#this text file includes the options used in comparative modelling used by cm_main_comb.pl
###############################Software and Data Settings####################
#prosys script dir
script_dir = /home/chengji/casp8/csblast/script

meta_dir=/home/chengji/casp8/csblast/
#prosys dir
prosys_dir = /home/chengji/software/prosys/

#blast tool dir
#blast_dir = /home/jianlinc/pspro/blast2.2.8/
#blast_dir = /home/chengji/software/prosys/blast-2.2.9/
blast_dir = /home/chengji/software/prosys/blast-2.2.17/bin

csblast_dir = /home/chengji/software/csblast-2.1.0-linux32 

#modeller 7.0 dir
#modeller_dir = /home/chengji/software/prosys/modeller7v7/
#modeller_dir = /home/chengji/software/modeller9v7/
modeller_dir = /home/tools/modeller-9.16/

#formated pdb database dir
#pdb_db_dir = /home/jianlinc/prosys/database/cm_lib/
#pdb_db_dir = /home/chengji/software/prosys_database/cm_lib_casp7/
pdb_db_dir = /home/chengji/software/prosys_database/cm_lib/
#pdb_db_dir = /var/preserve/eval/cm_lib/

#use non-redundant db dir (should always use non-redundant database)
#nr_dir = /home/jianlinc/pspro/data/nr/
#nr_dir = /var/preserve/nr/
nr_dir = /home/chengji/software/prosys_database/nr_latest/
#nr_dir = /home/chengji/cheng_group/cd-hit-2/


#not use nr (should never choose this option. its performance is worse)
#nr_dir = none

#atom files dir
#atom_dir = /home/jianlinc/prosys/database/atom/
atom_dir = /home/chengji/software/prosys_database/atom/

#meta common dir
meta_common_dir=/home/chengji/casp8/meta/
############################End of Software and Data Settings#################

#################################PDB blasting options#######################
#Not used any more. evalue threshold for msa alignment generation. 
#Should we change it to 1.0?
#this value is not used anymore. (collpased with cm_blast_evalue)
#cm_align_evalue = 0.5
cm_align_evalue = 0.001

#evalue threshold for template blasting and selection on PDB. 
#Reasonable values: 1.0, 0.1, 0.01, 0.001. 
#psi-blast default evalue is 1.0. (-e option)
#casp6, some paper suggest: 0.01. (we may choose this one)
#cm_blast_evalue = 1.0
cm_blast_evalue = 5 

#number of iteration of blasting on PDB. (-j option)
cm_blast_iteration = 5

#evalue threshold of including into profile on PDB (-h option)
#in old version: we didn't set this value. defalut is 0.001?
#cm_including_evalue = 0.001
#this is the same as default.
cm_including_evalue = 0.001
##############################End of PDB blasting option#################

#############################NR profile building option###################
#number of iterations of blasting on NR for profile building. (-j option)
nr_iteration_num = 3

#evalue threshold for returning from blasting on NR database
#and is is also the initial blast evalue (psi-blast default is 1.0)(-e option)
nr_return_evalue = 0.001 

#evalue threshold for including in profile building on NR database (-h option)
#old value (and still used by SSpro, FR feature generation is 1e-10, too small?)
#nr_including_evalue = 0.001
#this is used in sspro, better?
nr_including_evalue = 0.0000001
###############################End of NR profile building options#########

#############################Alignment Combination Options##############
#maximum allowed gap for stopping the alignment generation
#cm_max_gap_size = 20
cm_max_gap_size = -1

#minimum covered size for one template to be chosen
#cm_min_cover_size = 20
cm_min_cover_size = 5 

#Modeller Option
#From blast comparative modeling, how many 
#models to simulate. One model with lowest energy will be chosen.
cm_model_num = 5 

#set the combination method
#1. blast_comb (first version of simple combination). 
#if set to this option, cm_align_blast.pl will be used.
#2. new_comb (latest version of alignment combination)
#if set to this option, blast_align_comb.pl will be used.
cm_comb_method=new_comb
#cm_comb_method=blast_comb

#option for advanced combination only (new_comb && cm_max_liner_size>=0)
#<0: don't join the adjacent fragments(no gaps)
#>=0: join adjacent fragments (allow gaps)
#this option controls the maximum allowed intermedite
#regions betweew two fragments for joining.
adv_comb_join_max_size=15


#option to use simple/advanced combination
#>=0: use advanced combination. value is the max linker size at two ends
#<0: use simple combination
#must be an integer
cm_max_linker_size=5

#threshold to include significant matched templates
#templates with evalue lower than e^value will always
#be included no matter how many gaps are filled by this alignment.
#must be 0 or a negative integer.
#for negative number: the real evalue is: 1e^num (always positive)
#for 0: means only combined if it can cover gaps disregard significance.
#for 0: don't simply combine significant templates with low evalues
#cm_evalue_comb=0
cm_evalue_comb=-30
#cm_evalue_comb=-20

#option to decide if the redundant alignments should be removed
#yes: remove, no: not remove
cm_clean_redundant_align=yes

#for the unconditional evalue combination, this option control the evalue difference
#threshold of adding a less significant templates
#e.g., 10: means the evalue exponent difference must be less than 10
cm_evalue_diff=10


#number of cm templates to use
easy_model_num=10

#output model prefix name
output_prefix_name=csiblast
#########################End of Alignment Combination Options#################


##########################Options for sorting blast local alignment###########

#The file containing resolution/method/match ratio for all chains
#chain_stx_info=/home/jianlinc/prosys/database/cm_lib/chain_stx_info
chain_stx_info=/home/chengji/software/prosys_database/cm_lib/chain_stx_info

#resort blast local alignment according to stx quality.
#yes: resort, no: don't sort
sort_blast_align=no

#ratio of evalue to be considered in resorting (must > 1).
#only be valid if sort_blast_align is set to yes.
#only if the ratio of two evalues is between 1 and ratio to
#be considered for exchanging positions.
#smaller, more strict.
sort_blast_local_ratio=2

#ratio of resolution difference for being considered exchange.
#in Angstrom.
#only valid if sort_blast_align is set to yes.
sort_blast_local_delta_resolution=2

#Option for adding stx information and remove identical by resolution
#yes: do it. no: don't.
add_stx_info_rm_identical=no

#resolution difference that decide if the redundant alignment will 
#be removed. bigger, more strict.
rm_identical_resolution=2

###############################End of sorting and stx information option#######