diff --git a/ariaec/commands.py b/ariaec/commands.py index bcdf35df05e24c07a7f09ec6168c12b98ec504b3..9bb45c519be89d0aae386ead44f7c254ccd2af48 100644 --- a/ariaec/commands.py +++ b/ariaec/commands.py @@ -48,9 +48,10 @@ class AriaEcCommand: u"into ARIA restraints", u"Convert contacts in bbcontact format", u"Contactmap tool") - contact_types = ("plmdca", "evfold", "bbcontacts", "pconsc", "gremlin", - "metapsicov", "pdb", "native", "native_full", - "contactlist") + contact_types = ("plmdca", "evfold", "bbcontacts", "pconsc", "pconsc1", + "pconsc2", "psicov", "metapsicovhb", "metapsicov_stg1", + "metapsicov_stg2", "gremlin", "pdb", "native", + "native_full", "contactlist") default_confile = "conf/aria_ec.ini" def __init__(self, custom_logging=None): diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc index 7c8986d2a6e6b569ba7916bde0c9c7d57ac41e8b..dd3a1f06de367d2488b513a28012a210a5706243 100644 Binary files a/ariaec/commands.pyc and b/ariaec/commands.pyc differ diff --git a/ariaec/protmap.py b/ariaec/protmap.py index a8e43c492253afb50d51f9ea57ab60ebfad7b922..49a93593a582b3d32eee95777a1b1da02e070237 100644 --- a/ariaec/protmap.py +++ b/ariaec/protmap.py @@ -10,7 +10,7 @@ import os import re import matplotlib -matplotlib.use("pdf", warn=False) +matplotlib.use("Agg", warn=False) import logging import collections import itertools diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc index d10f399e814bce41679022e99d7d9a99d66ec753..b365e3c270a24ae8b9a12515799741e478126d3d 100644 Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ diff --git a/ariaec/reader.py b/ariaec/reader.py index 3f203f4f2e7ce2d7bd3f5c5e8b6d5b3228d053e7..cc187b669c9759c51ca912664a7f3be2407dfc3b 100644 --- a/ariaec/reader.py +++ b/ariaec/reader.py @@ -49,6 +49,7 @@ class MapFile(RegexFile): # List of 3tuples ("regex_file", "filetype", "sort_field") # sort_field allow sorting lines with values into this field # TODO: wrong regex for native_full ? + # TODO: smarter dict ... types = { "plmdca": { "regex": re.compile("^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+" @@ -74,7 +75,31 @@ class MapFile(RegexFile): '(?P<ec_score>\-?\d+\.\d+e?\-?\d*)$'), "score_field": "ec_score" }, - "metapsicov": { + "pconsc1": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) ' + '(?P<ec_score>\-?\d+\.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "pconsc2": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) ' + '(?P<ec_score>\-?\d+\.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "metapsicov_stg1": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) ' + '(?P<ec_score>\-?\d+.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "metapsicov_stg2": { + "regex": re.compile( + '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) ' + '(?P<ec_score>\-?\d+.\d+e?\-?\d*)$'), + "score_field": "ec_score" + }, + "psicov": { "regex": re.compile( '^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) ' '(?P<ec_score>\-?\d+.\d+e?\-?\d*)$'), diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc index 5eeb4d61ab4ba9568ce24f11b49683d31a4434f0..634fc3685c92e411635247e68d197a2fa87372bd 100644 Binary files a/ariaec/reader.pyc and b/ariaec/reader.pyc differ