Is there a good way to save these as their own files during this loop and then to plot them in different colors?

Question

list_of_coordinates = []
i = 0
while i < len(list_of_structures):
    for models in list_of_structures:
        for model in models:
            chains = model.get_chains()
            for chain in chains:
                residues = chain.get_residues()
                for residue in residues:
                    atoms = residue.get_atoms()
                    for atom in atoms:
                        atom_name = atom.get_name()
                        print(atom_name)
                        if atom_name == "CA":
                            CA_coord = atom.get_coord()
                            list_of_coordinates.append(CA_coord)

    i += 1
v = np.array(list_of_coordinates)

f = open("test.txt","w")
f.write(str(v))
f.close()
print(type(list_of_coordinates))


fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(v[:,0],v[:,1],v[:,2],c="r")
plt.show()

What I do is find the coordinates of these particular files in this loop and save them to a list then it graphs all of them, is there a better way to do this so that I can make a new file for each of them to save as well as seeing all of them in the scatter plot but maybe in differing colors? Thanks!

Do you want to save coordinates of α-C atoms for every structure in separate files, & put them into one scatter plot but with different colours for every structure? — Vovin, Sep 03 '22 at 16:43
change list_of_coordinates.append(CA_coord) indentation, add save list_of_coordinates , reset to zero list_of_coordinates before moving to a next structure (you called them models) in the loop — pippo1980, Sep 05 '22 at 17:46
@pippo1980 could you show me how this works, I am not fully sure what you mean with the reset to 0 spot? — Sam Taylor, Sep 06 '22 at 14:35
Yes this is what I would like to do. Most importantly saving the files separate. The graphing all in different colors would be an added bonus. @Vovin — Sam Taylor, Sep 06 '22 at 14:36

pippo1980 · Accepted Answer · 2022-09-06T22:20:01.200

Sorry about not being able to make scrollable windows smaller for my 4 input pdbs

ok my 4 short pdbs:

prova_1.pdb :

<!-- begin snippet: js hide: true -->
ATOM      1  N   ALA A   1       1.142 129.955  31.316  1.00 56.83           N  
ATOM      2  CA  ALA A   1       2.084 128.961  31.798  1.00 53.73           C  
ATOM      3  C   ALA A   1       1.743 127.771  30.885  1.00 51.56           C  
ATOM      4  O   ALA A   1       0.650 127.715  30.320  1.00 57.57           O  
ATOM      5  CB  ALA A   1       1.831 128.558  33.261  1.00 52.29           C  
ATOM      6  N   SER A   2       2.806 127.064  30.572  1.00 41.24           N  
ATOM      7  CA  SER A   2       2.887 125.804  29.847  1.00 30.35           C  
ATOM      8  C   SER A   2       4.352 125.681  30.149  1.00 25.48           C  
ATOM      9  O   SER A   2       5.074 126.672  29.968  1.00 26.70           O  
ATOM     10  CB  SER A   2       2.663 125.911  28.338  1.00 29.47           C  
ATOM     11  OG  SER A   2       3.604 125.369  27.417  1.00 27.34           O  
ATOM     12  N   ASN A   3       4.844 124.603  30.720  1.00 17.84           N  
ATOM     13  CA  ASN A   3       6.248 124.631  31.023  1.00 11.19           C  
ATOM     14  C   ASN A   3       6.959 124.045  29.845  1.00 12.66           C  
ATOM     15  O   ASN A   3       8.170 123.897  29.905  1.00 13.73           O  
ATOM     16  CB  ASN A   3       6.501 123.860  32.290  1.00 10.22           C  
ATOM     17  CG  ASN A   3       5.985 122.446  32.339  1.00 12.32           C  
ATOM     18  OD1 ASN A   3       5.592 121.848  31.329  1.00 14.90           O  
ATOM     19  ND2 ASN A   3       5.947 121.897  33.544  1.00 13.65           N  
ATOM     20  N   PHE A   4       6.300 123.727  28.742  1.00 10.37           N  
ATOM     21  CA  PHE A   4       7.002 123.152  27.631  1.00  7.74           C  
ATOM     22  C   PHE A   4       7.609 124.278  26.791  1.00 10.17           C  
ATOM     23  O   PHE A   4       7.070 124.663  25.739  1.00 13.33           O  
ATOM     24  CB  PHE A   4       6.016 122.339  26.846  1.00  3.48           C  
ATOM     25  CG  PHE A   4       6.675 121.292  25.996  1.00  2.00           C  
ATOM     26  CD1 PHE A   4       8.050 121.171  25.900  1.00  3.04           C  
ATOM     27  CD2 PHE A   4       5.871 120.419  25.326  1.00  2.88           C  
ATOM     28  CE1 PHE A   4       8.600 120.173  25.132  1.00  7.56           C  
ATOM     29  CE2 PHE A   4       6.433 119.413  24.560  1.00  5.85           C  
ATOM     30  CZ  PHE A   4       7.794 119.276  24.451  1.00  6.77           C  
ATOM     31  N   THR A   5       8.689 124.868  27.263  1.00 13.06           N  
ATOM     32  CA  THR A   5       9.399 125.914  26.575  1.00 14.10           C  
ATOM     33  C   THR A   5      10.827 125.601  26.227  1.00 14.87           C  
ATOM     34  O   THR A   5      11.407 124.627  26.688  1.00 19.07           O  
ATOM     35  CB  THR A   5       9.385 127.148  27.412  1.00 15.81           C  
ATOM     36  OG1 THR A   5       9.866 126.836  28.721  1.00 22.56           O  
ATOM     37  CG2 THR A   5       7.973 127.704  27.421  1.00 21.49           C  
ATOM     38  N   GLN A   6      11.427 126.455  25.419  1.00 16.45           N  
ATOM     39  CA  GLN A   6      12.807 126.328  24.979  1.00 13.21           C  
ATOM     40  C   GLN A   6      13.708 126.721  26.125  1.00  9.91           C  
ATOM     41  O   GLN A   6      13.263 127.501  26.962  1.00 12.35           O  
ATOM     42  CB  GLN A   6      12.909 127.234  23.821  1.00 16.85           C  
ATOM     43  CG  GLN A   6      14.074 128.176  23.710  1.00 32.72           C  
ATOM     44  CD  GLN A   6      13.915 128.964  22.425  1.00 40.53           C  
ATOM     45  OE1 GLN A   6      13.071 129.853  22.332  1.00 50.30           O  
ATOM     46  NE2 GLN A   6      14.649 128.668  21.360  1.00 47.53           N

prova_2.pdb :

ATOM     20  N   PHE A   4       6.300 123.727  28.742  1.00 10.37           N  
ATOM     21  CA  PHE A   4       7.002 123.152  27.631  1.00  7.74           C  
ATOM     22  C   PHE A   4       7.609 124.278  26.791  1.00 10.17           C  
ATOM     23  O   PHE A   4       7.070 124.663  25.739  1.00 13.33           O  
ATOM     24  CB  PHE A   4       6.016 122.339  26.846  1.00  3.48           C  
ATOM     25  CG  PHE A   4       6.675 121.292  25.996  1.00  2.00           C  
ATOM     26  CD1 PHE A   4       8.050 121.171  25.900  1.00  3.04           C  
ATOM     27  CD2 PHE A   4       5.871 120.419  25.326  1.00  2.88           C  
ATOM     28  CE1 PHE A   4       8.600 120.173  25.132  1.00  7.56           C  
ATOM     29  CE2 PHE A   4       6.433 119.413  24.560  1.00  5.85           C  
ATOM     30  CZ  PHE A   4       7.794 119.276  24.451  1.00  6.77           C  
ATOM     31  N   THR A   5       8.689 124.868  27.263  1.00 13.06           N  
ATOM     32  CA  THR A   5       9.399 125.914  26.575  1.00 14.10           C  
ATOM     33  C   THR A   5      10.827 125.601  26.227  1.00 14.87           C  
ATOM     34  O   THR A   5      11.407 124.627  26.688  1.00 19.07           O  
ATOM     35  CB  THR A   5       9.385 127.148  27.412  1.00 15.81           C  
ATOM     36  OG1 THR A   5       9.866 126.836  28.721  1.00 22.56           O  
ATOM     37  CG2 THR A   5       7.973 127.704  27.421  1.00 21.49           C  
ATOM     38  N   GLN A   6      11.427 126.455  25.419  1.00 16.45           N  
ATOM     39  CA  GLN A   6      12.807 126.328  24.979  1.00 13.21           C  
ATOM     40  C   GLN A   6      13.708 126.721  26.125  1.00  9.91           C  
ATOM     41  O   GLN A   6      13.263 127.501  26.962  1.00 12.35           O  
ATOM     42  CB  GLN A   6      12.909 127.234  23.821  1.00 16.85           C  
ATOM     43  CG  GLN A   6      14.074 128.176  23.710  1.00 32.72           C  
ATOM     44  CD  GLN A   6      13.915 128.964  22.425  1.00 40.53           C  
ATOM     45  OE1 GLN A   6      13.071 129.853  22.332  1.00 50.30           O  
ATOM     46  NE2 GLN A   6      14.649 128.668  21.360  1.00 47.53           N  
ATOM     47  N   PHE A   7      14.919 126.202  26.225  1.00  5.73           N  
ATOM     48  CA  PHE A   7      15.810 126.623  27.269  1.00  3.86           C  
ATOM     49  C   PHE A   7      17.240 126.457  26.803  1.00  6.24           C  
ATOM     50  O   PHE A   7      17.478 125.796  25.772  1.00  5.25           O  
ATOM     51  CB  PHE A   7      15.604 125.811  28.542  1.00  5.26           C  
ATOM     52  CG  PHE A   7      15.786 124.310  28.465  1.00  4.68           C  
ATOM     53  CD1 PHE A   7      14.771 123.513  27.996  1.00  3.85           C  
ATOM     54  CD2 PHE A   7      16.956 123.734  28.906  1.00  5.00           C  
ATOM     55  CE1 PHE A   7      14.937 122.144  27.986  1.00  4.19           C  
ATOM     56  CE2 PHE A   7      17.100 122.356  28.883  1.00  4.10           C  
ATOM     57  CZ  PHE A   7      16.096 121.548  28.426  1.00  2.00           C  
ATOM     58  N   VAL A   8      18.223 127.039  27.507  1.00  3.69           N  
ATOM     59  CA  VAL A   8      19.557 126.886  26.986  1.00  5.87           C  
ATOM     60  C   VAL A   8      20.166 125.775  27.807  1.00  5.50           C  
ATOM     61  O   VAL A   8      20.120 125.788  29.027  1.00  7.32           O  
ATOM     62  CB  VAL A   8      20.422 128.260  27.014  1.00  2.82           C  
ATOM     63  CG1 VAL A   8      19.663 129.298  27.677  1.00  2.00           C  
ATOM     64  CG2 VAL A   8      21.770 128.137  27.715  1.00  3.72           C

prova_3.pdb :

ATOM     73  N   VAL A  10      23.392 124.455  27.156  1.00  5.70           N  
ATOM     74  CA  VAL A  10      24.815 124.609  27.396  1.00  5.41           C  
ATOM     75  C   VAL A  10      25.028 126.086  27.368  1.00  9.58           C  
ATOM     76  O   VAL A  10      24.818 126.713  26.326  1.00  9.54           O  
ATOM     77  CB  VAL A  10      25.628 123.971  26.302  1.00  2.00           C  
ATOM     78  CG1 VAL A  10      27.079 124.222  26.538  1.00  2.00           C  
ATOM     79  CG2 VAL A  10      25.376 122.481  26.258  1.00  2.00           C  
ATOM     80  N   ASP A  11      25.389 126.678  28.476  1.00 15.18           N  
ATOM     81  CA  ASP A  11      25.625 128.089  28.463  1.00 24.10           C  
ATOM     82  C   ASP A  11      27.083 128.378  28.236  1.00 30.71           C  
ATOM     83  O   ASP A  11      27.898 128.328  29.144  1.00 32.07           O  
ATOM     84  CB  ASP A  11      25.172 128.683  29.773  1.00 30.45           C  
ATOM     85  CG  ASP A  11      25.315 130.192  29.952  1.00 37.30           C  
ATOM     86  OD1 ASP A  11      25.407 130.948  28.981  1.00 45.67           O  
ATOM     87  OD2 ASP A  11      25.313 130.633  31.097  1.00 44.21           O  
ATOM     88  N   ASN A  12      27.436 128.753  27.011  1.00 39.07           N  
ATOM     89  CA  ASN A  12      28.802 129.152  26.729  1.00 45.49           C  
ATOM     90  C   ASN A  12      28.900 130.664  26.783  1.00 48.93           C  
ATOM     91  O   ASN A  12      29.429 131.343  25.917  1.00 49.83           O  
ATOM     92  CB  ASN A  12      29.205 128.648  25.361  1.00 46.75           C  
ATOM     93  CG  ASN A  12      29.704 127.218  25.445  1.00 52.76           C  
ATOM     94  OD1 ASN A  12      30.437 126.808  26.353  1.00 54.40           O  
ATOM     95  ND2 ASN A  12      29.301 126.405  24.473  1.00 53.69           N  
ATOM     96  N   GLY A  13      28.311 131.227  27.831  1.00 52.11           N  
ATOM     97  CA  GLY A  13      28.324 132.661  28.085  1.00 59.39           C  
ATOM     98  C   GLY A  13      27.829 133.558  26.960  1.00 63.90           C  
ATOM     99  O   GLY A  13      28.566 134.446  26.526  1.00 66.52           O  
ATOM    100  N   GLY A  14      26.592 133.376  26.480  1.00 66.67           N  
ATOM    101  CA  GLY A  14      26.057 134.186  25.374  1.00 68.42           C  
ATOM    102  C   GLY A  14      26.542 133.759  23.967  1.00 70.75           C  
ATOM    103  O   GLY A  14      25.755 133.710  23.007  1.00 70.95           O  
ATOM    104  N   THR A  15      27.806 133.373  23.782  1.00 71.35           N  
ATOM    105  CA  THR A  15      28.357 133.033  22.479  1.00 73.39           C  
ATOM    106  C   THR A  15      28.563 131.530  22.201  1.00 70.75           C  
ATOM    107  O   THR A  15      29.560 130.900  22.623  1.00 71.27           O  
ATOM    108  CB  THR A  15      29.681 133.863  22.345  1.00 77.53           C  
ATOM    109  OG1 THR A  15      30.518 133.626  23.492  1.00 80.95           O  
ATOM    110  CG2 THR A  15      29.362 135.367  22.204  1.00 79.90           C  
ATOM    111  N   GLY A  16      27.650 130.909  21.451  1.00 64.68           N  
ATOM    112  CA  GLY A  16      27.780 129.467  21.198  1.00 55.83           C  
ATOM    113  C   GLY A  16      27.063 128.651  22.265  1.00 47.59           C  
ATOM    114  O   GLY A  16      27.463 127.543  22.627  1.00 46.78           O

prova_4.pdb :

ATOM      1  N   PHE A   4       8.005 121.707  30.748  1.00 10.37           N  
ATOM      2  CA  PHE A   4       8.609 121.187  29.556  1.00  7.74           C  
ATOM      3  C   PHE A   4       9.157 122.352  28.728  1.00 10.17           C  
ATOM      4  O   PHE A   4       8.537 122.794  27.744  1.00 13.33           O  
ATOM      5  CB  PHE A   4       7.556 120.420  28.814  1.00  3.48           C  
ATOM      6  CG  PHE A   4       8.135 119.416  27.860  1.00  2.00           C  
ATOM      7  CD1 PHE A   4       9.496 119.294  27.647  1.00  3.04           C  
ATOM      8  CD2 PHE A   4       7.272 118.583  27.214  1.00  2.88           C  
ATOM      9  CE1 PHE A   4       9.974 118.334  26.787  1.00  7.56           C  
ATOM     10  CE2 PHE A   4       7.761 117.615  26.355  1.00  5.85           C  
ATOM     11  CZ  PHE A   4       9.107 117.477  26.128  1.00  6.77           C  
ATOM     12  N   THR A   5      10.276 122.912  29.140  1.00 13.06           N  
ATOM     13  CA  THR A   5      10.937 123.990  28.452  1.00 14.10           C  
ATOM     14  C   THR A   5      12.329 123.688  27.973  1.00 14.87           C  
ATOM     15  O   THR A   5      12.936 122.690  28.335  1.00 19.07           O  
ATOM     16  CB  THR A   5      11.001 125.178  29.348  1.00 15.81           C  
ATOM     17  CG2 THR A   5       9.600 125.740  29.502  1.00 21.49           C  
ATOM     18  OG1 THR A   5      11.584 124.797  30.597  1.00 22.56           O  
ATOM     19  N   GLN A   6      12.870 124.580  27.164  1.00 16.45           N  
ATOM     20  CA  GLN A   6      14.208 124.470  26.607  1.00 13.21           C  
ATOM     21  C   GLN A   6      15.202 124.799  27.694  1.00  9.91           C  
ATOM     22  O   GLN A   6      14.833 125.537  28.604  1.00 12.35           O  
ATOM     23  CB  GLN A   6      14.224 125.434  25.493  1.00 16.85           C  
ATOM     24  CG  GLN A   6      15.384 126.376  25.335  1.00 32.72           C  
ATOM     25  CD  GLN A   6      15.129 127.229  24.110  1.00 40.53           C  
ATOM     26  NE2 GLN A   6      15.771 126.986  22.975  1.00 47.53           N  
ATOM     27  OE1 GLN A   6      14.288 128.126  24.131  1.00 50.30           O  
ATOM     28  N   PHE A   7      16.413 124.270  27.669  1.00  5.73           N  
ATOM     29  CA  PHE A   7      17.389 124.633  28.657  1.00  3.86           C  
ATOM     30  C   PHE A   7      18.775 124.484  28.068  1.00  6.24           C  
ATOM     31  O   PHE A   7      18.923 123.876  26.988  1.00  5.25           O  
ATOM     32  CB  PHE A   7      17.280 123.757  29.900  1.00  5.26           C  
ATOM     33  CG  PHE A   7      17.442 122.261  29.731  1.00  4.68           C  
ATOM     34  CD1 PHE A   7      16.386 121.493  29.306  1.00  3.85           C  
ATOM     35  CD2 PHE A   7      18.639 121.658  30.045  1.00  5.00           C  
ATOM     36  CE1 PHE A   7      16.538 120.126  29.213  1.00  4.19           C  
ATOM     37  CE2 PHE A   7      18.768 120.282  29.940  1.00  4.10           C  
ATOM     38  CZ  PHE A   7      17.723 119.503  29.525  1.00  2.00           C  
ATOM     39  N   VAL A   8      19.818 125.025  28.719  1.00  3.69           N  
ATOM     40  CA  VAL A   8      21.103 124.892  28.084  1.00  5.87           C  
ATOM     41  C   VAL A   8      21.767 123.739  28.795  1.00  5.50           C  
ATOM     42  O   VAL A   8      21.820 123.688  30.013  1.00  7.32           O  
ATOM     43  CB  VAL A   8      21.980 126.259  28.112  1.00  2.82           C  
ATOM     44  CG1 VAL A   8      21.285 127.265  28.886  1.00  2.00           C  
ATOM     45  CG2 VAL A   8      23.379 126.094  28.694  1.00  3.72           C  
TER   
END

my code :

import matplotlib.pyplot as plt

from itertools import cycle

prop_cycle = plt.rcParams['axes.prop_cycle']
colors = cycle(prop_cycle.by_key()['color'])


from Bio.PDB import PDBParser



list_of_structures = []

parser = PDBParser(PERMISSIVE=1, QUIET=1)

list_of_structures.extend([parser.get_structure("prova_1", "prova_1.pdb") ,
                           parser.get_structure("prova_2", "prova_2.pdb"),
                           parser.get_structure("prova_3", "prova_3.pdb"),
                          parser.get_structure("prova_3", "prova_4.pdb")])

print(list_of_structures)


list_of_struct = []

colorz = 'red'

i = 1
while i < len(list_of_structures):
    for models in list_of_structures:
        
        list_of_coordinates = []       
        
        for model in models:
            #print(model)
            chains = model.get_chains()
            for chain in chains:
                #print(chain)
                residues = chain.get_residues()
                for residue in residues:
                    #print(residue)
                    atoms = residue.get_atoms()
                    for atom in atoms:
                        atom_name = atom.get_name()
                        #print(atom_name)
                        if atom_name == "CA":
                            CA_coord = atom.get_coord()
                            
                            #print(CA_coord)
                            list_of_coordinates.append([i for i in CA_coord])
    
        i += 1
        list_of_struct.append(list_of_coordinates)


for i in list_of_struct:                            
            print(i)



f = open("test.txt","w")
f.write(str(list_of_struct))
f.close()
print(type(list_of_struct))

atomlist_full = list_of_struct


fig = plt.figure()
ax = plt.axes(projection="3d")

for i in range(len(list_of_struct)):
    
        atomlist = atomlist_full[i]
        
        for p in atomlist:       #print CA as dots
            ax.scatter3D(p[0], p[1], p[2],  color = colorz)
            print(p)
        
            
        for i in range(0,len(atomlist)-1):   #connect with a line CA n with n+1
            x,y,z = [atomlist[i+1][0],atomlist[i][0]],[atomlist[i+1][1],atomlist[i][1]],[atomlist[i+1][2],atomlist[i][2]]
            ax.plot(x,y,z, color = colorz)  
            
        
        colorz = next(colors)


plt.show()

output :

[[[2.084, 128.961, 31.798], [2.887, 125.804, 29.847], [6.248, 124.631, 31.023], [7.002, 123.152, 27.631], [9.399, 125.914, 26.575], [12.807, 126.328, 24.979]], [[7.002, 123.152, 27.631], [9.399, 125.914, 26.575], [12.807, 126.328, 24.979], [15.81, 126.623, 27.269], [19.557, 126.886, 26.986]], [[24.815, 124.609, 27.396], [25.625, 128.089, 28.463], [28.802, 129.152, 26.729], [28.324, 132.661, 28.085], [26.057, 134.186, 25.374], [28.357, 133.033, 22.479], [27.78, 129.467, 21.198]], [[8.609, 121.187, 29.556], [10.937, 123.99, 28.452], [14.208, 124.47, 26.607], [17.389, 124.633, 28.657], [21.103, 124.892, 28.084]]]

image of plot :

every different color line is a c-alpha of from one of the pdbs

Can change block after end of main loop with

for i in range(len(list_of_struct)):
    
    print(list_of_structures[i])



    f = open(list_of_structures[i].id+'_'+str(i)+'_'+'.txt',"w")
    f.write(str(list_of_struct[i]))
    f.close()
    print(type(list_of_struct))

to save each pdb coordinates in a single text file named with structure id such as prova_1_0_.txt for first pdb

Is there a good way to save these as their own files during this loop and then to plot them in different colors?

1 Answers1