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Nicolas MAILLET
rpg
Commits
18551f60
Commit
18551f60
authored
May 25, 2021
by
Nicolas MAILLET
Browse files
Add IPC2 to RPG and make it the default one
parent
dce7a910
Pipeline
#57012
passed with stages
in 50 seconds
Changes
4
Pipelines
1
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rpg/RapidPeptidesGenerator.py
View file @
18551f60
...
...
@@ -272,9 +272,9 @@ def main():
"error(s) (--quiet enable, overwrite -v). If output "
"filename already exists, output file will be "
"overwritten."
)
parser
.
add_argument
(
"-p"
,
"--pka"
,
metavar
=
""
,
choices
=
[
'ipc'
,
'stryer'
],
default
=
"ipc"
,
help
=
"Define pKa values. Either 'ipc' "
"
or
'stryer' (default: ipc)"
)
parser
.
add_argument
(
"-p"
,
"--pka"
,
metavar
=
""
,
choices
=
[
'ipc
2
'
,
'stryer'
,
'ipc'
],
default
=
"ipc
2
"
,
help
=
"Define pKa values. Either 'ipc
2
' "
"'stryer'
or 'ipc' (deprecated)
(default: ipc
2
)"
)
group_output
=
parser
.
add_mutually_exclusive_group
()
group_output
.
add_argument
(
"-o"
,
"--outputfile"
,
type
=
str
,
metavar
=
""
,
default
=
""
,
help
=
"Optional result file "
...
...
@@ -306,9 +306,11 @@ def main():
args
.
miscleavage
=
[]
# No miscleavage on concurrent, infinite time
# --pka option
aa_pka
=
core
.
AA_PKA_IPC
aa_pka
=
core
.
AA_PKA_IPC
_2
if
args
.
pka
==
"stryer"
:
aa_pka
=
core
.
AA_PKA_S
elif
args
.
pka
==
"ipc"
:
aa_pka
=
core
.
AA_PKA_IPC
# --list option
if
args
.
list
:
...
...
rpg/core.py
View file @
18551f60
...
...
@@ -86,6 +86,17 @@ AA_PKA_IPC = {"Nterm" : 9.564,
"Y"
:
10.071
,
"Cterm"
:
2.383
}
"""pKa of important amino acid to compute pI (from IPC_peptide. See http://isoelectric.org/theory.html for details)."""
# IPC_peptide2
AA_PKA_IPC_2
=
{
"Nterm"
:
7.947
,
"C"
:
9.454
,
"D"
:
3.969
,
"E"
:
4.507
,
"H"
:
6.439
,
"K"
:
8.165
,
"R"
:
11.493
,
"Y"
:
9.153
,
"Cterm"
:
2.977
}
"""pKa of important amino acid to compute pI (from IPC_peptide2. See http://www.ipc2-isoelectric-point.org/ for details)."""
def
handle_errors
(
message
=
""
,
err
=
1
,
error_type
=
""
):
"""Custom handling of errors and warnings.
...
...
rpg/sequence.py
View file @
18551f60
...
...
@@ -68,9 +68,11 @@ class Peptide:
# self representation for print
def
__repr__
(
self
):
pka
=
"IPC"
pka
=
"IPC
2
"
if
self
.
aa_pka
==
core
.
AA_PKA_S
:
pka
=
"Stryer"
elif
self
.
aa_pka
==
core
.
AA_PKA_IPC
:
pka
=
"IPC"
return
"Original header: "
+
self
.
header
+
"
\n
No. peptide: "
+
\
str
(
self
.
nb_peptide
)
+
"
\n
Enzyme: "
+
self
.
enzyme_name
+
\
"
\n
Cleav. pos: "
+
str
(
self
.
position
)
+
"
\n
Pep. size: "
+
\
...
...
tests/test_functional.py
View file @
18551f60
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