Commit 330e140c authored by Fabrice Allain's avatar Fabrice Allain
Browse files

Added plmc and plm as contact map types

parent d5b75029
...@@ -64,7 +64,7 @@ class AriaEcCommand(object): ...@@ -64,7 +64,7 @@ class AriaEcCommand(object):
u"Convert contacts in bbcontact format", u"Convert contacts in bbcontact format",
u"Contactmap tool", u"Contactmap tool",
u"Quality tool for pdb file(s)") u"Quality tool for pdb file(s)")
contact_types = ("plmdca", "evfold", "bbcontacts", "pconsc", "pconsc1", contact_types = ("evfold", "plmev", "plm", "plmdca", "plmc", "bbcontacts", "pconsc", "pconsc1",
"pconsc2", "psicov", "metapsicovhb", "metapsicov_stg1", "pconsc2", "psicov", "metapsicovhb", "metapsicov_stg1",
"metapsicov_stg2", "gremlin", "pdb", "native", "metapsicov_stg2", "gremlin", "pdb", "native",
"native_full", "contactlist") "native_full", "contactlist")
......
No preview for this file type
...@@ -18,7 +18,7 @@ import textwrap ...@@ -18,7 +18,7 @@ import textwrap
import aria.legacy.AminoAcid as AminoAcid import aria.legacy.AminoAcid as AminoAcid
from .base import get_filename from .base import get_filename
from .protein import Protein from .protein import Protein
from .reader import ProtFileListReader from .reader import MapFileListReader
from .protmap import (ResAtmMap, ResMap) from .protmap import (ResAtmMap, ResMap)
from mako.template import Template from mako.template import Template
from aria.Molecule import Molecule from aria.Molecule import Molecule
...@@ -39,7 +39,7 @@ class AriaEcBbConverter(object): ...@@ -39,7 +39,7 @@ class AriaEcBbConverter(object):
# TODO: check_type settings (AriaEcSettings) # TODO: check_type settings (AriaEcSettings)
self.settings = settings self.settings = settings
self.protein = Protein(settings) self.protein = Protein(settings)
self.reader = ProtFileListReader() self.reader = MapFileListReader()
self.outprefix = '' self.outprefix = ''
def run(self): def run(self):
......
No preview for this file type
...@@ -8,7 +8,7 @@ import sys ...@@ -8,7 +8,7 @@ import sys
import json import json
import logging import logging
from .base import get_filename from .base import get_filename
from .reader import ProtFileListReader from .reader import MapFileListReader
from .protmap import MapFilter from .protmap import MapFilter
from .protein import Protein from .protein import Protein
...@@ -24,7 +24,7 @@ class AriaEcContactMap(object): ...@@ -24,7 +24,7 @@ class AriaEcContactMap(object):
# TODO: check_type settings (AriaEcSettings) # TODO: check_type settings (AriaEcSettings)
self.settings = settings self.settings = settings
self.protein = Protein(settings) self.protein = Protein(settings)
self.file_reader = ProtFileListReader( self.file_reader = MapFileListReader(
cont_def=settings.contactdef.config) cont_def=settings.contactdef.config)
self.filter = MapFilter(settings.setup.config) self.filter = MapFilter(settings.setup.config)
self.outprefix = '' self.outprefix = ''
......
No preview for this file type
...@@ -68,6 +68,27 @@ class MapFile(RegexFile): ...@@ -68,6 +68,27 @@ class MapFile(RegexFile):
r"(?P<plm_score>--?\d+\.\d+)\s*$"), r"(?P<plm_score>--?\d+\.\d+)\s*$"),
"score_field": "plm_score" "score_field": "plm_score"
}, },
"plm": {
"regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
r"(?P<mi_score>\d)\s+"
r"(?P<plm_score>--?\d+\.\d+)\s*$"),
"score_field": "plm_score"
},
"plmev": {
"regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
r"(?P<mi_score>\d)\s+"
r"(?P<plm_score>--?\d+\.\d+)\s*$"),
"score_field": "plm_score"
},
"plmc": {
"regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
r"(?P<mi_score>\d)\s+"
r"(?P<plm_score>--?\d+\.\d+)\s*$"),
"score_field": "plm_score"
},
"evfold": { "evfold": {
"regex": re.compile( "regex": re.compile(
r'^(?P<res1_nb>\d+),(?P<res2_nb>\d+),' r'^(?P<res1_nb>\d+),(?P<res2_nb>\d+),'
...@@ -598,7 +619,7 @@ class DistanceMapFile(MapFile): ...@@ -598,7 +619,7 @@ class DistanceMapFile(MapFile):
# return DistanceMap # return DistanceMap
class ProtFileListReader(object): class MapFileListReader(object):
""" """
List of file object List of file object
""" """
......
No preview for this file type
...@@ -9,7 +9,7 @@ import json ...@@ -9,7 +9,7 @@ import json
import logging import logging
from .protein import Protein from .protein import Protein
from .reader import ProtFileListReader from .reader import MapFileListReader
from .base import get_filename from .base import get_filename
from .protmap import MapFilter from .protmap import MapFilter
from .econverter import AriaEcXMLConverter from .econverter import AriaEcXMLConverter
...@@ -33,7 +33,7 @@ class AriaEcSetup(object): ...@@ -33,7 +33,7 @@ class AriaEcSetup(object):
self.settings = settings self.settings = settings
self.protein = Protein(settings) self.protein = Protein(settings)
self.outprefix = '' self.outprefix = ''
self.reader = ProtFileListReader(cont_def=settings.contactdef.config) self.reader = MapFileListReader(cont_def=settings.contactdef.config)
self.allresmap = {} self.allresmap = {}
self.targetmap = None self.targetmap = None
self.refmaps = None self.refmaps = None
......
No preview for this file type
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment