)):178    #print ("counter_index ",counter_index[i]) #ok  179     180for sheet_index in range (0,len(beta_sheet)): # 5 should be number of beta stand in one beta sheet181    #print("love ",beta_sheet[sheet_index][10])182   183    atom_start_index=(int(beta_sheet[sheet_index][6]))184    #print("start index ",atom_start_index) #ok185    atom_end_index=(int(beta_sheet[sheet_index][9])) 186    #print("end index ",atom_end_index) #ok187    sheet_chain = beta_sheet[sheet_index][5]188    #print sheet_chain189190    mid_point = []191    array_strand_index =[]192    amino_acid_array = []193    aa_index = []194    #array_strand_index = [[0 for i in range(2)] for i in range(2)] #2 should be change according to length of one beta sheet195    array_x = []196    array_y = []197    array_z = []198    CA_x = []199    CA_y = []200    CA_z = []201    202    #print (count_atom)203    204    for i in range (0,count_atom) : 205        206        if (atom_start_index <= int(atom[i][5].strip()) <=  atom_end_index)  :207            208            if  atom[i][2].strip() == 'N' or atom[i][2].strip() == 'C': 209                #print "duplicate ", int(atom[i][5].strip())210                211                if sheet_chain == atom[i][4].strip(): #this is needed to differentiate same startindex & endindex but different chains212                    array_strand_index.append(atom[i][5].strip())                  213                    array_x.append(atom[i][6].strip())214                    array_y.append(atom[i][7].strip())215                    array_z.append(atom[i][8].strip())216                    length=len(array_strand_index)  217            if atom[i][2].strip() == 'CA':218                if sheet_chain == atom[i][4].strip():219                    aa_index.append( i )             220                    amino_acid_array.append(atom[i][3].strip())        221                    CA_x.append(atom[i][6].strip())222                    CA_y.append(atom[i][7].strip())223                    CA_z.append(atom[i][8].strip())224                    length_CA = len (CA_x)225    #print ("strand index  ",array_strand_index) #ok226   # print (aa_index)227    #print ("Amino acid  ",amino_acid_array)  #ok        228   229   230   231    232    if direction == 0: #forward direction #ok233        midpoint_x_bef = []234        midpoint_y_bef = []235        midpoint_z_bef = []  236        237      238        239        midpoint_x = []240        midpoint_y = []241        midpoint_z = []242        243        new_x = []244        new_y = []245        new_z = []  246        247       248        #coef = [1,1,1,1,1,1,1,1]249        #coef = []250        251        c_index = 1252        n_index = 2253        while c_index < length-1 and n_index <  length-1 :  #mid point calculation254            #print ("c_index ",c_index, "n_index ", n_index)255            midpoint_x_bef.append((float(array_x[c_index]) + float(array_x[n_index]))/float(2.0))    #making midpoint       256            midpoint_y_bef.append((float(array_y[c_index]) + float(array_y[n_index]))/float(2.0))   #making midpoint 257            midpoint_z_bef.append((float(array_z[c_index]) + float(array_z[n_index]))/float(2.0))  #making midpoint 258           259            c_index = c_index + 2260            n_index = n_index +2  261        262        #print ("midpoint_x_bef  ", midpoint_x_bef ) 263        #print ("midpoint_y_bef  ", midpoint_y_bef  )264        #print ("midpoint_z_bef  ", midpoint_z_bef  )265        midpoint_x=midpoint_x_bef266        midpoint_y=midpoint_y_bef267        midpoint_z=midpoint_z_bef268        '''269        midpoint_draw = []270        draw_index = 0271        while draw_index < len (midpoint_x_bef) :272            midpoint_point = []273            mid_x = midpoint_x_bef [draw_index]274            mid_y = midpoint_y_bef [draw_index]275            mid_z = midpoint_z_bef [draw_index]           276            midpoint_point.append (mid_x)277            midpoint_point.append (mid_y)278            midpoint_point.append (mid_z)279            midpoint_draw.append (midpoint_point) 280            draw_index = draw_index + 1281        #print   (midpoint_draw)  #ok282        pdb_format = '6s5s1s4s1s3s1s1s4s1s3s8s8s6s10s2s3s'283        #shape = 'ATOM 1 N LEU A 81 25.865 39.612 19.376 1.00 53.28 N '284        shape = ['ATOM', '1','N', 'LEU', 'A', '81', '25.865', '39.612', '19.376']285        if len(midpoint_draw) <= 2:286             midpoint_x=midpoint_x_bef287             midpoint_y=midpoint_y_bef288             midpoint_z=midpoint_z_bef289             290             for i in range (len( midpoint_x)):291                poi = poi +1292                                           293                #print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s\n"%tuple(shape) ok294                print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi,'S','LEU', 'A', '81',round(midpoint_x[i],3),round(midpoint_y[i],3),round(midpoint_z[i],3)]) #print new atom position in PDB file295                296             297        else:    298            value = draw_interpolation (midpoint_draw)   #making 3D cubic spline interpolation for midpoints299            #print value[0] #ok300            midpoint_x=value[0]  #new midpoint after cubic spline301            midpoint_y=value[1]  #new midpoint after cubic spline302            midpoint_z=value[2]   #new midpoint after cubic spline303        304            305           306            pdb_length = len( midpoint_x)307          308            for i in range (pdb_length):309                poi = poi +1          310                print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi,'S','LEU', 'A', '81',round(midpoint_x[i],3),round(midpoint_y[i],3),round(midpoint_z[i],3)]) #print new atom position in PDB file311           '''     312       313       314        315        316       317        #print ("midpoint_x ", midpoint_x ) 318         319        320     321     322        length_midpoint_array = len(midpoint_x)323        vector_array =[]324        cen_array = []325        midpoint_index = 1326        while midpoint_index < length_midpoint_array:327            point = []328            cen_point = []329            temp_mid_index = midpoint_index - 1330            vec_x = midpoint_x [temp_mid_index] -  midpoint_x [temp_mid_index+1]  #making midpoint vector331            vec_y = midpoint_y [temp_mid_index] -  midpoint_y [temp_mid_index+1]  #making midpoint vector332            vec_z = midpoint_z [temp_mid_index] -  midpoint_z [temp_mid_index+1]  #making midpoint vector333            334            cen_x = (float(midpoint_x [temp_mid_index]) + float( midpoint_x [temp_mid_index+1])) / float(2.0)  #making center of midpoint vector335            cen_y =(float( midpoint_y [temp_mid_index]) + float(midpoint_y [temp_mid_index+1]))/float(2.0)   #making center of midpoint vector336            cen_z = (float(midpoint_z [temp_mid_index]) + float( midpoint_z [temp_mid_index+1]))/float(2.0)   #making center of midpoint vector337            338            #print ("vector x ",vec_x) 339           # print ("vector y ",vec_y) 340           # print ("vector z ",vec_z) 341            #make unit vector342            magnitude = math.sqrt(pow(vec_x, 2) + pow(vec_y, 2) + pow(vec_z, 2))343            344           345            #print("vector length ",magnitude)346            347            point.append(vec_x/magnitude) # unit vector348            point.append(vec_y/magnitude)  # unit vector349            point.append(vec_z/magnitude)  # unit vector350            351      352            #point.append(vec_x) #ok353            #point.append(vec_y)354            #point.append(vec_z)355      356         357            cen_point.append(cen_x) #ok358            cen_point.append(cen_y)359            cen_point.append(cen_z)360            361            362            363            364            vector_array.append(point)365            366            cen_array.append(cen_point)367            368            midpoint_index = midpoint_index +1369        #print "vector array ",vector_array370        371        372        aa = []373        aa_index = 1374        while aa_index < len(amino_acid_array) - 1:   # to get amino acid value375             aa.append(amino_acid_array[aa_index]) 376             aa_index = aa_index +1377        amino_acid.append(aa)378        379        #print ("x cordinate of CA in each strand" CA_x )380    381        #print("length ", length)382        #print ("CA length ",length_CA)383        CA_x_new = []384        CA_y_new = []385        CA_z_new = []386        CA_vector = []387        CA_index = 1388        while CA_index < length_CA - 1:389            CA_point = []390            CA_x_new=(float(CA_x[CA_index]))391            CA_y_new=(float(CA_y[CA_index]))392            CA_z_new=(float(CA_z[CA_index]))393            CA_point.append (CA_x_new)394            CA_point.append (CA_y_new)395            CA_point.append (CA_z_new)396            CA_vector.append (CA_point)   397            CA_index = CA_index + 1398        #draw_interpolation (CA_vector) #draw spline according to carbon alpha 399400        CA_vector_between_strand.append(CA_vector)401        #draw_interpolation (CA_vector_between_strand)402403         404    if direction_opposite == 1:   #backword direction405    406        midpoint_x_bef_opposite = []407        midpoint_y_bef_opposite = []408        midpoint_z_bef_opposite = []  409410        midpoint_x_opposite = []411        midpoint_y_opposite = []412        midpoint_z_opposite = [] 413        414       415        416        c_index_opposite = length-3417        n_index_opposite = length-2418        while c_index_opposite > 0  and n_index_opposite > 0 : 419            #print ("c_index ",c_index, "n_index ", n_index)420            midpoint_x_bef_opposite.append((float(array_x[c_index_opposite]) + float(array_x[n_index_opposite]))/float(2.0))421            midpoint_y_bef_opposite.append((float(array_y[c_index_opposite]) + float(array_y[n_index_opposite]))/float(2.0))422            midpoint_z_bef_opposite.append((float(array_z[c_index_opposite]) + float(array_z[n_index_opposite]))/float(2.0)) 423            c_index_opposite = c_index_opposite - 2424            n_index_opposite = n_index_opposite - 2   425       426       427        midpoint_x_opposite = midpoint_x_bef_opposite428        midpoint_y_opposite = midpoint_y_bef_opposite429        midpoint_z_opposite = midpoint_z_bef_opposite430       431        '''432        midpoint_draw_opposite = []433        draw_index_opposite = len (midpoint_x_bef_opposite) -1434        while draw_index_opposite >= 0 :435            midpoint_point_opposite = []436            mid_x_opposite = midpoint_x_bef_opposite [draw_index_opposite]437            mid_y_opposite = midpoint_y_bef_opposite [draw_index_opposite]438            mid_z_opposite = midpoint_z_bef_opposite [draw_index_opposite]           439            midpoint_point_opposite.append (mid_x_opposite)440            midpoint_point_opposite.append (mid_y_opposite)441            midpoint_point_opposite.append (mid_z_opposite)442            midpoint_draw_opposite.append (midpoint_point_opposite) 443            draw_index_opposite = draw_index_opposite - 1444            445        #draw_interpolation (midpoint_draw)446       447        if len(midpoint_draw_opposite) <= 2:448             midpoint_x_opposite = midpoint_x_bef_opposite 449             midpoint_y_opposite = midpoint_y_bef_opposite450             midpoint_z_opposite = midpoint_z_bef_opposite451             452             for i in range (len( midpoint_x_opposite)):453                poi_opposite = poi_opposite +1454                                           455                #print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s\n"%tuple(shape) ok456               # print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi_opposite,'S','LEU', 'A', '81',round(midpoint_x_opposite[i],3),round(midpoint_y_opposite[i],3),round(midpoint_z_opposite[i],3)]) #print new atom position in PDB file457                458             459        else:    460            value_opposite = draw_interpolation (midpoint_draw_opposite)   #making 3D cubic spline interpolation for midpoints461            #print value_opposite[0] #ok462            midpoint_x_opposite = value_opposite[0]  #new midpoint after cubic spline463            midpoint_y_opposite = value_opposite[1]  #new midpoint after cubic spline464            midpoint_z_opposite = value_opposite[2]   #new midpoint after cubic spline465        466            467           468            pdb_length_opposite = len( midpoint_x_opposite)469          470            for i in range (pdb_length_opposite):471                poi_opposite = poi_opposite +1          472                #print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi_opposite,'S','LEU', 'A', '81',round(midpoint_x_opposite[i],3),round(midpoint_y_opposite[i],3),round(midpoint_z_opposite[i],3)]) #print new atom position in PDB file473                474       475       476        midpoint_x_opposite = midpoint_x_bef_opposite477        midpoint_y_opposite = midpoint_y_bef_opposite478        midpoint_z_opposite = midpoint_z_bef_opposite479        '''480    481        #print ("midpoint_x ", midpoint_x )      482        length_midpoint_array_opposite = len (midpoint_x_opposite)   483        vector_array_opposite =[]484        cen_array_opposite = []485        486        #midpoint_index_opposite = length_midpoint_array487        #while midpoint_index > 1:488        489        midpoint_index_opposite = 1 #big change in this loop490        while midpoint_index_opposite < length_midpoint_array_opposite:491            point_opposite = []492            cen_point_opposite = []493            494            temp_mid_index_opposite = midpoint_index_opposite - 1495            #vec_x = midpoint_x [temp_mid_index] -  midpoint_x [temp_mid_index-1]496            #vec_y = midpoint_y [temp_mid_index] -  midpoint_y [temp_mid_index-1]497            #vec_z = midpoint_z [temp_mid_index] -  midpoint_z [temp_mid_index-1]498            499            vec_x_opposite = midpoint_x_opposite [temp_mid_index_opposite] -  midpoint_x_opposite [temp_mid_index_opposite+1]500            vec_y_opposite = midpoint_y_opposite [temp_mid_index_opposite] -  midpoint_y_opposite [temp_mid_index_opposite+1]501            vec_z_opposite = midpoint_z_opposite [temp_mid_index_opposite] -  midpoint_z_opposite [temp_mid_index_opposite+1]502            503            #print ("vector ",vec_x,vec_y,vec_z) 504            505            #cen_x = (float(midpoint_x [temp_mid_index]) + float( midpoint_x [temp_mid_index-1])) / float(2.0)  #making center of midpoint vector506            #cen_y =(float( midpoint_y [temp_mid_index]) + float(midpoint_y [temp_mid_index-1]))/float(2.0)   #making center of midpoint vector507            #cen_z = (float(midpoint_z [temp_mid_index]) + float( midpoint_z [temp_mid_index-1]))/float(2.0)   #making center of midpoint vector508            509            cen_x_opposite = (float(midpoint_x_opposite [temp_mid_index_opposite]) + float( midpoint_x_opposite [temp_mid_index_opposite+1])) / float(2.0)  #making center of midpoint vector510            cen_y_opposite =(float( midpoint_y_opposite [temp_mid_index_opposite]) + float(midpoint_y_opposite [temp_mid_index_opposite+1]))/float(2.0)   #making center of midpoint vector511            cen_z_opposite = (float(midpoint_z_opposite [temp_mid_index_opposite]) + float( midpoint_z_opposite [temp_mid_index_opposite+1]))/float(2.0)   #making center of midpoint vector512            513              #make unit vector514            magnitude_opposite = math.sqrt(pow(vec_x_opposite, 2) + pow(vec_y_opposite, 2) + pow(vec_z_opposite, 2))515            #print("vector length opposite ",magnitude_opposite)516            #point.append(vec_x/magnitude) #not ok517            #point.append(vec_y/magnitude)518            #point.append(vec_z/magnitude)519            520            '''521            point_opposite.append(vec_x_opposite) #ok522            point_opposite.append(vec_y_opposite)523            point_opposite.append(vec_z_opposite)524            '''525            point_opposite.append(vec_x_opposite/magnitude_opposite) #ok526            point_opposite.append(vec_y_opposite/magnitude_opposite)527            point_opposite.append(vec_z_opposite/magnitude_opposite)528            529            530            531            cen_point_opposite.append(cen_x_opposite) #ok532            cen_point_opposite.append(cen_y_opposite)533            cen_point_opposite.append(cen_z_opposite)534     535            vector_array_opposite.append(point_opposite)536            537            cen_array_opposite.append(cen_point_opposite)538            539            midpoint_index_opposite = midpoint_index_opposite + 1540            541            #midpoint_index = midpoint_index - 1 542        543        aa_opposite = []544        aa_index_opposite = len(amino_acid_array) - 2545        while aa_index_opposite > 0:   # to get amino acid value546             aa_opposite.append(amino_acid_array[aa_index_opposite]) 547             aa_index_opposite = aa_index_opposite - 1 548        amino_acid_opposite.append(aa_opposite)549   550   551        #print ("x cordinate of CA in each strand", CA_x )552    553        #print("length ", length)554        #print ("CA length ",length_CA)555        CA_x_new_opposite = []556        CA_y_new_opposite = []557        CA_z_new_opposite = []558        CA_vector_opposite = []559        CA_index_opposite = length_CA - 2560        while CA_index_opposite > 0 :561            CA_point_opposite = []562            CA_x_new_opposite=(float(CA_x[CA_index_opposite]))563            CA_y_new_opposite=(float(CA_y[CA_index_opposite]))564            CA_z_new_opposite=(float(CA_z[CA_index_opposite]))565            CA_point_opposite.append (CA_x_new_opposite)566            CA_point_opposite.append (CA_y_new_opposite)567            CA_point_opposite.append (CA_z_new_opposite)568            CA_vector_opposite.append (CA_point_opposite)   569            CA_index_opposite = CA_index_opposite - 1570        CA_vector_between_strand_opposite.append(CA_vector_opposite)571        572        573    strand_vector.append(vector_array)  574    575    center_vector.append(cen_array)576    577    #for hydrogen bond calculation578    strand_vector_opposite.append(vector_array_opposite)  579    580    center_vector_opposite.append(cen_array_opposite)581    582   #print(beta_sheet[sheet_index][1])  583    584    585586 587   588    589    '''590    print ("vector ",vector_array)591    print (atom_start_index)592    print (array_strand_index) 593    print(length)594    595    print (array_x) 596    print (array_y) 597    print (array_z) 598    print (midpoint_x)599    print (midpoint_y)600    print (midpoint_z)601    print (length_midpoint_array)602    '''603print "\n"604length_strand_vector = len(strand_vector)605#print (strand_vector)606#print(amino_acid) # ok607#print ("vector strand length ",length_strand_vector)608#print ("CA_vector_between_strand ",len(CA_vector_between_strand)) # ok.  vector_strand length and CA_vector same609#print ("CA_vector_between_strand ",CA_vector_between_strand) 610#draw_interpolation (CA_vector_between_strand)611612def distance(x,y):   613    return numpy.sqrt(numpy.sum((x-y)**2))614615616def find_nearest_distance(a,B, pair_aa1, pair_aa2):617    618    619    #print ("a ", a)620    min_point = B[0]621    #min_dist = abs(numpy.linalg.norm(a- numpy.array(B[0])))622    min_dist = math.sqrt ( pow((a[0]-B[0][0]),2) + pow((a[1]-B[0][1]),2) + pow((a[2]-B[0][2]),2)  )623    #min_dist = 12000624   # print ("mindistance ", min_dist)625    #print("len of B",len(B)) #ok626    aa_min_index = 0627    for i in range (0, len(B)): 628        #dist = []629                       630        b = numpy.array(B[i])        631        #print ("b ", b) #ok632        #dist=(numpy.linalg.norm(a-b))633        try_dist = math.sqrt ( pow((a[0]-b[0]),2) + pow((a[1]-b[1]),2) + pow((a[2]-b[2]),2)  )634        #print ("distance ", try_dist)635        #dist=abs(distance(a,b))636        if try_dist < min_dist:637            min_dist = try_dist638            min_point = b639            aa_min_index = i640 641    642    return (min_point, aa_min_index)643644645def calculate_twist_angle(a,minimum_dist_point,j,aa_min_index2):646        647    #print ("mindist point ", minimum_dist_point)648    dot_product = numpy.dot(a,minimum_dist_point) # A.B649    #print (dot_product)650       651    a_sum = pow(a[0],2)+pow(a[1],2)+pow(a[2],2)652    a_root=math.sqrt(a_sum)653    b_sum = pow(minimum_dist_point[0],2)+pow(minimum_dist_point[1],2)+pow(minimum_dist_point[2],2)654    b_root=math.sqrt(b_sum)655    a_b = a_root*b_root656    657    angle_dot = math.acos(dot_product/a_b)658    #print (angle_dot)659    twist_angle = math.degrees(angle_dot)660    661    '''662    ### cross product ###663    cross_product = numpy.cross(a,minimum_dist_point) # A*B664    #print (cross_product)665    sum_square_cross_product = pow(cross_product[0],2) +  pow(cross_product[1],2)+ pow(cross_product[2],2)666    #print (sum_square_cross_product)667    root_sum_square_cross_product = math.sqrt(sum_square_cross_product)668    #print (root_sum_square_cross_product)669   670   671   672    angle_cross = math.asin(root_sum_square_cross_product/a_b)673    #print (angle_cross)674    print(math.degrees(angle_cross))675    ######## end of cross product ###########676    '''677    if twist_angle > 90.:678        twist_angle = 180.0 - twist_angle679   # sys.stdout = original680   # print(" Amino Acid",pair_aa1[j], " and ", pair_aa2[aa_min_index2],":", "Twist angle::" , twist_angle) #necessary681    #print("Twist angle::" , round(twist_angle,3)) #necessary682    out_char = "Twist angle:: " + str(round(twist_angle,3)) + '\n'683    outf.write(out_char)684    return twist_angle685       # print ( "amino acid ", pair_aa1[j], " ", pair_aa2[aa_min_index2])686minimum_dist_point = []  687minimum_dist_point_dup = []688flag = 0689all_avg_twist_angle = []  690avg_count = 0    691avg_track = 1692pair_array = []693len_array = []694i = 0695while i < length_strand_vector : # pairwise calculation 696    #print ("beta sheet index", beta_sheet[i][1])697    #print ("beta strand", beta_sheet[i])698    699    #print(int(beta_sheet[i][1]), " : ", int(beta_sheet[i][3]))700    #print ("i ", i)701    #print ("flag ",flag)702    avg_twist_count = []703            704    if(int(beta_sheet[i][1])>=int(beta_sheet[i][3])):705        flag = int(beta_sheet[i][1])706        avg_count = 0707       708        #print ("avg count ",avg_count)709    else:710        flag = flag + 1711        avg_count = avg_count + 1712        A_t = []713        B_t= []714        A = []715        B = []716        717        #for hydrogen bond718        A_t_opposite = []719        B_t_opposite  = []720        A_opposite  = []721        B_opposite  = []722        723        alpha_A_t = []724        alpha_B_t = []725        alpha_A = []726        alpha_B = []727        728          #for hydrogen bond729        alpha_A_t_opposite = []730        alpha_B_t_opposite = []731        alpha_A_opposite = []732        alpha_B_opposite = []733        734        pair_aa1_t = []735        pair_aa2_t = []736        pair_aa1 = []737        pair_aa2 = []738        739         740        #for hydrogen bond741        pair_aa1_t_opposite = []742        pair_aa2_t_opposite = []743        pair_aa1_opposite = []744        pair_aa2_opposite = []745        746        747        index_vec = i748        A_t = strand_vector[i] #copy strand to A array749        B_t = strand_vector[index_vec+1] #copy strand to B array 750        751        #for hydrogen bond752        A_t_opposite = strand_vector_opposite[i] #copy strand to A array753        B_t_opposite = strand_vector_opposite[index_vec+1] #copy strand to B array 754        755        #alpha carbon756        alpha_A_t = CA_vector_between_strand[i] #copy strand to A array757        alpha_B_t = CA_vector_between_strand[index_vec+1] #copy strand to B array 758        759         #for hydrogen bond760        alpha_A_t_opposite = CA_vector_between_strand_opposite[i] #copy strand to A array (alpha-carbon) backword direction761        alpha_B_t_opposite = CA_vector_between_strand_opposite[index_vec+1] #copy strand to B array (alpha-carbon) backword direction762        763        '''764        #center vector765        alpha_A_t = center_vector[i] #copy strand to A array766        alpha_B_t = center_vector[index_vec+1] #copy strand to B array 767        768         #for hydrogen bond769        alpha_A_t_opposite = center_vector_opposite[i] #copy strand to A array (alpha-carbon) backword direction770        alpha_B_t_opposite = center_vector_opposite[index_vec+1] #copy strand to B array (alpha-carbon) backword direction771        '''772        773        pair_aa1_t = amino_acid[i] #copy strand to A array774        pair_aa2_t = amino_acid[index_vec+1] #copy strand to B array 775        776        #hydrogen bond777        pair_aa1_t_opposite = amino_acid_opposite[i] #copy strand to A array778        pair_aa2_t_opposite = amino_acid_opposite[index_vec+1] #copy strand to B array 779        780        781      #  print ("A_t ",A_t)782       783      #  print ("B_t ",B_t)784       # sys.stdout = original785        #print ("beta strand 1", beta_sheet[i]) #necessary786        #print ("beta strand 2", beta_sheet[i+1]) #necessary787        out_char = "beta strand 1" + str(beta_sheet[i]) + '\n'788        outf.write(out_char)789        out_char = "beta strand 2" + str(beta_sheet[i+1]) + '\n'790        outf.write(out_char)791        #print ("A_t ",len(A_t))792       793        #print ("B_t ",len(B_t))794        if len(A_t) > len(B_t):795            A = B_t796            B = A_t797            798            #hydrogen bond799            A_opposite = B_t_opposite800            B_opposite = A_t_opposite801            802            alpha_A = alpha_B_t803            alpha_B = alpha_A_t804            805             #hydrogen bond806            alpha_A_opposite = alpha_B_t_opposite807            alpha_B_opposite = alpha_A_t_opposite808            809            pair_aa1 = pair_aa2_t810            pair_aa2 = pair_aa1_t811            812            #hydrogen bond813            pair_aa1_opposite = pair_aa2_t_opposite814            pair_aa2_opposite = pair_aa1_t_opposite815        else:816            A = A_t817            B = B_t818            819             #hydrogen bond820            A_opposite = A_t_opposite821            B_opposite = B_t_opposite822            823            alpha_A = alpha_A_t824            alpha_B = alpha_B_t 825            826            #hydrogen bond827            alpha_A_opposite = alpha_A_t_opposite828            alpha_B_opposite = alpha_B_t_opposite829            830            pair_aa1 = pair_aa1_t831            pair_aa2 = pair_aa2_t832            833             #hydrogen bond834            pair_aa1_opposite = pair_aa1_t_opposite835            pair_aa2_opposite = pair_aa2_t_opposite836        837        #aa_min_index2 = 0838        k = 0839        twist_angle_return = 0.0840        add_1 = 0 841        add_n = 0842        add_hp = 0 #hydrogen bond843        pick_index = 0844        845        '''for calculation of avg twist angle between two beta strands'''846        twist_count = 0847        sum_twist_angle = 0.0848        avg_twist_angle = []849        850        #taking minimum of 4 consecutive  angles' sum851        cons_twist_angle = []852       853        854        for j in range (0, len(A_opposite)):855            a = numpy.array(A[j])  856            857            #hydrogen bond858            a_opposite = numpy.array(A_opposite[j])859            860            alpha_a = numpy.array(alpha_A[j])  #this is needed for calculating center of vector in 3D space861            862            #hydrogen bond863            alpha_a_opposite = numpy.array(alpha_A_opposite[j])864           865               866            #minimum_dist_point, aa_min_index2 = find_nearest_distance(a, B, pair_aa1[j], pair_aa2)867            #print ("k ", k)868            if k == 0  : # determining first pair869              870                minimum_dist_point, aa_min_index2 = find_nearest_distance(alpha_a, alpha_B, pair_aa1[j], pair_aa2)#nearest neighbour checking it will work for determining first pair871                #minimum_dist_point, aa_min_index2 = find_nearest_distance(a, B, pair_aa1[j], pair_aa2)872               #hydrogen bond873                minimum_dist_point_opposite, aa_min_index2_opposite = find_nearest_distance(alpha_a_opposite, alpha_B_opposite, pair_aa1_opposite[j], pair_aa2_opposite)#nearest neighbour checking it will work for determining first pair874                #minimum_dist_point_opposite, aa_min_index2_opposite = find_nearest_distance(a_opposite, B_opposite, pair_aa1_opposite[j], pair_aa2_opposite)875               876               # sys.stdout = original877                print(" MIN_INDEX_Forward", aa_min_index2)   878                print(" MIN_INDEX_Backword", aa_min_index2_opposite)    879                #print(" MIN_POINT ", minimum_dist_point)880                #print(" MIN_B ", B[aa_min_index2])881                882                '''883                twist_angle_return = calculate_twist_angle(a,B[aa_min_index2],j,aa_min_index2)884                sum_twist_angle = sum_twist_angle + twist_angle_return885                twist_count = twist_count + 1             886                pick_index = aa_min_index2887                '''888                889                if aa_min_index2 == 0 and len(A) <= aa_min_index2_opposite: #hydrogen bond parallel and anti-parallel case equal length strand or small strand is inside of big strand (complete overlap)890                    add_1 = 1891                    892                    twist_angle_return = calculate_twist_angle(a,B[aa_min_index2],j,aa_min_index2)893                    cons_twist_angle.append(twist_angle_return)   894                    sum_twist_angle = sum_twist_angle + twist_angle_return895                    twist_count = twist_count + 1             896                    pick_index = aa_min_index2897                    898                if aa_min_index2 == 0  and len(A) > aa_min_index2_opposite: #hydrogen bond parallel and anti-parallel case   small strand is outside (partial overlap) of big strand899                    add_hp = 1900                    901                    twist_angle_return = calculate_twist_angle(a_opposite,B_opposite[aa_min_index2_opposite],j,aa_min_index2)902                    cons_twist_angle.append(twist_angle_return)   903                    sum_twist_angle = sum_twist_angle + twist_angle_return904                    twist_count = twist_count + 1             905                    pick_index = aa_min_index2_opposite906                    907                if aa_min_index2 != 0:908                    add_n = 1909                    twist_angle_return = calculate_twist_angle(a,B[aa_min_index2],j,aa_min_index2)910                    cons_twist_angle.append(twist_angle_return)   911                    sum_twist_angle = sum_twist_angle + twist_angle_return912                    twist_count = twist_count + 1             913                    pick_index = aa_min_index2914                915            else: #next pairs916                if add_1 == 1 and k < len(B):917                    minimum_dist_point_dup = B[k]918                    pick_index = k919                    twist_angle_return = calculate_twist_angle(a,minimum_dist_point_dup,j,pick_index)920                    cons_twist_angle.append(twist_angle_return)   921                    cons_twist_angle.append(twist_angle_return)   922                    sum_twist_angle = sum_twist_angle + twist_angle_return923                    twist_count = twist_count + 1924                    925                if add_hp == 1 and  int(beta_sheet[i+1][11])!=-1  and  pick_index < len(B_opposite) - 1:		#parallel  small strand is outside (partial overlap) of big strand                         926                   # j = pick_index - 1927                    pick_index = pick_index + 1928                  929                    print "k ",k930                    print "pick_index",pick_index931                    minimum_dist_point_dup = B_opposite[pick_index]932                    #print "minimum_dist_point_dup ",minimum_dist_point_dup #ok933                   # print "a_opposite ",a_opposite934            935                    twist_angle_return = calculate_twist_angle(a_opposite,minimum_dist_point_dup,j,pick_index)936                    cons_twist_angle.append(twist_angle_return)   937                    sum_twist_angle = sum_twist_angle + twist_angle_return938                    twist_count = twist_count + 1939                    940                if add_hp == 1 and  int(beta_sheet[i+1][11])==-1  and  pick_index != 0: # anti-parallel  small strand is outside (partial overlap) of big strand                         941                   # j = pick_index - 1942                    pick_index = pick_index - 1 #may be need to change later 943                  944                    print "k ",k945                    print "pick_index",pick_index946                    minimum_dist_point_dup = B_opposite[pick_index]947                    #print "minimum_dist_point_dup ",minimum_dist_point_dup #ok948                   # print "a_opposite ",a_opposite949                    950                   951                    twist_angle_return = calculate_twist_angle(a_opposite,minimum_dist_point_dup,j,pick_index)952                    cons_twist_angle.append(twist_angle_return)   953                    sum_twist_angle = sum_twist_angle + twist_angle_return954                    twist_count = twist_count + 1955                956                957                if add_n == 1 and  int(beta_sheet[i+1][11])!=-1 and k < len(B) - aa_min_index2: # Parallel beta strands 	958                    pick_index = pick_index + 1959                    minimum_dist_point_dup = B[pick_index]960                    twist_angle_return = calculate_twist_angle(a,minimum_dist_point_dup,j,pick_index)961                    cons_twist_angle.append(twist_angle_return)   962                    sum_twist_angle = sum_twist_angle + twist_angle_return963                    twist_count = twist_count + 1964                    965                if add_n == 1 and   int(beta_sheet[i+1][11])==-1  and pick_index!=0: # anti-Parallel beta strands 		966                    pick_index = pick_index - 1           967                    minimum_dist_point_dup = B[pick_index]968                    twist_angle_return = calculate_twist_angle(a,minimum_dist_point_dup,j,pick_index)969                    cons_twist_angle.append(twist_angle_return)   970                    sum_twist_angle = sum_twist_angle + twist_angle_return971                    twist_count = twist_count + 1972            973                                                                   974            k = k + 1975                 976        if  twist_count != 0:  977            avg_twist_angle.append (float(sum_twist_angle) / float(twist_count))  978           979            cons_sum_array = []980            if len(cons_twist_angle) > 4:981                for c in range (0,len(cons_twist_angle) - 3):982                    cons_sum = 0.0983                    for cc in range (c,c+4):       984                         cons_sum = cons_twist_angle[cc] + cons_sum985                    cons_sum_array.append(cons_sum)986                pair_array.append((round(min(cons_sum_array)  / 4.0,3)))987                len_array.append(len(cons_sum_array))988                #print "sum of consecutive 4 angles ", cons_sum_array989                #print "min of consecutive 4 angles ",min(cons_sum_array)990                out_char = "min of sum of consecutive 4 angles :: " + str(round(min(cons_sum_array),3)) + '\n'991                outf.write(out_char)992                out_char = "Twist per angle :: " + str(round(min(cons_sum_array)  / 4.0 ,3)) + '\n'993                outf.write(out_char)994            995            elif len(cons_twist_angle) == 4:996                for c in range (0,len(cons_twist_angle) - 2):997                    cons_sum = 0.0998                    for cc in range (c,c+3):       999                         cons_sum = cons_twist_angle[cc] + cons_sum1000                    cons_sum_array.append(cons_sum)1001                pair_array.append((round(min(cons_sum_array)  / 3.0,3)))1002                len_array.append(len(cons_sum_array))1003                #print "sum of consecutive 4 angles ", cons_sum_array1004                #print "min of consecutive 4 angles ",min(cons_sum_array)1005                out_char = "min of sum of consecutive 3 angles :: " + str(round(min(cons_sum_array),3)) + '\n'1006                outf.write(out_char)  1007                out_char = "Twist per angle :: " + str(round(min(cons_sum_array) / 3.0 ,3) ) + '\n'1008                outf.write(out_char)1009                1010            elif len(cons_twist_angle) == 2 or len(cons_twist_angle) == 3 or len(cons_twist_angle) == 1:1011               #print "smallest twist ",min(cons_twist_angle)1012                pair_array.append((round(min(cons_twist_angle) , 3 )))1013                len_array.append(len(cons_sum_array))1014                out_char = "smallest angles :: " + str(round(min(cons_twist_angle),3)) + '\n'1015                outf.write(out_char)1016            avg_track = 11017        else:1018            avg_track = 01019        1020        for t in range (len(avg_twist_angle)):   1021            #print ("avg_twist_angle between strands ", round(avg_twist_angle[t],3)) #necessary1022            #print ( round(avg_twist_angle[t],3)) #necessary1023            out_char = "avg_twist_angle between strands  " + str( round(avg_twist_angle[t],3) ) + '\n'1024            outf.write(out_char)1025            all_avg_twist_angle.append(avg_twist_angle[t])            1026     1027        #print ("...........................")#necessary1028        #print cons_twist_angle#ok1029      1030        outf.write("................................................"+"\n")1031   1032    i = i +11033#print ("avg_twist_angle between strands ", all_avg_twist_angle) #ok     103410351036'''for calculation of avg twist angle in a beta sheet'''1037outf.write("\n\n")10381039twist_angle_beta_sheet = []1040avg_avg_twist_angle_beta_sheet = []1041jc = 0   1042for i in range (len(counter_index)):  1043    sum_avg_twist_angle = 0.0  1044    j = jc1045    #print jc, " ", counter_index[i]-1, " ",j #ok1046    while j < (jc + counter_index[i]-1):1047        #print "j ",j1048        sum_avg_twist_angle = sum_avg_twist_angle + all_avg_twist_angle[j]  1049        sum_avg_twist_angle = round(sum_avg_twist_angle,3)       1050        j = j + 1    1051    jc = jc + counter_index[i]-11052    #avg_avg_twist_angle_beta_sheet.append(sum_avg_twist_angle)1053    twist_angle_beta_sheet.append(float(sum_avg_twist_angle)/float(counter_index[i]-1))1054    #print ("avg_twist angle in all beta sheets ", round(twist_angle_beta_sheet[i],3)) #necessary1055  1056    #print ( round(twist_angle_beta_sheet[i],3)) 1057    out_char = "avg_twist angle in all beta sheets " + str( round(twist_angle_beta_sheet[i],3)) + '\n'1058    outf.write(out_char)1059   1060#print ("avg_twist angle in all beta sheets ", float(avg_avg_twist_angle_beta_sheet[0])/float(counter_index[0]-1))1061#print pair_array #ok10621063outf.write("................................................"+"\n")10641065#print pair_array # ok1066#print len_array #ok1067'''1068#### According to minimum value pair #############10691070kc = 01071for i in range (len(counter_index)):  1072    j = kc1073    min_arr = []1074    while j < (kc + counter_index[i]-1):1075        min_arr.append (pair_array[j])1076        1077        j = j + 1  1078    kc = kc + counter_index[i]-11079    arr = numpy.array (min_arr) 1080    ind1 , ind2 = arr.argsort()[:2] 1081    min_val1 =   arr[ind1]1082    min_val2 =   arr[ind2]1083    #print min_val1, min_val21084    out_char = "Min pair val1, val2 :: " + str(min_val1) + ",  "+ str(min_val2)+'\n'1085    outf.write(out_char)1086    1087    min_avg_twist = float(min_val1 + min_val2)/2.01088    #print min_avg_twist1089    out_char = "Min Twist :: " + str(min_avg_twist) + '\n'1090    outf.write(out_char)10911092outf.write("................................................"+"\n")10931094#### According to longest pair #############1095kl = 01096for il in range (len(counter_index)):  1097    jl = kl1098    min_arr_l = []1099    while jl < (kl + counter_index[il]-1):1100        min_arr_l.append (len_array[jl])1101        1102        jl = jl + 1  1103    kl = kl + counter_index[il]-11104    arr_len = numpy.array (len_array) 1105    ind1 , ind2 = arr_len.argsort()[::-1][:2]1106    max_val1 =   pair_array[ind1]1107    max_val2 =   pair_array[ind2]1108   # print ind1, ind2 #ok1109    out_char = "longest pair val1, val2 :: " + str(max_val1) + ",  "+ str(max_val2)+'\n'1110    outf.write(out_char)1111    1112    min_avg_twist_long_pair = float(max_val1 + max_val2)/2.01113    #print min_avg_twist_long_pair1114    out_char = "Avg MinTwist according to longest pair :: " + str(min_avg_twist_long_pair) + '\n'1115    outf.write(out_char)11161117'''111811191120#print (beta_sheet)1121#print (beta_sheet[0][6])1122#print (beta_sheet[0][9])1123#print (atom[0])1124#print (atom[0][5])1125#print (a)1126#f.close()1127
...

twist_region_unitlength_spline.py

Source:twist_region_unitlength_spline.py

1# -*- coding: utf-8 -*-2"""3Created on Fri Oct 14 23:01:08 201645@author: tunaz6"""789import sys1011import re12import numpy13import math1415from scipy import interpolate1617from mpl_toolkits.mplot3d import Axes3D18import matplotlib.pyplot as plt192021class Tee(object):22    def __init__(self, *files):23        self.files = files24    def write(self, obj):25        for f in self.files:26            f.write(obj)27            f.flush() # If you want the output to be visible immediately28    def flush(self) :29        for f in self.files:30            f.flush()31            32            33if len(sys.argv) == 1 or len(sys.argv) == 2 or len(sys.argv) > 3  :34    print "Usage: python twist_region.py pdbfilename.pdb direction"35    sys.exit(0)363738lines_File = [lines1.rstrip('\n') for lines1 in open(sys.argv[1], 'r')]   394041try:42    direction = int(sys.argv[2]) # give direction as input43    '''44    direction= 0 means forward direction, 45    direction = 1 means backword direction 46    '''47    if direction != 0 and direction != 1 :48        print "please input either 0 or 1. 0 = forward, 1 = backword"49        sys.exit(0)50except ValueError:  51        print "please input either 0 or 1. 0 = forward, 1 = backword"52        sys.exit(0)          5354#sys.stdout = open("output_all.pdb", "w")55out_filename = 'twist_angles.txt'56outf = open(out_filename, 'w')5758sys.stdout = open('output_pdb.pdb','w')59#outf2 = open(out_filename2, 'w')60#lines_File = [lines1.rstrip('\n') for lines1 in open('1aky.pdb')]    61#lines_File = [lines1.rstrip('\n') for lines1 in open('1aop.pdb')]  62#lines_File = [lines1.rstrip('\n') for lines1 in open('2p8y.pdb')] #index problem63#lines_File = [lines1.rstrip('\n') for lines1 in open('1s04.pdb')] #complex structure (multple same chain duplicate index)64#lines_File = [lines1.rstrip('\n') for lines1 in open('1atz.pdb')] 65#lines_File = [lines1.rstrip('\n') for lines1 in open('2qtr.pdb')] 66#lines_File = [lines1.rstrip('\n') for lines1 in open('1d5t.pdb')] 67#lines_File = [lines1.rstrip('\n') for lines1 in open('1elu.pdb')]68#lines_File = [lines1.rstrip('\n') for lines1 in open('1a12.pdb')]69#lines_File = [lines1.rstrip('\n') for lines1 in open('1b3a.pdb')]7071#direction = 0 # direction= 0 means forward direction, direction = 1 means backword direction so change here        72            73def draw_interpolation(input_array):74    #print "input  ", input_array75    #print "length  ", len(input_array)76    if  len(input_array) > 2 :77        data = numpy.array(input_array)78        data = data.astype(float)79        80       # print data #ok81           82        data = data[0:100].transpose()83        #print "hi", data #ok84        #now we get all the knots and info about the interpolated spline85		#spacing = int(len(input_array)/.3)86        tck, u= interpolate.splprep(data,k=2)   87        #new = interpolate.splev(numpy.linspace(0,1,50), tck)88        #new = interpolate.splev(numpy.linspace(0,1,int(len(input_array)/.8)), tck) #unit length given 0.189        #new = interpolate.splev(numpy.linspace(0,1,int(len(input_array)/.5)), tck) #we used it for ACM_BCB90        new = interpolate.splev(numpy.linspace(0, 1, int(len(input_array) /.4)), tck) #vector length 1.19192        #now lets plot it!93        94        #fig = plt.figure()95        #ax = Axes3D(fig)96        #ax.plot(data[0], data[1], data[2], label='originalpoints', lw =2, c='Dodgerblue')97        #ax.plot(new[0], new[1], new[2], label='fit', lw =2, c='red')98        #ax.legend()99        #plt.savefig('junk.png')100        #plt.show() 101        return new[0], new[1], new[2]             102103104#print (lines_File1)105106direction_opposite = 1 #hydrogen bond 107108count_beta_sheet = 0109count_beta_strand = 0110counter = 0111counter_index = []112problem = 0113a=[]114beta_sheet = []115atom = []116splitted_line = []117count_atom = 0118for sheet_line in lines_File: #find each line in all lines119     if sheet_line.startswith('SHEET'):     #find those lines start with "SHEET"120         #count_atom = count_atom+1121         #print (sheet_line)       #print the lines started with "SHEET"        122         #beta_sheet.append ( re.sub("\s\s+" , " ",sheet_line).split()) #ok for all except 1123         beta_sheet.append([sheet_line[0:6], sheet_line[7:10], sheet_line[11:14], sheet_line[14:16],sheet_line[17:20], sheet_line[21], sheet_line[22:27], sheet_line[28:31], sheet_line[32], sheet_line[33:37], sheet_line[37], sheet_line[38:40],sheet_line[41:45],sheet_line[45:48], sheet_line[49], sheet_line[50:55], sheet_line[56:60], sheet_line[60:63], sheet_line[64], sheet_line[65:69], sheet_line[69]])124     if sheet_line.startswith('ATOM'):  #find those lines start with "ATOM"125         count_atom = count_atom+1126         #print (sheet_line)       #print the lines started with "ATOM"127         atom.append( [sheet_line[:6], sheet_line[6:11], sheet_line[12:16], sheet_line[17:20], sheet_line[21], sheet_line[22:26], sheet_line[30:38], sheet_line[38:46], sheet_line[46:54]])128         #atom.append( [sheet_line[0:6], sheet_line[6:11], sheet_line[12:16], sheet_line[16:17],sheet_line[17:20], sheet_line[21:22], sheet_line[22:26], sheet_line[26:27], sheet_line[30:38], sheet_line[38:46], sheet_line[46:54], sheet_line[46:54], sheet_line[54:60], sheet_line[60:66], sheet_line[76:78], sheet_line[78:80]])129         #atom.append ( re.sub("\s\s+" , " ",sheet_line).split())130#print (int(atom[1836][5].strip()))131#print (atom[1836])132133strand_vector=[]134center_vector = []135CA_vector_between_strand = []136amino_acid = []137138139#common hydrogen bond140strand_vector_opposite=[]141center_vector_opposite = []142CA_vector_between_strand_opposite = []143amino_acid_opposite = []144145146poi = 0147track = 1148149poi_opposite = 0 #hydrogen bond150151152for sheet_index in range (0,len(beta_sheet)): # handle if there is less than 3 atoms in a strand153    if int(beta_sheet[sheet_index][1]) == int(beta_sheet[sheet_index][3]):154        counter = counter + 1155156#print ("number of beta sheet ",counter) #ok157out_char = "number of beta sheet " + str(counter) + '\n\n'158outf.write(out_char)            159for sheet_index in range (0,len(beta_sheet)): # handle if there is less than 3 atoms in a strand160    if abs((int(beta_sheet[sheet_index][9]))  - int(beta_sheet[sheet_index][6])) >= 2 :161        if int(beta_sheet[sheet_index][1]) == int(beta_sheet[sheet_index][3]):162            #counter = counter + 1163            if track == 0 :164                counter_index.append(int(beta_sheet[sheet_index][1]) - problem)165                track = 1166            else:   167                counter_index.append(int(beta_sheet[sheet_index][1]))168                track = 1169    else:170        #print "hi " #ok171        if  (int(beta_sheet[sheet_index][3]) > 2):           172             problem = problem + 1173             #print problem  #ok174             track = 0175            176            177#for i in range (0,len(counter_index)):178    #print ("counter_index ",counter_index[i]) #ok  179     180for sheet_index in range (0,len(beta_sheet)): # 5 should be number of beta stand in one beta sheet181    #print("love ",beta_sheet[sheet_index][10])182   183    atom_start_index=(int(beta_sheet[sheet_index][6]))184    #print("start index ",atom_start_index) #ok185    atom_end_index=(int(beta_sheet[sheet_index][9])) 186    #print("end index ",atom_end_index) #ok187    sheet_chain = beta_sheet[sheet_index][5]188    #print sheet_chain189190    mid_point = []191    array_strand_index =[]192    amino_acid_array = []193    aa_index = []194    #array_strand_index = [[0 for i in range(2)] for i in range(2)] #2 should be change according to length of one beta sheet195    array_x = []196    array_y = []197    array_z = []198    CA_x = []199    CA_y = []200    CA_z = []201    202    #print (count_atom)203    204    for i in range (0,count_atom) : 205        206        if (atom_start_index <= int(atom[i][5].strip()) <=  atom_end_index)  :207            208            if  atom[i][2].strip() == 'N' or atom[i][2].strip() == 'C': 209                #print "duplicate ", int(atom[i][5].strip())210                211                if sheet_chain == atom[i][4].strip(): #this is needed to differentiate same startindex & endindex but different chains212                    array_strand_index.append(atom[i][5].strip())                  213                    array_x.append(atom[i][6].strip())214                    array_y.append(atom[i][7].strip())215                    array_z.append(atom[i][8].strip())216                    length=len(array_strand_index)  217            if atom[i][2].strip() == 'CA':218                if sheet_chain == atom[i][4].strip():219                    aa_index.append( i )             220                    amino_acid_array.append(atom[i][3].strip())        221                    CA_x.append(atom[i][6].strip())222                    CA_y.append(atom[i][7].strip())223                    CA_z.append(atom[i][8].strip())224                    length_CA = len (CA_x)225    #print ("strand index  ",array_strand_index) #ok226   # print (aa_index)227    #print ("Amino acid  ",amino_acid_array)  #ok        228   229   230   231    232    if direction == 0: #forward direction #ok233        midpoint_x_bef = []234        midpoint_y_bef = []235        midpoint_z_bef = []  236        237      238        239        midpoint_x = []240        midpoint_y = []241        midpoint_z = []242        243        new_x = []244        new_y = []245        new_z = []  246        247       248        #coef = [1,1,1,1,1,1,1,1]249        #coef = []250        251        c_index = 1252        n_index = 2253        while c_index < length-1 and n_index <  length-1 :  #mid point calculation254            #print ("c_index ",c_index, "n_index ", n_index)255            midpoint_x_bef.append((float(array_x[c_index]) + float(array_x[n_index]))/float(2.0))    #making midpoint       256            midpoint_y_bef.append((float(array_y[c_index]) + float(array_y[n_index]))/float(2.0))   #making midpoint 257            midpoint_z_bef.append((float(array_z[c_index]) + float(array_z[n_index]))/float(2.0))  #making midpoint 258           259            c_index = c_index + 2260            n_index = n_index +2  261        262        #print ("midpoint_x_bef  ", midpoint_x_bef ) 263        #print ("midpoint_y_bef  ", midpoint_y_bef  )264        #print ("midpoint_z_bef  ", midpoint_z_bef  )265            266        midpoint_draw = []267        draw_index = 0268        while draw_index < len (midpoint_x_bef) :269            midpoint_point = []270            mid_x = midpoint_x_bef [draw_index]271            mid_y = midpoint_y_bef [draw_index]272            mid_z = midpoint_z_bef [draw_index]           273            midpoint_point.append (mid_x)274            midpoint_point.append (mid_y)275            midpoint_point.append (mid_z)276            midpoint_draw.append (midpoint_point) 277            draw_index = draw_index + 1278        #print   (midpoint_draw)  #ok279        pdb_format = '6s5s1s4s1s3s1s1s4s1s3s8s8s6s10s2s3s'280        #shape = 'ATOM 1 N LEU A 81 25.865 39.612 19.376 1.00 53.28 N '281        shape = ['ATOM', '1','N', 'LEU', 'A', '81', '25.865', '39.612', '19.376']282        if len(midpoint_draw) <= 2:283             midpoint_x=midpoint_x_bef284             midpoint_y=midpoint_y_bef285             midpoint_z=midpoint_z_bef286             287             for i in range (len( midpoint_x)):288                poi = poi +1289                                           290                #print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s\n"%tuple(shape) ok291                print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi,'S','LEU', 'A', '81',round(midpoint_x[i],3),round(midpoint_y[i],3),round(midpoint_z[i],3)]) #print new atom position in PDB file292                293             294        else:    295            value = draw_interpolation (midpoint_draw)   #making 3D cubic spline interpolation for midpoints296            #print value[0] #ok297            midpoint_x=value[0]  #new midpoint after cubic spline298            midpoint_y=value[1]  #new midpoint after cubic spline299            midpoint_z=value[2]   #new midpoint after cubic spline300        301            302           303            pdb_length = len( midpoint_x)304          305            for i in range (pdb_length):306                poi = poi +1          307                print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi,'S','LEU', 'A', '81',round(midpoint_x[i],3),round(midpoint_y[i],3),round(midpoint_z[i],3)]) #print new atom position in PDB file308                309       310       311        312        313       314        #print ("midpoint_x ", midpoint_x ) 315         316        317     318     319        length_midpoint_array = len(midpoint_x)320        vector_array =[]321        cen_array = []322        midpoint_index = 1323        while midpoint_index < length_midpoint_array:324            point = []325            cen_point = []326            temp_mid_index = midpoint_index - 1327            vec_x = midpoint_x [temp_mid_index] -  midpoint_x [temp_mid_index+1]  #making midpoint vector328            vec_y = midpoint_y [temp_mid_index] -  midpoint_y [temp_mid_index+1]  #making midpoint vector329            vec_z = midpoint_z [temp_mid_index] -  midpoint_z [temp_mid_index+1]  #making midpoint vector330            331            cen_x = (float(midpoint_x [temp_mid_index]) + float( midpoint_x [temp_mid_index+1])) / float(2.0)  #making center of midpoint vector332            cen_y =(float( midpoint_y [temp_mid_index]) + float(midpoint_y [temp_mid_index+1]))/float(2.0)   #making center of midpoint vector333            cen_z = (float(midpoint_z [temp_mid_index]) + float( midpoint_z [temp_mid_index+1]))/float(2.0)   #making center of midpoint vector334            335            #print ("vector x ",vec_x) 336           # print ("vector y ",vec_y) 337           # print ("vector z ",vec_z) 338            #make unit vector339            magnitude = math.sqrt(pow(vec_x, 2) + pow(vec_y, 2) + pow(vec_z, 2))340            341           342            print("vector length ",magnitude)343            344            point.append(vec_x/magnitude) # unit vector345            point.append(vec_y/magnitude)  # unit vector346            point.append(vec_z/magnitude)  # unit vector347            348      349            #point.append(vec_x) #ok350            #point.append(vec_y)351            #point.append(vec_z)352      353         354            cen_point.append(cen_x) #ok355            cen_point.append(cen_y)356            cen_point.append(cen_z)357            358            359            360            361            vector_array.append(point)362            363            cen_array.append(cen_point)364            365            midpoint_index = midpoint_index +1366        #print "vector array ",vector_array367        368        369        aa = []370        aa_index = 1371        while aa_index < len(amino_acid_array) - 1:   # to get amino acid value372             aa.append(amino_acid_array[aa_index]) 373             aa_index = aa_index +1374        amino_acid.append(aa)375        376        #print ("x cordinate of CA in each strand" CA_x )377    378        #print("length ", length)379        #print ("CA length ",length_CA)380        CA_x_new = []381        CA_y_new = []382        CA_z_new = []383        CA_vector = []384        CA_index = 1385        while CA_index < length_CA - 1:386            CA_point = []387            CA_x_new=(float(CA_x[CA_index]))388            CA_y_new=(float(CA_y[CA_index]))389            CA_z_new=(float(CA_z[CA_index]))390            CA_point.append (CA_x_new)391            CA_point.append (CA_y_new)392            CA_point.append (CA_z_new)393            CA_vector.append (CA_point)   394            CA_index = CA_index + 1395        #draw_interpolation (CA_vector) #draw spline according to carbon alpha 396397        CA_vector_between_strand.append(CA_vector)398        #draw_interpolation (CA_vector_between_strand)399400         401    if direction_opposite == 1:   #backword direction402    403        midpoint_x_bef_opposite = []404        midpoint_y_bef_opposite = []405        midpoint_z_bef_opposite = []  406407        midpoint_x_opposite = []408        midpoint_y_opposite = []409        midpoint_z_opposite = [] 410        411       412        413        c_index_opposite = length-3414        n_index_opposite = length-2415        while c_index_opposite > 0  and n_index_opposite > 0 : 416            #print ("c_index ",c_index, "n_index ", n_index)417            midpoint_x_bef_opposite.append((float(array_x[c_index_opposite]) + float(array_x[n_index_opposite]))/float(2.0))418            midpoint_y_bef_opposite.append((float(array_y[c_index_opposite]) + float(array_y[n_index_opposite]))/float(2.0))419            midpoint_z_bef_opposite.append((float(array_z[c_index_opposite]) + float(array_z[n_index_opposite]))/float(2.0)) 420            c_index_opposite = c_index_opposite - 2421            n_index_opposite = n_index_opposite - 2   422       423       424       425        midpoint_draw_opposite = []426        draw_index_opposite = len (midpoint_x_bef_opposite) -1427        while draw_index_opposite >= 0 :428            midpoint_point_opposite = []429            mid_x_opposite = midpoint_x_bef_opposite [draw_index_opposite]430            mid_y_opposite = midpoint_y_bef_opposite [draw_index_opposite]431            mid_z_opposite = midpoint_z_bef_opposite [draw_index_opposite]           432            midpoint_point_opposite.append (mid_x_opposite)433            midpoint_point_opposite.append (mid_y_opposite)434            midpoint_point_opposite.append (mid_z_opposite)435            midpoint_draw_opposite.append (midpoint_point_opposite) 436            draw_index_opposite = draw_index_opposite - 1437            438        #draw_interpolation (midpoint_draw)439       440        if len(midpoint_draw_opposite) <= 2:441             midpoint_x_opposite = midpoint_x_bef_opposite 442             midpoint_y_opposite = midpoint_y_bef_opposite443             midpoint_z_opposite = midpoint_z_bef_opposite444             445             for i in range (len( midpoint_x_opposite)):446                poi_opposite = poi_opposite +1447                                           448                #print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s\n"%tuple(shape) ok449               # print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi_opposite,'S','LEU', 'A', '81',round(midpoint_x_opposite[i],3),round(midpoint_y_opposite[i],3),round(midpoint_z_opposite[i],3)]) #print new atom position in PDB file450                451             452        else:    453            value_opposite = draw_interpolation (midpoint_draw_opposite)   #making 3D cubic spline interpolation for midpoints454            #print value_opposite[0] #ok455            midpoint_x_opposite = value_opposite[0]  #new midpoint after cubic spline456            midpoint_y_opposite = value_opposite[1]  #new midpoint after cubic spline457            midpoint_z_opposite = value_opposite[2]   #new midpoint after cubic spline458        459            460           461            pdb_length_opposite = len( midpoint_x_opposite)462          463            for i in range (pdb_length_opposite):464                poi_opposite = poi_opposite +1          465                #print "%-6s%5s %4s %3s %s%4s    %8s%8s%8s"%tuple(['ATOM',poi_opposite,'S','LEU', 'A', '81',round(midpoint_x_opposite[i],3),round(midpoint_y_opposite[i],3),round(midpoint_z_opposite[i],3)]) #print new atom position in PDB file466                467       468       469        midpoint_x_opposite = midpoint_x_bef_opposite470        midpoint_y_opposite = midpoint_y_bef_opposite471        midpoint_z_opposite = midpoint_z_bef_opposite472        473    474        #print ("midpoint_x ", midpoint_x )      475        length_midpoint_array_opposite = len (midpoint_x_opposite)   476        vector_array_opposite =[]477        cen_array_opposite = []478        479        #midpoint_index_opposite = length_midpoint_array480        #while midpoint_index > 1:481        482        midpoint_index_opposite = 1 #big change in this loop483        while midpoint_index_opposite < length_midpoint_array_opposite:484            point_opposite = []485            cen_point_opposite = []486            487            temp_mid_index_opposite = midpoint_index_opposite - 1488            #vec_x = midpoint_x [temp_mid_index] -  midpoint_x [temp_mid_index-1]489            #vec_y = midpoint_y [temp_mid_index] -  midpoint_y [temp_mid_index-1]490            #vec_z = midpoint_z [temp_mid_index] -  midpoint_z [temp_mid_index-1]491            492            vec_x_opposite = midpoint_x_opposite [temp_mid_index_opposite] -  midpoint_x_opposite [temp_mid_index_opposite+1]493            vec_y_opposite = midpoint_y_opposite [temp_mid_index_opposite] -  midpoint_y_opposite [temp_mid_index_opposite+1]494            vec_z_opposite = midpoint_z_opposite [temp_mid_index_opposite] -  midpoint_z_opposite [temp_mid_index_opposite+1]495            496            #print ("vector ",vec_x,vec_y,vec_z) 497            498            #cen_x = (float(midpoint_x [temp_mid_index]) + float( midpoint_x [temp_mid_index-1])) / float(2.0)  #making center of midpoint vector499            #cen_y =(float( midpoint_y [temp_mid_index]) + float(midpoint_y [temp_mid_index-1]))/float(2.0)   #making center of midpoint vector500            #cen_z = (float(midpoint_z [temp_mid_index]) + float( midpoint_z [temp_mid_index-1]))/float(2.0)   #making center of midpoint vector501            502            cen_x_opposite = (float(midpoint_x_opposite [temp_mid_index_opposite]) + float( midpoint_x_opposite [temp_mid_index_opposite+1])) / float(2.0)  #making center of midpoint vector503            cen_y_opposite =(float( midpoint_y_opposite [temp_mid_index_opposite]) + float(midpoint_y_opposite [temp_mid_index_opposite+1]))/float(2.0)   #making center of midpoint vector504            cen_z_opposite = (float(midpoint_z_opposite [temp_mid_index_opposite]) + float( midpoint_z_opposite [temp_mid_index_opposite+1]))/float(2.0)   #making center of midpoint vector505            506              #make unit vector507            magnitude_opposite = math.sqrt(pow(vec_x_opposite, 2) + pow(vec_y_opposite, 2) + pow(vec_z_opposite, 2))508            #print("vector length opposite ",magnitude_opposite)509            #point.append(vec_x/magnitude) #not ok510            #point.append(vec_y/magnitude)511            #point.append(vec_z/magnitude)512            513            '''514            point_opposite.append(vec_x_opposite) #ok515            point_opposite.append(vec_y_opposite)516            point_opposite.append(vec_z_opposite)517            '''518            point_opposite.append(vec_x_opposite/magnitude_opposite) #ok519            point_opposite.append(vec_y_opposite/magnitude_opposite)520            point_opposite.append(vec_z_opposite/magnitude_opposite)521            522            523            524            cen_point_opposite.append(cen_x_opposite) #ok525            cen_point_opposite.append(cen_y_opposite)526            cen_point_opposite.append(cen_z_opposite)527     528            vector_array_opposite.append(point_opposite)529            530            cen_array_opposite.append(cen_point_opposite)531            532            midpoint_index_opposite = midpoint_index_opposite + 1533            534            #midpoint_index = midpoint_index - 1 535        536        aa_opposite = []537        aa_index_opposite = len(amino_acid_array) - 2538        while aa_index_opposite > 0:   # to get amino acid value539             aa_opposite.append(amino_acid_array[aa_index_opposite]) 540             aa_index_opposite = aa_index_opposite - 1 541        amino_acid_opposite.append(aa_opposite)542   543   544        #print ("x cordinate of CA in each strand", CA_x )545    546        #print("length ", length)547        #print ("CA length ",length_CA)548        CA_x_new_opposite = []549        CA_y_new_opposite = []550        CA_z_new_opposite = []551        CA_vector_opposite = []552        CA_index_opposite = length_CA - 2553        while CA_index_opposite > 0 :554            CA_point_opposite = []555            CA_x_new_opposite=(float(CA_x[CA_index_opposite]))556            CA_y_new_opposite=(float(CA_y[CA_index_opposite]))557            CA_z_new_opposite=(float(CA_z[CA_index_opposite]))558            CA_point_opposite.append (CA_x_new_opposite)559            CA_point_opposite.append (CA_y_new_opposite)560            CA_point_opposite.append (CA_z_new_opposite)561            CA_vector_opposite.append (CA_point_opposite)   562            CA_index_opposite = CA_index_opposite - 1563        CA_vector_between_strand_opposite.append(CA_vector_opposite)564        565        566    strand_vector.append(vector_array)  567    568    center_vector.append(cen_array)569    570    #for hydrogen bond calculation571    strand_vector_opposite.append(vector_array_opposite)  572    573    center_vector_opposite.append(cen_array_opposite)574    575   #print(beta_sheet[sheet_index][1])  576    577    578579 580   581    582    '''583    print ("vector ",vector_array)584    print (atom_start_index)585    print (array_strand_index) 586    print(length)587    588    print (array_x) 589    print (array_y) 590    print (array_z) 591    print (midpoint_x)592    print (midpoint_y)593    print (midpoint_z)594    print (length_midpoint_array)595    '''596print "\n"597length_strand_vector = len(strand_vector)598#print (strand_vector)599#print(amino_acid) # ok600#print ("vector strand length ",length_strand_vector)601#print ("CA_vector_between_strand ",len(CA_vector_between_strand)) # ok.  vector_strand length and CA_vector same602#print ("CA_vector_between_strand ",CA_vector_between_strand) 603#draw_interpolation (CA_vector_between_strand)604605def distance(x,y):   606    return numpy.sqrt(numpy.sum((x-y)**2))607608609def find_nearest_distance(a,B, pair_aa1, pair_aa2):610    611    612    #print ("a ", a)613    min_point = B[0]614    #min_dist = abs(numpy.linalg.norm(a- numpy.array(B[0])))615    min_dist = math.sqrt ( pow((a[0]-B[0][0]),2) + pow((a[1]-B[0][1]),2) + pow((a[2]-B[0][2]),2)  )616    #min_dist = 12000617   # print ("mindistance ", min_dist)618    #print("len of B",len(B)) #ok619    aa_min_index = 0620    for i in range (0, len(B)): 621        #dist = []622                       623        b = numpy.array(B[i])        624        #print ("b ", b) #ok625        #dist=(numpy.linalg.norm(a-b))626        try_dist = math.sqrt ( pow((a[0]-b[0]),2) + pow((a[1]-b[1]),2) + pow((a[2]-b[2]),2)  )627        #print ("distance ", try_dist)628        #dist=abs(distance(a,b))629        if try_dist < min_dist:630            min_dist = try_dist631            min_point = b632            aa_min_index = i633 634    635    return (min_point, aa_min_index)636637638def calculate_twist_angle(a,minimum_dist_point,j,aa_min_index2):639        640    #print ("mindist point ", minimum_dist_point)641    dot_product = numpy.dot(a,minimum_dist_point) # A.B642    #print (dot_product)643       644    a_sum = pow(a[0],2)+pow(a[1],2)+pow(a[2],2)645    a_root=math.sqrt(a_sum)646    b_sum = pow(minimum_dist_point[0],2)+pow(minimum_dist_point[1],2)+pow(minimum_dist_point[2],2)647    b_root=math.sqrt(b_sum)648    a_b = a_root*b_root649    650    angle_dot = math.acos(dot_product/a_b)651    #print (angle_dot)652    twist_angle = math.degrees(angle_dot)653    654    '''655    ### cross product ###656    cross_product = numpy.cross(a,minimum_dist_point) # A*B657    #print (cross_product)658    sum_square_cross_product = pow(cross_product[0],2) +  pow(cross_product[1],2)+ pow(cross_product[2],2)659    #print (sum_square_cross_product)660    root_sum_square_cross_product = math.sqrt(sum_square_cross_product)661    #print (root_sum_square_cross_product)662   663   664   665    angle_cross = math.asin(root_sum_square_cross_product/a_b)666    #print (angle_cross)667    print(math.degrees(angle_cross))668    ######## end of cross product ###########669    '''670    if twist_angle > 90.:671        twist_angle = 180.0 - twist_angle672   # sys.stdout = original673   # print(" Amino Acid",pair_aa1[j], " and ", pair_aa2[aa_min_index2],":", "Twist angle::" , twist_angle) #necessary674    #print("Twist angle::" , round(twist_angle,3)) #necessary675    out_char = "Twist angle:: " + str(round(twist_angle,3)) + '\n'676    outf.write(out_char)677    return twist_angle678       # print ( "amino acid ", pair_aa1[j], " ", pair_aa2[aa_min_index2])679minimum_dist_point = []  680minimum_dist_point_dup = []681flag = 0682all_avg_twist_angle = []  683avg_count = 0    684avg_track = 1685pair_array = []686len_array = []687i = 0688while i < length_strand_vector : # pairwise calculation 689    #print ("beta sheet index", beta_sheet[i][1])690    #print ("beta strand", beta_sheet[i])691    692    #print(int(beta_sheet[i][1]), " : ", int(beta_sheet[i][3]))693    #print ("i ", i)694    #print ("flag ",flag)695    avg_twist_count = []696            697    if(int(beta_sheet[i][1])>=int(beta_sheet[i][3])):698        flag = int(beta_sheet[i][1])699        avg_count = 0700       701        #print ("avg count ",avg_count)702    else:703        flag = flag + 1704        avg_count = avg_count + 1705        A_t = []706        B_t= []707        A = []708        B = []709        710        #for hydrogen bond711        A_t_opposite = []712        B_t_opposite  = []713        A_opposite  = []714        B_opposite  = []715        716        alpha_A_t = []717        alpha_B_t = []718        alpha_A = []719        alpha_B = []720        721          #for hydrogen bond722        alpha_A_t_opposite = []723        alpha_B_t_opposite = []724        alpha_A_opposite = []725        alpha_B_opposite = []726        727        pair_aa1_t = []728        pair_aa2_t = []729        pair_aa1 = []730        pair_aa2 = []731        732         733        #for hydrogen bond734        pair_aa1_t_opposite = []735        pair_aa2_t_opposite = []736        pair_aa1_opposite = []737        pair_aa2_opposite = []738        739        740        index_vec = i741        A_t = strand_vector[i] #copy strand to A array742        B_t = strand_vector[index_vec+1] #copy strand to B array 743        744        #for hydrogen bond745        A_t_opposite = strand_vector_opposite[i] #copy strand to A array746        B_t_opposite = strand_vector_opposite[index_vec+1] #copy strand to B array 747        748        749        #alpha_A_t = CA_vector_between_strand[i] #copy strand to A array750        #alpha_B_t = CA_vector_between_strand[index_vec+1] #copy strand to B array 751        752         #for hydrogen bond753        #alpha_A_t_opposite = CA_vector_between_strand_opposite[i] #copy strand to A array (alpha-carbon) backword direction754        #alpha_B_t_opposite = CA_vector_between_strand_opposite[index_vec+1] #copy strand to B array (alpha-carbon) backword direction755        756        757        alpha_A_t = center_vector[i] #copy strand to A array758        alpha_B_t = center_vector[index_vec+1] #copy strand to B array 759        760         #for hydrogen bond761        alpha_A_t_opposite = center_vector_opposite[i] #copy strand to A array (alpha-carbon) backword direction762        alpha_B_t_opposite = center_vector_opposite[index_vec+1] #copy strand to B array (alpha-carbon) backword direction763        764        765        pair_aa1_t = amino_acid[i] #copy strand to A array766        pair_aa2_t = amino_acid[index_vec+1] #copy strand to B array 767        768        #hydrogen bond769        pair_aa1_t_opposite = amino_acid_opposite[i] #copy strand to A array770        pair_aa2_t_opposite = amino_acid_opposite[index_vec+1] #copy strand to B array 771        772        773      #  print ("A_t ",A_t)774       775      #  print ("B_t ",B_t)776       # sys.stdout = original777        #print ("beta strand 1", beta_sheet[i]) #necessary778        #print ("beta strand 2", beta_sheet[i+1]) #necessary779        out_char = "beta strand 1" + str(beta_sheet[i]) + '\n'780        outf.write(out_char)781        out_char = "beta strand 2" + str(beta_sheet[i+1]) + '\n'782        outf.write(out_char)783        #print ("A_t ",len(A_t))784       785        #print ("B_t ",len(B_t))786        if len(A_t) > len(B_t):787            A = B_t788            B = A_t789            790            #hydrogen bond791            A_opposite = B_t_opposite792            B_opposite = A_t_opposite793            794            alpha_A = alpha_B_t795            alpha_B = alpha_A_t796            797             #hydrogen bond798            alpha_A_opposite = alpha_B_t_opposite799            alpha_B_opposite = alpha_A_t_opposite800            801            pair_aa1 = pair_aa2_t802            pair_aa2 = pair_aa1_t803            804            #hydrogen bond805            pair_aa1_opposite = pair_aa2_t_opposite806            pair_aa2_opposite = pair_aa1_t_opposite807        else:808            A = A_t809            B = B_t810            811             #hydrogen bond812            A_opposite = A_t_opposite813            B_opposite = B_t_opposite814            815            alpha_A = alpha_A_t816            alpha_B = alpha_B_t 817            818            #hydrogen bond819            alpha_A_opposite = alpha_A_t_opposite820            alpha_B_opposite = alpha_B_t_opposite821            822            pair_aa1 = pair_aa1_t823            pair_aa2 = pair_aa2_t824            825             #hydrogen bond826            pair_aa1_opposite = pair_aa1_t_opposite827            pair_aa2_opposite = pair_aa2_t_opposite828        829        #aa_min_index2 = 0830        k = 0831        twist_angle_return = 0.0832        add_1 = 0 833        add_n = 0834        add_hp = 0 #hydrogen bond835        pick_index = 0836        837        '''for calculation of avg twist angle between two beta strands'''838        twist_count = 0839        sum_twist_angle = 0.0840        avg_twist_angle = []841        842        #taking minimum of 4 consecutive  angles' sum843        cons_twist_angle = []844       845        846        for j in range (0, len(A_opposite)):847            a = numpy.array(A[j])  848            849            #hydrogen bond850            a_opposite = numpy.array(A_opposite[j])851            852            alpha_a = numpy.array(alpha_A[j])  #this is needed for calculating center of vector in 3D space853            854            #hydrogen bond855            alpha_a_opposite = numpy.array(alpha_A_opposite[j])856           857               858            #minimum_dist_point, aa_min_index2 = find_nearest_distance(a, B, pair_aa1[j], pair_aa2)859            #print ("k ", k)860            if k == 0  : # determining first pair861              862                minimum_dist_point, aa_min_index2 = find_nearest_distance(alpha_a, alpha_B, pair_aa1[j], pair_aa2)#nearest neighbour checking it will work for determining first pair863                #minimum_dist_point, aa_min_index2 = find_nearest_distance(a, B, pair_aa1[j], pair_aa2)864               #hydrogen bond865                minimum_dist_point_opposite, aa_min_index2_opposite = find_nearest_distance(alpha_a_opposite, alpha_B_opposite, pair_aa1_opposite[j], pair_aa2_opposite)#nearest neighbour checking it will work for determining first pair866                #minimum_dist_point_opposite, aa_min_index2_opposite = find_nearest_distance(a_opposite, B_opposite, pair_aa1_opposite[j], pair_aa2_opposite)867               868               # sys.stdout = original869                print(" MIN_INDEX_Forward", aa_min_index2)   870                print(" MIN_INDEX_Backword", aa_min_index2_opposite)    871                #print(" MIN_POINT ", minimum_dist_point)872                #print(" MIN_B ", B[aa_min_index2])873                874                '''875                twist_angle_return = calculate_twist_angle(a,B[aa_min_index2],j,aa_min_index2)876                sum_twist_angle = sum_twist_angle + twist_angle_return877                twist_count = twist_count + 1             878                pick_index = aa_min_index2879                '''880                881                if aa_min_index2 == 0 and len(A) <= aa_min_index2_opposite: #hydrogen bond parallel and anti-parallel case equal length strand or small strand is inside of big strand (complete overlap)882                    add_1 = 1883                    884                    twist_angle_return = calculate_twist_angle(a,B[aa_min_index2],j,aa_min_index2)885                    cons_twist_angle.append(twist_angle_return)   886                    sum_twist_angle = sum_twist_angle + twist_angle_return887                    twist_count = twist_count + 1             888                    pick_index = aa_min_index2889                    890                if aa_min_index2 == 0  and len(A) > aa_min_index2_opposite: #hydrogen bond parallel and anti-parallel case   small strand is outside (partial overlap) of big strand891                    add_hp = 1892                    893                    twist_angle_return = calculate_twist_angle(a_opposite,B_opposite[aa_min_index2_opposite],j,aa_min_index2)894                    cons_twist_angle.append(twist_angle_return)   895                    sum_twist_angle = sum_twist_angle + twist_angle_return896                    twist_count = twist_count + 1             897                    pick_index = aa_min_index2_opposite898                    899                if aa_min_index2 != 0:900                    add_n = 1901                    twist_angle_return = calculate_twist_angle(a,B[aa_min_index2],j,aa_min_index2)902                    cons_twist_angle.append(twist_angle_return)   903                    sum_twist_angle = sum_twist_angle + twist_angle_return904                    twist_count = twist_count + 1             905                    pick_index = aa_min_index2906                907            else: #next pairs908                print aa_min_index2," ",len(B), " ",aa_min_index2_opposite909                if add_1 == 1 and k < len(B):910                    minimum_dist_point_dup = B[k]911                    pick_index = k912                    twist_angle_return = calculate_twist_angle(a,minimum_dist_point_dup,j,pick_index)913                    cons_twist_angle.append(twist_angle_return)   914                    cons_twist_angle.append(twist_angle_return)   915                    sum_twist_angle = sum_twist_angle + twist_angle_return916                    twist_count = twist_count + 1917                    918                if add_hp == 1 and  int(beta_sheet[i+1][11])!=-1  and  pick_index < len(B_opposite) - 1:		#parallel  small strand is outside (partial overlap) of big strand                         919                   # j = pick_index - 1920                    pick_index = pick_index + 1921                  922                    print "k ",k923                    print "pick_index",pick_index924                    minimum_dist_point_dup = B_opposite[pick_index]925                    #print "minimum_dist_point_dup ",minimum_dist_point_dup #ok926                   # print "a_opposite ",a_opposite927            928                    twist_angle_return = calculate_twist_angle(a_opposite,minimum_dist_point_dup,j,pick_index)929                    cons_twist_angle.append(twist_angle_return)   930                    sum_twist_angle = sum_twist_angle + twist_angle_return931                    twist_count = twist_count + 1932                    933                if add_hp == 1 and  int(beta_sheet[i+1][11])==-1  and  pick_index != 0: # anti-parallel  small strand is outside (partial overlap) of big strand                         934                   # j = pick_index - 1935                    pick_index = pick_index - 1 #may be need to change later 936                  937                    print "k ",k938                    print "pick_index",pick_index939                    minimum_dist_point_dup = B_opposite[pick_index]940                    #print "minimum_dist_point_dup ",minimum_dist_point_dup #ok941                   # print "a_opposite ",a_opposite942                    943                   944                    twist_angle_return = calculate_twist_angle(a_opposite,minimum_dist_point_dup,j,pick_index)945                    cons_twist_angle.append(twist_angle_return)   946                    sum_twist_angle = sum_twist_angle + twist_angle_return947                    twist_count = twist_count + 1948                949                950                if add_n == 1 and  int(beta_sheet[i+1][11])!=-1 and k < len(B) - aa_min_index2: # Parallel beta strands 	951                    pick_index = pick_index + 1952                    minimum_dist_point_dup = B[pick_index]953                    twist_angle_return = calculate_twist_angle(a,minimum_dist_point_dup,j,pick_index)954                    cons_twist_angle.append(twist_angle_return)   955                    sum_twist_angle = sum_twist_angle + twist_angle_return956                    twist_count = twist_count + 1957                    958                if add_n == 1 and   int(beta_sheet[i+1][11])==-1  and pick_index!=0: # anti-Parallel beta strands 		959                    pick_index = pick_index - 1           960                    minimum_dist_point_dup = B[pick_index]961                    twist_angle_return = calculate_twist_angle(a,minimum_dist_point_dup,j,pick_index)962                    cons_twist_angle.append(twist_angle_return)   963                    sum_twist_angle = sum_twist_angle + twist_angle_return964                    twist_count = twist_count + 1965            966                                                                   967            k = k + 1968                 969        if  twist_count != 0:  970            avg_twist_angle.append (float(sum_twist_angle) / float(twist_count))  971           972            cons_sum_array = []973            if len(cons_twist_angle) > 4:974                for c in range (0,len(cons_twist_angle) - 3):975                    cons_sum = 0.0976                    for cc in range (c,c+4):       977                         cons_sum = cons_twist_angle[cc] + cons_sum978                    cons_sum_array.append(cons_sum)979                pair_array.append((round(min(cons_sum_array)  / 4.0,3)))980                len_array.append(len(cons_sum_array))981                #print "sum of consecutive 4 angles ", cons_sum_array982                #print "min of consecutive 4 angles ",min(cons_sum_array)983                out_char = "min of sum of consecutive 4 angles :: " + str(round(min(cons_sum_array),3)) + '\n'984                outf.write(out_char)985                out_char = "Twist per angle :: " + str(round(min(cons_sum_array)  / 4.0 ,3)) + '\n'986                outf.write(out_char)987            988            elif len(cons_twist_angle) == 4:989                for c in range (0,len(cons_twist_angle) - 2):990                    cons_sum = 0.0991                    for cc in range (c,c+3):       992                         cons_sum = cons_twist_angle[cc] + cons_sum993                    cons_sum_array.append(cons_sum)994                pair_array.append((round(min(cons_sum_array)  / 3.0,3)))995                len_array.append(len(cons_sum_array))996                #print "sum of consecutive 4 angles ", cons_sum_array997                #print "min of consecutive 4 angles ",min(cons_sum_array)998                out_char = "min of sum of consecutive 3 angles :: " + str(round(min(cons_sum_array),3)) + '\n'999                outf.write(out_char)  1000                out_char = "Twist per angle :: " + str(round(min(cons_sum_array) / 3.0 ,3) ) + '\n'1001                outf.write(out_char)1002                1003            elif len(cons_twist_angle) == 2 or len(cons_twist_angle) == 3 or len(cons_twist_angle) == 1:1004               #print "smallest twist ",min(cons_twist_angle)1005                pair_array.append((round(min(cons_twist_angle) , 3 )))1006                len_array.append(len(cons_sum_array))1007                out_char = "smallest angles :: " + str(round(min(cons_twist_angle),3)) + '\n'1008                outf.write(out_char)1009            avg_track = 11010        else:1011            avg_track = 01012        1013        for t in range (len(avg_twist_angle)):   1014            #print ("avg_twist_angle between strands ", round(avg_twist_angle[t],3)) #necessary1015            #print ( round(avg_twist_angle[t],3)) #necessary1016            out_char = "avg_twist_angle between strands  " + str( round(avg_twist_angle[t],3) ) + '\n'1017            outf.write(out_char)1018            all_avg_twist_angle.append(avg_twist_angle[t])            1019     1020        #print ("...........................")#necessary1021        #print cons_twist_angle#ok1022      1023        outf.write("................................................"+"\n")1024   1025    i = i +11026#print ("avg_twist_angle between strands ", all_avg_twist_angle) #ok     102710281029'''for calculation of avg twist angle in a beta sheet'''1030outf.write("\n\n")10311032twist_angle_beta_sheet = []1033avg_avg_twist_angle_beta_sheet = []1034jc = 0   1035for i in range (len(counter_index)):  1036    sum_avg_twist_angle = 0.0  1037    j = jc1038    #print jc, " ", counter_index[i]-1, " ",j #ok1039    while j < (jc + counter_index[i]-1):1040        #print "j ",j1041        sum_avg_twist_angle = sum_avg_twist_angle + all_avg_twist_angle[j]  1042        sum_avg_twist_angle = round(sum_avg_twist_angle,3)       1043        j = j + 1    1044    jc = jc + counter_index[i]-11045    #avg_avg_twist_angle_beta_sheet.append(sum_avg_twist_angle)1046    twist_angle_beta_sheet.append(float(sum_avg_twist_angle)/float(counter_index[i]-1))1047    #print ("avg_twist angle in all beta sheets ", round(twist_angle_beta_sheet[i],3)) #necessary1048  1049    #print ( round(twist_angle_beta_sheet[i],3)) 1050    out_char = "avg_twist angle in all beta sheets " + str( round(twist_angle_beta_sheet[i],3)) + '\n'1051    outf.write(out_char)1052   1053#print ("avg_twist angle in all beta sheets ", float(avg_avg_twist_angle_beta_sheet[0])/float(counter_index[0]-1))1054#print pair_array #ok10551056outf.write("................................................"+"\n")10571058#print pair_array # ok1059#print len_array #ok1060'''1061#### According to minimum value pair #############10621063kc = 01064for i in range (len(counter_index)):  1065    j = kc1066    min_arr = []1067    while j < (kc + counter_index[i]-1):1068        min_arr.append (pair_array[j])1069        1070        j = j + 1  1071    kc = kc + counter_index[i]-11072    arr = numpy.array (min_arr) 1073    ind1 , ind2 = arr.argsort()[:2] 1074    min_val1 =   arr[ind1]1075    min_val2 =   arr[ind2]1076    #print min_val1, min_val21077    out_char = "Min pair val1, val2 :: " + str(min_val1) + ",  "+ str(min_val2)+'\n'1078    outf.write(out_char)1079    1080    min_avg_twist = float(min_val1 + min_val2)/2.01081    #print min_avg_twist1082    out_char = "Min Twist :: " + str(min_avg_twist) + '\n'1083    outf.write(out_char)10841085outf.write("................................................"+"\n")10861087#### According to longest pair #############1088kl = 01089for il in range (len(counter_index)):  1090    jl = kl1091    min_arr_l = []1092    while jl < (kl + counter_index[il]-1):1093        min_arr_l.append (len_array[jl])1094        1095        jl = jl + 1  1096    kl = kl + counter_index[il]-11097    arr_len = numpy.array (len_array) 1098    ind1 , ind2 = arr_len.argsort()[::-1][:2]1099    max_val1 =   pair_array[ind1]1100    max_val2 =   pair_array[ind2]1101   # print ind1, ind2 #ok1102    out_char = "longest pair val1, val2 :: " + str(max_val1) + ",  "+ str(max_val2)+'\n'1103    outf.write(out_char)1104    1105    min_avg_twist_long_pair = float(max_val1 + max_val2)/2.01106    #print min_avg_twist_long_pair1107    out_char = "Avg MinTwist according to longest pair :: " + str(min_avg_twist_long_pair) + '\n'1108    outf.write(out_char)11091110'''111111121113#print (beta_sheet)1114#print (beta_sheet[0][6])1115#print (beta_sheet[0][9])1116#print (atom[0])1117#print (atom[0][5])1118#print (a)1119#f.close()1120
...

merge_sample.py

Source:merge_sample.py

1from extractor.models import *2def compare_stretch_with_confusions(first,second, all_indexes):3    inside_if=04    '''check if my is inside of opposite5    check if opposite is inside of my6    check of my and opposite contain each other for at least 50%7    '''8    # SELECT AVG(percentage_based_on_chars) from extractor_compatibility;9    for my in first:10        overlap = []11        for opposite in second:12            state = 0 # 1 = first if is true, 2 = second if is true13            if my[1]>=opposite[1] and my[2]<=opposite[2]:14                state = 115            if my[2]>=opposite[1] and my[1]<=opposite[1] and (my[2]-opposite[1])>=((my[2]-my[1])/2):16                state = 217            if state==1 or state==2:18                if my[3]==opposite[3] \19                        or (my[3]==1 and opposite[3]==4) or (my[3]==4 and opposite[3]==1) \20                        or (my[3]==1 and opposite[3]==2) or (my[3]==2 and opposite[3]==1)\21                        or (my[3]==1 and opposite[3]==12) or (my[3]==12 and opposite[3]==1)\22                        or (my[3]==1 and opposite[3]==10) or (my[3]==10 and opposite[3]==1)\23                        or (my[3]==2 and opposite[3]==7) or (my[3]==7 and opposite[3]==2)\24                        or (my[3]==1 and opposite[3]==8) or (my[3]==8 and opposite[3]==1)\25                        or (my[3]==8 and opposite[3]==9) or (my[3]==9 and opposite[3]==8)\26                        or (my[3]==1 and opposite[3]==6) or (my[3]==6 and opposite[3]==1)\27                        or (my[3]==2 and opposite[3]==4) or (my[3]==4 and opposite[3]==2)\28                        or (my[3]==7 and opposite[3]==8) or (my[3]==8 and opposite[3]==7)\29                        or (my[3]==8 and opposite[3]==4) or (my[3]==4 and opposite[3]==8)\30                        or (my[3]==5 and opposite[3]==7) or (my[3]==7 and opposite[3]==5)\31                        or (my[3]==2 and opposite[3]==5) or (my[3]==5 and opposite[3]==2):32                    inside_if+=133                    all_indexes.update({my[0]:True})34                    all_indexes.update({opposite[0]:True})35                    break36        #     if state==1:37        #         overlap.append((my[3],opposite[3],my[0],opposite[0],my[2]-my[3]))38        #     if state==2:39        #         overlap.append((my[3],opposite[3],my[0],opposite[0],my[2]-opposite[1]))40        # if len(overlap)>0:41        #     to_save = max(overlap,key=itemgetter(4))42        #     save_confusion(to_save)43    return inside_if44def save_confusion(as_list):45    atype = KnowledgeType.objects.get(id=as_list[0])46    btype = KnowledgeType.objects.get(id=as_list[1])47    aid = MarkedUnit.objects.get(id=(max(as_list[2],as_list[3])))48    bid = MarkedUnit.objects.get(id=(min(as_list[2],as_list[3])))49    try:50        change_entry = Confusions.objects.get(idofa=aid,idofb=bid)51        change_entry.atype = atype52        change_entry.btype = btype53        change_entry.length = as_list[4]54    except Confusions.DoesNotExist:55        Confusions.objects.create(atype=atype,56                                  btype=btype,57                                  idofa=aid,58                                  idofb=bid,59                                  length=as_list[4])...

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