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Raise exceptions instead of sys.exit #62

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Raise exceptions instead of sys.exit #62

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2212ecb
Raise exceptions instead of sys.exit in module functions
ollyfutur Mar 20, 2024
f28ab02
Alias np.float deprecated in modern numpy versions
ollyfutur Mar 20, 2024
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35 changes: 14 additions & 21 deletions barnaba/functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -237,8 +237,7 @@ def rmsd_traj(reference,traj,out=None,heavy_atom=False):
assert(len(nn_traj.ok_residues)==len(nn_ref.ok_residues))
# check that sequence is identical when using heavy atoms
if(nn_traj.rna_seq_id!=nn_ref.rna_seq_id and heavy_atom==True):
sys.stderr.write("# Sequences are not identical, cannot superimpose using all heavy atoms. ")
sys.exit(1)
raise ValueError("Sequences are not identical, cannot superimpose using all heavy atoms.")

# loop over residues and find common heavy atoms
idx_ref = []
Expand Down Expand Up @@ -272,9 +271,7 @@ def rmsd_traj(reference,traj,out=None,heavy_atom=False):
print("# found ",len(idx_ref), "atoms in common")

if(len(idx_ref)<3):
warn = "# Only %d atoms in common. abort.\n" % len(idx_ref)
sys.stderr.write(warn)
sys.exit(1)
raise ValueError("Only %d atoms in common." % len(idx_ref))

traj.superpose(reference,atom_indices=idx_target, ref_atom_indices=idx_ref)
if(out!=None): traj.save(out)
Expand Down Expand Up @@ -334,11 +331,8 @@ def backbone_angles_traj(traj,residues=None,angles=None):
if(angles[i] in definitions.bb_angles):
idx_angles.append(definitions.bb_angles.index(angles[i]))
else:
msg = "# Fatal error. requested angle \"%s\" not available.\n" % angles[i]
msg += "# Choose from: %s \n" % definitions.bb_angles
sys.stderr.write(msg)
sys.exit(1)

raise ValueError("Requested angle '%s' not available. Choose from: %s." %
(angles[i], definitions.bb_angles))

idxs = (all_idx[:,idx_angles,:]).reshape(-1,4)
missing = np.where(np.sum(idxs,axis=1)==0)
Expand Down Expand Up @@ -403,10 +397,9 @@ def sugar_angles_traj(traj,residues=None,angles=None):
if(angles[i] in definitions.sugar_angles):
idx_angles.append(definitions.sugar_angles.index(angles[i]))
else:
msg = "# Fatal error. requested angle \"%s\" not available.\n" % angles[i]
msg += "# Choose from: %s \n" % (definitions.sugar_angles)
sys.stderr.write(msg)
sys.exit(1)
raise ValueError("Requested angle '%s' not available. Choose from: %s." %
(angles[i], definitions.sugar_angles))


idxs = (all_idx[:,idx_angles,:]).reshape(-1,4)
missing = np.where(np.sum(idxs,axis=1)==0)
Expand Down Expand Up @@ -543,10 +536,10 @@ def jcouplings_traj(traj,residues=None,couplings=None,raw=False):
idx_angles.append(definitions.couplings_idx[couplings[i]])
idx_angles1.append(i)
else:
msg = "# Fatal error. requested coupling \"%s\" not available.\n" % couplings[i]
msg += "# Choose from: %s \n" % definitions.couplings_idx
sys.stderr.write(msg)
sys.exit(1)
raise ValueError("Requested coupling '%s' not available. Choose from: %s." %
(couplings[i], definitions.couplings_idx))



idxs = (all_idx[:,idx_angles,:]).reshape(-1,4)
missing = np.where(np.sum(idxs,axis=1)==0)
Expand Down Expand Up @@ -1298,7 +1291,7 @@ def parse_dotbracket(threshold, file, weights):
if len(dotbr) != len(sequence):
print(mult_chain)
if not mult_chain:
sys.exit("Dot-bracket length does not match sequence length")
raise ValueError("Dot-bracket length does not match sequence length.")
else:
dotbr = dotbr[:len(sequence)]
base_pairs = parse_dotbr(dotbr)
Expand All @@ -1316,7 +1309,7 @@ def parse_dotbracket(threshold, file, weights):
dotbr = l[1]
if len(dotbr) != len(sequence):
if not mult_chain:
sys.exit("Dot-bracket length does not match sequence length")
raise ValueError("Dot-bracket length does not match sequence length.")
else:
dotbr = dotbr[:len(sequence)]
n_frames += 1
Expand All @@ -1337,7 +1330,7 @@ def parse_dotbracket(threshold, file, weights):
else:
ann_list[bp[0], bp[1], "WCc"] += weights[n_frames-1]
if len(list_base_pairs) == 0:
sys.exit("No basepairs found.")
raise ValueError("No basepairs found.")
if traj:
for ann, value in ann_list.items():
if len(weights) == 0:
Expand Down
2 changes: 1 addition & 1 deletion barnaba/kde.py
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Expand Up @@ -239,7 +239,7 @@ def evaluate(self, points):
self.d)
raise ValueError(msg)

result = zeros((m,), dtype=np.float)
result = zeros((m,), dtype=float)

if m >= self.n:
# there are more points than data, so loop over data
Expand Down
3 changes: 1 addition & 2 deletions barnaba/model.py
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Expand Up @@ -29,8 +29,7 @@ def __init__(self,data,set_lcs=False):

ll = len(data)
if(ll==0):
sys.stderr.write("# Fatal error. No valid residues in pdb file \n")
sys.exit(1)
raise ValueError("No valid residues in pdb file.")

# array with all coordinates
self.coords = np.array([data[i][5:8] for i in range(ll)])
Expand Down
23 changes: 8 additions & 15 deletions barnaba/nucleic.py
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Expand Up @@ -81,9 +81,7 @@ def __init__(self,topology,modified=True):
self.indeces_lcs = np.asarray(indeces_lcs).T

if(len(self.ok_residues)<1):
warn = "# Only %d found in structure. Exiting \n" % len(self.ok_residues)
sys.stderr.write(warn)
sys.exit(1)
raise ValueError("Only %d found in structure." % len(self.ok_residues))
#else:
# warn = "# %d nucleotides found in structure \n" % len(ok_residues)
# sys.stderr.write(warn)
Expand All @@ -101,10 +99,8 @@ def get_bb_torsion_idx(self, residues=None):
if(residues[k] in self.rna_seq):
idx_residues.append((self.rna_seq).index(residues[k]))
else:
msg = "# Fatal error. Residue \"%s\" not found \n" % residues[k]
msg += "# The list of residues is: %s \n" % self.rna_seq
sys.stderr.write(msg)
sys.exit(1)
raise ValueError("Residue '%s' not found. The list of residues is: %s" %
(residues[k], self.rna_seq))
else:
idx_residues = np.arange(ll)

Expand Down Expand Up @@ -184,10 +180,9 @@ def get_sugar_torsion_idx(self,residues=None):
if(residues[k] in self.rna_seq):
idx_residues.append((self.rna_seq).index(residues[k]))
else:
msg = "# Fatal error. Residue \"%s\" not found \n" % residues[k]
msg += "# The list of residues is: %s \n" % self.rna_seq
sys.stderr.write(msg)
sys.exit(1)
raise ValueError("Residue '%s' not found. The list of residues is: %s" %
(residues[k], self.rna_seq))

else:
idx_residues = np.arange(ll)

Expand Down Expand Up @@ -230,10 +225,8 @@ def get_coupling_idx(self,residues=None):
if(residues[k] in self.rna_seq):
idx_residues.append((self.rna_seq).index(residues[k]))
else:
msg = "# Fatal error. Residue \"%s\" not found \n" % residues[k]
msg += "# The list of residues is: %s \n" % self.rna_seq
sys.stderr.write(msg)
sys.exit(1)
raise ValueError("Residue '%s' not found. The list of residues is: %s" %
(residues[k], self.rna_seq))
else:
idx_residues = np.arange(ll)

Expand Down
3 changes: 1 addition & 2 deletions barnaba/smm.py
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Expand Up @@ -24,8 +24,7 @@ def __init__(self,gvecs,eps,weights=[]):
print("# Sequence lenght =",slen)
self.slen = slen
else:
print("# Error - check your gmat file")
sys.exit(1)
raise ValueError("Check your gmat file")

# calculate distance matrix
dmat_sq = cdist(gvecs,gvecs,'sqeuclidean')
Expand Down
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