Commit ea0d92df authored by Fabrice Allain's avatar Fabrice Allain
Browse files

Using mako library to generate dynamically iteration tag in the project template

parent 0fe842e1
No preview for this file type
[main] [main]
; ------------------------- Main parameters ---------------------------------- # ; ------------------------- Main parameters ---------------------------------- #
; 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
; 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: ss_dist_file:
scsc_min_file: scsc_min_file:
ariaproject_template: ariaproject_template: 2.3.0
[contactdef] [contactdef]
; Contact definition section used to define contactmap from pdb file. ; Contact definition section used to define contactmap from pdb file.
...@@ -113,13 +118,6 @@ md_parameters_random_seed: 89764443 ...@@ -113,13 +118,6 @@ md_parameters_random_seed: 89764443
md_parameters_steps_high: 10000 md_parameters_steps_high: 10000
md_parameters_steps_cool1: 5000 md_parameters_steps_cool1: 5000
md_parameters_steps_cool2: 4000 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_solvent: water
water_refinement_n_structures: 10 water_refinement_n_structures: 10
water_refinement_enabled: no water_refinement_enabled: no
...@@ -133,6 +131,30 @@ whatif_enabled: yes ...@@ -133,6 +131,30 @@ whatif_enabled: yes
clashlist_executable: clashlist_executable:
clahlist_enabled: no clahlist_enabled: no
pickle_output: 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]
; -------------------------- Contactmap parameters --------------------------- # ; -------------------------- Contactmap parameters --------------------------- #
......
...@@ -19,6 +19,7 @@ from .base import get_filename, Capturing ...@@ -19,6 +19,7 @@ from .base import get_filename, Capturing
from .protein import Protein from .protein import Protein
from .reader import ProtFileListReader from .reader import ProtFileListReader
from .protmap import (ResAtmMap, ResMap) from .protmap import (ResAtmMap, ResMap)
from mako.template import Template
from aria.Molecule import Molecule from aria.Molecule import Molecule
from aria.tools import string_to_segid from aria.tools import string_to_segid
from aria.AriaXML import AriaXMLPickler from aria.AriaXML import AriaXMLPickler
...@@ -725,20 +726,19 @@ class AriaEcXMLConverter(AriaXMLConverter): ...@@ -725,20 +726,19 @@ class AriaEcXMLConverter(AriaXMLConverter):
:param desc: :param desc:
:return: :return:
""" """
logger.info("Reading aria template file %s" % aria_template) logger.info("Loading aria template file %s" % aria_template)
if aria_template:
template = os.path.abspath(aria_template)
try: templatepath = os.path.abspath(aria_template)
t = open(template, 'r') ariaproj_template = Template(filename=templatepath,
except Exception, msg: module_directory="/tmp/mako_modules")
sys.exit("""Can't open "%s" file. %s""" % (template, msg))
aria_project_template = t.read() try:
t.close() t = open(templatepath, 'r')
else: except Exception, msg:
aria_project_template = pkgr.resource_string( sys.exit("""Can't open "%s" file. %s""" % (templatepath, msg))
__name__, self.settings.ARIAPROJ_TEMPLATE)
aria_project_template = t.read()
t.close()
aria_project_dict = {} aria_project_dict = {}
...@@ -822,12 +822,10 @@ class AriaEcXMLConverter(AriaXMLConverter): ...@@ -822,12 +822,10 @@ class AriaEcXMLConverter(AriaXMLConverter):
data_dihedrals = {'dihed_angle_file': tbl_files["dihed"]} data_dihedrals = {'dihed_angle_file': tbl_files["dihed"]}
aria_project_dict.update(data_dihedrals) aria_project_dict.update(data_dihedrals)
if self.settings.setup.config['cpus']: aria_project_dict['n_cpus'] = self.settings.setup.config.get('cpus',
aria_project_dict['n_cpus'] = self.settings.setup.config['cpus'] '20')
else:
aria_project_dict['n_cpus'] = '20'
proj_file = "%s/ariaproject.xml" % work_dir proj_file = "%s/ariaproject.xml" % work_dir
with open(proj_file, 'w') as proj_xml: with open(proj_file, 'w') as proj_xml:
logger.info("Writing ARIA project file (%s)" % proj_file) 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))
No preview for this file type
...@@ -75,14 +75,12 @@ class Settings(object): ...@@ -75,14 +75,12 @@ class Settings(object):
class AriaEcSettings(Settings): 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__)), # ss_dist = os.path.join(os.path.dirname(os.path.realpath(__file__)),
# 'conf/ss_dist.txt') # 'conf/ss_dist.txt')
# TODO: move these constant variable in objects which can read these file !! # TODO: move these constant variable in objects which can read these file !!
# TODO: Baseclass inspired from this class and ariabase class. All # TODO: Baseclass inspired from this class and ariabase class. All
# objects in this package should extend the base object # 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' SS_DIST = 'data/ss_dist.txt'
SCSC_MIN = 'data/scsc_min.p' SCSC_MIN = 'data/scsc_min.p'
TOPO = 'data/topallhdg5.3.pro' TOPO = 'data/topallhdg5.3.pro'
...@@ -136,10 +134,12 @@ class AriaEcSettings(Settings): ...@@ -136,10 +134,12 @@ class AriaEcSettings(Settings):
@property @property
def template(self): def template(self):
if not self._template: if not self._template:
if self.main.config["ariaproject_template"] and \ templatepath = "templates/aria_project_v%s.xml" % str(self.main.config["ariaproject_template"])
os.path.exists(self.main.config["ariaproject_template"]): if os.path.exists(pkgr.resource_filename(__name__, templatepath)):
self._template = self.main.config["ariaproject_template"] self._template = pkgr.resource_filename(__name__, templatepath)
else: 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._template = pkgr.resource_filename(__name__,
self.ARIAPROJ_TEMPLATE) self.ARIAPROJ_TEMPLATE)
return self._template return self._template
......
No preview for this file type
No preview for this file type
No preview for this file type
No preview for this file type
No preview for this file type
<!DOCTYPE project SYSTEM "project1.0.dtd"> <!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> <data>
<ccpn_model filename=""/> <ccpn_model filename=""/>
<molecule file="%(molecule_file)s" format="xml" ccpn_id=""> <molecule file="${molecule_file}" format="xml" ccpn_id="">
<linkage_definition name="automatic" filename=""/> <linkage_definition name="automatic" filename=""/>
<parameter_definition name="%(parameter_definition)s" filename=""/> <parameter_definition name="${parameter_definition}" filename=""/>
<topology_definition name="automatic" filename=""/> <topology_definition name="automatic" filename=""/>
</molecule>%(unambiguous_distance_restraints)s %(ambiguous_distance_restraints)s </molecule>${unambiguous_distance_restraints} ${ambiguous_distance_restraints}
<hbonds file="%(hbond_dist_file)s" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/> <hbonds file="${hbond_dist_file}" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<dihedrals file="%(dihed_angle_file)s" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/> <dihedrals file="${dihed_angle_file}" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="no"/> <symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="no"/>
<initial_structure file="" format="iupac" ccpn_id="" enabled="no"/> <initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
</data> </data>
<structure_generation engine="cns"> <structure_generation engine="cns">
<cns local_executable="%(cns_executable)s" keep_output="%(cns_keep_output)s" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" nonbonded_parameters="PROLSQ"> <cns local_executable="${cns_executable}" keep_output="${cns_keep_output}" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" nonbonded_parameters="PROLSQ">
<annealing_parameters> <annealing_parameters>
<unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="%(unambiguous_restraints_k_cool1_initial)s" k_cool1_final="%(unambiguous_restraints_k_cool1_final)s" k_cool2="%(unambiguous_restraints_k_cool2)s"/> <unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="${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"/> <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"/> <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="${hbond_restraints_k_cool2}"/>
<dihedral_restraints k_hot="5.0" k_cool1="%(dihedral_restraints_k_cool1)s" k_cool2="%(dihedral_restraints_k_cool2)s"/> <dihedral_restraints k_hot="5.0" k_cool1="${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="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="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="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 @@ ...@@ -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"/> <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"/> <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"/> <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"/> <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)s" weight_rama="1.0"/> <rama_potential enabled="${rama_potential_enabled}" weight_rama="1.0"/>
</annealing_parameters> </annealing_parameters>
<md_parameters dynamics="torsion" random_seed="%(md_parameters_random_seed)s" tad_temp_high="10000.0" tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="%(md_parameters_steps_high)s" steps_refine="4000" steps_cool1="%(md_parameters_steps_cool1)s" steps_cool2="%(md_parameters_steps_cool2)s"/> <md_parameters dynamics="torsion" random_seed="${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="${md_parameters_steps_cool2}"/>
</cns> </cns>
<job_manager default_command="csh -f"> <job_manager default_command="csh -f">
<host enabled="yes" command="%(host_command)s" executable="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" n_cpu="%(n_cpus)s" use_absolute_path="yes"/> <host enabled="yes" command="${host_command}" executable="/baycells/home/bardiaux/bin/cns1.21_aria_logn_linux_x86_64_intel.exe" n_cpu="${n_cpus}" use_absolute_path="yes"/>
</job_manager> </job_manager>
</structure_generation> </structure_generation>
<protocol floating_assignment="yes"> <protocol floating_assignment="yes">
<iteration number="0" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s"> % for iter in range(0, int(iterations + 1)):
<iteration number="${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/> <assignment/>
<merging method="standard"/> <merging method="${merging_method}"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/> <calibration relaxation_matrix="${calib_relaxation_matrix}" distance_cutoff="${calib_distance_cutoff}" estimator="${calib_estimator}" error_estimator="${calib_error_estimator}"/>
<violation_analysis violation_tolerance="1000.0" violation_threshold="%(violation_analysis_violation_threshold)s"/> <violation_analysis violation_tolerance="${viol_violation_tolerance[iter]}" violation_threshold="${viol_violation_threshold}"/>
<partial_assignment weight_threshold="1.0" max_contributions="%(max_contribution)s" exponent="%(exponent)s"/> <partial_assignment weight_threshold="${partassign_weight_threshold[iter]}" max_contributions="${partassign_max_contributions}"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/> <network_anchoring high_residue_threshold="${netanch_high_residue_threshold}" enabled="${netanch_enabled}" min_residue_threshold="${netanch_min_residue_threshold}" min_atom_threshold="${netanch_min_atom_threshold}"/>
</iteration> </iteration>
<iteration number="1" n_structures="%(iteration_n_structures)s" sort_criterion="total_energy" n_best_structures="%(iteration_n_best_structures)s" n_kept_structures="%(iteration_n_kept_structures)s"> % endfor
<assignment/> <water_refinement solvent="${water_refinement_solvent}" n_structures="${water_refinement_n_structures}" enabled="${water_refinement_enabled}" write_solvent_molecules="${water_refinement_write_solvent_molecules}"/>
<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> </protocol>
<analysis> <analysis>
<structures_analysis enabled="yes"/> <structures_analysis enabled="yes"/>
<procheck executable="%(procheck_executable)s" enabled="%(procheck_enabled)s"/> <procheck executable="${procheck_executable}" enabled="${procheck_enabled}"/>
<prosa executable="%(prosa_executable)s" enabled="%(prosa_enabled)s"/> <prosa executable="${prosa_executable}" enabled="${prosa_enabled}"/>
<whatif executable="%(whatif_executable)s" enabled="%(whatif_enabled)s"/> <whatif executable="${whatif_executable}" enabled="${whatif_enabled}"/>
<clashlist executable="%(clashlist_executable)s" enabled="%(clahlist_enabled)s"/> <clashlist executable="${clashlist_executable}" enabled="${clahlist_enabled}"/>
</analysis> </analysis>
<report> <report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/> <ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
<molmol enabled="yes"/> <molmol enabled="yes"/>
<noe_restraint_list pickle_output="%(pickle_output)s" text_output="yes" xml_output="no"/> <noe_restraint_list pickle_output="${pickle_output}" text_output="yes" xml_output="no"/>
<spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/> <spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/>
</report> </report>
</project> </project>
<!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>
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment