mmagnus /
rna-tools
| @@ 1630-1659 (lines=30) @@ | ||
| 1627 | # |
|
| 1628 | # fix missing G (the whole base at the moment) |
|
| 1629 | # |
|
| 1630 | if str(r.get_resname()).strip() == "G" and fix_missing_atoms: |
|
| 1631 | for a in r: |
|
| 1632 | if a.id == "N1": |
|
| 1633 | break |
|
| 1634 | else: |
|
| 1635 | G_struc = PDB.PDBParser().get_structure('', path + '/data/G.pdb') |
|
| 1636 | G = [G_atom for G_atom in G_struc[0].get_residues()][0] |
|
| 1637 | ||
| 1638 | r_atoms = [r["O4'"], r["C2'"], r["C1'"]] |
|
| 1639 | G_atoms = [G["O4'"], G["C2'"], G["C1'"]] |
|
| 1640 | ||
| 1641 | sup = PDB.Superimposer() |
|
| 1642 | sup.set_atoms(r_atoms, G_atoms) |
|
| 1643 | rms = round(sup.rms, 3) |
|
| 1644 | ||
| 1645 | sup.apply(G_struc.get_atoms()) # to all atoms of G |
|
| 1646 | ||
| 1647 | r.add(G["N9"]) |
|
| 1648 | r.add(G["C8"]) |
|
| 1649 | r.add(G["N7"]) |
|
| 1650 | r.add(G["C5"]) |
|
| 1651 | r.add(G["C6"]) |
|
| 1652 | r.add(G["O6"]) |
|
| 1653 | r.add(G["N1"]) |
|
| 1654 | r.add(G["C2"]) |
|
| 1655 | r.add(G["N2"]) |
|
| 1656 | r.add(G["N3"]) |
|
| 1657 | r.add(G["C4"]) |
|
| 1658 | ||
| 1659 | fixed.append(['add the whole base G', chain.id, r, r.id[1]]) |
|
| 1660 | # |
|
| 1661 | # fix missing A (the whole base at the moment) |
|
| 1662 | # |
|
| @@ 1663-1691 (lines=29) @@ | ||
| 1660 | # |
|
| 1661 | # fix missing A (the whole base at the moment) |
|
| 1662 | # |
|
| 1663 | if str(r.get_resname()).strip() == "A" and fix_missing_atoms: |
|
| 1664 | for a in r: |
|
| 1665 | if a.id == "N1": |
|
| 1666 | break |
|
| 1667 | else: |
|
| 1668 | A_struc = PDB.PDBParser().get_structure('', path + '/data/A.pdb') |
|
| 1669 | A = [A_atom for A_atom in A_struc[0].get_residues()][0] |
|
| 1670 | ||
| 1671 | r_atoms = [r["O4'"], r["C2'"], r["C1'"]] |
|
| 1672 | A_atoms = [A["O4'"], A["C2'"], A["C1'"]] |
|
| 1673 | ||
| 1674 | sup = PDB.Superimposer() |
|
| 1675 | sup.set_atoms(r_atoms, A_atoms) |
|
| 1676 | rms = round(sup.rms, 3) |
|
| 1677 | ||
| 1678 | sup.apply(A_struc.get_atoms()) # to all atoms of A |
|
| 1679 | ||
| 1680 | r.add(A["N9"]) |
|
| 1681 | r.add(A["C8"]) |
|
| 1682 | r.add(A["N7"]) |
|
| 1683 | r.add(A["C5"]) |
|
| 1684 | r.add(A["C6"]) |
|
| 1685 | r.add(A["N6"]) |
|
| 1686 | r.add(A["N1"]) |
|
| 1687 | r.add(A["C2"]) |
|
| 1688 | r.add(A["N3"]) |
|
| 1689 | r.add(A["C4"]) |
|
| 1690 | ||
| 1691 | fixed.append(['add the whole base A', chain.id, r, r.id[1]]) |
|
| 1692 | ||
| 1693 | # |
|
| 1694 | # strip residues of extra atoms, not in G_ATOMS in this case |
|
