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Commit ea0d92df authored by Fabrice Allain's avatar Fabrice Allain
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Using mako library to generate dynamically iteration tag in the project template

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ariaec/commands.pyc
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ariaec/conf/aria_ec.ini
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[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 --------------------------- #
......
ariaec/econverter.py
View file @ ea0d92df
......@@ -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))
ariaec/econverter.pyc
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ariaec/ecsettings.py
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......@@ -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
......
ariaec/ecsettings.pyc
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ariaec/maplot.pyc
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ariaec/protein.pyc
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ariaec/protmap.pyc
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ariaec/setup.pyc
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ariaec/templates/aria_project.xml → ariaec/templates/aria_project_v2.3.0.xml
View file @ ea0d92df
<!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">
<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)s" format="xml" ccpn_id="">
<molecule file="${molecule_file}" format="xml" ccpn_id="">
<linkage_definition name="automatic" filename=""/>
<parameter_definition name="%(parameter_definition)s" filename=""/>
<parameter_definition name="${parameter_definition}" 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"/>
</molecule>${unambiguous_distance_restraints} ${ambiguous_distance_restraints}
<hbonds file="${hbond_dist_file}" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<dihedrals file="${dihed_angle_file}" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="no"/>
<initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
</data>
<structure_generation engine="cns">
<cns local_executable="%(cns_executable)s" keep_output="%(cns_keep_output)s" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" nonbonded_parameters="PROLSQ">
<cns local_executable="${cns_executable}" keep_output="${cns_keep_output}" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" nonbonded_parameters="PROLSQ">
<annealing_parameters>
<unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="%(unambiguous_restraints_k_cool1_initial)s" k_cool1_final="%(unambiguous_restraints_k_cool1_final)s" k_cool2="%(unambiguous_restraints_k_cool2)s"/>
<unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="${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)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"/>
<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="${dihedral_restraints_k_cool2}"/>
<karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
......@@ -31,101 +31,39 @@
<rdc_restraints parameter_class="5" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
<flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" m_rswitch_cool2="0.5" rswitch_hot="0.5" rswitch_cool1="0.5" rswitch_cool2="0.5" m_asymptote_hot="-1.0" m_asymptote_cool1="-1.0" m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" asymptote_cool2="0.1"/>
<symmetry_restraints k_packing_hot="15.0" k_packing_cool1="10.0" k_packing_cool2="5.0" last_iteration_packing="8" k_ncs="50.0"/>
<logharmonic_potential enabled="%(logharmonic_potential_enabled)s" use_auto_weight="%(logharmonic_potential_use_auto_weight)s" weight_unambig="%(logharmonic_potential_weight_unambig)s" weight_ambig="%(logharmonic_potential_weight_ambig)s" weight_hbond="%(logharmonic_potential_weight_hbond)s"/>
<rama_potential enabled="%(rama_potential_enabled)s" weight_rama="1.0"/>
<logharmonic_potential enabled="${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="${rama_potential_enabled}" weight_rama="1.0"/>
</annealing_parameters>
<md_parameters dynamics="torsion" random_seed="%(md_parameters_random_seed)s" tad_temp_high="10000.0" tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="%(md_parameters_steps_high)s" steps_refine="4000" steps_cool1="%(md_parameters_steps_cool1)s" steps_cool2="%(md_parameters_steps_cool2)s"/>
<md_parameters dynamics="torsion" random_seed="${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="${md_parameters_steps_cool2}"/>
</cns>
<job_manager default_command="csh -f">
<host enabled="yes" command="%(host_command)s" executable="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" n_cpu="%(n_cpus)s" use_absolute_path="yes"/>
<host enabled="yes" command="${host_command}" executable="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" n_cpu="${n_cpus}" use_absolute_path="yes"/>
</job_manager>
</structure_generation>
<protocol floating_assignment="yes">
<iteration number="0" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s">
% for iter in range(0, int(iterations + 1)):
<iteration number="${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="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"/>
<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>
<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"/>
% endfor
<water_refinement solvent="${water_refinement_solvent}" n_structures="${water_refinement_n_structures}" enabled="${water_refinement_enabled}" write_solvent_molecules="${water_refinement_write_solvent_molecules}"/>
</protocol>
<analysis>
<structures_analysis enabled="yes"/>
<procheck executable="%(procheck_executable)s" enabled="%(procheck_enabled)s"/>
<prosa executable="%(prosa_executable)s" enabled="%(prosa_enabled)s"/>
<whatif executable="%(whatif_executable)s" enabled="%(whatif_enabled)s"/>
<clashlist executable="%(clashlist_executable)s" enabled="%(clahlist_enabled)s"/>
<procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
<clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
<molmol enabled="yes"/>
<noe_restraint_list pickle_output="%(pickle_output)s" text_output="yes" xml_output="no"/>
<noe_restraint_list pickle_output="${pickle_output}" text_output="yes" xml_output="no"/>
<spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/>
</report>
</project>
ariaec/templates/aria_project_v2.3.2.xml 0 → 100644
View file @ ea0d92df
<!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>
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