Commit 76fa3942 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Updated tempate files

parent 5244de67
Path<!DOCTYPE project SYSTEM "project1.0.dtd">
<!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=""/>
......
## Template with hbdb tag
<!-- Template with hbdb tag -->
<!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>
......
## Template with clustering tag
<!-- Template with clustering tag -->
<!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>
......
## Template with scoring tag
<!-- Template with scoring tag -->
<!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>
......
## Template with avg_exponent field in ambiguous restraint tag
<!-- Template with avg_exponent field in ambiguous restraint tag -->
<!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>
......
## Template with method field in clustering tag
<!-- Template with method field in clustering tag -->
<!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>
......
......@@ -36,13 +36,13 @@ from past.builtins import cmp
from threading import Thread
QUALITY_CHECKS_HEADER = \
"""
Summary for quality checks:
---------------------------
Created: %(time)s
"""
"""
Summary for quality checks:
---------------------------
Created: %(time)s
"""
def checksum(filename):
......@@ -683,7 +683,7 @@ class Project(AriaBaseClass):
codes = ",".join(molsystem_id[1:])
self.message(
'Retrieving molecular system "%s", chain code(s) "%s"...' % (
molsystem_id[0], codes))
molsystem_id[0], codes))
else:
molsystem_id = None
......@@ -702,7 +702,7 @@ class Project(AriaBaseClass):
restraints_names[d].append(c['ccpn_id'])
self.message(
'Retrieving Constraint List "%s" of type "%s" ...' % (
c['ccpn_id'], d))
c['ccpn_id'], d))
##
# BARDIAUX Models
......@@ -908,11 +908,13 @@ class Project(AriaBaseClass):
ioRole='input')
convert_to_aria = cType in [DC.DATA_AMBIGUOUS,
DC.DATA_UNAMBIGUOUS] and (
X[cType][i]['add_to_network'] == YES or
X[cType][i]['calibrate'] != NO or
X[cType][i][
'filter_contributions'] == YES)
DC.DATA_UNAMBIGUOUS] and (
X[cType][i][
'add_to_network'] == YES or
X[cType][i][
'calibrate'] != NO or
X[cType][i][
'filter_contributions'] == YES)
if convert_to_aria:
# CCPN Restraint added to distance restraints list
......@@ -1038,7 +1040,7 @@ class Project(AriaBaseClass):
# this is not supported for now.
if xx['peaks']['format'] == 'ccpn' or \
xx['shifts']['format'] == 'ccpn':
xx['shifts']['format'] == 'ccpn':
val = xx
# BARDIAUX 2.2
......@@ -1904,6 +1906,7 @@ class Project(AriaBaseClass):
class ProjectSingleton(Project, Singleton):
"""ProjectSingleton constructor class"""
def __init__(self, *args, **kw):
Singleton.__init__(self)
Project.__init__(self, *args, **kw)
......@@ -1960,7 +1963,7 @@ class ProjectXMLPickler(XMLBasePickler):
def setStructGenPickler(self):
from . cns import CNSXMLPickler
from .cns import CNSXMLPickler
from . import JobManager as JobManager
self.cns = CNSXMLPickler()
......
......@@ -15,7 +15,12 @@
-->
<!ELEMENT project (data, structure_generation, protocol, analysis, report)>
<!ELEMENT project (
data,
structure_generation,
protocol,
analysis,
report)>
<!ATTLIST project
name CDATA ""
version CDATA "1.0"
......@@ -28,25 +33,46 @@
temp_root CDATA #REQUIRED
run CDATA "1"
file_root CDATA #REQUIRED
cache (yes | no) "yes"
cache (yes | no) "no"
cleanup (yes | no) "yes">
<!ELEMENT data (ccpn_model, molecule, spectrum+, unambiguous_distance_restraints*, ambiguous_distance_restraints*, jcouplings*, rdcs*, hbonds*, dihedrals*, ssbonds?, ssbridge*, hispatch*, template_structure*, initial_structure, symmetry)>
<!ELEMENT data (
ccpn_model,
molecule,
spectrum*,
unambiguous_distance_restraints*,
ambiguous_distance_restraints*,
jcouplings*,
rdcs*,
hbonds*,
dihedrals*,
ssbonds*,
ssbridge*,
hispatch*,
cispropatch*,
znpatch*,
isopatch*,
other_data*,
template_structure*,
initial_structure,
symmetry)>
<!ELEMENT ccpn_model EMPTY>
<!ATTLIST ccpn_model
filename CDATA "">
<!ELEMENT molecule (linkage_definition, topology_definition, parameter_definition)>
<!ELEMENT molecule (
linkage_definition,
topology_definition,
parameter_definition)>
<!ATTLIST molecule
file CDATA #REQUIRED
format (xml) "xml"
format (xml|ccpn) "xml"
ccpn_id CDATA "">
<!ELEMENT linkage_definition EMPTY>
<!ATTLIST linkage_definition
name (automatic|user_defined|dna-rna.link|topallhdg.pep|topallhdg5.3.pep) "automatic"
name (automatic|user_defined|dna-rna.link|dna-rna-pho.link|topallhdg.pep|topallhdg5.3.pep) "automatic"
filename CDATA "">
<!ELEMENT topology_definition EMPTY>
......@@ -56,35 +82,42 @@
<!ELEMENT parameter_definition EMPTY>
<!ATTLIST parameter_definition
name (automatic|user_defined|dna-rna-allatom.param|parallhdg5.0.pro|parallhdg5.1.pro|parallhdg5.2.pro|parallhdg5.3.pro) "automatic"
name (automatic|user_defined|dna-rna-allatom.param|parallhdg5.0.pro|parallhdg5.1.pro|parallhdg5.2.pro|parallhdg5.3.pro|parallhdg5.3softbig.pro) "automatic"
filename CDATA "">
<!ELEMENT spectrum (shifts, peaks, experiment_data?)>
<!ELEMENT spectrum (
shifts,
peaks,
experiment_data?)>
<!ATTLIST spectrum
enabled (yes|no) "yes"
use_assignments (yes|no) "yes"
trust_assigned_peaks (yes|no) "no"
structural_rules (yes|no) "no"
filter_diagonal_peaks (yes|no) "no">
filter_diagonal_peaks (yes|no) "no"
filter_unassigned_peaks (yes|no) "no">
<!ELEMENT shifts EMPTY>
<!ATTLIST shifts
file CDATA #REQUIRED
format (xml) "xml"
format (xml|ccpn) "xml"
ccpn_id CDATA ""
default_shift_error CDATA "0.01"
ccpn_id CDATA "">
use_shift_error (yes|no) "yes">
<!ELEMENT peaks (lower_bound_correction,
<!ELEMENT peaks (
lower_bound_correction,
upper_bound_correction)>
<!ATTLIST peaks
file CDATA #REQUIRED
format (xml) "xml"
format (xml|ccpn) "xml"
ccpn_id CDATA ""
peak_size (volume|intensity) "volume"
freq_window_proton1 CDATA "0.04"
freq_window_hetero1 CDATA "0.5"
freq_window_proton2 CDATA "0.02"
freq_window_hetero2 CDATA "0.5"
ccpn_id CDATA "">
use_bounds (yes|no) "no">
<!ELEMENT lower_bound_correction EMPTY>
<!ATTLIST lower_bound_correction
......@@ -106,22 +139,22 @@
<!ELEMENT unambiguous_distance_restraints EMPTY>
<!ATTLIST unambiguous_distance_restraints
file CDATA #REQUIRED
format (tbl|xml) "tbl"
format (tbl|xml|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes"
add_to_network (yes|no) "no"
calibrate (yes|no) "no"
calibrate (all_iterations|all_iterations_except_first|no) "no"
run_network_anchoring (yes|no) "no"
filter_contributions (yes|no) "no">
<!ELEMENT ambiguous_distance_restraints EMPTY>
<!ATTLIST ambiguous_distance_restraints
file CDATA #REQUIRED
format (tbl|xml) "tbl"
format (tbl|xml|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes"
add_to_network (yes|no) "no"
calibrate (yes|no) "no"
calibrate (all_iterations|all_iterations_except_first|no) "no"
run_network_anchoring (yes|no) "no"
filter_contributions (yes|no) "no"
avg_exponent CDATA "6">
......@@ -129,39 +162,47 @@
<!ELEMENT jcouplings EMPTY>
<!ATTLIST jcouplings
file CDATA #REQUIRED
format (tbl) "tbl"
parameter_class (1 | 2 | 3 | 4 | 5) "1"
enabled (yes|no) "yes">
format (tbl|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes"
parameter_class (1 | 2 | 3 | 4 | 5) "1">
<!ELEMENT rdcs EMPTY>
<!ATTLIST rdcs
file CDATA #REQUIRED
format (tbl) "tbl"
format (tbl|ccpn) "tbl"
ccpn_id CDATA ""
parameter_class (1 | 2 | 3 | 4 | 5) "1"
enabled (yes|no) "yes">
<!ELEMENT hbonds EMPTY>
<!ATTLIST hbonds
file CDATA #REQUIRED
format (tbl) "tbl"
data_type (standard | csi) "standard"
format (tbl|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes"
ccpn_id CDATA "">
data_type (standard | csi) "standard">
<!ELEMENT dihedrals EMPTY>
<!ATTLIST dihedrals
file CDATA #REQUIRED
format (tbl) "tbl"
data_type (standard | talos | csi) "standard"
format (tbl|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes"
ccpn_id CDATA "">
data_type (standard | talos | csi) "standard">
<!ELEMENT ssbonds EMPTY>
<!ELEMENT ssbonds (cyspatch*)>
<!ATTLIST ssbonds
file CDATA #REQUIRED
format (tbl) "tbl"
format (tbl|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes">
<!ELEMENT cyspatch EMPTY>
<!ATTLIST cyspatch
residue CDATA #REQUIRED
segid CDATA "">
<!ELEMENT ssbridge EMPTY>
<!ATTLIST ssbridge
residue1 CDATA #REQUIRED
......@@ -175,15 +216,52 @@
segid CDATA ""
proton (HISD|HISE) "HISD">
<!ELEMENT cispropatch EMPTY>
<!ATTLIST cispropatch
residue CDATA #REQUIRED
segid CDATA "">
<!ELEMENT znpatch EMPTY>
<!ATTLIST znpatch
type (SSSS|SSSE|SSSD|SSEE|SSDD|SSDE) "SSSS"
residue_zn CDATA #REQUIRED
segid_zn CDATA ""
residue1 CDATA #REQUIRED
segid1 CDATA ""
residue2 CDATA #REQUIRED
segid2 CDATA ""
residue3 CDATA #REQUIRED
segid3 CDATA ""
residue4 CDATA #REQUIRED
segid4 CDATA "">
<!ELEMENT isopatch EMPTY>
<!ATTLIST isopatch
type (cis|trans) "trans"
residue1 CDATA #REQUIRED
segid1 CDATA ""
residue2 CDATA #REQUIRED
segid2 CDATA "">
<!ELEMENT other_data EMPTY>
<!ATTLIST other_data
file CDATA #REQUIRED
format (tbl|ccpn) "tbl"
ccpn_id CDATA ""
enabled (yes|no) "yes"
data_type (planarity) "planarity">
<!ELEMENT template_structure EMPTY>
<!ATTLIST template
format (iupac | cns | dyana) "iupac"
file CDATA #REQUIRED
format (iupac | cns | dyana | ccpn) "iupac"
ccpn_id CDATA ""
enabled (yes|no) "yes">
<!ELEMENT initial_structure EMPTY>
<!ATTLIST initial_structure
format (iupac | cns | dyana) "iupac"
format (iupac | cns | dyana | ccpn) "iupac"
file CDATA #REQUIRED
enabled (yes|no) "yes"
ccpn_id CDATA "">
......@@ -197,23 +275,26 @@
ncs_enabled (yes|no) "yes"
packing_enabled (yes|no) "yes">
<!ELEMENT structure_generation (cns, job_manager)>
<!ELEMENT structure_generation (
cns,
job_manager)>
<!ATTLIST structure_generation engine (cns) "cns">
<!ELEMENT job_manager (host+)>
<!ELEMENT job_manager (host*)>
<!ATTLIST job_manager
default_command CDATA "csh -f">
<!ELEMENT host EMPTY>
<!ATTLIST host
enabled (yes|no) "yes"
command CDATA "default"
executable CDATA "default"
command CDATA "csh"
executable CDATA #REQUIRED
n_cpu CDATA "1"
use_absolute_path CDATA (yes|no) "yes">
<!ELEMENT cns (annealing_parameters, md_parameters)>
<!ELEMENT cns (
annealing_parameters,
md_parameters)>
<!ATTLIST cns
local_executable CDATA #REQUIRED
keep_output (yes|gzip|no) "yes"
......@@ -222,25 +303,39 @@
generate_template (yes|no|always) "yes"
nonbonded_parameters (PROLSQ|PARMALLH6|PARALLHDG|OPSLX) "PROLSQ">
<!ELEMENT annealing_parameters (unambiguous_restraints, ambiguous_restraints, hbond_restraints, dihedral_restraints, karplus_restraints+, rdc_restraints+, flat_bottom_harmonic_wall, symmetry_restraints, logharmonic_potential, rama_potential, hbdb_potential, scoring)>
<!ELEMENT annealing_parameters (
unambiguous_restraints,
ambiguous_restraints,
hbond_restraints,
dihedral_restraints,
karplus_restraints+,
rdc_restraints+,
flat_bottom_harmonic_wall,
symmetry_restraints,
logharmonic_potential,
rama_potential,
hbdb_potential,
scoring)>
<!--TODO: averaging attribute ?-->
<!ELEMENT unambiguous_restraints EMPTY>
<!ATTLIST unambiguous_restraints
first_iteration CDATA "0"
k_hot CDATA "10"
k_cool1_initial CDATA "10"
k_cool1_final CDATA "50"
k_cool2 CDATA "50"
averaging (sum) "sum">
k_cool2 CDATA "50">
<!--averaging (sum) "sum"-->
<!--TODO: averaging attribute ?-->
<!ELEMENT ambiguous_restraints EMPTY>
<!ATTLIST ambiguous_restraints
first_iteration CDATA "0"
k_hot CDATA "10"
k_cool1_initial CDATA "10"
k_cool1_final CDATA "50"
k_cool2 CDATA "50"
averaging (sum) "sum">
k_cool2 CDATA "50">
<!--averaging (sum) "sum"-->
<!ELEMENT hbond_restraints EMPTY>
<!ATTLIST hbond_restraints
......@@ -248,8 +343,7 @@
k_hot CDATA "10"
k_cool1_initial CDATA "10"
k_cool1_final CDATA "50"
k_cool2 CDATA "50"
averaging (sum) "sum">
k_cool2 CDATA "50">
<!ELEMENT dihedral_restraints EMPTY>
<!ATTLIST dihedral_restraints
......@@ -364,7 +458,8 @@
enabled (yes|no) "yes"
write_solvent_molecules (yes|no) "no">
<!ELEMENT iteration (assignment,
<!ELEMENT iteration (
assignment,
merging,
calibration,
violation_analysis,
......@@ -379,7 +474,9 @@
n_best_structures CDATA "7"
n_kept_structures CDATA "10">
<!--TODO: Meaning of this empty tag ?-->
<!ELEMENT assignment EMPTY>
<!ELEMENT merging EMPTY>
<!ATTLIST merging
method (standard|no_merging|combination2_1|combination4_4) "standard">
......@@ -387,6 +484,7 @@
<!ELEMENT calibration EMPTY>
<!ATTLIST calibration
distance_cutoff CDATA "6.0"
volume_or_intensity (volume|intensity) "volume"
estimator (ratio_of_averages) "ratio_of_averages"
relaxation_matrix (yes|no) "no"
error_estimator (distance|intensity) "distance">
......@@ -399,10 +497,12 @@
<!ELEMENT partial_assignment EMPTY>
<!ATTLIST partial_assignment
weight_threshold CDATA "0.8"
weight_threshold CDATA "1.0"
max_contributions CDATA "20"
exponent CDATA "6">
<!--TODO: find something to avoid putting private settings in the DTD if we
generate automatically this file in the future-->
<!ELEMENT network_anchoring EMPTY>
<!ATTLIST network_anchoring
enabled (yes|no) "no"
......
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