From 1cf6e97fa155f6eb48ea14aea30ee805c4962801 Mon Sep 17 00:00:00 2001
From: fabrice <fabrice.allain@pasteur.fr>
Date: Wed, 2 Mar 2016 14:31:22 +0100
Subject: [PATCH] Bug fixe: wrong atom list when pair_list set to all (add
terminal atoms)
---
ariaec/econverter.py | 264 ++++++++++++++++++++----------------------
ariaec/econverter.pyc | Bin 28647 -> 27429 bytes
ariaec/maplot.py | 2 +-
ariaec/maplot.pyc | Bin 5130 -> 5130 bytes
ariaec/protmap.pyc | Bin 45110 -> 45110 bytes
ariaec/setup.py | 15 +--
ariaec/setup.pyc | Bin 7791 -> 7818 bytes
7 files changed, 137 insertions(+), 144 deletions(-)
diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index 0f5ac00..cfbfd10 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -15,12 +15,15 @@ import json
import re
import pkg_resources as pkgr
import aria.legacy.AminoAcid as AminoAcid
-import aria.ConversionTable as ConversionTable
-import aria.conversion
-from .base import (Capturing, get_filename)
+from .base import get_filename, Capturing
from .protein import Protein
from .reader import ProtFileListReader
from .protmap import (ResAtmMap, ResMap)
+from aria.Molecule import Molecule
+from aria.tools import string_to_segid
+from aria.AriaXML import AriaXMLPickler
+from aria.conversion import Converter, SequenceList, MoleculeSettings
+
logger = logging.getLogger(__name__)
@@ -90,10 +93,52 @@ class AriaEcBbConverter(object):
return math.sqrt(n) / float(l)
-class AriaXMLConverter(object):
- def __init__(self):
- # TODO: stock here pickle file path for cns donor/ acceptor dict
- pass
+class AriaXMLConverter(Converter, object):
+ def __init__(self, settings):
+ Converter.__init__(self)
+ self._mol_set = MoleculeSettings()
+ self._pickler = AriaXMLPickler()
+ self.outprefix = ""
+ self.settings = settings
+ self.molecule = None
+
+ def load_molecule(self, seqpath):
+ self._mol_set['format'] = 'seq'
+ self._mol_set['input'] = seqpath
+ self._mol_set['output'] = os.path.join(self.settings.infra["xml"],
+ self.outprefix + ".xml")
+ self._mol_set['type'] = 'PROTEIN'
+ self._mol_set['segid'] = ' '
+ self._mol_set['first_residue_number'] = 1
+ self._mol_set['naming_convention'] = ''
+ self._mol_set['name'] = self.outprefix
+
+ segids = self._mol_set['segid']
+ segids = segids.split('/')
+
+ segids = [string_to_segid(segid) for segid in segids]
+ # Recup molecule
+ chain_types = {}
+ for s in segids:
+ chain_types[s] = self._mol_set['type']
+
+ sequence = SequenceList(chain_types, self._mol_set['first_residue_number'])
+
+ with Capturing() as output:
+ sequence.parse(self._mol_set['input'], self._mol_set['format'],
+ self._mol_set['naming_convention'])
+
+ logger.info("\n" + "".join(output))
+
+ factory = self.create_factory()
+
+ factory.reset()
+ factory.unfreeze()
+
+ chains = sequence.create_chains(factory)
+
+ self.molecule = Molecule(self._mol_set['name'])
+ [self.molecule.add_chain(chains[seg]) for seg in segids]
@staticmethod
def deff(distance_list, dpow=6):
@@ -350,11 +395,35 @@ assign (resid {res1} and name n) (resid {res1} and name ca) (resid {res1} and na
class AriaEcXMLConverter(AriaXMLConverter):
- def __init__(self, settings):
+ def __init__(self, *args, **kwargs):
self.restraint_list = []
- self.settings = settings
- self.protname = ""
- super(AriaEcXMLConverter, self).__init__()
+ super(AriaEcXMLConverter, self).__init__(*args, **kwargs)
+
+ def atm_product(self, idx1, res1, idx2, res2, prod_type="min"):
+
+ def resname(res):
+ return AminoAcid.AminoAcid(res)[0]
+
+ def min_atms(aa1, aa2, atms):
+ # Function to minimize atom pair list between aa1 & aa2
+ return [
+ atmpair for atmpair in atms if atmpair in (
+ ('CA', 'CA'),
+ ('CB', 'CB'),
+ self.settings.scsc_min[resname(aa1)][resname(aa2)])]
+ atms1 = self.molecule.get_chains()[0].getResidues()[idx1].atoms.keys()
+ atms2 = self.molecule.get_chains()[0].getResidues()[idx2].atoms.keys()
+ if prod_type == "min":
+ return min_atms(res1, res2, list(itertools.product(atms1, atms2)))
+ elif prod_type == "heavy":
+ atms1 = filter(ResAtmMap.heavy_reg.match, atms1)
+ atms2 = filter(ResAtmMap.heavy_reg.match, atms2)
+ return list(itertools.product(atms1, atms2))
+ elif prod_type == "all":
+ return list(itertools.product(atms1, atms2))
+ else:
+ logger.error("Wrong pair_list option. Pair_list set to min")
+ return min_atms(res1, res2, list(itertools.product(atms1, atms2)))
def targetdistmap(self, distype, sequence, distfile=None, groupby=None):
# TODO: valeur par defaut de distfile au fichier contenant les infos
@@ -451,79 +520,14 @@ class AriaEcXMLConverter(AriaXMLConverter):
pair_flag = self.settings.setup.config["pair_list"]
target_dist = self.settings.setup.config["restraint_distance"]
- conv_table = ConversionTable.ConversionTable().table['AMINO_ACID'][
- 'iupac']
-
- # TODO: atm_pair method
- if pair_flag == "min":
- def min_atms(aa1, aa2, atms):
- # Function to minimize atom pair list between aa1 & aa2
- return [
- atmpair for atmpair in atms if atmpair in (
- ('CA', 'CA'),
- ('CB', 'CB'),
- self.settings.scsc_min[aa1][aa2])]
- aa_atm = dict((AminoAcid.AminoAcid(aa)[0],
- filter(contactmap.heavy_reg.match, atms.keys()))
- for aa, atms in conv_table.items())
- aa_atm_pair = \
- {
- (aa1, aa2): min_atms(aa1, aa2, list(itertools.product(atms1,
- atms2)))
- for aa1, atms1 in aa_atm.items()
- for aa2, atms2 in aa_atm.items()
- }
- elif pair_flag == "heavy":
- # Dict giving all atms foreach aa
- aa_heav_atm = dict((AminoAcid.AminoAcid(aa)[0],
- filter(contactmap.heavy_reg.match, atms.keys()))
- for aa, atms in conv_table.items())
-
- # Dict giving atoms product for each res-res pair
- aa_atm_pair = {(aa1, aa2): list(itertools.product(atms1, atms2))
- for aa1, atms1 in aa_heav_atm.items()
- for aa2, atms2 in aa_heav_atm.items()
- }
- elif pair_flag == "all":
- # Dict giving all atms foreach aa
- aa_atm = dict((AminoAcid.AminoAcid(aa)[0],
- filter(contactmap.all_reg.match, atms.keys()))
- for aa, atms in conv_table.items())
-
- # Dict giving atoms product for each res-res pair
- aa_atm_pair = {(aa1, aa2): list(itertools.product(atms1, atms2))
- for aa1, atms1 in aa_atm.items()
- for aa2, atms2 in aa_atm.items()
- }
- else:
- logger.error("Wrong pair_list option. Pair_list set to min")
-
- def min_atms(aa1, aa2, atms):
- # Function to minimize atom pair list between aa1 & aa2
- return [
- atmpair for atmpair in atms if atmpair in (
- ('CA', 'CA'),
- ('CB', 'CB'),
- self.settings.scsc_min[aa1][aa2])]
- aa_atm = dict((AminoAcid.AminoAcid(aa)[0],
- filter(contactmap.heavy_reg.match, atms.keys()))
- for aa, atms in conv_table.items())
- aa_atm_pair = \
- {
- (aa1, aa2): min_atms(aa1, aa2, list(itertools.product(atms1,
- atms2)))
- for aa1, atms1 in aa_atm.items()
- for aa2, atms2 in aa_atm.items()
- }
-
def min_ind(ind):
return ind if ind >= 0 else 0
def max_ind(ind, max_idx):
return ind if ind <= max_idx else max_idx
- def resname(residx):
- return AminoAcid.AminoAcid(contactmap.index.values[residx][-3:])[0]
+ def resname_3l(residx):
+ return AminoAcid.AminoAcid(contactmap.index.values[residx][-3:])[1]
max_seqidx = len(contactmap.sequence)
restraint_dict = collections.OrderedDict()
@@ -531,18 +535,19 @@ class AriaEcXMLConverter(AriaXMLConverter):
contrib_id = 0
for contactidx, contact in enumerate(pair_list):
- # /!\ humanidx in contact must start at 1 !n_factor
- # Add neighbors if neigh_flag
logger.debug("Contact %s" % str(contact))
+
+ # Add neighbors if neigh_flag
resx_idx = range(min_ind(contact[0] - 1),
max_ind(contact[0] + 2, max_seqidx)) if \
neigh_flag else [contact[0]]
resy_idx = range(min_ind(contact[1] - 1),
max_ind(contact[1] + 2, max_seqidx)) if \
neigh_flag else [contact[1]]
- contactweight = weight_list[contactidx]
+ contactweight = weight_list[contactidx]
dist_list = []
+
if adr_flag:
rest_id += 1
# TODO: Autre dist_list if target != ResMap
@@ -576,22 +581,27 @@ class AriaEcXMLConverter(AriaXMLConverter):
target_dist = self.settings.setup.confn_factorig[
"restraint_distance"]
- for resx in resx_idx:
- for resy in resy_idx:
- resxn = targetdist.index.levels[0][resx]
- resyn = targetdist.index.levels[0][resy]
- for atm_pair in aa_atm_pair[(resname(resx),
- resname(resy))]:
+ for idx_x in resx_idx:
+ for idx_y in resy_idx:
+ mapidx_x = targetdist.index.levels[0][idx_x]
+ mapidx_y = targetdist.index.levels[0][idx_y]
+ res_x = resname_3l(idx_x)
+ res_y = resname_3l(idx_y)
+
+ atm_pairs = self.atm_product(idx_x, res_x, idx_y, res_y,
+ pair_flag)
+
+ for atm_pair in atm_pairs:
if adr_flag:
contrib_id += 1
else:
if len(targetdist.index.levels) == 2:
- target_dist = targetdist.loc[resxn,
- atm_pair[0]][resyn,
+ target_dist = targetdist.loc[mapidx_x,
+ atm_pair[0]][mapidx_y,
atm_pair[1]]
else:
- target_dist = "%.2f" % targetdist.iat[resx,
- resy]
+ target_dist = "%.2f" % targetdist.iat[idx_x,
+ idx_y]
if target_dist is None:
# In case missing distance values
@@ -600,7 +610,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
logger.warning(
"Target distance is missing for restraint "
"%s-%s (%s). Using default distance (%s)"
- % (resx + 1, resy + 1, atm_pair, target_dist))
+ % (idx_x + 1, idx_y + 1, atm_pair, target_dist))
rest_id += 1
contrib_id = 1
@@ -636,12 +646,12 @@ class AriaEcXMLConverter(AriaXMLConverter):
"weight": 1.0
},
"spin_pair": {
- resx + 1: atm_pair[0],
- resy + 1: atm_pair[1]
+ idx_x + 1: atm_pair[0],
+ idx_y + 1: atm_pair[1]
}
}
xml_file = self.settings.infra["xml"] + "/" + "_".join((
- self.protname, listname)) + ".xml"
+ self.outprefix, listname)) + ".xml"
self.write_dist_xml(restraint_dict, xml_file)
return xml_file, pair_list
@@ -667,11 +677,11 @@ class AriaEcXMLConverter(AriaXMLConverter):
:param hbmap: Extra hbond map (eg: metapsicov hbonds)
:return:
"""
- dihed_file = os.path.join(self.settings.infra["tbl"], self.protname +
+ dihed_file = os.path.join(self.settings.infra["tbl"], self.outprefix +
"_dihed.tbl")
- hb_file = os.path.join(self.settings.infra["tbl"], self.protname +
+ hb_file = os.path.join(self.settings.infra["tbl"], self.outprefix +
"_hbond.tbl")
- ssdist_file = os.path.join(self.settings.infra["tbl"], self.protname +
+ ssdist_file = os.path.join(self.settings.infra["tbl"], self.outprefix +
"_ssdist.tbl")
self.write_dihedral_tbl(protein.sec_struct.ss_matrix, dihed_file)
self.write_hb_tbl(protein, hb_file,
@@ -684,39 +694,21 @@ class AriaEcXMLConverter(AriaXMLConverter):
ssdist_file)
return {'hbond': hb_file, 'dihed': dihed_file, 'ssdist': ssdist_file}
- def write_xmlseq(self, seqpath):
- xml_file = os.path.join(self.settings.infra["xml"], self.protname +
- ".xml")
-
- m = aria.conversion.MoleculeSettings()
- m['format'] = 'seq'
- m['input'] = seqpath
- m['output'] = xml_file
- m['type'] = 'PROTEIN'
- m['segid'] = ' '
- m['first_residue_number'] = 1
- m['naming_convention'] = ''
- m['name'] = self.protname
-
- c = aria.conversion.ConverterSettings()
- c.reset()
- c['molecule'] = m
- c['project_name'] = self.protname
-
- converter = aria.conversion.Converter()
- converter.setSettings(c)
-
- # TODO: generate xml in order to use convert method ??
- # converter.convert()
- with Capturing() as output:
- converter._convert_sequence()
+ def write_xmlseq(self):
- logger.info("\n" + "".join(output))
+ try:
+
+ self._pickler.dump(self.molecule, self._mol_set[
+ 'output'])
+
+ except Exception, msg:
+
+ logger.error("Error writing xml seq file : %s" % msg)
- return xml_file
+ return self._mol_set['output']
- def write_project(self, aria_template, seqfile, dist_files, tbl_files,
- desc=""):
+ def write_ariaproject(self, aria_template, seqfile, dist_files, tbl_files,
+ desc=""):
if aria_template:
template = os.path.abspath(aria_template)
@@ -755,21 +747,21 @@ class AriaEcXMLConverter(AriaXMLConverter):
for direct in (work_dir, temp_root):
- if not os.path.exists(os.path.join(direct, self.protname)):
- os.makedirs(os.path.join(direct, self.protname))
+ if not os.path.exists(os.path.join(direct, self.outprefix)):
+ os.makedirs(os.path.join(direct, self.outprefix))
- if not os.path.exists(os.path.join(direct, self.protname, desc)):
- os.makedirs(os.path.join(direct, self.protname, desc))
+ if not os.path.exists(os.path.join(direct, self.outprefix, desc)):
+ os.makedirs(os.path.join(direct, self.outprefix, desc))
- work_dir = os.path.join(work_dir, self.protname, desc)
- temp_root = os.path.join(temp_root, self.protname, desc)
+ work_dir = os.path.join(work_dir, self.outprefix, desc)
+ temp_root = os.path.join(temp_root, self.outprefix, desc)
aria_project_dict['working_directory'] = work_dir
aria_project_dict['temp_root'] = temp_root
- project = {'project_name': "_".join((self.protname, desc)),
+ project = {'project_name': "_".join((self.outprefix, desc)),
'date': datetime.date.today().isoformat(),
- 'file_root': "_".join((self.protname, desc))}
+ 'file_root': "_".join((self.outprefix, desc))}
aria_project_dict.update(project)
data_molecule = {'molecule_file': seqfile}
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index b625787498e3efd62d67472e4b42a83b28e25c1c..12fd3dfe9c8a55270612d758122c6bc87f40bac5 100644
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diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index e5b834e..ba351a5 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -80,7 +80,7 @@ class AriaEcContactMap(object):
# Use only position filter
# self.filter(fo.mapdict, fo.filetype, fo.contactlist,
# self.protein, clashlist=fo.clashlist,
- # protname=self.protname,
+ # outprefix=self.outprefix,
# outdir=self.settings.outdir, mapfilters="pos")
self.allresmap[(fo.filename, fo.filetype)] = fo.mapdict
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index a461771fb53bdf1b0630d498d1820a065b5c73ae..a21fef1bed62dd942c979bb3f41cec9c39e17d56 100644
GIT binary patch
delta 16
XcmeCu=+a<k{>;nOx8~|bc4iR(E?Naw
delta 16
XcmeCu=+a<k{>;m@@AA=&?93tnFhm8O
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index 3c211cc7e6fb5eb7499d1a522e96e82ce70facdb..53032a74ad2c6c3e5e53856f5b9c34f2eb8551d1 100644
GIT binary patch
delta 16
Ycmdn?fN9$UCRXOpyj(^bSq(P;06E(R3;+NC
delta 16
Ycmdn?fN9$UCRXOpyj;c`Sq(P;06E|W4FCWD
diff --git a/ariaec/setup.py b/ariaec/setup.py
index fe2f1db..1aebaa8 100644
--- a/ariaec/setup.py
+++ b/ariaec/setup.py
@@ -54,7 +54,7 @@ class AriaEcSetup:
# -------------------------------------------------------------------- #
self.outprefix = get_filename(self.settings.setup.args.get("seq",
None))
- self.converter.protname = self.outprefix
+ self.converter.outprefix = self.outprefix
# ------------------------- Load sequence ---------------------------- #
self.protein.set_aa_sequence(self.settings.setup.args.get("seq", None))
# -------------- Load secondary structure prediction ----------------- #
@@ -69,7 +69,7 @@ class AriaEcSetup:
# ---------------------------- Processing ---------------------------- #
# -------------------------------------------------------------------- #
# TODO: write submatrix in a file
- # TODO: change read method in reader to __call__ ?
+ # TODO: change read method in reader to __call__
# -------------------------- contact maps ---------------------------- #
self.reader.read(self.settings.setup.args.get("infiles"),
filetypelist=self.settings.setup.args.get("contact_types"),
@@ -142,7 +142,8 @@ class AriaEcSetup:
# ----------------------------- SEQ file ----------------------------- #
self.protein.write_seq(os.path.join(self.settings.infra.get("others", ''),
self.outprefix + ".seq"))
-
+ # Load aria molecule object from generated seq file
+ self.converter.load_molecule(self.protein.seqfile_path)
# --------------------------- TBL restraints ------------------------- #
# Setting contact number limit for hbmap
n_hb = int(len(self.protein.aa_sequence.sequence) *
@@ -159,16 +160,16 @@ class AriaEcSetup:
self.allresmap, self.targetmap)
# --------------------------- XML SEQ file --------------------------- #
- seq_file = self.converter.write_xmlseq(self.protein.seqfile_path)
+ 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_project(aria_template,
- seq_file, dist_files, tbl_files,
- desc="_".join(sorted(self.allresmap.keys())))
+ self.converter.write_ariaproject(aria_template,
+ xmlseq_file, dist_files, tbl_files,
+ desc="_".join(sorted(self.allresmap.keys())))
# ------------------------------ others ------------------------------ #
self.write_optional_files()
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index fc95c7c9edf6e7ecf1230d01559c4f2a62b55c5b..4f16a2b361a1c02638a25850235bf1943cb5f8fb 100644
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--
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