##########################################################
# This config file is designed to allow you to set AMPLE
# settings easier and in a more convenient format.
# It allows you to set directory/executable paths as well
# as other settings specific to the AMPLE/MrBUMP pipeline.
#
# IMPORTANT:
#       Although filenames can be set in this config file,
#       please consider that you might encounter
#       unexpected or unspotted errors in future runs.
#
# Author: hlfsimko
# Date: 10.01.2016
##########################################################

[General]
allow_his_tag    = False
benchmark_mode   = False
ccp4_jobid       = None
debug            = False
devel_mode       = False
dry_run          = False
early_terminate  = True
max_array_jobs   = None
name             = ampl
nmr_process      = None
nmr_remodel      = False
no_gui           = False
nproc            = 1
output_pdb       = ample_output.pdb
purge            = False
quick_mode       = False
rcdir            = None
run_dir          = None
submit_array     = True
submit_cluster   = False 
submit_max_array = None
submit_pe_lsf    = None 
submit_pe_sge    = None 
submit_qtype     = None
submit_queue     = None
webserver_uri    = None

[Executables]
blast_dir                = None
fast_protein_cluster_exe = None
gesamt_exe               = None
LGA                      = None
maxcluster_exe           = None
mustang_exe              = None
phenix_exe               = None
rosetta_AbinitioRelax    = None
rosetta_dir              = None
rosetta_fragments_exe    = None
scwrl_exe                = None
shelxe_exe               = None
spicker_exe              = None
theseus_exe              = None

[Databases]
nr         = None
rosetta_db = None

[Restraints]
distance_to_neighbour   = 5
domain_termini_distance = 0
energy_function         = FADE
native_cutoff           = 8
restraints_factor       = 1.0
restraints_weight       = 0.0
use_contacts            = False

[Modelling]
all_atom        = True
import_models   = False
make_frags      = True
make_models     = True
nmodels         = 1000
quark_models    = False
rg_reweight     = None
ROSETTA_cluster = None
rosetta_version = None
transmembrane   = False
transmembrane2  = False
use_homs        = True

[Ensembling]
cluster_method        		= spicker
ensemble_options      		= None
ensembler_timeout               = 3600
homologs              		= False
homolog_aligner       		= gesamt
import_cluster        		= False
import_ensembles      		= False
improve_template      		= None
max_ensemble_models   		= 30
make_ensembles        		= True
missing_domain        		= False
num_clusters          		= 1
percent               		= 5
side_chain_treatments 		= None
single_model_mode	  		= False
subcluster_program    		= maxcluster
top_model_only        		= False
truncation_method     		= percent
truncation_pruning    		= None
truncation_scorefile_header = None
use_scwrl             		= False

[Molecular_Replacement]
arpwarp_cycles           = 10
buccaneer_cycles         = 5
do_mr                    = True
F                        = None
FREE                     = None
ideal_helices            = False
molrep_only              = False
mrbump_programs          = None
mrbump_scripts           = None
mr_keys                  = None
mr_sg_all                = None
nmasu                    = 0
phaser_kill              = 360
phaser_only              = True
phaser_rms               = 0.1
shelx_cycles             = 15
shelxe_rebuild           = False
shelxe_rebuild_arpwarp   = False
shelxe_rebuild_buccaneer = False
SIGF                     = None
use_arpwarp              = True
use_buccaneer            = True
use_shelxe               = True

[Files]
## These files should ideally be parsed via the command line
## to avoid problems when using the same configuration file across
## multiple jobs
alignment_file                  = None
bbcontacts_file                 = None
cluster_dir                     = None
config_file                     = None
contact_file                    = None
disulfide_constraints_file      = None
domain_all_chains_pdb           = None
fasta                           = None
frags_3mers                     = None
frags_9mers                     = None
models                          = None
models_dir                      = None
mrbump_dir                      = None
mr_sequence                     = None
mtz                             = None
native_pdb                      = None
nmr_model_in                    = None
nmr_remodel_fasta               = None
psipred_ss2                     = None
restart_pkl                     = None
restraints_file                 = None
score_matrix                    = None
score_matrix_file_list          = None
sf_cif                          = None
transmembrane_octopusfile       = None
transmembrane_lipofile          = None
transmembrane_spanfile          = None
truncation_scorefile  	    	= None
work_dir                        = None 

#cmdline_flags= None
#make_mr = True
#success = False
#AMPLE_finished = False