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6 deletions
... | @@ -1405,14 +1405,14 @@ def basepair_flat_angle(res, pair): | ... | @@ -1405,14 +1405,14 @@ def basepair_flat_angle(res, pair): |
1405 | """ | 1405 | """ |
1406 | measurement of the plane angles formed by the vectors C1->B1 of the paired nucleotides | 1406 | measurement of the plane angles formed by the vectors C1->B1 of the paired nucleotides |
1407 | """ | 1407 | """ |
1408 | - if res.get_resname()=='A' or res.get_resname()=='G' or res.get_resname()=='C' or res.get_resname()=='U' : | 1408 | + if res.get_resname()=='C' or res.get_resname()=='U' : |
1409 | atom_c4_res = [ atom.get_coord() for atom in res if "C4'" in atom.get_fullname() ] | 1409 | atom_c4_res = [ atom.get_coord() for atom in res if "C4'" in atom.get_fullname() ] |
1410 | atom_c1p_res = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ] | 1410 | atom_c1p_res = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ] |
1411 | atom_b1_res = pos_b1(res) | 1411 | atom_b1_res = pos_b1(res) |
1412 | a1_res = Vector(atom_c4_res[0]) | 1412 | a1_res = Vector(atom_c4_res[0]) |
1413 | a2_res = Vector(atom_c1p_res[0]) | 1413 | a2_res = Vector(atom_c1p_res[0]) |
1414 | a3_res = Vector(atom_b1_res[0]) | 1414 | a3_res = Vector(atom_b1_res[0]) |
1415 | - if res.get_resname()=='C' or res.get_resname()=='U' : | 1415 | + if res.get_resname()=='A' or res.get_resname()=='G' : |
1416 | atom_c1p_res = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ] | 1416 | atom_c1p_res = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ] |
1417 | atom_b1_res = pos_b1(res) | 1417 | atom_b1_res = pos_b1(res) |
1418 | atom_b2_res = pos_b2(res) | 1418 | atom_b2_res = pos_b2(res) |
... | @@ -1420,14 +1420,14 @@ def basepair_flat_angle(res, pair): | ... | @@ -1420,14 +1420,14 @@ def basepair_flat_angle(res, pair): |
1420 | a2_res = Vector(atom_b1_res[0]) | 1420 | a2_res = Vector(atom_b1_res[0]) |
1421 | a3_res = Vector(atom_b2_res[0]) | 1421 | a3_res = Vector(atom_b2_res[0]) |
1422 | 1422 | ||
1423 | - if pair.get_resname()=='A' or pair.get_resname()=='G' or pair.get_resname()=='C' or pair.get_resname()=='U' : | 1423 | + if pair.get_resname()=='C' or pair.get_resname()=='U' : |
1424 | atom_c4_pair = [ atom.get_coord() for atom in pair if "C4'" in atom.get_fullname() ] | 1424 | atom_c4_pair = [ atom.get_coord() for atom in pair if "C4'" in atom.get_fullname() ] |
1425 | atom_c1p_pair = [ atom.get_coord() for atom in pair if "C1'" in atom.get_fullname() ] | 1425 | atom_c1p_pair = [ atom.get_coord() for atom in pair if "C1'" in atom.get_fullname() ] |
1426 | atom_b1_pair = pos_b1(pair) | 1426 | atom_b1_pair = pos_b1(pair) |
1427 | a1_pair = Vector(atom_c4_pair[0]) | 1427 | a1_pair = Vector(atom_c4_pair[0]) |
1428 | a2_pair = Vector(atom_c1p_pair[0]) | 1428 | a2_pair = Vector(atom_c1p_pair[0]) |
1429 | a3_pair = Vector(atom_b1_pair) | 1429 | a3_pair = Vector(atom_b1_pair) |
1430 | - if pair.get_resname()=='C' or pair.get_resname()=='U' : | 1430 | + if pair.get_resname()=='A' or pair.get_resname()=='G' : |
1431 | atom_c1p_pair = [ atom.get_coord() for atom in pair if "C1'" in atom.get_fullname() ] | 1431 | atom_c1p_pair = [ atom.get_coord() for atom in pair if "C1'" in atom.get_fullname() ] |
1432 | atom_b1_pair = pos_b1(pair) | 1432 | atom_b1_pair = pos_b1(pair) |
1433 | atom_b2_pair = pos_b2(pair) | 1433 | atom_b2_pair = pos_b2(pair) |
... | @@ -1627,7 +1627,6 @@ def measures_aa(name, s, thr_idx): | ... | @@ -1627,7 +1627,6 @@ 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 | - | ||
1631 | op3_p = get_euclidian_distance(atom_op3[0], atom_p[0]) | 1630 | op3_p = get_euclidian_distance(atom_op3[0], atom_p[0]) |
1632 | 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[0], atom_p[0]) # link with the previous nucleotide |
1633 | p_op1 = get_euclidian_distance(atom_op1[0], atom_p[0]) | 1632 | p_op1 = get_euclidian_distance(atom_op1[0], atom_p[0]) |
... | @@ -1685,7 +1684,7 @@ def measures_aa(name, s, thr_idx): | ... | @@ -1685,7 +1684,7 @@ def measures_aa(name, s, thr_idx): |
1685 | df=pd.concat([df_comm, df_pur, df_pyr], axis = 1) | 1684 | df=pd.concat([df_comm, df_pur, df_pyr], axis = 1) |
1686 | pbar.close() | 1685 | pbar.close() |
1687 | 1686 | ||
1688 | - df.to_csv(runDir+"/results/geometry/all-atoms/distances/dist_atoms "+name+".csv") | 1687 | + df.to_csv(runDir + "/results/geometry/all-atoms/distances/dist_atoms " + name + ".csv") |
1689 | 1688 | ||
1690 | @trace_unhandled_exceptions | 1689 | @trace_unhandled_exceptions |
1691 | def measures_hrna(name, s, thr_idx): | 1690 | def measures_hrna(name, s, thr_idx): | ... | ... |
-
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