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Sec struct #35

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Sec struct #35

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83c2626
Fixed single pdb problems
sreisser May 29, 2018
e014b75
replaced deprecated expm3 with expm
sreisser May 29, 2018
cc8552a
Merge remote branch 'origin/master' into sec_struct
sreisser May 29, 2018
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73 changes: 26 additions & 47 deletions barnaba/functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1236,57 +1236,36 @@ def parse_dotbracket(threshold, file, weights):
# mult_chain = True
if not line.startswith("#"):
l = line.split()
if "pdb" in l[0].lower():
dotbr = l[1]
if len(dotbr) != len(sequence):
print(mult_chain)
if not mult_chain:
sys.exit("Dot-bracket length does not match sequence length")
else:
dotbr = dotbr[:len(sequence)]
base_pairs = parse_dotbr(dotbr)
for bp in base_pairs:
ann_list[bp[0], bp[1], "WCc"] = 1.
list_base_pairs = base_pairs
ann_lists.append(dict(ann_list))
ann_list = {}
else:
try: int(l[0])
except ValueError:
continue
dotbr = l[1]
if len(dotbr) != len(sequence):
if not mult_chain:
sys.exit("Dot-bracket length does not match sequence length")
else:
traj = True
dotbr = l[1]
if len(dotbr) != len(sequence):
if not mult_chain:
sys.exit("Dot-bracket length does not match sequence length")
else:
dotbr = dotbr[:len(sequence)]
n_frames += 1
base_pairs = parse_dotbr(dotbr)
for bp in base_pairs:
if bp not in list_base_pairs:
list_base_pairs.append(bp)
try:
ann_list[bp[0], bp[1], "WCc"]
except:
if len(weights) == 0:
ann_list[bp[0], bp[1], "WCc"] = 1.
else:
ann_list[bp[0], bp[1], "WCc"] = weights[n_frames-1]
else:
if len(weights) == 0:
ann_list[bp[0], bp[1], "WCc"] += 1.
else:
dotbr = dotbr[:len(sequence)]
n_frames += 1
base_pairs = parse_dotbr(dotbr)
for bp in base_pairs:
if bp not in list_base_pairs:
list_base_pairs.append(bp)
try:
ann_list[bp[0], bp[1], "WCc"]
except:
if len(weights) == 0:
ann_list[bp[0], bp[1], "WCc"] = 1.
else:
ann_list[bp[0], bp[1], "WCc"] = weights[n_frames-1]
else:
if len(weights) == 0:
ann_list[bp[0], bp[1], "WCc"] += 1.
else:
ann_list[bp[0], bp[1], "WCc"] += weights[n_frames-1]
if len(list_base_pairs) == 0:
sys.exit("No basepairs found.")
if traj:
for ann, value in ann_list.items():
if len(weights) == 0:
ann_list[ann] /= n_frames
else:
ann_list[ann] /= sum(weights)
for ann, value in ann_list.items():
if len(weights) == 0:
ann_list[ann] /= n_frames
else:
ann_list[ann] /= sum(weights)
chains = [0]
return sequence, ann_list, list_base_pairs, n_frames

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7 changes: 5 additions & 2 deletions bin/barnaba
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Original file line number Diff line number Diff line change
Expand Up @@ -316,15 +316,18 @@ def annotate(args):
for i in range(len(args.pdbs)):
st, pair, res = bb.annotate(args.pdbs[i])
stri_p += "# SEQ " + (" ".join([f for f in res]) + "\n")
stri_p += "# sequence %s\n" % "-".join(res)
stri_p += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
stri_p += "".join([ "%-10s %-10s %4s \n" % (res[pair[0][0][e][0]],res[pair[0][0][e][1]],pair[0][1][e]) for e in range(len(pair[0][0]))])

stri_s += "# sequence %s\n" % "-".join(res)
stri_s += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
stri_s += "".join([ "%-10s %-10s %4s \n" % (res[st[0][0][e][0]],res[st[0][0][e][1]],st[0][1][e]) for e in range(len(st[0][0]))])

if(args.dotbr):
dotbr,ss = bb.dot_bracket(pair,res)
stri_dot += "# SEQ %s" % ss
stri_dot += "# sequence %s\n" % "-".join(res)
stri_dot += "%-20s %s\n" %(args.pdbs[i].split("/")[-1],dotbr[0])


Expand Down Expand Up @@ -724,13 +727,13 @@ def sec_structure(args):
output += "%8d%10.2e%10.2e%10.2e%10d\n" % (i, E, max_F, h, r_i)
print( i, " steps of minmization")
output += "%d steps of minmization\n" % (i)
from scipy.linalg import expm3, norm
from scipy.linalg import expm, norm

av_stem_vector = np.mean([pos[int(param_stem[0][1])], pos[int(param_stem[0][2])]], axis=0) - np.mean([pos[int(param_stem[len(param_stem)-1][1])], pos[int(param_stem[len(param_stem)-1][2])]], axis=0)
theta = np.arctan2(-av_stem_vector[0], -av_stem_vector[1])

def M(axis, theta):
return expm3(np.cross(np.eye(3), axis/norm(axis)*theta))
return expm(np.cross(np.eye(3), axis/norm(axis)*theta))
axis = [0,0,1]
m0 = M(axis, theta)
trans_pos = np.full((len(pos),3), [dimensions*.5, dimensions*.5, 0])
Expand Down