Aglaé TABOT

Merge branch 'stage_aglae' of ssh://forge.ibisc.univ-evry.fr:6622/lbecquey/RNANet into stage_aglae


Former-commit-id: 5827efe2
...@@ -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):
......