diff --git a/ariaec/commands.pyc b/ariaec/commands.pyc
index 6cb3f4ce9085f01222fdf50166463871c2fb80a2..2d377707d3f28aea7f677e655f4cea34ee2eddeb 100644
Binary files a/ariaec/commands.pyc and b/ariaec/commands.pyc differ
diff --git a/ariaec/conf/aria_ec.ini b/ariaec/conf/aria_ec.ini
index e8822f37bd867c2341b05f0f8092a89989ed8289..b9ea1fc14c816845660ba3965aaf809aa1596481 100644
--- a/ariaec/conf/aria_ec.ini
+++ b/ariaec/conf/aria_ec.ini
@@ -1,9 +1,14 @@
[main]
; ------------------------- Main parameters ---------------------------------- #
; Leave these fields empty in order to use default files
+; ariaproject_template : Since there is several differences between
+; aria version in template tags, this package
+; can switch between 2 version actually: 2.3.0
+; with ramachandran potential tag and 2.3.2 with
+; exponent tag
ss_dist_file:
scsc_min_file:
-ariaproject_template:
+ariaproject_template: 2.3.0
[contactdef]
; Contact definition section used to define contactmap from pdb file.
@@ -113,13 +118,6 @@ md_parameters_random_seed: 89764443
md_parameters_steps_high: 10000
md_parameters_steps_cool1: 5000
md_parameters_steps_cool2: 4000
-iteration_n_structures: 100
-iteration_n_best_structures: 15
-iteration_n_kept_structures: 0
-exponent: 20
-max_contribution: 1000
-merging_method: standard
-violation_analysis_violation_threshold: 0.5
water_refinement_solvent: water
water_refinement_n_structures: 10
water_refinement_enabled: no
@@ -133,6 +131,30 @@ whatif_enabled: yes
clashlist_executable:
clahlist_enabled: no
pickle_output: no
+; --------------------------- Iteration parameters --------------------------- #
+; /!\ Parameters below can be formatted as a list if we want different values
+; foreach iteration. Actually, only parameters can be set with different
+; values for each iterations (violation tolerance and partial assignment weight
+; treshold)
+iterations: 8
+iteration_n_structures: 100
+iteration_sort_criterion: total_energy
+iteration_n_best_structures: 15
+iteration_n_kept_structures: 0
+merging_method: standard
+calib_relaxation_matrix: no
+calib_distance_cutoff: 6.0
+calib_estimator: ratio_of_averages
+calib_error_estimator: distance
+viol_violation_tolerance: 1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1
+viol_violation_threshold: 0.5
+partassign_weight_threshold: 1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8
+partassign_max_contributions: 1000
+partassign_exponent: 6
+netanch_high_residue_threshold: 4.0
+netanch_enabled: no
+netanch_min_residue_threshold: 1.0
+netanch_min_atom_threshold: 0.25
[contactmap]
; -------------------------- Contactmap parameters --------------------------- #
diff --git a/ariaec/econverter.py b/ariaec/econverter.py
index 3555110c93d4e8db3100d97ecf25f0c7373e46c0..453bb85d4e5cd9e4d2e3ca5a5c1bca299250d207 100644
--- a/ariaec/econverter.py
+++ b/ariaec/econverter.py
@@ -19,6 +19,7 @@ from .base import get_filename, Capturing
from .protein import Protein
from .reader import ProtFileListReader
from .protmap import (ResAtmMap, ResMap)
+from mako.template import Template
from aria.Molecule import Molecule
from aria.tools import string_to_segid
from aria.AriaXML import AriaXMLPickler
@@ -725,20 +726,19 @@ class AriaEcXMLConverter(AriaXMLConverter):
:param desc:
:return:
"""
- logger.info("Reading aria template file %s" % aria_template)
- if aria_template:
- template = os.path.abspath(aria_template)
+ logger.info("Loading aria template file %s" % aria_template)
- try:
- t = open(template, 'r')
- except Exception, msg:
- sys.exit("""Can't open "%s" file. %s""" % (template, msg))
+ templatepath = os.path.abspath(aria_template)
+ ariaproj_template = Template(filename=templatepath,
+ module_directory="/tmp/mako_modules")
- aria_project_template = t.read()
- t.close()
- else:
- aria_project_template = pkgr.resource_string(
- __name__, self.settings.ARIAPROJ_TEMPLATE)
+ try:
+ t = open(templatepath, 'r')
+ except Exception, msg:
+ sys.exit("""Can't open "%s" file. %s""" % (templatepath, msg))
+
+ aria_project_template = t.read()
+ t.close()
aria_project_dict = {}
@@ -822,12 +822,10 @@ class AriaEcXMLConverter(AriaXMLConverter):
data_dihedrals = {'dihed_angle_file': tbl_files["dihed"]}
aria_project_dict.update(data_dihedrals)
- if self.settings.setup.config['cpus']:
- aria_project_dict['n_cpus'] = self.settings.setup.config['cpus']
- else:
- aria_project_dict['n_cpus'] = '20'
+ aria_project_dict['n_cpus'] = self.settings.setup.config.get('cpus',
+ '20')
proj_file = "%s/ariaproject.xml" % work_dir
with open(proj_file, 'w') as proj_xml:
logger.info("Writing ARIA project file (%s)" % proj_file)
- proj_xml.write(aria_project_template % aria_project_dict)
+ proj_xml.write(ariaproj_template.render(**aria_project_dict))
diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index 6d3501f5d813cfc8988d2752f1c152586a65384a..c228c656db48ed9ff2ff44183a90af3b16f69558 100644
Binary files a/ariaec/econverter.pyc and b/ariaec/econverter.pyc differ
diff --git a/ariaec/ecsettings.py b/ariaec/ecsettings.py
index 8eecb1cf5c65d3d91ac21a06cffc9a57437b52b5..dd131a4fb30c5e3e5437f9d023c6d0f2a1197d06 100644
--- a/ariaec/ecsettings.py
+++ b/ariaec/ecsettings.py
@@ -75,14 +75,12 @@ class Settings(object):
class AriaEcSettings(Settings):
- template = os.path.join(os.path.dirname(os.path.realpath(__file__)),
- 'templates/aria_project.xml')
# ss_dist = os.path.join(os.path.dirname(os.path.realpath(__file__)),
# 'conf/ss_dist.txt')
# TODO: move these constant variable in objects which can read these file !!
# TODO: Baseclass inspired from this class and ariabase class. All
# objects in this package should extend the base object
- ARIAPROJ_TEMPLATE = 'templates/aria_project.xml'
+ ARIAPROJ_TEMPLATE = 'templates/aria_project_v2.3.0.xml'
SS_DIST = 'data/ss_dist.txt'
SCSC_MIN = 'data/scsc_min.p'
TOPO = 'data/topallhdg5.3.pro'
@@ -136,10 +134,12 @@ class AriaEcSettings(Settings):
@property
def template(self):
if not self._template:
- if self.main.config["ariaproject_template"] and \
- os.path.exists(self.main.config["ariaproject_template"]):
- self._template = self.main.config["ariaproject_template"]
+ templatepath = "templates/aria_project_v%s.xml" % str(self.main.config["ariaproject_template"])
+ if os.path.exists(pkgr.resource_filename(__name__, templatepath)):
+ self._template = pkgr.resource_filename(__name__, templatepath)
else:
+ logger.error("Template version for aria project (%s) is not "
+ "supported" % self.main.config.get("ariaproject_template"))
self._template = pkgr.resource_filename(__name__,
self.ARIAPROJ_TEMPLATE)
return self._template
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index de9ac5fb88e2143023317d03576a8d895716bfba..255ed5031f4cbbcd88e62c1a883bc47f6365371f 100644
Binary files a/ariaec/ecsettings.pyc and b/ariaec/ecsettings.pyc differ
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index 7cc29e955233c6673ff0495a9fa094cfb16255ff..52c27a55568ff104dddf5f68a89fe949ec82cd0d 100644
Binary files a/ariaec/maplot.pyc and b/ariaec/maplot.pyc differ
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 44407c48708b929725c1e5963072313920b55827..3df5777c7f7fa6aa966518bc7a9d3fbd82c53a12 100644
Binary files a/ariaec/protein.pyc and b/ariaec/protein.pyc differ
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index 9608866141f32929e6046b770d1ff1e170af4106..97bdf80fc6bac046dfcd28c7d8a8f59c05779b2f 100644
Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ
diff --git a/ariaec/setup.pyc b/ariaec/setup.pyc
index 4017775356dffc582cc0d28878907f1eb8fbb147..61472e585722d579ed2c331f857e43d791d42641 100644
Binary files a/ariaec/setup.pyc and b/ariaec/setup.pyc differ
diff --git a/ariaec/templates/aria_project.xml b/ariaec/templates/aria_project.xml
deleted file mode 100644
index 898fb7e8a7bcbeab878962b262922cf3a19cab88..0000000000000000000000000000000000000000
--- a/ariaec/templates/aria_project.xml
+++ /dev/null
@@ -1,131 +0,0 @@
-<!DOCTYPE project SYSTEM "project1.0.dtd">
-<project name="%(project_name)s" version="1.0" author="" date="%(date)s" description="" comment="" references="" working_directory="%(working_directory)s" temp_root="%(temp_root)s" run="%(runid)s" file_root="%(file_root)s" cache="yes" cleanup="yes">
- <data>
- <ccpn_model filename=""/>
- <molecule file="%(molecule_file)s" format="xml" ccpn_id="">
- <linkage_definition name="automatic" filename=""/>
- <parameter_definition name="%(parameter_definition)s" filename=""/>
- <topology_definition name="automatic" filename=""/>
- </molecule>%(unambiguous_distance_restraints)s %(ambiguous_distance_restraints)s
- <hbonds file="%(hbond_dist_file)s" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
- <dihedrals file="%(dihed_angle_file)s" 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)s" keep_output="%(cns_keep_output)s" 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)s" k_cool1_final="%(unambiguous_restraints_k_cool1_final)s" k_cool2="%(unambiguous_restraints_k_cool2)s"/>
- <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)s" k_cool1_final="%(hbond_restraints_k_cool1_final)s" k_cool2="%(hbond_restraints_k_cool2)s"/>
- <dihedral_restraints k_hot="5.0" k_cool1="%(dihedral_restraints_k_cool1)s" k_cool2="%(dihedral_restraints_k_cool2)s"/>
- <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)s" use_auto_weight="%(logharmonic_potential_use_auto_weight)s" weight_unambig="%(logharmonic_potential_weight_unambig)s" weight_ambig="%(logharmonic_potential_weight_ambig)s" weight_hbond="%(logharmonic_potential_weight_hbond)s"/>
- <rama_potential enabled="%(rama_potential_enabled)s" weight_rama="1.0"/>
- </annealing_parameters>
- <md_parameters dynamics="torsion" random_seed="%(md_parameters_random_seed)s" 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)s" steps_refine="4000" steps_cool1="%(md_parameters_steps_cool1)s" steps_cool2="%(md_parameters_steps_cool2)s"/>
- </cns>
- <job_manager default_command="csh -f">
- <host enabled="yes" command="%(host_command)s" executable="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" n_cpu="%(n_cpus)s" use_absolute_path="yes"/>
- </job_manager>
- </structure_generation>
- <protocol floating_assignment="yes">
- <iteration number="0" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="1000.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="1.0" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="1" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="5.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.9999" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="2" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="3.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.999" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="3" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="1.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.99" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="4" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="1.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.98" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="5" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="1.0" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.96" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="6" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="0.1" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.93" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="7" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="standard"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="0.1" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.9" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <iteration number="8" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
- <assignment/>
- <merging method="%(merging_method)s"/>
- <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
- <violation_analysis violation_tolerance="0.1" violation_threshold="%(violation_analysis_violation_threshold)s"/>
- <partial_assignment weight_threshold="0.8" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/>
- <network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
- </iteration>
- <water_refinement solvent="%(water_refinement_solvent)s" n_structures="%(water_refinement_n_structures)s" enabled="%(water_refinement_enabled)s" write_solvent_molecules="%(water_refinement_write_solvent_molecules)s"/>
- </protocol>
- <analysis>
- <structures_analysis enabled="yes"/>
- <procheck executable="%(procheck_executable)s" enabled="%(procheck_enabled)s"/>
- <prosa executable="%(prosa_executable)s" enabled="%(prosa_enabled)s"/>
- <whatif executable="%(whatif_executable)s" enabled="%(whatif_enabled)s"/>
- <clashlist executable="%(clashlist_executable)s" enabled="%(clahlist_enabled)s"/>
- </analysis>
- <report>
- <ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
- <molmol enabled="yes"/>
- <noe_restraint_list pickle_output="%(pickle_output)s" text_output="yes" xml_output="no"/>
- <spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/>
- </report>
-</project>
diff --git a/ariaec/templates/aria_project_v2.3.0.xml b/ariaec/templates/aria_project_v2.3.0.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f6c304269e6900858edc2f462328595d187513dd
--- /dev/null
+++ b/ariaec/templates/aria_project_v2.3.0.xml
@@ -0,0 +1,69 @@
+<!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="${rama_potential_enabled}" weight_rama="1.0"/>
+ </annealing_parameters>
+ <md_parameters dynamics="torsion" random_seed="${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="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" 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="${viol_violation_threshold}"/>
+ <partial_assignment weight_threshold="${partassign_weight_threshold[iter]}" max_contributions="${partassign_max_contributions}"/>
+ <network_anchoring high_residue_threshold="${netanch_high_residue_threshold}" enabled="${netanch_enabled}" min_residue_threshold="${netanch_min_residue_threshold}" min_atom_threshold="${netanch_min_atom_threshold}"/>
+ </iteration>
+ % endfor
+ <water_refinement solvent="${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>
diff --git a/ariaec/templates/aria_project_v2.3.2.xml b/ariaec/templates/aria_project_v2.3.2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..63816698dd0e9e3330207471ac9da9f3782d2e3d
--- /dev/null
+++ b/ariaec/templates/aria_project_v2.3.2.xml
@@ -0,0 +1,69 @@
+<!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="${rama_potential_enabled}" weight_rama="1.0"/>
+ </annealing_parameters>
+ <md_parameters dynamics="torsion" random_seed="${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="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" 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="${viol_violation_threshold}"/>
+ <partial_assignment weight_threshold="${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}"/>
+ </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>