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ariaec
Commit 8d077988 authored by fabrice's avatar fabrice
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Bug fixe: only heavy atoms when atom list set to all + upp_bound not fixed... 

Bug fixe: only heavy atoms when atom list set to all + upp_bound not fixed when ambig_restraint turn on
parent fa3f608d
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Showing with 58 additions and 18 deletions
ariaec/conf/aria_ec.ini
View file @ 8d077988
......@@ -34,8 +34,9 @@ hb_dplus: 0.5
; --------------------------- Contacts parameters ---------------------------- #
; evfold_weight : use EVFold weight -> 10/i (i:contact rank)
; neighborhood_contact : add neighbors when writing restraint
; pair_list : all, min [min]; use all atom pairs or
; minimized list (CA-CA, CB-CB, SC-SC)
; pair_list : all, heavy, min [min]; use all atom pairs,
; heavy atms or minimized list
; (CA-CA, CB-CB, SC-SC)
; ambiguous_distance_restraint : use Ambiguous Distance Restraints
; ambiguous_distance_type : min, deff [min]; compute Deff from target
; distance iif ADR
......@@ -53,6 +54,7 @@ groupby_method: min
restraint_distance: 2.5
lower_bound: 1.0
def_upper_bound: 4.0
; Specific tresholds only for unambig restraints
ca_upper_bound: 7.0
cb_upper_bound: 7.0
; ---------------------------- Filter parameters ----------------------------- #
......@@ -106,10 +108,10 @@ md_parameters_random_seed: 89764443
md_parameters_steps_high: 10000
md_parameters_steps_cool1: 5000
md_parameters_steps_cool2: 4000
iteration_n_structures: 1000
iteration_n_structures: 100
iteration_n_best_structures: 15
iteration_n_kept_structures: 0
max_contribution: 20
max_contribution: 1000
merging_method: standard
violation_analysis_violation_threshold: 0.5
water_refinement_solvent: water
......
ariaec/econverter.py
View file @ 8d077988
......@@ -454,16 +454,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
conv_table = ConversionTable.ConversionTable().table['AMINO_ACID'][
'iupac']
# Dict giving all atms foreach aa
aa_atm = dict((AminoAcid.AminoAcid(aa)[0],
filter(contactmap.heavy_reg.match, v.keys())) for
aa, v 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()
}
# TODO: atm_pair method
if pair_flag == "min":
def min_atms(aa1, aa2, atms):
# Function to minimize atom pair list between aa1 & aa2
......@@ -472,6 +463,51 @@ class AriaEcXMLConverter(AriaXMLConverter):
('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,
......@@ -510,7 +546,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
if adr_flag:
rest_id += 1
# TODO: Autre dist_list if target != ResMap
# dist_list containt all atm-atm dist foren_factorach res-res (+ neigh)
# dist_list containt all atm-atm dist foreach res-res (+ neigh)
# if target is a ResAtmMap or only one dist foreach res-res
# !!!!! Utiliser stack pour eviter les distances en doubles ????
if isinstance(targetdist, ResAtmMap) or len(
......@@ -573,9 +609,9 @@ class AriaEcXMLConverter(AriaXMLConverter):
if restraint_dict.get(rest_id, None) is None:
# If restraint doesn't exist
# TODO: set upper and lower bound if sdv not None
if atm_pair == ("CA", "CA"):
if atm_pair == ("CA", "CA") and not adr_flag:
upp_bound = self.settings.setup.config["ca_upper_bound"]
elif atm_pair == ("CB", "CB"):
elif atm_pair == ("CB", "CB") and not adr_flag:
upp_bound = self.settings.setup.config["cb_upper_bound"]
else:
upp_bound = self.settings.setup.config[
......@@ -698,7 +734,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
aria_project_dict = {}
# Check if ratio cool1 / cool2 is 5:4
# Check if ratio cool1 / cool2 is 5:4 ... (relevant ?)
steps_1 = float(self.settings.setup.config['md_parameters_steps_cool1'])
steps_2 = float(self.settings.setup.config['md_parameters_steps_cool2'])
if steps_1 / steps_2 != float(5) / int(4):
......
ariaec/econverter.pyc
View file @ 8d077988
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ariaec/protmap.py
View file @ 8d077988
......@@ -511,8 +511,10 @@ class ResAtmMap(ProteinMap):
CG 1.391024 1.379875 1.478053 2.505414 0.000000 2.790403
"""
# TODO: matrix should be not only for heavy atoms
# Matrix only for heavy atoms.
heavy_reg = re.compile(r"[CNOS][ABGDEZH][0-9]?")
all_reg = re.compile(r"^((?!cns|dyana).*)$")
# TODO: Autre methodes de dist
distance_method = 'euclidean'
......
ariaec/protmap.pyc
View file @ 8d077988
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