Aglaé TABOT

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

......@@ -1405,14 +1405,14 @@ def basepair_flat_angle(res, pair):
"""
measurement of the plane angles formed by the vectors C1->B1 of the paired nucleotides
"""
if res.get_resname()=='A' or res.get_resname()=='G' or res.get_resname()=='C' or res.get_resname()=='U' :
if res.get_resname()=='C' or res.get_resname()=='U' :
atom_c4_res = [ atom.get_coord() for atom in res if "C4'" in atom.get_fullname() ]
atom_c1p_res = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ]
atom_b1_res = pos_b1(res)
a1_res = Vector(atom_c4_res[0])
a2_res = Vector(atom_c1p_res[0])
a3_res = Vector(atom_b1_res[0])
if res.get_resname()=='C' or res.get_resname()=='U' :
if res.get_resname()=='A' or res.get_resname()=='G' :
atom_c1p_res = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ]
atom_b1_res = pos_b1(res)
atom_b2_res = pos_b2(res)
......@@ -1420,14 +1420,14 @@ def basepair_flat_angle(res, pair):
a2_res = Vector(atom_b1_res[0])
a3_res = Vector(atom_b2_res[0])
if pair.get_resname()=='A' or pair.get_resname()=='G' or pair.get_resname()=='C' or pair.get_resname()=='U' :
if pair.get_resname()=='C' or pair.get_resname()=='U' :
atom_c4_pair = [ atom.get_coord() for atom in pair if "C4'" in atom.get_fullname() ]
atom_c1p_pair = [ atom.get_coord() for atom in pair if "C1'" in atom.get_fullname() ]
atom_b1_pair = pos_b1(pair)
a1_pair = Vector(atom_c4_pair[0])
a2_pair = Vector(atom_c1p_pair[0])
a3_pair = Vector(atom_b1_pair)
if pair.get_resname()=='C' or pair.get_resname()=='U' :
if pair.get_resname()=='A' or pair.get_resname()=='G' :
atom_c1p_pair = [ atom.get_coord() for atom in pair if "C1'" in atom.get_fullname() ]
atom_b1_pair = pos_b1(pair)
atom_b2_pair = pos_b2(pair)
......@@ -1627,7 +1627,6 @@ def measures_aa(name, s, thr_idx):
atom_n4 = [ atom.get_coord() for atom in res if "N4" in atom.get_fullname() ]
atom_o4 = [ atom.get_coord() for atom in res if atom.get_name() == "O4"]
op3_p = get_euclidian_distance(atom_op3[0], atom_p[0])
last_o3p_p = get_euclidian_distance(last_o3p[0], atom_p[0]) # link with the previous nucleotide
p_op1 = get_euclidian_distance(atom_op1[0], atom_p[0])
......@@ -1685,7 +1684,7 @@ def measures_aa(name, s, thr_idx):
df=pd.concat([df_comm, df_pur, df_pyr], axis = 1)
pbar.close()
df.to_csv(runDir+"/results/geometry/all-atoms/distances/dist_atoms "+name+".csv")
df.to_csv(runDir + "/results/geometry/all-atoms/distances/dist_atoms " + name + ".csv")
@trace_unhandled_exceptions
def measures_hrna(name, s, thr_idx):
......