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bis-aria
ariaec
Commits
41e1ac0e
Commit
41e1ac0e
authored
Nov 16, 2016
by
Fabrice Allain
Browse files
Updated several doctypes & config file
parent
330e140c
Changes
7
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ariaec/commands.pyc
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41e1ac0e
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ariaec/conf/aria_ec.ini
View file @
41e1ac0e
...
@@ -3,9 +3,10 @@
...
@@ -3,9 +3,10 @@
; Leave these fields empty in order to use default files
; Leave these fields empty in order to use default files
; ariaproject_template : Since there is several differences between
; ariaproject_template : Since there is several differences between
; aria version in template tags, this package
; aria version in template tags, this package
; can switch between 2 version actually: 2.3.0
; can switch between 2 version actually:
; with ramachandran potential tag and 2.3.2 with
; - 2.3.0 with ramachandran potential tag
; exponent tag
; - 2.3.2 with exponent tag
; - 2.3.3 with clustering tag
ss_dist_file:
ss_dist_file:
scsc_min_file:
scsc_min_file:
ariaproject_template:
2.3.0
ariaproject_template:
2.3.0
...
@@ -164,6 +165,9 @@ netanch_high_residue_threshold: 4.0
...
@@ -164,6 +165,9 @@ netanch_high_residue_threshold: 4.0
netanch_enabled:
no
netanch_enabled:
no
netanch_min_residue_threshold:
1.0
netanch_min_residue_threshold:
1.0
netanch_min_atom_threshold:
0.25
netanch_min_atom_threshold:
0.25
clustering_enabled:
no
clustering_mask:
CA
clustering_nclusters:
2
[contactmap]
[contactmap]
; -------------------------- Contactmap parameters --------------------------- #
; -------------------------- Contactmap parameters --------------------------- #
...
...
ariaec/econverter.py
View file @
41e1ac0e
...
@@ -140,7 +140,7 @@ class AriaXMLConverter(Converter, object):
...
@@ -140,7 +140,7 @@ class AriaXMLConverter(Converter, object):
segids
=
segids
.
split
(
'/'
)
segids
=
segids
.
split
(
'/'
)
segids
=
[
string_to_segid
(
segid
)
for
segid
in
segids
]
segids
=
[
string_to_segid
(
segid
)
for
segid
in
segids
]
#
Recup
molecule
#
Fetch
molecule
chain_types
=
{}
chain_types
=
{}
for
s
in
segids
:
for
s
in
segids
:
chain_types
[
s
]
=
self
.
_mol_set
[
'type'
]
chain_types
[
s
]
=
self
.
_mol_set
[
'type'
]
...
...
ariaec/protein.py
View file @
41e1ac0e
...
@@ -494,7 +494,6 @@ class Protein(object):
...
@@ -494,7 +494,6 @@ class Protein(object):
# TODO: same as above, trouble with unicode calls inside capturing
# TODO: same as above, trouble with unicode calls inside capturing
# with Capturing() as output:
# with Capturing() as output:
self
.
aa_sequence
.
WriteSeq
(
text_type
(
outfile
))
self
.
aa_sequence
.
WriteSeq
(
text_type
(
outfile
))
# LOG.info(''.join(output))
self
.
seqfile_path
=
outfile
self
.
seqfile_path
=
outfile
...
...
ariaec/protein.pyc
View file @
41e1ac0e
No preview for this file type
ariaec/templates/aria_project_v2.3.3.xml
0 → 100644
View file @
41e1ac0e
<!DOCTYPE project SYSTEM "project1.0.dtd">
<project
name=
"${project_name}"
version=
"1.0"
author=
""
date=
"${date}"
description=
""
comment=
""
references=
""
working_directory=
"${working_directory}"
temp_root=
"${temp_root}"
run=
"${runid}"
file_root=
"${file_root}"
cache=
"yes"
cleanup=
"yes"
>
<data>
<ccpn_model
filename=
""
/>
<molecule
file=
"${molecule_file}"
format=
"xml"
ccpn_id=
""
>
<linkage_definition
name=
"automatic"
filename=
""
/>
<parameter_definition
name=
"${parameter_definition}"
filename=
""
/>
<topology_definition
name=
"automatic"
filename=
""
/>
</molecule>
${unambiguous_distance_restraints} ${ambiguous_distance_restraints}
<hbonds
file=
"${hbond_dist_file}"
format=
"tbl"
ccpn_id=
""
enabled=
"yes"
data_type=
"standard"
/>
<dihedrals
file=
"${dihed_angle_file}"
format=
"tbl"
ccpn_id=
""
enabled=
"yes"
data_type=
"standard"
/>
<symmetry
enabled=
"no"
method=
"standard"
n_monomers=
"1"
symmetry_type=
"None"
ncs_enabled=
"no"
packing_enabled=
"no"
/>
<initial_structure
file=
""
format=
"iupac"
ccpn_id=
""
enabled=
"no"
/>
</data>
<structure_generation
engine=
"cns"
>
<cns
local_executable=
"${cns_executable}"
keep_output=
"${cns_keep_output}"
keep_restraint_files=
"yes"
create_psf_file=
"yes"
generate_template=
"yes"
nonbonded_parameters=
"PROLSQ"
>
<annealing_parameters>
<unambiguous_restraints
first_iteration=
"0"
k_hot=
"10.0"
k_cool1_initial=
"${unambiguous_restraints_k_cool1_initial}"
k_cool1_final=
"${unambiguous_restraints_k_cool1_final}"
k_cool2=
"${unambiguous_restraints_k_cool2}"
/>
<ambiguous_restraints
first_iteration=
"0"
k_hot=
"10.0"
k_cool1_initial=
"10.0"
k_cool1_final=
"50.0"
k_cool2=
"50.0"
/>
<hbond_restraints
first_iteration=
"0"
k_hot=
"10.0"
k_cool1_initial=
"${hbond_restraints_k_cool1_initial}"
k_cool1_final=
"${hbond_restraints_k_cool1_final}"
k_cool2=
"${hbond_restraints_k_cool2}"
/>
<dihedral_restraints
k_hot=
"5.0"
k_cool1=
"${dihedral_restraints_k_cool1}"
k_cool2=
"${dihedral_restraints_k_cool2}"
/>
<karplus_restraints
parameter_class=
"1"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"2"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"3"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"4"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"5"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<rdc_restraints
parameter_class=
"1"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"2"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"3"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"4"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"5"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<flat_bottom_harmonic_wall
m_rswitch_hot=
"0.5"
m_rswitch_cool1=
"0.5"
m_rswitch_cool2=
"0.5"
rswitch_hot=
"0.5"
rswitch_cool1=
"0.5"
rswitch_cool2=
"0.5"
m_asymptote_hot=
"-1.0"
m_asymptote_cool1=
"-1.0"
m_asymptote_cool2=
"-0.1"
asymptote_hot=
"1.0"
asymptote_cool1=
"1.0"
asymptote_cool2=
"0.1"
/>
<symmetry_restraints
k_packing_hot=
"15.0"
k_packing_cool1=
"10.0"
k_packing_cool2=
"5.0"
last_iteration_packing=
"8"
k_ncs=
"50.0"
/>
<logharmonic_potential
enabled=
"${logharmonic_potential_enabled}"
use_auto_weight=
"${logharmonic_potential_use_auto_weight}"
weight_unambig=
"${logharmonic_potential_weight_unambig}"
weight_ambig=
"${logharmonic_potential_weight_ambig}"
weight_hbond=
"${logharmonic_potential_weight_hbond}"
/>
<rama_potential
enabled=
"${rama_potential_enabled}"
weight_rama=
"1.0"
/>
<hbdb_potential
enabled=
"${hbdb_potential_enabled}"
/>
</annealing_parameters>
<md_parameters
dynamics=
"torsion"
random_seed=
"${md_parameters_random_seed}"
tad_temp_high=
"10000.0"
tad_timestep_factor=
"9.0"
cartesian_temp_high=
"2000.0"
cartesian_first_iteration=
"0"
timestep=
"0.003"
temp_cool1_final=
"1000.0"
temp_cool2_final=
"50.0"
steps_high=
"${md_parameters_steps_high}"
steps_refine=
"4000"
steps_cool1=
"${md_parameters_steps_cool1}"
steps_cool2=
"${md_parameters_steps_cool2}"
/>
</cns>
<job_manager
default_command=
"csh -f"
>
<host
enabled=
"yes"
command=
"${host_command}"
executable=
"${host_executable}"
n_cpu=
"${n_cpus}"
use_absolute_path=
"yes"
/>
</job_manager>
</structure_generation>
<protocol
floating_assignment=
"yes"
>
% for iter in range(0, int(iterations + 1)):
<iteration
number=
"${iter}"
n_structures=
"${iteration_n_structures}"
sort_criterion=
"${iteration_sort_criterion}"
n_best_structures=
"${iteration_n_best_structures}"
n_kept_structures=
"${iteration_n_kept_structures}"
>
<assignment/>
<merging
method=
"${merging_method}"
/>
<calibration
relaxation_matrix=
"${calib_relaxation_matrix}"
distance_cutoff=
"${calib_distance_cutoff}"
estimator=
"${calib_estimator}"
error_estimator=
"${calib_error_estimator}"
/>
<violation_analysis
violation_tolerance=
"${viol_violation_tolerance[iter]}"
violation_threshold=
"${viol_violation_threshold}"
sigma_mode=
"${viol_sigma_mode}"
/>
<partial_assignment
weight_threshold=
"${partassign_weight_threshold[iter]}"
max_contributions=
"${partassign_max_contributions}"
exponent=
"${partassign_exponent}"
/>
<network_anchoring
high_residue_threshold=
"${netanch_high_residue_threshold}"
enabled=
"${netanch_enabled}"
min_residue_threshold=
"${netanch_min_residue_threshold}"
min_atom_threshold=
"${netanch_min_atom_threshold}"
/>
<clustering
enabled=
"${clustering_enabled}"
mask=
"${clustering_mask}"
n_clusters=
"${clustering_nclusters}"
/>
</iteration>
% endfor
<water_refinement
solvent=
"${water_refinement_solvent}"
n_structures=
"${water_refinement_n_structures}"
enabled=
"${water_refinement_enabled}"
write_solvent_molecules=
"${water_refinement_write_solvent_molecules}"
/>
</protocol>
<analysis>
<structures_analysis
enabled=
"yes"
/>
<procheck
executable=
"${procheck_executable}"
enabled=
"${procheck_enabled}"
/>
<prosa
executable=
"${prosa_executable}"
enabled=
"${prosa_enabled}"
/>
<whatif
executable=
"${whatif_executable}"
enabled=
"${whatif_enabled}"
/>
<clashlist
executable=
"${clashlist_executable}"
enabled=
"${clahlist_enabled}"
/>
</analysis>
<report>
<ccpn
export_assignments=
"no"
export_noe_restraint_list=
"no"
export_structures=
"no"
/>
<molmol
enabled=
"yes"
/>
<noe_restraint_list
pickle_output=
"${pickle_output}"
text_output=
"yes"
xml_output=
"no"
/>
<spectra
write_assigned=
"no"
write_assigned_force=
"no"
iteration=
"last"
write_unambiguous_only=
"yes"
/>
</report>
</project>
bin/ec2aria.py
View file @
41e1ac0e
...
@@ -18,6 +18,10 @@ LOG = logging.getLogger(__name__)
...
@@ -18,6 +18,10 @@ LOG = logging.getLogger(__name__)
def
main
():
def
main
():
"""
Launch ariaec command interface
:return:
"""
mylog
=
CustomLogging
(
desc
=
__doc__
)
mylog
=
CustomLogging
(
desc
=
__doc__
)
...
...
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