diff --git a/ariaec/conf/aria_ec.ini b/ariaec/conf/aria_ec.ini index 0b05166d9627e80cfdf297788c2603a1fb3c696a..d47d9cf3470ad2653ff0e813f3319df6c04f0204 100644 --- a/ariaec/conf/aria_ec.ini +++ b/ariaec/conf/aria_ec.ini @@ -53,7 +53,7 @@ groupby_method: min ; Parameters below used only when distance_type is set to "fixed" restraint_distance: 2.5 lower_bound: 1.0 -def_upper_bound: 4.0 +def_upper_bound: 5.0 ; Specific tresholds only for unambig restraints ca_upper_bound: 7.0 cb_upper_bound: 7.0 diff --git a/ariaec/econverter.py b/ariaec/econverter.py index cfbfd10705f31018d722d03d097de79867fd7410..ea6211843985c309edbf4a9e22b8e0200a957ccf 100644 --- a/ariaec/econverter.py +++ b/ariaec/econverter.py @@ -485,7 +485,9 @@ class AriaEcXMLConverter(AriaXMLConverter): :param scoremap: sorted list of contacts :return: """ - # Number of selected contacts + # Number of selected contact + # If there isn't enough contacts in input contact map after filtering + # step, change nb_c nb_c = nb_c if nb_c < len(contactmap.contactset()) else len( contactmap.contactset()) @@ -652,6 +654,7 @@ class AriaEcXMLConverter(AriaXMLConverter): } xml_file = self.settings.infra["xml"] + "/" + "_".join(( self.outprefix, listname)) + ".xml" + logger.info("Write %d xml distance restraints in %s" % (nb_c, xml_file)) self.write_dist_xml(restraint_dict, xml_file) return xml_file, pair_list diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc index 12fd3dfe9c8a55270612d758122c6bc87f40bac5..1e89d37d3a6835f86c91c4bcacca99b2cd3c8bbe 100644 Binary files a/ariaec/econverter.pyc and b/ariaec/econverter.pyc differ diff --git a/ariaec/protmap.py b/ariaec/protmap.py index a844b75252934edfbcf7171729ac43b7b02bce91..93892550562a3f72c3c930fbb90b02e4da13c58d 100644 --- a/ariaec/protmap.py +++ b/ariaec/protmap.py @@ -18,7 +18,7 @@ import pandas as pd import seaborn as sns import numpy as np import datetime -from .ndconv import net_deconv +# from .ndconv import net_deconv from matplotlib import pyplot as plt import aria.ConversionTable as ConversionTable import aria.legacy.AminoAcid as AminoAcid @@ -70,8 +70,6 @@ class Map(pd.DataFrame): self.sym = sym self.desc = desc - - def sortedset(self, human_idx=False): # Remove duplicate in sort_list n = 1 if human_idx else 0 diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc index 53032a74ad2c6c3e5e53856f5b9c34f2eb8551d1..f99062db6e3547d723a669c9252b023a9f829c85 100644 Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ diff --git a/version.py b/version.py index 4806173bad632d69a870f4f3c1115c7ff58643e8..70bb33137bbb9bab28eb1bf82564e7980edaa20f 100644 --- a/version.py +++ b/version.py @@ -1,2 +1,2 @@ # Do not edit this file, pipeline versioning is governed by git tags -__version__=v0.1.8-dev2 \ No newline at end of file +__version__=v0.1.11-dev1 \ No newline at end of file