diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index b8bb092ec43388bd39e87153c8cc6cbfe19e9e15..3555110c93d4e8db3100d97ecf25f0c7373e46c0 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -686,12 +686,16 @@ class AriaEcXMLConverter(AriaXMLConverter):
"_hbond.tbl")
ssdist_file = os.path.join(self.settings.infra["tbl"], self.outprefix +
"_ssdist.tbl")
+ logger.info(" Dihedral restraints (%s)" % dihed_file)
self.write_dihedral_tbl(protein.sec_struct.ss_matrix, dihed_file)
+ logger.info(" Helix bond restraints (%s)" % hb_file)
self.write_hb_tbl(protein, hb_file,
hbmap=hbmap, n_hb=n_hb,
lr_type=self.settings.setup.config['longrange_hbtype'],
dminus=self.settings.setup.config['hb_dminus'],
dplus=self.settings.setup.config['hb_dplus'])
+ logger.info(" Secondary structure restraints (%s)" %
+ ssdist_file)
self.write_ssdist_tbl(protein.sec_struct.ss_matrix,
protein.sec_struct.ssdist,
ssdist_file)
@@ -721,18 +725,18 @@ class AriaEcXMLConverter(AriaXMLConverter):
:param desc:
:return:
"""
+ logger.info("Reading aria template file %s" % 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)
+ except Exception, msg:
+ sys.exit("""Can't open "%s" file. %s""" % (template, msg))
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)
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index 911bdea6e1338309d118f619cc0cd84cea25f521..6d3501f5d813cfc8988d2752f1c152586a65384a 100644
Binary files a/ariaec/econverter.pyc and b/ariaec/econverter.pyc differ
diff --git a/ariaec/ecsettings.py b/ariaec/ecsettings.py
index ebad6247d37da8d6f810d0b566b422a01ba8c7c3..8eecb1cf5c65d3d91ac21a06cffc9a57437b52b5 100644
--- a/ariaec/ecsettings.py
+++ b/ariaec/ecsettings.py
@@ -92,7 +92,7 @@ class AriaEcSettings(Settings):
"bbconv", "contactdef"))
self._infra = {}
self._scsc_min = None
- self._ss_dist = None
+ self._ssdist = None
self._template = None
self.outdir = os.getcwd()
self.name = name
@@ -123,10 +123,29 @@ class AriaEcSettings(Settings):
if self.infra:
self._up_infra()
+ @property
+ def ssdist(self):
+ if not self._ssdist:
+ if self.main.config["ss_dist_file"] and \
+ os.path.exists(self.main.config["ss_dist_file"]):
+ self._ssdist = self.main.config["ss_dist_file"]
+ else:
+ self._ssdist = pkgr.resource_filename(__name__, self.SS_DIST)
+ return self._ssdist
+
+ @property
+ def template(self):
+ if not self._template:
+ if self.main.config["ariaproject_template"] and \
+ os.path.exists(self.main.config["ariaproject_template"]):
+ self._template = self.main.config["ariaproject_template"]
+ else:
+ self._template = pkgr.resource_filename(__name__,
+ self.ARIAPROJ_TEMPLATE)
+ return self._template
+
@property
def scsc_min(self):
- # TODO: use cpickle only if we can't read scsc file in .ini conf !!!
- # Otherwise use another format ...
# If scsc_min already computed
if not self._scsc_min:
try:
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index 14a6ab0431a6f0549d2010cb1be33f34717c8df2..de9ac5fb88e2143023317d03576a8d895716bfba 100644
Binary files a/ariaec/ecsettings.pyc and b/ariaec/ecsettings.pyc differ
diff --git a/ariaec/protein.py b/ariaec/protein.py
index d0802bcac3646b4c293e93bcbce6c2adf78273b3..8b5a48fc3842a35fa68f2382bea14ccc93e5d1ad 100644
--- a/ariaec/protein.py
+++ b/ariaec/protein.py
@@ -207,12 +207,14 @@ class SsList:
"""
filename = os.path.abspath(ssdistpath) if ssdistpath else None
+ logger.info("Loading ss dist file")
try:
with open(filename) as f:
self._read_ssdist(f, filename=filename)
- except IOError:
+ except Exception, message:
+ logger.error("%s" % message)
logger.error("Can't load given ss dist file...")
- logger.info("Loading default ss dist file")
+ logger.error("Loading default ss dist file")
with pkgr.resource_stream(__name__, self.settings.SS_DIST) as f:
self._read_ssdist(f, filename=self.settings.SS_DIST)
@@ -457,8 +459,13 @@ class Protein:
if ssdist_filename:
# Read secondary distance matrix
self.sec_struct.read_ssdist(ssdist_filename)
+ else:
+ logger.error("No secondary structure distance file found. Please "
+ "check configuration file")
if self.aa_sequence.sequence:
# Synchronise sec structure sequence with aa sequence
+ logger.info("Align secondary structure sequence with protein "
+ "sequence")
self.sec_struct.seq_sublist(self.aa_sequence.sequence)
if ssidx:
logger.info("Using secondary structure index for amino acid "
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 9384a753ca62347a0205225fbddc43a197d46c95..44407c48708b929725c1e5963072313920b55827 100644
Binary files a/ariaec/protein.pyc and b/ariaec/protein.pyc differ
diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index 0bba9ebb679adea283309819b2aa2f7d39fd4b0f..fcb55694aaa7f4ecf2e802e91cfccddb3785d3c7 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -614,7 +614,7 @@ class ResAtmMap(ProteinMap):
newmap[:] = self.copy().stack().groupby(level=0).min()
return newmap
- def contact_map(self, contactdef, scsc_min=None):
+ def contact_map(self, contactdef, scsc_min=None, def_cut=5.0):
"""
Contact map generator from all atoms distance map. There's a contact
with 2 residues iff dist between 2 atoms are below the given treshold
@@ -632,12 +632,13 @@ class ResAtmMap(ProteinMap):
# Initialize contact map to a boolean matrix filled with False
contact_map = ResAtmMap(sequence=self.sequence, mtype="contact",
desc=self.desc, sym=self.sym, path=self.path)
+ def_cutoff = float(contactdef.get("default_cutoff")) if float(
+ contactdef.get("default_cutoff")) else def_cut
if type(contactdef) == float:
contact_map[:] = self.applymap(lambda x: x < contactdef)
- elif sum(x is not None for x in contactdef.values()) == 1 and \
- contactdef.get("default_cutoff"):
+ elif sum(x is not None for x in contactdef.values()) == 1 and def_cutoff:
logger.info("Using default cutoff")
contact_map[:] = self.applymap(lambda x: x < contactdef.get("default_cutoff"))
@@ -649,8 +650,12 @@ class ResAtmMap(ProteinMap):
for pair in contactdef.keys():
if pair == "default_cutoff":
continue
- treshold = contactdef[pair]
pair = tuple(pair.upper().split("_"))
+ if contactdef[pair] > def_cutoff:
+ treshold = contactdef[pair]
+ else:
+ logger.warning("Treshold for %s ignored (lower than "
+ "the default cutoff)" % str(pair))
logger.info(
"Filtering values in matrix related to %s (%s)" %
(str(pair), str(treshold)))
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index a6a0cfb3e5065b7c22b52cd6b6e910aff70fdace..9608866141f32929e6046b770d1ff1e170af4106 100644
Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ
diff --git a/ariaec/setup.py b/ariaec/setup.py
index 1aebaa8f0e969fd26bf637d7160e87491ff98945..335a376c45c399144b5dc9e1d2d1fa5d58150f0e 100644
--- a/ariaec/setup.py
+++ b/ariaec/setup.py
@@ -58,11 +58,9 @@ class AriaEcSetup:
# ------------------------- Load sequence ---------------------------- #
self.protein.set_aa_sequence(self.settings.setup.args.get("seq", None))
# -------------- Load secondary structure prediction ----------------- #
- ss_file = self.settings.main.config["ss_dist_file"] if \
- self.settings.main.config["ss_dist_file"] else None
self.protein.set_sec_struct(self.settings.setup.args.get("sspred",
None),
- ss_file,
+ ssdist_filename=self.settings.ssdist,
ssidx=self.settings.setup.args.get(
"ssidx", False))
# -------------------------------------------------------------------- #
@@ -148,6 +146,7 @@ class AriaEcSetup:
# Setting contact number limit for hbmap
n_hb = int(len(self.protein.aa_sequence.sequence) *
self.settings.setup.config.get("nf_longrange_hb"))
+ logger.info("Writing tbl files ...")
tbl_files = self.converter.write_tbl_restraints(
self.protein, hbmap=self.hbmaps, n_hb=n_hb)
@@ -163,11 +162,7 @@ class AriaEcSetup:
xmlseq_file = self.converter.write_xmlseq()
# ---------------------- 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 None
- self.converter.write_ariaproject(aria_template,
+ self.converter.write_ariaproject(self.settings.template,
xmlseq_file, dist_files, tbl_files,
desc="_".join(sorted(self.allresmap.keys())))
# ------------------------------ others ------------------------------ #
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index 9acd618838fbdac5ab9e9b455d1417883426c65d..4017775356dffc582cc0d28878907f1eb8fbb147 100644
Binary files a/ariaec/setup.pyc and b/ariaec/setup.pyc differ
diff --git a/version.py b/version.py
index 282defff11555733eda4731f253d20d680bfeec7..e0ce9534e68845f3859089100de0c3af44c750c3 100644
--- a/version.py
+++ b/version.py
@@ -1,2 +1,2 @@
# Do not edit this file, pipeline versioning is governed by git tags
-__version__=v0.1.11-dev2
\ No newline at end of file
+__version__=v0.1.11-dev2-8-g4239f50
\ No newline at end of file