Louis BECQUEY / RNANet

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Louis BECQUEY
ec43d66b 1 parent 0e22c8ff

fixed missing atom declaration

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Showing 1 changed file with 28 additions and 28 deletions
......@@ -1484,6 +1484,7 @@ def measures_wadley(name, s, thr_idx):
if res.get_resname() not in ['ATP', 'CCC', 'A3P', 'A23', 'GDP', 'RIA', "2BA"] :
atom_p = [ atom.get_coord() for atom in res if atom.get_name() == "P"]
atom_c1p = [ atom.get_coord() for atom in res if "C1'" in atom.get_fullname() ]
atom_c4p = [ atom.get_coord() for atom in res if "C4'" in atom.get_fullname() ]
if len(atom_c1p) > 1:
for atom in res:
if "C1'" in atom.get_fullname():
......@@ -2454,8 +2455,8 @@ def gmm_hrna():
c1p_b1 = list(df["C1'-B1"][~ np.isnan(df["C1'-B1"])])
b1_b2 = list(df["B1-B2"][~ np.isnan(df["B1-B2"])])
os.makedirs(runDir + "/results/figures/HiRE-RNA/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/HiRE-RNA/distances/")
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/distances/")
GMM_histo(o5p_c5p, "O5'-C5'")
GMM_histo(b1_b2, "B1-B2")
......@@ -2476,7 +2477,7 @@ def gmm_hrna():
axes.set_ylim(0, 100)
plt.xlabel("Distance (Angström)")
plt.title("GMM des distances entre atomes HiRE-RNA")
plt.savefig(runDir + "/results/figures/HiRE-RNA/distances/GMM des distances entre atomes HiRE-RNA.png")
plt.savefig(runDir + "/results/figures/GMM/HiRE-RNA/distances/GMM des distances entre atomes HiRE-RNA.png")
plt.close()
# Angles
......@@ -2491,8 +2492,8 @@ def gmm_hrna():
c4p_c1p_b1 = list(df["C4'-C1'-B1"][~ np.isnan(df["C4'-C1'-B1"])])
c1p_b1_b2 = list(df["C1'-B1-B2"][~ np.isnan(df["C1'-B1-B2"])])
os.makedirs(runDir + "/results/figures/HiRE-RNA/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/HiRE-RNA/distances/")
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/distances/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/distances/")
GMM_histo(lastc4p_p_o5p, "C4'-P-O5'", toric=True)
GMM_histo(lastc1p_lastc4p_p, "C1'-C4'-P", toric=True)
......@@ -2515,7 +2516,7 @@ def gmm_hrna():
axes.set_ylim(0, 100)
plt.xlabel("Angle (Degré)")
plt.title("GMM des angles entre atomes HiRE-RNA")
plt.savefig(runDir + "/results/figures/HiRE-RNA/angles/GMM des angles entre atomes HiRE-RNA.png")
plt.savefig(runDir + "/results/figures/GMM/HiRE-RNA/angles/GMM des angles entre atomes HiRE-RNA.png")
plt.close()
# Torsions
......@@ -2530,8 +2531,8 @@ def gmm_hrna():
c4_psuiv_o5suiv_c5suiv = list(df["C4'-P°-O5'°-C5'°"][~ np.isnan(df["C4'-P°-O5'°-C5'°"])])
c1_c4_psuiv_o5suiv = list(df["C1'-C4'-P°-O5'°"][~ np.isnan(df["C1'-C4'-P°-O5'°"])])
os.makedirs(runDir + "/results/figures/HiRE-RNA/torsions/", exist_ok=True)
os.chdir(runDir + "/results/figures/HiRE-RNA/torsions/")
os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/torsions/", exist_ok=True)
os.chdir(runDir + "/results/figures/GMM/HiRE-RNA/torsions/")
GMM_histo(p_o5_c5_c4, "P-O5'-C5'-C4'", toric=True)
GMM_histo(o5_c5_c4_c1, "O5'-C5'-C4'-C1'", toric=True)
......@@ -2945,10 +2946,10 @@ if __name__ == "__main__":
# Define the tasks
joblist = []
# Do eta/theta plots
if n_unmapped_chains and DO_WADLEY_ANALYSIS:
joblist.append(Job(function=reproduce_wadley_results, args=(1, False, (1,4), res_thr)))
joblist.append(Job(function=reproduce_wadley_results, args=(4, False, (1,4), res_thr)))
# # Do eta/theta plots
# if n_unmapped_chains and DO_WADLEY_ANALYSIS:
# joblist.append(Job(function=reproduce_wadley_results, args=(1, False, (1,4), res_thr)))
# joblist.append(Job(function=reproduce_wadley_results, args=(4, False, (1,4), res_thr)))
# Do distance matrices for each family excl. LSU/SSU (will be processed later)
if DO_AVG_DISTANCE_MATRIX:
......@@ -2963,18 +2964,17 @@ if __name__ == "__main__":
joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, True, False)))
joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, False, False)))
# Do general family statistics
joblist.append(Job(function=stats_len)) # Computes figures about chain lengths
joblist.append(Job(function=stats_freq)) # updates the database (nucleotide frequencies in families)
for f in famlist:
joblist.append(Job(function=parallel_stats_pairs, args=(f,))) # updates the database (intra-chain basepair types within a family)
if f not in ignored:
joblist.append(Job(function=to_id_matrix, args=(f,))) # updates the database (identity matrices of families)
# # Do general family statistics
# joblist.append(Job(function=stats_len)) # Computes figures about chain lengths
# joblist.append(Job(function=stats_freq)) # updates the database (nucleotide frequencies in families)
# for f in famlist:
# joblist.append(Job(function=parallel_stats_pairs, args=(f,))) # updates the database (intra-chain basepair types within a family)
# if f not in ignored:
# joblist.append(Job(function=to_id_matrix, args=(f,))) # updates the database (identity matrices of families)
# Do geometric measures on all chains
if n_unmapped_chains:
os.makedirs(runDir+"/results/geometry/all-atoms/distances/", exist_ok=True)
os.makedirs(runDir+"/results/geometry/all-atoms/angles/", exist_ok=True)
f_prec = os.listdir(path_to_3D_data + "rna_only")[0]
for f in os.listdir(path_to_3D_data + "rna_only"):
joblist.append(Job(function=measure_from_structure, args=(f,), how_many_in_parallel=nworkers)) # All-atom distances
......@@ -2992,7 +2992,7 @@ if __name__ == "__main__":
#exit()
# process_jobs(joblist)
process_jobs(joblist)
# Now process the memory-heavy tasks family by family
if DO_AVG_DISTANCE_MATRIX:
......@@ -3016,15 +3016,15 @@ if __name__ == "__main__":
os.makedirs(runDir+"/results/figures/GMM/", exist_ok=True)
os.makedirs(runDir+"/results/geometry/json/", exist_ok=True)
joblist = []
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/all-atoms/distances/', 'dist_atoms.csv')))
if DO_HIRE_RNA_MEASURES:
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/distances/', 'dist_atoms_hire_RNA.csv')))
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/angles/', 'angles_hire_RNA.csv')))
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/torsions/', 'angles_torsion_hire_RNA.csv')))
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/basepairs/', 'basepairs.csv')))
# joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/all-atoms/distances/', 'dist_atoms.csv')))
# if DO_HIRE_RNA_MEASURES:
# joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/distances/', 'dist_atoms_hire_RNA.csv')))
# joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/angles/', 'angles_hire_RNA.csv')))
# joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/torsions/', 'angles_torsion_hire_RNA.csv')))
# joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/HiRE-RNA/basepairs/', 'basepairs.csv')))
if DO_WADLEY_ANALYSIS:
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/Pyle/distances/', 'distances_wadley.csv')))
joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/Pyle/angles/', 'angles_plans_wadley.csv')))
# joblist.append(Job(function=concat_dataframes, args=(runDir + '/results/geometry/Pyle/angles/', 'angles_plans_wadley.csv')))
process_jobs(joblist)
joblist = []
joblist.append(Job(function=gmm_aa_dists, args=()))
......