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bis-aria
ariaec
Commits
34b074a5
Commit
34b074a5
authored
Jan 18, 2016
by
fabrice
Browse files
bug fixes when template or contactfilter fields are empty in ini file
parent
35d8304e
Changes
7
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Inline
Side-by-side
ariaec/conf/aria_ec.ini
View file @
34b074a5
...
...
@@ -7,10 +7,10 @@ ariaproject_template:
[contactdef]
; Contact definition section used to define contactmap from pdb file
default_cutoff:
8
.0
ca_ca:
cb_cb:
sc_sc:
default_cutoff:
7
.0
ca_ca:
7.0
cb_cb:
7.0
sc_sc:
5.0
; Add other contact cutoff below folowwing the syntax atm1_atm2
[setup]
...
...
@@ -60,9 +60,10 @@ cb_upper_bound: 7.0
; ---------------------------- Filter parameters ----------------------------- #
; n_factor : Number of EC selected: n * n_factor (n: sequence length)
; contactfilter : all or combinaison of pos, cons, cys, ssclash, nd
; separated by "+" character [all]
; separated by "+" character [all]. If empty, use only position
; filter (avoid short range restraints)
n_factor:
1.0
contactfilter:
contactfilter:
all
conservation_treshold:
95
position_treshold:
5
nd_beta:
0.99
...
...
ariaec/econverter.py
View file @
34b074a5
...
...
@@ -13,7 +13,7 @@ import os
import
sys
import
json
import
re
import
pkg_resources
as
pkgr
import
aria.legacy.AminoAcid
as
AminoAcid
import
aria.ConversionTable
as
ConversionTable
import
aria.conversion
...
...
@@ -127,6 +127,7 @@ reliable="{reliable}" list_name="{list_name}">
for
contrib_id
in
restraint_dict
[
restraint_id
][
"contrib"
]:
res_id
=
restraint_dict
[
restraint_id
][
"contrib"
][
contrib_id
][
"spin_pair"
].
keys
()
print
(
res_id
)
xml_file
.
write
(
'''
\
<contribution id="{id}" weight="{weight}">
<spin_pair>
...
...
@@ -500,7 +501,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
for
contactidx
,
contact
in
enumerate
(
pair_list
):
# /!\ humanidx in contact must start at 1 !n_factor
print
(
contact
)
# Add neighbors if neigh_flag
resx_idx
=
range
(
min_ind
(
contact
[
0
]
-
1
),
max_ind
(
contact
[
0
]
+
2
,
max_seqidx
))
if
\
...
...
@@ -610,6 +611,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
}
xml_file
=
self
.
settings
.
infra
[
"xml"
]
+
"/"
+
"_"
.
join
((
self
.
outprefix
,
listname
))
+
".xml"
print
(
restraint_dict
)
self
.
write_dist_xml
(
restraint_dict
,
xml_file
)
return
xml_file
,
pair_list
...
...
@@ -685,14 +687,20 @@ class AriaEcXMLConverter(AriaXMLConverter):
def
write_project
(
self
,
aria_template
,
seqfile
,
dist_files
,
tbl_files
,
desc
=
""
):
template
=
os
.
path
.
abspath
(
aria_template
)
if
aria_template
:
template
=
os
.
path
.
abspath
(
aria_template
)
try
:
t
=
open
(
template
,
'r'
)
except
IOError
:
sys
.
exit
(
"""Can't open "%s" file."""
%
template
)
try
:
t
=
open
(
template
,
'r'
)
except
IOError
:
sys
.
exit
(
"""Can't open "%s" file."""
%
template
)
aria_project_template
=
t
.
read
()
aria_project_template
=
t
.
read
()
t
.
close
()
else
:
logger
.
info
(
"Reading default aria template file %s"
%
self
.
settings
.
ARIAPROJ_TEMPLATE
)
aria_project_template
=
pkgr
.
resource_string
(
__name__
,
self
.
settings
.
ARIAPROJ_TEMPLATE
)
aria_project_dict
=
{}
...
...
@@ -794,5 +802,3 @@ class AriaEcXMLConverter(AriaXMLConverter):
with
open
(
proj_file
,
'w'
)
as
proj_xml
:
logger
.
info
(
"Writing ARIA project file (%s)"
%
proj_file
)
proj_xml
.
write
(
aria_project_template
%
aria_project_dict
)
t
.
close
()
ariaec/econverter.pyc
View file @
34b074a5
No preview for this file type
ariaec/protmap.py
View file @
34b074a5
...
...
@@ -946,8 +946,7 @@ class MapFilter:
if
mapfilters
==
"all"
:
mapfilters
=
self
.
filter_types
elif
not
mapfilters
:
logger
.
info
(
"No filter with %s map!"
%
mtype
)
return
mapdict
mapfilters
=
(
"pos"
,)
else
:
mapfilters
=
[
elm
for
elm
in
mapfilters
if
elm
in
self
.
filter_types
]
logger
.
info
(
"Filtering %s contact map"
%
mtype
)
...
...
ariaec/protmap.pyc
View file @
34b074a5
No preview for this file type
ariaec/setup.py
View file @
34b074a5
...
...
@@ -154,8 +154,9 @@ class AriaEcSetup:
# ---------------------- ARIA XML project file ----------------------- #
aria_template
=
self
.
settings
.
main
.
config
[
"ariaproject_template"
]
if
\
self
.
settings
.
main
.
config
[
"ariaproject_template"
]
and
\
os
.
path
.
exists
(
self
.
settings
.
main
.
config
[
"ariaproject_template"
])
\
else
self
.
settings
.
templat
e
else
Non
e
self
.
converter
.
write_project
(
aria_template
,
seq_file
,
dist_files
,
tbl_files
,
desc
=
"_"
.
join
(
sorted
(
self
.
allresmap
.
keys
())))
...
...
ariaec/setup.pyc
View file @
34b074a5
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