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| ... | @@ -1627,51 +1627,51 @@ def measures_aa(name, s, thr_idx): | ... | @@ -1627,51 +1627,51 @@ def measures_aa(name, s, thr_idx): |
| 1627 | atom_n4 = [ atom.get_coord() for atom in res if "N4" in atom.get_fullname() ] | 1627 | atom_n4 = [ atom.get_coord() for atom in res if "N4" in atom.get_fullname() ] |
| 1628 | atom_o4 = [ atom.get_coord() for atom in res if atom.get_name() == "O4"] | 1628 | atom_o4 = [ atom.get_coord() for atom in res if atom.get_name() == "O4"] |
| 1629 | 1629 | ||
| 1630 | - op3_p = get_euclidian_distance(atom_op3[0], atom_p[0]) | 1630 | + op3_p = get_euclidian_distance(atom_op3, atom_p) |
| 1631 | - last_o3p_p = get_euclidian_distance(last_o3p[0], atom_p[0]) # link with the previous nucleotide | 1631 | + last_o3p_p = get_euclidian_distance(last_o3p, atom_p) # link with the previous nucleotide |
| 1632 | - p_op1 = get_euclidian_distance(atom_op1[0], atom_p[0]) | 1632 | + p_op1 = get_euclidian_distance(atom_op1, atom_p) |
| 1633 | - p_op2 = get_euclidian_distance(atom_op2[0], atom_p[0]) | 1633 | + p_op2 = get_euclidian_distance(atom_op2, atom_p) |
| 1634 | - p_o5p = get_euclidian_distance(atom_o5p[0], atom_p[0]) | 1634 | + p_o5p = get_euclidian_distance(atom_o5p, atom_p) |
| 1635 | - o5p_c5p = get_euclidian_distance(atom_o5p[0], atom_c5p[0]) | 1635 | + o5p_c5p = get_euclidian_distance(atom_o5p, atom_c5p) |
| 1636 | - c5p_c4p = get_euclidian_distance(atom_c5p[0], atom_c4p[0]) | 1636 | + c5p_c4p = get_euclidian_distance(atom_c5p, atom_c4p) |
| 1637 | - c4p_o4p = get_euclidian_distance(atom_c4p[0], atom_o4p[0]) | 1637 | + c4p_o4p = get_euclidian_distance(atom_c4p, atom_o4p) |
| 1638 | - c4p_c3p = get_euclidian_distance(atom_c4p[0], atom_c3p[0]) | 1638 | + c4p_c3p = get_euclidian_distance(atom_c4p, atom_c3p) |
| 1639 | - o4p_c1p = get_euclidian_distance(atom_o4p[0], atom_c1p[0]) | 1639 | + o4p_c1p = get_euclidian_distance(atom_o4p, atom_c1p) |
| 1640 | - c1p_c2p = get_euclidian_distance(atom_c1p[0], atom_c2p[0]) | 1640 | + c1p_c2p = get_euclidian_distance(atom_c1p, atom_c2p) |
| 1641 | - c2p_o2p = get_euclidian_distance(atom_c2p[0], atom_o2p[0]) | 1641 | + c2p_o2p = get_euclidian_distance(atom_c2p, atom_o2p) |
| 1642 | - c2p_c3p = get_euclidian_distance(atom_c2p[0], atom_c3p[0]) | 1642 | + c2p_c3p = get_euclidian_distance(atom_c2p, atom_c3p) |
| 1643 | - c3p_o3p = get_euclidian_distance(atom_c3p[0], atom_o3p[0]) | 1643 | + c3p_o3p = get_euclidian_distance(atom_c3p, atom_o3p) |
| 1644 | 1644 | ||
| 1645 | last_o3p=atom_o3p # o3' of this residue becomes the previous o3' of the following | 1645 | last_o3p=atom_o3p # o3' of this residue becomes the previous o3' of the following |
| 1646 | 1646 | ||
| 1647 | #different cases for the aromatic cycles | 1647 | #different cases for the aromatic cycles |
| 1648 | if res.get_resname()=='A' or res.get_resname()=='G': | 1648 | if res.get_resname()=='A' or res.get_resname()=='G': |
| 1649 | # computes the distances between atoms of aromatic cycles | 1649 | # computes the distances between atoms of aromatic cycles |
| 1650 | - c1p_n9 = get_euclidian_distance(atom_c1p[0], atom_n9[0]) | 1650 | + c1p_n9 = get_euclidian_distance(atom_c1p, atom_n9) |
| 1651 | - n9_c8 = get_euclidian_distance(atom_n9[0], atom_c8[0]) | 1651 | + n9_c8 = get_euclidian_distance(atom_n9, atom_c8) |
| 1652 | - c8_n7 = get_euclidian_distance(atom_c8[0], atom_n7[0]) | 1652 | + c8_n7 = get_euclidian_distance(atom_c8, atom_n7) |
| 1653 | - n7_c5 = get_euclidian_distance(atom_n7[0], atom_c5[0]) | 1653 | + n7_c5 = get_euclidian_distance(atom_n7, atom_c5) |
| 1654 | - c5_c6 = get_euclidian_distance(atom_c5[0], atom_c6[0]) | 1654 | + c5_c6 = get_euclidian_distance(atom_c5, atom_c6) |
| 1655 | - c6_o6 = get_euclidian_distance(atom_c6[0], atom_o6[0]) | 1655 | + c6_o6 = get_euclidian_distance(atom_c6, atom_o6) |
| 1656 | - c6_n6 = get_euclidian_distance(atom_c6[0], atom_n6[0]) | 1656 | + c6_n6 = get_euclidian_distance(atom_c6, atom_n6) |
| 1657 | - c6_n1 = get_euclidian_distance(atom_c6[0], atom_n1[0]) | 1657 | + c6_n1 = get_euclidian_distance(atom_c6, atom_n1) |
| 1658 | - n1_c2 = get_euclidian_distance(atom_n1[0], atom_c2[0]) | 1658 | + n1_c2 = get_euclidian_distance(atom_n1, atom_c2) |
| 1659 | - c2_n2 = get_euclidian_distance(atom_c2[0], atom_n2[0]) | 1659 | + c2_n2 = get_euclidian_distance(atom_c2, atom_n2) |
| 1660 | - c2_n3 = get_euclidian_distance(atom_c2[0], atom_n3[0]) | 1660 | + c2_n3 = get_euclidian_distance(atom_c2, atom_n3) |
| 1661 | - n3_c4 = get_euclidian_distance(atom_n3[0], atom_c4[0]) | 1661 | + n3_c4 = get_euclidian_distance(atom_n3, atom_c4) |
| 1662 | - c4_n9 = get_euclidian_distance(atom_c4[0], atom_n9[0]) | 1662 | + c4_n9 = get_euclidian_distance(atom_c4, atom_n9) |
| 1663 | - c4_c5 = get_euclidian_distance(atom_c4[0], atom_c5[0]) | 1663 | + c4_c5 = get_euclidian_distance(atom_c4, atom_c5) |
| 1664 | if res.get_resname()=='C' or res.get_resname()=='U' : | 1664 | if res.get_resname()=='C' or res.get_resname()=='U' : |
| 1665 | - c1p_n1 = get_euclidian_distance(atom_c1p[0], atom_n1[0]) | 1665 | + c1p_n1 = get_euclidian_distance(atom_c1p, atom_n1) |
| 1666 | - n1_c6 = get_euclidian_distance(atom_n1[0], atom_c6[0]) | 1666 | + n1_c6 = get_euclidian_distance(atom_n1, atom_c6) |
| 1667 | - c6_c5 = get_euclidian_distance(atom_c6[0], atom_c5[0]) | 1667 | + c6_c5 = get_euclidian_distance(atom_c6, atom_c5) |
| 1668 | - c5_c4 = get_euclidian_distance(atom_c5[0], atom_c4[0]) | 1668 | + c5_c4 = get_euclidian_distance(atom_c5, atom_c4) |
| 1669 | - c4_n3 = get_euclidian_distance(atom_c4[0], atom_n3[0]) | 1669 | + c4_n3 = get_euclidian_distance(atom_c4, atom_n3) |
| 1670 | - n3_c2 = get_euclidian_distance(atom_n3[0], atom_c2[0]) | 1670 | + n3_c2 = get_euclidian_distance(atom_n3, atom_c2) |
| 1671 | - c2_o2 = get_euclidian_distance(atom_c2[0], atom_o2[0]) | 1671 | + c2_o2 = get_euclidian_distance(atom_c2, atom_o2) |
| 1672 | - c2_n1 = get_euclidian_distance(atom_c2[0], atom_n1[0]) | 1672 | + c2_n1 = get_euclidian_distance(atom_c2, atom_n1) |
| 1673 | - c4_n4 = get_euclidian_distance(atom_c4[0], atom_n4[0]) | 1673 | + c4_n4 = get_euclidian_distance(atom_c4, atom_n4) |
| 1674 | - c4_o4 = get_euclidian_distance(atom_c4[0], atom_o4[0]) | 1674 | + c4_o4 = get_euclidian_distance(atom_c4, atom_o4) |
| 1675 | 1675 | ||
| 1676 | liste_common.append([res.get_resname(), last_o3p_p, op3_p, p_op1, p_op2, p_o5p, o5p_c5p, c5p_c4p, c4p_o4p, c4p_c3p, o4p_c1p, c1p_c2p, c2p_o2p, c2p_c3p, c3p_o3p] ) | 1676 | liste_common.append([res.get_resname(), last_o3p_p, op3_p, p_op1, p_op2, p_o5p, o5p_c5p, c5p_c4p, c4p_o4p, c4p_c3p, o4p_c1p, c1p_c2p, c2p_o2p, c2p_c3p, c3p_o3p] ) |
| 1677 | liste_purines.append([c1p_n9, n9_c8, c8_n7, n7_c5, c5_c6, c6_o6, c6_n6, c6_n1, n1_c2, c2_n2, c2_n3, n3_c4, c4_n9, c4_c5]) | 1677 | liste_purines.append([c1p_n9, n9_c8, c8_n7, n7_c5, c5_c6, c6_o6, c6_n6, c6_n1, n1_c2, c2_n2, c2_n3, n3_c4, c4_n9, c4_c5]) |
| ... | @@ -3004,6 +3004,7 @@ if __name__ == "__main__": | ... | @@ -3004,6 +3004,7 @@ if __name__ == "__main__": |
| 3004 | joblist.append(Job(function=measure_from_structure, args=(f,), how_many_in_parallel=nworkers)) # All-atom distances | 3004 | joblist.append(Job(function=measure_from_structure, args=(f,), how_many_in_parallel=nworkers)) # All-atom distances |
| 3005 | 3005 | ||
| 3006 | # Basepair geometries statistics (from RNACifs/ 3D files) | 3006 | # Basepair geometries statistics (from RNACifs/ 3D files) |
| 3007 | + | ||
| 3007 | ld = os.listdir(path_to_3D_data +'datapoints') | 3008 | ld = os.listdir(path_to_3D_data +'datapoints') |
| 3008 | if '4zdo_1_E' in ld : | 3009 | if '4zdo_1_E' in ld : |
| 3009 | ld.remove('4zdo_1_E') # weird cases to remove for now | 3010 | ld.remove('4zdo_1_E') # weird cases to remove for now |
| ... | @@ -3016,6 +3017,7 @@ if __name__ == "__main__": | ... | @@ -3016,6 +3017,7 @@ if __name__ == "__main__": |
| 3016 | 3017 | ||
| 3017 | #exit() | 3018 | #exit() |
| 3018 | 3019 | ||
| 3020 | + | ||
| 3019 | process_jobs(joblist) | 3021 | process_jobs(joblist) |
| 3020 | 3022 | ||
| 3021 | # Now process the memory-heavy tasks family by family | 3023 | # Now process the memory-heavy tasks family by family |
| ... | @@ -3029,7 +3031,7 @@ if __name__ == "__main__": | ... | @@ -3029,7 +3031,7 @@ if __name__ == "__main__": |
| 3029 | 3031 | ||
| 3030 | print() | 3032 | print() |
| 3031 | print() | 3033 | print() |
| 3032 | - | 3034 | + |
| 3033 | # finish the work after the parallel portions | 3035 | # finish the work after the parallel portions |
| 3034 | 3036 | ||
| 3035 | per_chain_stats() # per chain base frequencies en basepair types | 3037 | per_chain_stats() # per chain base frequencies en basepair types |
| ... | @@ -3060,3 +3062,4 @@ if __name__ == "__main__": | ... | @@ -3060,3 +3062,4 @@ if __name__ == "__main__": |
| 3060 | joblist.append(Job(function=gmm_wadley, args=())) | 3062 | joblist.append(Job(function=gmm_wadley, args=())) |
| 3061 | if len(joblist): | 3063 | if len(joblist): |
| 3062 | process_jobs(joblist) | 3064 | process_jobs(joblist) |
| 3065 | + | ... | ... |
-
mentioned in commit 4b50dab0
-
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