From 402cdec9a6e037dbcc4ad0ca504299c50ee9f040 Mon Sep 17 00:00:00 2001
From: fabrice <fabrice.allain@pasteur.fr>
Date: Wed, 3 Feb 2016 17:12:32 +0100
Subject: [PATCH] pep8tized v3
---
ariaec/__init__.py | 5 +-
ariaec/__init__.pyc | Bin 170 -> 235 bytes
ariaec/base.py | 45 +++++-
ariaec/base.pyc | Bin 9787 -> 9798 bytes
ariaec/econtacts.py | 304 ++++++++++++++++++++--------------------
ariaec/econverter.pyc | Bin 26548 -> 26548 bytes
ariaec/protein.py | 100 ++++++++++++-
ariaec/protein.pyc | Bin 14778 -> 14791 bytes
ariaec/protmap.pyc | Bin 43457 -> 43653 bytes
ariaec/reader.py | 39 ++++++
ariaec/reader.pyc | Bin 18499 -> 19059 bytes
ariaec/setup.py | 13 ++
ariaec/test/__init__.py | 4 +-
13 files changed, 350 insertions(+), 160 deletions(-)
diff --git a/ariaec/__init__.py b/ariaec/__init__.py
index 139597f..697ee03 100644
--- a/ariaec/__init__.py
+++ b/ariaec/__init__.py
@@ -1,2 +1,3 @@
-
-
+"""
+ Aria EC module
+"""
diff --git a/ariaec/__init__.pyc b/ariaec/__init__.pyc
index cc787257a928f0d8da01c0067a690129bc1b5871..aaad1100aa43704a4c4d15ca44c9edcec7c634b0 100644
GIT binary patch
literal 235
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N*l))SWETT50{|O?GN%9l
delta 124
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ru_!Y!J~dfC5lY9$XXa&=#K-FuRF-f6HQMCnr<CTT+JTHJ2AKo^z^NIv
diff --git a/ariaec/base.py b/ariaec/base.py
index 0705509..ce0501d 100644
--- a/ariaec/base.py
+++ b/ariaec/base.py
@@ -102,9 +102,9 @@ def format_str(string):
:param string:
:return:
"""
- if re.search(r"^\s*true\s*$", string, re.I):
+ if re.search(r"^\s*(true|yes)\s*$", string, re.I):
return True
- elif re.search(r"^\s*false\s*$", string, re.I):
+ elif re.search(r"^\s*(false|no)\s*$", string, re.I):
return False
elif re.search(r"^\s*\d+\s*$", string):
return int(string)
@@ -114,7 +114,7 @@ def format_str(string):
return string.split(',')
elif "+" in string:
return string.split('+')
- elif re.search(r"[/\\w]+", string):
+ elif re.search(r"[/\w]+", string):
return string
else:
if string:
@@ -133,12 +133,23 @@ def format_str(string):
def format_dict(indict):
+ """
+
+ :param indict:
+ :return:
+ """
for key in indict:
indict[key] = format_str(indict[key])
return indict
def ppdict(indict, indent=2):
+ """
+
+ :param indict:
+ :param indent:
+ :return:
+ """
return json.dumps(indict, indent=indent)
@@ -197,6 +208,12 @@ class CustomLogging:
default_file = "conf/logging.json"
def __init__(self, level=logging.INFO, desc=None):
+ """
+
+ :param level:
+ :param desc:
+ :return:
+ """
# TODO: detect path log filenames and makedirs if not exists
logging.basicConfig(level=level)
if desc:
@@ -206,6 +223,11 @@ class CustomLogging:
self.config = self.default_config()
def update_msg(self, desc):
+ """
+
+ :param desc:
+ :return:
+ """
if type(self.msg) == list:
self.msg += desc
self.msg = " - ".join(self.msg)
@@ -213,6 +235,10 @@ class CustomLogging:
self.msg = " - ".join((self.msg, desc.capitalize()))
def default_config(self):
+ """
+
+ :return:
+ """
# with open(self.default_file, 'rt') as f:
with pkgr.resource_stream(__name__, self.default_file) as f:
config = json.load(f)
@@ -237,6 +263,10 @@ class CustomLogging:
logging.config.dictConfig(self.config)
def welcome(self):
+ """
+
+ :return:
+ """
desc = '''
================================================================================
@@ -249,6 +279,10 @@ class CustomLogging:
class Capturing(list):
def __enter__(self):
+ """
+
+ :return:
+ """
# Stock default stdout and redirect current stdout to this class
self._stdout = sys.stdout
# All print calls are saved into self._stringio
@@ -256,6 +290,11 @@ class Capturing(list):
return self
def __exit__(self, *args):
+ """
+
+ :param args:
+ :return:
+ """
self.extend("\n".join(self._stringio.getvalue().splitlines()))
sys.stdout = self._stdout
diff --git a/ariaec/base.pyc b/ariaec/base.pyc
index 005803ab55abad265e668c20803035f1de32b0a7..6ba57492ff0c8c8321e0c1a639df8d983482e33f 100644
GIT binary patch
delta 63
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B5KjOA
diff --git a/ariaec/econtacts.py b/ariaec/econtacts.py
index a130f07..66206d8 100644
--- a/ariaec/econtacts.py
+++ b/ariaec/econtacts.py
@@ -3,13 +3,13 @@
"""
from __future__ import absolute_import, division, print_function
-import math
-import re
-import numpy as np
-import pandas as pd
+# import re
+# import math
+# import numpy as np
+# import pandas as pd
from collections import namedtuple
-from .base import cart_dist
+# from .base import cart_dist
Contact = namedtuple("Contact", ["resid1", "resid2"])
@@ -18,154 +18,154 @@ Atom = namedtuple("Atom", ["name", "coords"])
# BBcontacts scripts #
# ---------------------------------------------------------------------------- #
-def diversityvalue(msa, l):
- """
- Compute diversityvalue for bbcontacts.py : sqrt(n)/L where n is the
- number of sequence in MSA and L the protein length
- :param msa: filepath (fasta format)
- :param l: protein length
- :return: diversityvalue (float)
- """
-
- # Compute n value
- msa_reg = re.compile(r"^>[A-Za-z0-9]+_[A-Za-z0-9]+")
- n = 0
-
- with open(msa) as f:
- for index, line in enumerate(f):
- match = msa_reg.match(line)
- if match and "deselect" not in line:
- n += 1
-
- return math.sqrt(n) / float(l)
-
-
-def indexup_bbcontact(bbcontact_dict, startind, out, prefix):
- """
- Index update if startind of coupling matrix is not eq 0
- :param out:
- :param prefix:
- :param bbcontact_dict:
- :param startind:
- :return:
- """
- up = int(startind) - 1
- col = ('identifier', 'diversity', 'direction', 'viterbiscore',
- 'indexpred', 'state', 'res1', 'res2')
- with open('%s/%s.filteredoutput_up.txt' % (out, prefix), 'w') as f:
- f.write("#{:>14}\t{:>10}\t{:>15}\t{:>15}\t{:>10}\t{:>10}\t{:>5}\t{"
- ":>5}".format(*col))
-
- for contact in bbcontact_dict:
- resid1 = int(bbcontact_dict[contact]['res1_nb'])
- resid2 = int(bbcontact_dict[contact]['res2_nb'])
- bbcontact_dict[contact]['res1'] = resid1 + up
- bbcontact_dict[contact]['res1_nb'] = resid1 + up
- bbcontact_dict[contact]['res2'] = resid2 + up
- bbcontact_dict[contact]['res2_nb'] = resid2 + up
- line = [bbcontact_dict[contact][x] for x in col]
- f.write("\n{:>15}\t{:>10}\t{:>15}\t{:>15}\t{:>10}\t{:>10}\t{"
- ":>5}\t{:>5}".format(*line))
-
-
-def contact_insertion(contacts_dict, insert_list, insertvalue, seq):
- """
- Insert
- :param contacts_dict:
- :param insert_list:
- :param insertvalue:
- :param seq:
- :return:
- """
- maxind = max(contacts_dict.keys())
- for insert in insert_list:
- if insert not in contacts_dict:
- contacts_dict[insert] = {'resname': seq[insert - 1]}
- tmp = {}
- # Init all contacts related to insert
- for contact in range(insert + 1, maxind + 1):
- tmp[contact] = float(insertvalue)
- contacts_dict[insert].update(tmp)
+# def diversityvalue(msa, l):
+# """
+# Compute diversityvalue for bbcontacts.py : sqrt(n)/L where n is the
+# number of sequence in MSA and L the protein length
+# :param msa: filepath (fasta format)
+# :param l: protein length
+# :return: diversityvalue (float)
+# """
+#
+# Compute n value
+# msa_reg = re.compile(r"^>[A-Za-z0-9]+_[A-Za-z0-9]+")
+# n = 0
+#
+# with open(msa) as f:
+# for index, line in enumerate(f):
+# match = msa_reg.match(line)
+# if match and "deselect" not in line:
+# n += 1
+#
+# return math.sqrt(n) / float(l)
+
+
+# def indexup_bbcontact(bbcontact_dict, startind, out, prefix):
+# """
+# Index update if startind of coupling matrix is not eq 0
+# :param out:
+# :param prefix:
+# :param bbcontact_dict:
+# :param startind:
+# :return:
+# """
+# up = int(startind) - 1
+# col = ('identifier', 'diversity', 'direction', 'viterbiscore',
+# 'indexpred', 'state', 'res1', 'res2')
+# with open('%s/%s.filteredoutput_up.txt' % (out, prefix), 'w') as f:
+# f.write("#{:>14}\t{:>10}\t{:>15}\t{:>15}\t{:>10}\t{:>10}\t{:>5}\t{"
+# ":>5}".format(*col))
+#
+# for contact in bbcontact_dict:
+# resid1 = int(bbcontact_dict[contact]['res1_nb'])
+# resid2 = int(bbcontact_dict[contact]['res2_nb'])
+# bbcontact_dict[contact]['res1'] = resid1 + up
+# bbcontact_dict[contact]['res1_nb'] = resid1 + up
+# bbcontact_dict[contact]['res2'] = resid2 + up
+# bbcontact_dict[contact]['res2_nb'] = resid2 + up
+# line = [bbcontact_dict[contact][x] for x in col]
+# f.write("\n{:>15}\t{:>10}\t{:>15}\t{:>15}\t{:>10}\t{:>10}\t{"
+# ":>5}\t{:>5}".format(*line))
+
+
+# def contact_insertion(contacts_dict, insert_list, insertvalue, seq):
+# """
+# Insert
+# :param contacts_dict:
+# :param insert_list:
+# :param insertvalue:
+# :param seq:
+# :return:
+# """
+# maxind = max(contacts_dict.keys())
+# for insert in insert_list:
+# if insert not in contacts_dict:
+# contacts_dict[insert] = {'resname': seq[insert - 1]}
+# tmp = {}
+# Init all contacts related to insert
+# for contact in range(insert + 1, maxind + 1):
+# tmp[contact] = float(insertvalue)
+# contacts_dict[insert].update(tmp)
# Contacts scripts #
# ---------------------------------------------------------------------------- #
-def pdb_to_contact(pdbpath, threshold):
- """
- List of contacts inside given pdb file
- :param threshold:
- :author: bardiaux
- :param pdbpath:
- :return:
- """
- mapy = []
- descmap = {}
-
- with open(pdbpath, 'r') as pdb:
- coords = {}
-
- while 1:
-
- l = pdb.readline()
-
- if not l:
- break
-
- elif l.startswith('ATOM'):
- # Foreach atom
-
- fields = l
- atom = fields[12:16].strip()
- resid = int(fields[23:26].strip())
-
- if atom[0] != "H":
-
- coords.setdefault(resid, [])
- coord = np.array([float(a) for a in [fields[30:38],
- fields[38:46],
- fields[46:54]]])
- coords[resid].append(Atom(name=atom, coords=coord))
-
- k = coords.keys()
- k.sort() # sorted resid list
-
- for ii in range(0, len(k)):
- # Foreach res i
- i = k[ii]
- at1 = coords[i] # (x, y, z) coords list (N, CA, C, ...)
- for jj in range(ii, len(k)):
- # foreach res j (i+1, i+2, ...)
- j = k[jj]
- found = False
- at2 = coords[j]
-
- for a in at1:
- # foreach atm of res i
- for b in at2:
- # foreach atm of res j
- if not found and cart_dist(a.coords, b.coords) < \
- float(
- threshold):
- # If no contact found between 2 res and cart dist < t
- found = True
- if (i, j) not in mapy:
- # If contact not already found
- mapy.append((i, j))
- descmap[Contact(resid1=i, resid2=j)] = {"dist": "%.2f" % cart_dist(a.coords, b.coords),
- "atoms": (a.name, b.name)}
-
- return mapy, descmap
-
-
-def contact2dataframe(contacts, refseq):
- dim = len(refseq)
- matrix = np.zeros(shape=(dim, dim))
- matrix = pd.DataFrame(matrix)
- # print matrix
- # print contacts
- for contact in contacts:
- # Contactmatrix humanidx starts at 0 and input contacts at 1
- matrix.iloc[int(contact[0]) - 1, int(contact[1]) - 1] = 1
- matrix.iloc[int(contact[1]) - 1, int(contact[0]) - 1] = 1
-
- return matrix
+# def pdb_to_contact(pdbpath, threshold):
+# """
+# List of contacts inside given pdb file
+# :param threshold:
+# :author: bardiaux
+# :param pdbpath:
+# :return:
+# """
+# mapy = []
+# descmap = {}
+#
+# with open(pdbpath, 'r') as pdb:
+# coords = {}
+#
+# while 1:
+#
+# l = pdb.readline()
+#
+# if not l:
+# break
+#
+# elif l.startswith('ATOM'):
+# Foreach atom
+#
+# fields = l
+# atom = fields[12:16].strip()
+# resid = int(fields[23:26].strip())
+#
+# if atom[0] != "H":
+#
+# coords.setdefault(resid, [])
+# coord = np.array([float(a) for a in [fields[30:38],
+# fields[38:46],
+# fields[46:54]]])
+# coords[resid].append(Atom(name=atom, coords=coord))
+#
+# k = coords.keys()
+# k.sort() # sorted resid list
+#
+# for ii in range(0, len(k)):
+# Foreach res i
+# i = k[ii]
+# at1 = coords[i] # (x, y, z) coords list (N, CA, C, ...)
+# for jj in range(ii, len(k)):
+# foreach res j (i+1, i+2, ...)
+# j = k[jj]
+# found = False
+# at2 = coords[j]
+#
+# for a in at1:
+# foreach atm of res i
+# for b in at2:
+# foreach atm of res j
+# if not found and cart_dist(a.coords, b.coords) < \
+# float(
+# threshold):
+# If no contact found between 2 res and cart dist < t
+# found = True
+# if (i, j) not in mapy:
+# If contact not already found
+# mapy.append((i, j))
+# descmap[Contact(resid1=i, resid2=j)] = {"dist": "%.2f" % cart_dist(a.coords, b.coords),
+# "atoms": (a.name, b.name)}
+#
+# return mapy, descmap
+
+
+# def contact2dataframe(contacts, refseq):
+# dim = len(refseq)
+# matrix = np.zeros(shape=(dim, dim))
+# matrix = pd.DataFrame(matrix)
+# print matrix
+# print contacts
+# for contact in contacts:
+# Contactmatrix humanidx starts at 0 and input contacts at 1
+# matrix.iloc[int(contact[0]) - 1, int(contact[1]) - 1] = 1
+# matrix.iloc[int(contact[1]) - 1, int(contact[0]) - 1] = 1
+#
+# return matrix
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index f40bc0ebb91b323884eae2aaff8222fe42f6584e..cb31273d5e9ba6ae64853689ff210effa8750620 100644
GIT binary patch
delta 18
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diff --git a/ariaec/protein.py b/ariaec/protein.py
index de9efd8..d0802bc 100644
--- a/ariaec/protein.py
+++ b/ariaec/protein.py
@@ -13,8 +13,6 @@ import aria.legacy.SequenceList as SequenceList
import aria.legacy.AminoAcid as AmnAcd
from .base import (reg_load, Capturing, ppdict)
# import skbio.Protein as skprot
-
-
# TODO: interface skbio ??
@@ -38,6 +36,11 @@ class SsList:
ss_dist_reg = re.compile(r"\s+(\d+\.\d+) \( (\d+\.\d+)\)")
def __init__(self, sett):
+ """
+
+ :param sett:
+ :return:
+ """
self.settings = sett
self.ss_matrix = []
self.ssdict = {}
@@ -46,6 +49,10 @@ class SsList:
@property
def index(self):
+ """
+
+ :return:
+ """
if self.ss_matrix:
# Assuming human idx (1 ...) correspond to ss_matrix first column !!!
return [int(_) for _ in zip(*self.ss_matrix)[0]]
@@ -53,10 +60,21 @@ class SsList:
return []
def check_filetype(self, filename):
+ """
+
+ :param filename:
+ :return:
+ """
self.filetype = os.path.splitext(filename)[1][1:]
# TODO: check if given file is supported
def read(self, filename, sequence=''):
+ """
+
+ :param filename:
+ :param sequence:
+ :return:
+ """
self.check_filetype(filename)
logger.info("Reading secondary structure file %s [%s]" % (
filename,
@@ -73,6 +91,11 @@ class SsList:
self.seq_sublist(sequence)
def read_psipred(self, filename):
+ """
+
+ :param filename:
+ :return:
+ """
self.ssdict = reg_load(self.psipred_reg, filename)
# TODO: supprimer psipred_list dans les futures implementations
@@ -95,11 +118,22 @@ class SsList:
self.ssdict[line_id]['ss_conf']])
def write_ssfasta(self, filename, desc="pdbid"):
+ """
+
+ :param filename:
+ :param desc:
+ :return:
+ """
with open(filename, 'w') as psipred:
psipred.write("> %s\n" % desc)
psipred.write("".join([_[0] for _ in zip(*self.ss_matrix)[2]]))
def read_indextableplus(self, filename):
+ """
+
+ :param filename:
+ :return:
+ """
c = 0
error_list = []
ss_index_dict = {'H': 1, 'C': 1, 'E': 1}
@@ -134,6 +168,12 @@ class SsList:
str(error_list)))
def _read_ssdist(self, infile, filename=''):
+ """
+
+ :param infile:
+ :param filename:
+ :return:
+ """
logger.info("Reading distance file {0}".format(filename))
c = 0
atom_list = []
@@ -228,6 +268,13 @@ class AminoAcidSequence(SequenceList.SequenceList):
}
def __init__(self, topologyfile, *args, **kwargs):
+ """
+
+ :param topologyfile:
+ :param args:
+ :param kwargs:
+ :return:
+ """
SequenceList.SequenceList.__init__(self, *args, **kwargs)
self._topfile = topologyfile
self._topology = None
@@ -236,6 +283,10 @@ class AminoAcidSequence(SequenceList.SequenceList):
@property
def humanidx(self):
+ """
+
+ :return:
+ """
return range(1, len(self.sequence) + 1)
@property
@@ -254,13 +305,26 @@ class AminoAcidSequence(SequenceList.SequenceList):
return self._topology
def __getitem__(self, key):
+ """
+
+ :param key:
+ :return:
+ """
return self.aalist[key]
def __repr__(self):
+ """
+
+ :return:
+ """
return "Amino Acid sequence %s (%d)" % (self.sequence,
len(self.sequence))
def readtopo(self):
+ """
+
+ :return:
+ """
topo = {}
with pkgr.resource_stream(__name__, self._topfile) as tpf:
res_flag = False
@@ -302,6 +366,11 @@ class AminoAcidSequence(SequenceList.SequenceList):
return topo
def read(self, filename):
+ """
+
+ :param filename:
+ :return:
+ """
# TODO: smarter reader checking type of file (fasta, etc ...)
with Capturing() as output:
self.ReadFasta(filename)
@@ -315,6 +384,11 @@ class AminoAcidSequence(SequenceList.SequenceList):
class Protein:
def __init__(self, sett):
+ """
+
+ :param sett:
+ :return:
+ """
self.aa_sequence = AminoAcidSequence(sett.TOPO)
self.sec_struct = SsList(sett)
self.index = [] # Index starting from 1
@@ -345,9 +419,19 @@ class Protein:
@property
def topology(self):
+ """
+
+ :return:
+ """
return self.aa_sequence.topology
def set_aa_sequence(self, filename, ssidx=False):
+ """
+
+ :param filename:
+ :param ssidx:
+ :return:
+ """
self.aa_sequence.read(filename)
self.index = range(1, len(self.aa_sequence.sequence) + 1)
if self.sec_struct.ss_matrix:
@@ -359,6 +443,13 @@ class Protein:
self.sec_struct.index)
def set_sec_struct(self, filename, ssdist_filename='', ssidx=False):
+ """
+
+ :param filename:
+ :param ssdist_filename:
+ :param ssidx:
+ :return:
+ """
# TODO: Add test checking if both amino acid and sec_struct sequence
# have the same length after seq_sublist call
# Read secondary structure prediction file
@@ -376,6 +467,11 @@ class Protein:
self.sec_struct.index)
def write_seq(self, outfile):
+ """
+
+ :param outfile:
+ :return:
+ """
with Capturing() as output:
self.aa_sequence.WriteSeq(outfile)
logger.info(''.join(output))
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index d1705b8cec306250c959a81e7042ce8c4a265b99..bb3ccaa9234ccfc7e5c497e3221e2035e56ec577 100644
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diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index e62ac3d42b8bf007616fbbb32a42b4105c14abac..1491a80fcb6c161b11f21ee12cae5c2610f3ec42 100644
GIT binary patch
delta 915
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diff --git a/ariaec/reader.py b/ariaec/reader.py
index 6065ef7..62a14d3 100644
--- a/ariaec/reader.py
+++ b/ariaec/reader.py
@@ -183,6 +183,12 @@ class MapFile(RegexFile):
check_type = True
def __init__(self, *args, **kwargs):
+ """
+
+ :param args:
+ :param kwargs:
+ :return:
+ """
super(MapFile, self).__init__(*args, **kwargs)
if self.check_type:
self.regex, self.filetype, self.sort = self.check_maptype()
@@ -199,6 +205,16 @@ class MapFile(RegexFile):
def create_map(self, protein, contactdef, flaglist=None, offset=0, sym=True,
**kwargs):
+ """
+
+ :param protein:
+ :param contactdef:
+ :param flaglist:
+ :param offset:
+ :param sym:
+ :param kwargs:
+ :return:
+ """
raise NotImplementedError("Class %s doesn't implement create_map" %
self.__class__.__name__)
@@ -215,10 +231,19 @@ class MapFile(RegexFile):
"names in contact file at line %d !" % line)
def update_map(self, resmap):
+ """
+
+ :param resmap:
+ :return:
+ """
raise NotImplementedError("Class %s doesn't implement update_map" %
self.__class__.__name__)
def check_maptype(self):
+ """
+
+ :return:
+ """
logger.info("Checking format for file %s" % self.filepath)
# Check if given type is supported
# TODO: report this check into commands section
@@ -279,6 +304,14 @@ class MapFile(RegexFile):
def read(self, protein=None, contactdef=5.0, groupby_method="min",
scsc=None):
+ """
+
+ :param protein:
+ :param contactdef:
+ :param groupby_method:
+ :param scsc:
+ :return:
+ """
logger.info("Reading %s file" % self.filepath)
if self.filetype:
# Read file with regex related to filetype
@@ -339,6 +372,12 @@ class MapFile(RegexFile):
class ContactMapFile(MapFile):
# "plmdca", "evfold", "bbcontacts", "pconsc", "gremlin", "metapsicov",
def __init__(self, filepath, filetype):
+ """
+
+ :param filepath:
+ :param filetype:
+ :return:
+ """
super(self.__class__, self).__init__(filepath, filetype)
def update_map(self, resmap):
diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc
index 54d903a53dd0ac6cbfe5622a16d372710a27c4ef..cbaf7ae40f5c54325f1073688eef100c73a386b0 100644
GIT binary patch
delta 954
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diff --git a/ariaec/setup.py b/ariaec/setup.py
index f6e830f..b357532 100644
--- a/ariaec/setup.py
+++ b/ariaec/setup.py
@@ -21,6 +21,11 @@ logger = logging.getLogger(__name__)
class AriaEcSetup:
def __init__(self, settings):
+ """
+
+ :param settings:
+ :return:
+ """
# TODO: check_type settings (AriaEcSettings)
self.settings = settings
self.protein = Protein(settings)
@@ -34,6 +39,10 @@ class AriaEcSetup:
self.converter = AriaEcXMLConverter(settings)
def run(self):
+ """
+
+ :return:
+ """
# Check input
logger.debug("Settings:\n" + json.dumps(self.settings.setup.config,
indent=4))
@@ -162,6 +171,10 @@ class AriaEcSetup:
self.write_optional_files()
def write_optional_files(self):
+ """
+
+ :return:
+ """
# Indextableplus file (submatrix)
# Contacts_refined.out
for maptype in self.allresmap:
diff --git a/ariaec/test/__init__.py b/ariaec/test/__init__.py
index 43decae..0852314 100644
--- a/ariaec/test/__init__.py
+++ b/ariaec/test/__init__.py
@@ -1 +1,3 @@
-__author__ = 'raionic'
+"""
+ ARIA EC test module
+"""
--
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