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Christian Faber
BioHelpers
Commits
2df21f06
Commit
2df21f06
authored
10 months ago
by
Christian Faber
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clean up cmap
parent
aa1b1e41
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3 changed files
setup.py
+1
-1
1 addition, 1 deletion
setup.py
src/BioHelpers_FABER.egg-info/PKG-INFO
+1
-1
1 addition, 1 deletion
src/BioHelpers_FABER.egg-info/PKG-INFO
src/BioHelpers_FABER/cmap.py
+8
-6
8 additions, 6 deletions
src/BioHelpers_FABER/cmap.py
with
10 additions
and
8 deletions
setup.py
+
1
−
1
View file @
2df21f06
...
@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
...
@@ -5,7 +5,7 @@ with open("README.md", "r") as f:
setup
(
setup
(
name
=
"
BioHelpers_FABER
"
,
name
=
"
BioHelpers_FABER
"
,
version
=
"
0.1.2
0
"
,
version
=
"
0.1.2
1
"
,
description
=
"
Small collection of useful scripts for the computational work with RNA Data.
"
,
description
=
"
Small collection of useful scripts for the computational work with RNA Data.
"
,
url
=
"
https://gitlab.jsc.fz-juelich.de/faber1/biohelpers
"
,
url
=
"
https://gitlab.jsc.fz-juelich.de/faber1/biohelpers
"
,
package_dir
=
{
""
:
"
src
"
},
package_dir
=
{
""
:
"
src
"
},
...
...
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src/BioHelpers_FABER.egg-info/PKG-INFO
+
1
−
1
View file @
2df21f06
Metadata-Version: 2.1
Metadata-Version: 2.1
Name: BioHelpers-FABER
Name: BioHelpers-FABER
Version: 0.1.
18
Version: 0.1.
20
Summary: Small collection of useful scripts for the computational work with RNA Data.
Summary: Small collection of useful scripts for the computational work with RNA Data.
Home-page: https://gitlab.jsc.fz-juelich.de/faber1/biohelpers
Home-page: https://gitlab.jsc.fz-juelich.de/faber1/biohelpers
Author: Christian Faber
Author: Christian Faber
...
...
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src/BioHelpers_FABER/cmap.py
+
8
−
6
View file @
2df21f06
...
@@ -63,10 +63,12 @@ class Cmap:
...
@@ -63,10 +63,12 @@ class Cmap:
self
.
reference
=
reference
self
.
reference
=
reference
self
.
contact_threshold
=
contact_threshold
self
.
contact_threshold
=
contact_threshold
self
.
positioning
,
self
.
sequence
=
bm
.
get_sequence_position
(
filename
)
self
.
positioning
,
self
.
sequence
=
bm
.
get_sequence_position
(
filename
)
if
start_from_one
:
if
not
start_from_one
:
shift
=
self
.
positioning
[
0
]
-
1
self
.
positioning
=
[
e
-
shift
for
e
in
self
.
positioning
]
self
.
positioning
.
insert
(
0
,
0
)
self
.
positioning
.
insert
(
0
,
0
)
self
.
positioning
.
insert
(
0
,
0
)
self
.
positioning
.
insert
(
0
,
0
)
self
.
l
=
self
.
positioning
[
-
1
]
-
self
.
positioning
[
0
]
+
1
*
(
not
start_from_one
)
self
.
l
=
self
.
positioning
[
-
1
]
chain
=
next
(
pdb
.
PDBParser
().
get_structure
(
id
,
filename
)[
0
].
get_chains
())
chain
=
next
(
pdb
.
PDBParser
().
get_structure
(
id
,
filename
)[
0
].
get_chains
())
bm
.
cleanup_chain
(
chain
)
bm
.
cleanup_chain
(
chain
)
self
.
native_contacts
=
np
.
zeros
((
len
(
chain
),
len
(
chain
)))
self
.
native_contacts
=
np
.
zeros
((
len
(
chain
),
len
(
chain
)))
...
@@ -77,8 +79,8 @@ class Cmap:
...
@@ -77,8 +79,8 @@ class Cmap:
self
.
contacts
[
"
native
"
]
=
np
.
zeros
((
self
.
l
,
self
.
l
))
self
.
contacts
[
"
native
"
]
=
np
.
zeros
((
self
.
l
,
self
.
l
))
for
c
in
bm
.
arr_to_contact_list
(
self
.
native_contacts
):
for
c
in
bm
.
arr_to_contact_list
(
self
.
native_contacts
):
self
.
contacts
[
"
native
"
][
self
.
contacts
[
"
native
"
][
self
.
num_to_id
(
c
[
0
])
-
self
.
positioning
[
0
]
-
1
*
(
not
start_from_one
)
,
self
.
num_to_id
(
c
[
0
]),
self
.
num_to_id
(
c
[
1
])
-
self
.
positioning
[
0
]
-
1
*
(
not
start_from_one
)
,
self
.
num_to_id
(
c
[
1
]),
]
=
1
]
=
1
self
.
pdb_id
=
id
self
.
pdb_id
=
id
...
...
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