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/
RNANet
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Authored by
Aglaé TABOT
2021-06-14 09:57:11 +0200
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Commit
ab43d9d6641a75fcf555d2eebca7d8ca02784a16
ab43d9d6
1 parent
0270d00e
Added pbar to some functions
Hide whitespace changes
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Showing
1 changed file
with
26 additions
and
4 deletions
statistics.py
statistics.py
View file @
ab43d9d
...
...
@@ -1298,7 +1298,7 @@ def dist_atoms(f):
chain
=
next
(
s
[
0
]
.
get_chains
())
#1 chain per file
residues
=
list
(
chain
.
get_residues
())
pbar
=
tqdm
(
total
=
len
(
residues
),
position
=
thr_idx
+
1
,
desc
=
f
"Worker {thr_idx+1}: {f} dist_atoms"
,
unit
=
"
chain
"
,
leave
=
False
)
pbar
=
tqdm
(
total
=
len
(
residues
),
position
=
thr_idx
+
1
,
desc
=
f
"Worker {thr_idx+1}: {f} dist_atoms"
,
unit
=
"
residu
"
,
leave
=
False
)
pbar
.
update
(
0
)
for
res
in
chain
:
...
...
@@ -1624,9 +1624,17 @@ def dist_atoms_hire_RNA (f) :
name
=
str
.
split
(
f
,
'.'
)[
0
]
liste_dist
=
[]
last_c4p
=
[]
global
idxQueue
thr_idx
=
idxQueue
.
get
()
setproctitle
(
f
"RNANet statistics.py Worker {thr_idx+1} dist_atoms_hire_RNA({f})"
)
parser
=
MMCIFParser
()
s
=
parser
.
get_structure
(
name
,
os
.
path
.
abspath
(
"/home/data/RNA/3D/rna_only/"
+
f
))
chain
=
next
(
s
[
0
]
.
get_chains
())
residues
=
list
(
chain
.
get_residues
())
pbar
=
tqdm
(
total
=
len
(
residues
),
position
=
thr_idx
+
1
,
desc
=
f
"Worker {thr_idx+1}: {f} dist_atoms_hire_RNA"
,
unit
=
"residu"
,
leave
=
False
)
pbar
.
update
(
0
)
os
.
makedirs
(
runDir
+
"/results/distances_hRNA/"
,
exist_ok
=
True
)
for
res
in
chain
:
p_o5p
=
None
...
...
@@ -1692,9 +1700,13 @@ def dist_atoms_hire_RNA (f) :
liste_dist
.
append
([
res
.
get_resname
(),
last_c4p_p
,
p_o5p
,
o5p_c5p
,
c5p_c4p
,
c4p_c1p
,
c1p_b1
,
b1_b2
])
pbar
.
update
(
1
)
df
=
pd
.
DataFrame
(
liste_dist
,
columns
=
[
"Residu"
,
"C4'-P"
,
"P-O5'"
,
"O5'-C5'"
,
"C5'-C4'"
,
"C4'-C1'"
,
"C1'-B1"
,
"B1-B2"
])
pbar
.
close
()
df
.
to_csv
(
runDir
+
'/results/distances_hRNA/'
+
'dist_atoms_hire_RNA '
+
name
+
'.csv'
)
idxQueue
.
put
(
thr_idx
)
# replace the thread index in the queue
setproctitle
(
f
"RNANet statistics.py Worker {thr_idx+1} finished"
)
def
conversion_angles
(
bdd
):
'''
...
...
@@ -1771,13 +1783,19 @@ def angles_torsion_hire_RNA(f):
last_c4p
=
[]
last_c5p
=
[]
last_c1p
=
[]
global
idxQueue
thr_idx
=
idxQueue
.
get
()
setproctitle
(
f
"RNANet statistics.py Worker {thr_idx+1} angles_torsion_hire_RNA({f})"
)
os
.
makedirs
(
runDir
+
"/results/torsion_angles_hRNA/"
,
exist_ok
=
True
)
parser
=
MMCIFParser
()
s
=
parser
.
get_structure
(
name
,
os
.
path
.
abspath
(
"/home/data/RNA/3D/rna_only/"
+
f
))
chain
=
next
(
s
[
0
]
.
get_chains
())
residues
=
list
(
chain
.
get_residues
())
pbar
=
tqdm
(
total
=
len
(
residues
),
position
=
thr_idx
+
1
,
desc
=
f
"Worker {thr_idx+1}: {f} angles_torsion_hire_RNA"
,
unit
=
"residu"
,
leave
=
False
)
pbar
.
update
(
0
)
for
res
in
chain
:
p_o5_c5_c4
=
np
.
nan
...
...
@@ -1873,9 +1891,13 @@ def angles_torsion_hire_RNA(f):
last_c5p
=
atom_c5p
last_c1p
=
atom_c1p
liste_angles_torsion
.
append
([
res
.
get_resname
(),
p_o5_c5_c4
,
o5_c5_c4_c1
,
c5_c4_c1_b1
,
c4_c1_b1_b2
,
o5_c5_c4_psuiv
,
c5_c4_psuiv_o5suiv
,
c4_psuiv_o5suiv_c5suiv
,
c1_c4_psuiv_o5suiv
])
pbar
.
update
(
1
)
df
=
pd
.
DataFrame
(
liste_angles_torsion
,
columns
=
[
"Residu"
,
"P-O5'-C5'-C4'"
,
"O5'-C5'-C4'-C1'"
,
"C5'-C4'-C1'-B1"
,
"C4'-C1'-B1-B2"
,
"O5'-C5'-C4'-P°"
,
"C5'-C4'-P°-O5'°"
,
"C4'-P°-O5'°-C5'°"
,
"C1'-C4'-P°-O5'°"
])
pbar
.
close
()
df
.
to_csv
(
runDir
+
'/results/torsion_angles_hRNA/'
+
'angles_torsion_hire_RNA '
+
name
+
'.csv'
)
idxQueue
.
put
(
thr_idx
)
# replace the thread index in the queue
setproctitle
(
f
"RNANet statistics.py Worker {thr_idx+1} finished"
)
if
__name__
==
"__main__"
:
...
...
@@ -2014,7 +2036,7 @@ if __name__ == "__main__":
#conversion_eta_theta('/home/atabot/RNANet.db')
#exit()
f_prec
=
os
.
listdir
(
path_to_3D_data
+
"rna_only"
)[
0
]
for
f
in
os
.
listdir
(
path_to_3D_data
+
"rna_only"
)[:
100
]:
for
f
in
os
.
listdir
(
path_to_3D_data
+
"rna_only"
)[:
100
]:
joblist
.
append
(
Job
(
function
=
dist_atoms
,
args
=
(
f
,)))
joblist
.
append
(
Job
(
function
=
dist_atoms_hire_RNA
,
args
=
(
f
,)))
joblist
.
append
(
Job
(
function
=
angles_torsion_hire_RNA
,
args
=
(
f
,)))
...
...
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