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
Louis BECQUEY
2021-06-17 11:40:11 +0200
Browse Files
Options
Browse Files
Download
Email Patches
Plain Diff
Commit
574c6145372b97d0b7998039df81381adb650100
574c6145
1 parent
b334af48
correct atom names in basepairs
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
5 additions
and
6 deletions
statistics.py
statistics.py
View file @
574c614
...
...
@@ -1405,14 +1405,14 @@ def basepair_flat_angle(res, pair):
"""
measurement of the plane angles formed by the vectors C1->B1 of the paired nucleotides
"""
if
res
.
get_resname
()
==
'
A'
or
res
.
get_resname
()
==
'G'
or
res
.
get_resname
()
==
'
C'
or
res
.
get_resname
()
==
'U'
:
if
res
.
get_resname
()
==
'C'
or
res
.
get_resname
()
==
'U'
:
atom_c4_res
=
[
atom
.
get_coord
()
for
atom
in
res
if
"C4'"
in
atom
.
get_fullname
()
]
atom_c1p_res
=
[
atom
.
get_coord
()
for
atom
in
res
if
"C1'"
in
atom
.
get_fullname
()
]
atom_b1_res
=
pos_b1
(
res
)
a1_res
=
Vector
(
atom_c4_res
[
0
])
a2_res
=
Vector
(
atom_c1p_res
[
0
])
a3_res
=
Vector
(
atom_b1_res
[
0
])
if
res
.
get_resname
()
==
'
C'
or
res
.
get_resname
()
==
'U
'
:
if
res
.
get_resname
()
==
'
A'
or
res
.
get_resname
()
==
'G
'
:
atom_c1p_res
=
[
atom
.
get_coord
()
for
atom
in
res
if
"C1'"
in
atom
.
get_fullname
()
]
atom_b1_res
=
pos_b1
(
res
)
atom_b2_res
=
pos_b2
(
res
)
...
...
@@ -1420,14 +1420,14 @@ def basepair_flat_angle(res, pair):
a2_res
=
Vector
(
atom_b1_res
[
0
])
a3_res
=
Vector
(
atom_b2_res
[
0
])
if
pair
.
get_resname
()
==
'
A'
or
pair
.
get_resname
()
==
'G'
or
pair
.
get_resname
()
==
'
C'
or
pair
.
get_resname
()
==
'U'
:
if
pair
.
get_resname
()
==
'C'
or
pair
.
get_resname
()
==
'U'
:
atom_c4_pair
=
[
atom
.
get_coord
()
for
atom
in
pair
if
"C4'"
in
atom
.
get_fullname
()
]
atom_c1p_pair
=
[
atom
.
get_coord
()
for
atom
in
pair
if
"C1'"
in
atom
.
get_fullname
()
]
atom_b1_pair
=
pos_b1
(
pair
)
a1_pair
=
Vector
(
atom_c4_pair
[
0
])
a2_pair
=
Vector
(
atom_c1p_pair
[
0
])
a3_pair
=
Vector
(
atom_b1_pair
)
if
pair
.
get_resname
()
==
'
C'
or
pair
.
get_resname
()
==
'U
'
:
if
pair
.
get_resname
()
==
'
A'
or
pair
.
get_resname
()
==
'G
'
:
atom_c1p_pair
=
[
atom
.
get_coord
()
for
atom
in
pair
if
"C1'"
in
atom
.
get_fullname
()
]
atom_b1_pair
=
pos_b1
(
pair
)
atom_b2_pair
=
pos_b2
(
pair
)
...
...
@@ -1627,7 +1627,6 @@ 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
])
...
...
@@ -1685,7 +1684,7 @@ def measures_aa(name, s, thr_idx):
df
=
pd
.
concat
([
df_comm
,
df_pur
,
df_pyr
],
axis
=
1
)
pbar
.
close
()
df
.
to_csv
(
runDir
+
"/results/geometry/all-atoms/distances/dist_atoms "
+
name
+
".csv"
)
df
.
to_csv
(
runDir
+
"/results/geometry/all-atoms/distances/dist_atoms "
+
name
+
".csv"
)
@trace_unhandled_exceptions
def
measures_hrna
(
name
,
s
,
thr_idx
):
...
...
Please
register
or
login
to post a comment