Commit 41e1ac0e authored by Fabrice Allain's avatar Fabrice Allain
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Updated several doctypes & config file

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