Toggle navigation
Toggle navigation
This project
Loading...
Sign in
Louis BECQUEY
/
RNANet
Go to a project
Toggle navigation
Toggle navigation pinning
Projects
Groups
Snippets
Help
Project
Activity
Repository
Pipelines
Graphs
Issues
0
Merge Requests
0
Wiki
Network
Create a new issue
Builds
Commits
Authored by
Aglaé TABOT
2021-06-21 12:15:30 +0200
1
Browse Files
Options
Browse Files
Download
Email Patches
Plain Diff
Commit
8b616dd66e40afdeb4eef78b54c1682b1445e54a
8b616dd6
1 parent
beff1fea
removal of [0] in measures_aa
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
42 additions
and
39 deletions
statistics.py
statistics.py
View file @
8b616dd
...
...
@@ -1627,51 +1627,51 @@ 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
]
)
p_op2
=
get_euclidian_distance
(
atom_op2
[
0
],
atom_p
[
0
]
)
p_o5p
=
get_euclidian_distance
(
atom_o5p
[
0
],
atom_p
[
0
]
)
o5p_c5p
=
get_euclidian_distance
(
atom_o5p
[
0
],
atom_c5p
[
0
]
)
c5p_c4p
=
get_euclidian_distance
(
atom_c5p
[
0
],
atom_c4p
[
0
]
)
c4p_o4p
=
get_euclidian_distance
(
atom_c4p
[
0
],
atom_o4p
[
0
]
)
c4p_c3p
=
get_euclidian_distance
(
atom_c4p
[
0
],
atom_c3p
[
0
]
)
o4p_c1p
=
get_euclidian_distance
(
atom_o4p
[
0
],
atom_c1p
[
0
]
)
c1p_c2p
=
get_euclidian_distance
(
atom_c1p
[
0
],
atom_c2p
[
0
]
)
c2p_o2p
=
get_euclidian_distance
(
atom_c2p
[
0
],
atom_o2p
[
0
]
)
c2p_c3p
=
get_euclidian_distance
(
atom_c2p
[
0
],
atom_c3p
[
0
]
)
c3p_o3p
=
get_euclidian_distance
(
atom_c3p
[
0
],
atom_o3p
[
0
]
)
op3_p
=
get_euclidian_distance
(
atom_op3
,
atom_p
)
last_o3p_p
=
get_euclidian_distance
(
last_o3p
,
atom_p
)
# link with the previous nucleotide
p_op1
=
get_euclidian_distance
(
atom_op1
,
atom_p
)
p_op2
=
get_euclidian_distance
(
atom_op2
,
atom_p
)
p_o5p
=
get_euclidian_distance
(
atom_o5p
,
atom_p
)
o5p_c5p
=
get_euclidian_distance
(
atom_o5p
,
atom_c5p
)
c5p_c4p
=
get_euclidian_distance
(
atom_c5p
,
atom_c4p
)
c4p_o4p
=
get_euclidian_distance
(
atom_c4p
,
atom_o4p
)
c4p_c3p
=
get_euclidian_distance
(
atom_c4p
,
atom_c3p
)
o4p_c1p
=
get_euclidian_distance
(
atom_o4p
,
atom_c1p
)
c1p_c2p
=
get_euclidian_distance
(
atom_c1p
,
atom_c2p
)
c2p_o2p
=
get_euclidian_distance
(
atom_c2p
,
atom_o2p
)
c2p_c3p
=
get_euclidian_distance
(
atom_c2p
,
atom_c3p
)
c3p_o3p
=
get_euclidian_distance
(
atom_c3p
,
atom_o3p
)
last_o3p
=
atom_o3p
# o3' of this residue becomes the previous o3' of the following
#different cases for the aromatic cycles
if
res
.
get_resname
()
==
'A'
or
res
.
get_resname
()
==
'G'
:
# computes the distances between atoms of aromatic cycles
c1p_n9
=
get_euclidian_distance
(
atom_c1p
[
0
],
atom_n9
[
0
]
)
n9_c8
=
get_euclidian_distance
(
atom_n9
[
0
],
atom_c8
[
0
]
)
c8_n7
=
get_euclidian_distance
(
atom_c8
[
0
],
atom_n7
[
0
]
)
n7_c5
=
get_euclidian_distance
(
atom_n7
[
0
],
atom_c5
[
0
]
)
c5_c6
=
get_euclidian_distance
(
atom_c5
[
0
],
atom_c6
[
0
]
)
c6_o6
=
get_euclidian_distance
(
atom_c6
[
0
],
atom_o6
[
0
]
)
c6_n6
=
get_euclidian_distance
(
atom_c6
[
0
],
atom_n6
[
0
]
)
c6_n1
=
get_euclidian_distance
(
atom_c6
[
0
],
atom_n1
[
0
]
)
n1_c2
=
get_euclidian_distance
(
atom_n1
[
0
],
atom_c2
[
0
]
)
c2_n2
=
get_euclidian_distance
(
atom_c2
[
0
],
atom_n2
[
0
]
)
c2_n3
=
get_euclidian_distance
(
atom_c2
[
0
],
atom_n3
[
0
]
)
n3_c4
=
get_euclidian_distance
(
atom_n3
[
0
],
atom_c4
[
0
]
)
c4_n9
=
get_euclidian_distance
(
atom_c4
[
0
],
atom_n9
[
0
]
)
c4_c5
=
get_euclidian_distance
(
atom_c4
[
0
],
atom_c5
[
0
]
)
c1p_n9
=
get_euclidian_distance
(
atom_c1p
,
atom_n9
)
n9_c8
=
get_euclidian_distance
(
atom_n9
,
atom_c8
)
c8_n7
=
get_euclidian_distance
(
atom_c8
,
atom_n7
)
n7_c5
=
get_euclidian_distance
(
atom_n7
,
atom_c5
)
c5_c6
=
get_euclidian_distance
(
atom_c5
,
atom_c6
)
c6_o6
=
get_euclidian_distance
(
atom_c6
,
atom_o6
)
c6_n6
=
get_euclidian_distance
(
atom_c6
,
atom_n6
)
c6_n1
=
get_euclidian_distance
(
atom_c6
,
atom_n1
)
n1_c2
=
get_euclidian_distance
(
atom_n1
,
atom_c2
)
c2_n2
=
get_euclidian_distance
(
atom_c2
,
atom_n2
)
c2_n3
=
get_euclidian_distance
(
atom_c2
,
atom_n3
)
n3_c4
=
get_euclidian_distance
(
atom_n3
,
atom_c4
)
c4_n9
=
get_euclidian_distance
(
atom_c4
,
atom_n9
)
c4_c5
=
get_euclidian_distance
(
atom_c4
,
atom_c5
)
if
res
.
get_resname
()
==
'C'
or
res
.
get_resname
()
==
'U'
:
c1p_n1
=
get_euclidian_distance
(
atom_c1p
[
0
],
atom_n1
[
0
]
)
n1_c6
=
get_euclidian_distance
(
atom_n1
[
0
],
atom_c6
[
0
]
)
c6_c5
=
get_euclidian_distance
(
atom_c6
[
0
],
atom_c5
[
0
]
)
c5_c4
=
get_euclidian_distance
(
atom_c5
[
0
],
atom_c4
[
0
]
)
c4_n3
=
get_euclidian_distance
(
atom_c4
[
0
],
atom_n3
[
0
]
)
n3_c2
=
get_euclidian_distance
(
atom_n3
[
0
],
atom_c2
[
0
]
)
c2_o2
=
get_euclidian_distance
(
atom_c2
[
0
],
atom_o2
[
0
]
)
c2_n1
=
get_euclidian_distance
(
atom_c2
[
0
],
atom_n1
[
0
]
)
c4_n4
=
get_euclidian_distance
(
atom_c4
[
0
],
atom_n4
[
0
]
)
c4_o4
=
get_euclidian_distance
(
atom_c4
[
0
],
atom_o4
[
0
]
)
c1p_n1
=
get_euclidian_distance
(
atom_c1p
,
atom_n1
)
n1_c6
=
get_euclidian_distance
(
atom_n1
,
atom_c6
)
c6_c5
=
get_euclidian_distance
(
atom_c6
,
atom_c5
)
c5_c4
=
get_euclidian_distance
(
atom_c5
,
atom_c4
)
c4_n3
=
get_euclidian_distance
(
atom_c4
,
atom_n3
)
n3_c2
=
get_euclidian_distance
(
atom_n3
,
atom_c2
)
c2_o2
=
get_euclidian_distance
(
atom_c2
,
atom_o2
)
c2_n1
=
get_euclidian_distance
(
atom_c2
,
atom_n1
)
c4_n4
=
get_euclidian_distance
(
atom_c4
,
atom_n4
)
c4_o4
=
get_euclidian_distance
(
atom_c4
,
atom_o4
)
liste_common
.
append
([
res
.
get_resname
(),
last_o3p_p
,
op3_p
,
p_op1
,
p_op2
,
p_o5p
,
o5p_c5p
,
c5p_c4p
,
c4p_o4p
,
c4p_c3p
,
o4p_c1p
,
c1p_c2p
,
c2p_o2p
,
c2p_c3p
,
c3p_o3p
]
)
liste_purines
.
append
([
c1p_n9
,
n9_c8
,
c8_n7
,
n7_c5
,
c5_c6
,
c6_o6
,
c6_n6
,
c6_n1
,
n1_c2
,
c2_n2
,
c2_n3
,
n3_c4
,
c4_n9
,
c4_c5
])
...
...
@@ -3004,6 +3004,7 @@ if __name__ == "__main__":
joblist
.
append
(
Job
(
function
=
measure_from_structure
,
args
=
(
f
,),
how_many_in_parallel
=
nworkers
))
# All-atom distances
# Basepair geometries statistics (from RNACifs/ 3D files)
ld
=
os
.
listdir
(
path_to_3D_data
+
'datapoints'
)
if
'4zdo_1_E'
in
ld
:
ld
.
remove
(
'4zdo_1_E'
)
# weird cases to remove for now
...
...
@@ -3016,6 +3017,7 @@ if __name__ == "__main__":
#exit()
process_jobs
(
joblist
)
# Now process the memory-heavy tasks family by family
...
...
@@ -3029,7 +3031,7 @@ if __name__ == "__main__":
print
()
print
()
# finish the work after the parallel portions
per_chain_stats
()
# per chain base frequencies en basepair types
...
...
@@ -3060,3 +3062,4 @@ if __name__ == "__main__":
joblist
.
append
(
Job
(
function
=
gmm_wadley
,
args
=
()))
if
len
(
joblist
):
process_jobs
(
joblist
)
...
...
Aglaé TABOT
@atabot
2021-08-16 15:07:17 UTC
mentioned in commit
4b50dab0
Please
register
or
login
to post a comment