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bis-aria
ariaec
Commits
c6e18071
Commit
c6e18071
authored
May 30, 2017
by
Fabrice ALLAIN
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Pdbstat distance type functionnal
parent
998a96f1
Changes
9
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9 changed files
with
55717 additions
and
55724 deletions
+55717
-55724
ariaec/conf/config.ini
ariaec/conf/config.ini
+26
-29
ariaec/converter.py
ariaec/converter.py
+241
-260
ariaec/data/pdbdists/lowerbounds.intra.p
ariaec/data/pdbdists/lowerbounds.intra.p
+16290
-16290
ariaec/data/pdbdists/targetdists.inter.p
ariaec/data/pdbdists/targetdists.inter.p
+6561
-6561
ariaec/data/pdbdists/targetdists.intra.p
ariaec/data/pdbdists/targetdists.intra.p
+16290
-16290
ariaec/data/pdbdists/upperbounds.intra.p
ariaec/data/pdbdists/upperbounds.intra.p
+16290
-16290
ariaec/protein.py
ariaec/protein.py
+13
-0
ariaec/protmap.py
ariaec/protmap.py
+2
-2
ariaec/reader.py
ariaec/reader.py
+4
-2
No files found.
ariaec/conf/config.ini
View file @
c6e18071
...
...
@@ -72,26 +72,20 @@ hb_dplus: 0.5
; use all, heavy atms or from a minimized
; list (CA, CB, SC) for contribution list for
; each distance restraint
; pair_product : True, False [True]
; Define if there is more than one contribution
; per atom type. If True, compute pairwise
; product between contribution lists of the 2
; residues. Otherwise, pair_list will be a
; atoms_type : all, heavy, min [min]
; use all, heavy atms or from a minimized
; list (CA, CB, SC) for contribution list for
; each distance restraint
; contributions_type : same, allvsall, onevsall [same]
; By default contributions list will be a
; simple list between atoms of the same type
; (CA-CA, CB-CB, ...)
; ambiguous_distance_restraint : True, False [False]
; Generate Ambiguous Distance Restraints.
; Otherwise, each distance restraints will have
; only one contribution (unambiguous distance
; restraints)
; ambiguous_distance_type : min, deff [min]
; compute Deff or min distance as target
; distance if reference structure given
; ambiguous_restraint_type : allvsall, onevsall [allvsall]
; generate one ADR for all contribution pairs or
; one ADR foreach atom in first res against all
; the others in second res defined by
; contribution list
; (CA-CA, CB-CB, ...). Otherwise, compute
; pairwise product between contribution
; lists of the 2 residues (onevsall and
; allvsall). In the case of ADR, onevsall will
; generate one ADR for all contribution pairs
; between an atom of the first residue against
; all the other atoms in the second residue
; distance_type : fixed, pdbstat, distfile [fixed]
; Define distance use for target distance. By
; default the target distance is fixed by
...
...
@@ -100,22 +94,25 @@ hb_dplus: 0.5
; (not yet implemented) or given by the user can
; be used.
; pdbdistance_level : ss, res,
; groupby_method : mean, min [min]
; groupby_method : mean, min
, deff
[min]
; If a distance map is used for setting distance
; target, define if we use min or mean distance
; values at residu level.
; target, define if we use min, mean or deff
; distance on all the possible values.
; ambiguous_distance_restraint : True, False [False]
; Generate Ambiguous Distance Restraints.
; Otherwise, each distance restraints will have
; only one contribution (unambiguous distance
; restraints)
native_reliable:
False
evfold_weight:
False
neighborhood_contact:
False
pair_list:
min
pair_product:
True
ambiguous_distance_restraint:
False
ambiguous_restraint_type:
onevsall
ambiguous_distance_type:
min
deffpow:
6
atoms_type:
min
contributions_type:
same
distance_type:
fixed
pdbdistance_level:
ss
groupby_method:
min
deffpow:
6
pdbdistance_level:
ss
ambiguous_distance_restraint:
False
; Parameters below used only when distance_type is set to "fixed"
restraint_distance:
2.5
lower_bound:
1.0
...
...
ariaec/converter.py
View file @
c6e18071
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ariaec/data/pdbdists/lowerbounds.intra.p
View file @
c6e18071
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ariaec/data/pdbdists/targetdists.inter.p
View file @
c6e18071
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ariaec/data/pdbdists/targetdists.intra.p
View file @
c6e18071
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ariaec/data/pdbdists/upperbounds.intra.p
View file @
c6e18071
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ariaec/protein.py
View file @
c6e18071
...
...
@@ -61,6 +61,19 @@ class SsList(object):
else
:
return
[]
@
property
def
sequence
(
self
):
"""
Returns
-------
"""
if
self
.
ss_matrix
:
return
[
_
for
_
in
zip
(
*
self
.
ss_matrix
)[
2
]]
else
:
return
[]
def
check_filetype
(
self
,
filename
):
"""
...
...
ariaec/protmap.py
View file @
c6e18071
...
...
@@ -936,10 +936,10 @@ class ProteinMap(Map):
if
scoremap
is
not
None
:
score
=
scoremap
.
iat
[(
int
(
contact
[
0
])
-
offset
,
int
(
contact
[
1
])
-
offset
)]
outfile
.
write
(
"%d %d %.4f"
%
outfile
.
write
(
"%d %d %.4f
\n
"
%
(
contact
[
0
],
contact
[
1
],
score
))
else
:
outfile
.
write
(
"%d %d"
%
(
contact
[
0
],
contact
[
1
]))
outfile
.
write
(
"%d %d
\n
"
%
(
contact
[
0
],
contact
[
1
]))
class
ResAtmMap
(
ProteinMap
):
...
...
ariaec/reader.py
View file @
c6e18071
...
...
@@ -849,8 +849,10 @@ class MapFileListReader(object):
if
os
.
path
.
exists
(
filepath
):
# TODO: check_type functionstr
LOG
.
debug
(
"Adding %s file to watchlist"
,
maptypes
[
i
])
if
maptypes
[
i
].
lower
()
==
"pdb"
and
\
os
.
path
.
splitext
(
filepath
)[
1
][
1
:]
==
"pdb"
:
if
(
maptypes
[
i
].
lower
()
==
"pdb"
and
os
.
path
.
splitext
(
filepath
)[
1
][
1
:]
==
"pdb"
)
or
(
maptypes
[
i
].
lower
()
==
"distfile"
and
os
.
path
.
splitext
(
filepath
)[
1
][
1
:]
==
"pdb"
):
self
.
maps
.
append
(
PDBFile
(
filepath
))
else
:
self
.
maps
.
append
(
ContactMapFile
(
filepath
,
...
...
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