mmagnus /
rna-tools
| @@ 1828-1857 (lines=30) @@ | ||
| 1825 | # |
|
| 1826 | # fix missing G (the whole base at the moment) |
|
| 1827 | # |
|
| 1828 | if str(r.get_resname()).strip() == "G" and fix_missing_atoms: |
|
| 1829 | for a in r: |
|
| 1830 | if a.id == "N1": |
|
| 1831 | break |
|
| 1832 | else: |
|
| 1833 | G_struc = PDB.PDBParser().get_structure('', path + '/data/G.pdb') |
|
| 1834 | G = [G_atom for G_atom in G_struc[0].get_residues()][0] |
|
| 1835 | ||
| 1836 | r_atoms = [r["O4'"], r["C2'"], r["C1'"]] |
|
| 1837 | G_atoms = [G["O4'"], G["C2'"], G["C1'"]] |
|
| 1838 | ||
| 1839 | sup = PDB.Superimposer() |
|
| 1840 | sup.set_atoms(r_atoms, G_atoms) |
|
| 1841 | rms = round(sup.rms, 3) |
|
| 1842 | ||
| 1843 | sup.apply(G_struc.get_atoms()) # to all atoms of G |
|
| 1844 | ||
| 1845 | r.add(G["N9"]) |
|
| 1846 | r.add(G["C8"]) |
|
| 1847 | r.add(G["N7"]) |
|
| 1848 | r.add(G["C5"]) |
|
| 1849 | r.add(G["C6"]) |
|
| 1850 | r.add(G["O6"]) |
|
| 1851 | r.add(G["N1"]) |
|
| 1852 | r.add(G["C2"]) |
|
| 1853 | r.add(G["N2"]) |
|
| 1854 | r.add(G["N3"]) |
|
| 1855 | r.add(G["C4"]) |
|
| 1856 | ||
| 1857 | fixed.append(['add the whole base G', chain.id, r, r.id[1]]) |
|
| 1858 | # |
|
| 1859 | # fix missing A (the whole base at the moment) |
|
| 1860 | # |
|
| @@ 1861-1889 (lines=29) @@ | ||
| 1858 | # |
|
| 1859 | # fix missing A (the whole base at the moment) |
|
| 1860 | # |
|
| 1861 | if str(r.get_resname()).strip() == "A" and fix_missing_atoms: |
|
| 1862 | for a in r: |
|
| 1863 | if a.id == "N1": |
|
| 1864 | break |
|
| 1865 | else: |
|
| 1866 | A_struc = PDB.PDBParser().get_structure('', path + '/data/A.pdb') |
|
| 1867 | A = [A_atom for A_atom in A_struc[0].get_residues()][0] |
|
| 1868 | ||
| 1869 | r_atoms = [r["O4'"], r["C2'"], r["C1'"]] |
|
| 1870 | A_atoms = [A["O4'"], A["C2'"], A["C1'"]] |
|
| 1871 | ||
| 1872 | sup = PDB.Superimposer() |
|
| 1873 | sup.set_atoms(r_atoms, A_atoms) |
|
| 1874 | rms = round(sup.rms, 3) |
|
| 1875 | ||
| 1876 | sup.apply(A_struc.get_atoms()) # to all atoms of A |
|
| 1877 | ||
| 1878 | r.add(A["N9"]) |
|
| 1879 | r.add(A["C8"]) |
|
| 1880 | r.add(A["N7"]) |
|
| 1881 | r.add(A["C5"]) |
|
| 1882 | r.add(A["C6"]) |
|
| 1883 | r.add(A["N6"]) |
|
| 1884 | r.add(A["N1"]) |
|
| 1885 | r.add(A["C2"]) |
|
| 1886 | r.add(A["N3"]) |
|
| 1887 | r.add(A["C4"]) |
|
| 1888 | ||
| 1889 | fixed.append(['add the whole base A', chain.id, r, r.id[1]]) |
|
| 1890 | ||
| 1891 | # |
|
| 1892 | # strip residues of extra atoms, not in G_ATOMS in this case |
|
