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):
u"Convert contacts in bbcontact format",
u"Contactmap tool",
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",
"metapsicov_stg2", "gremlin", "pdb", "native",
"native_full", "contactlist")
......
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......@@ -18,7 +18,7 @@ import textwrap
import aria.legacy.AminoAcid as AminoAcid
from .base import get_filename
from .protein import Protein
from .reader import ProtFileListReader
from .reader import MapFileListReader
from .protmap import (ResAtmMap, ResMap)
from mako.template import Template
from aria.Molecule import Molecule
......@@ -39,7 +39,7 @@ class AriaEcBbConverter(object):
# TODO: check_type settings (AriaEcSettings)
self.settings = settings
self.protein = Protein(settings)
self.reader = ProtFileListReader()
self.reader = MapFileListReader()
self.outprefix = ''
def run(self):
......
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......@@ -8,7 +8,7 @@ import sys
import json
import logging
from .base import get_filename
from .reader import ProtFileListReader
from .reader import MapFileListReader
from .protmap import MapFilter
from .protein import Protein
......@@ -24,7 +24,7 @@ class AriaEcContactMap(object):
# TODO: check_type settings (AriaEcSettings)
self.settings = settings
self.protein = Protein(settings)
self.file_reader = ProtFileListReader(
self.file_reader = MapFileListReader(
cont_def=settings.contactdef.config)
self.filter = MapFilter(settings.setup.config)
self.outprefix = ''
......
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......@@ -68,6 +68,27 @@ class MapFile(RegexFile):
r"(?P<plm_score>--?\d+\.\d+)\s*$"),
"score_field": "plm_score"
},
"plm": {
"regex": re.compile(r"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"
r"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"
r"(?P<mi_score>\d)\s+"
r"(?P<plm_score>--?\d+\.\d+)\s*$"),
"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": {
"regex": re.compile(
r'^(?P<res1_nb>\d+),(?P<res2_nb>\d+),'
......@@ -598,7 +619,7 @@ class DistanceMapFile(MapFile):
# return DistanceMap
class ProtFileListReader(object):
class MapFileListReader(object):
"""
List of file object
"""
......
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......@@ -9,7 +9,7 @@ import json
import logging
from .protein import Protein
from .reader import ProtFileListReader
from .reader import MapFileListReader
from .base import get_filename
from .protmap import MapFilter
from .econverter import AriaEcXMLConverter
......@@ -33,7 +33,7 @@ class AriaEcSetup(object):
self.settings = settings
self.protein = Protein(settings)
self.outprefix = ''
self.reader = ProtFileListReader(cont_def=settings.contactdef.config)
self.reader = MapFileListReader(cont_def=settings.contactdef.config)
self.allresmap = {}
self.targetmap = None
self.refmaps = None
......
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