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# Description
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ARIA version compatible with evolutionary restraints 
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## Requirements
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Be sure to install these packages before running setup file
* pip (>= 9.0)
* setuptools (>= 18.0)
* numpy (>= 1.11)
* matplotlib
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## Installation
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```
# Ariaec directory or in a virtualenv, call the following command:
> pip install .
```
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# Command line
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The command line tool correspond to ariaec (or ec2aria for older versions)
command in the terminal
folder.
```
usage: ariaec [-h] -o OUTPUT_DIRECTORY [-c CONF_FILE] [--nolog] [-d]
              {setup,bbconv,maplot,pdbqual,analysis,tbl2xml,pdbdist,pdbstat}
              ...
positional arguments:
  {setup,bbconv,maplot,pdbqual,analysis,tbl2xml,pdbdist,pdbstat}
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optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT_DIRECTORY, --output OUTPUT_DIRECTORY
                        Output directory (default: None)
  -c CONF_FILE, --conf CONF_FILE
                        configuration file (default: None)
  --nolog               Don't generate log files (default: False)
  -d, --debug           Increase output verbosity (default: False)
```
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In order to change default parameters, the tool can accept a configuration file (.ini format). Default parameters are listed below:
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```
[main]
; ------------------------- Main parameters ---------------------------------- #
; Leave these fields empty in order to use default files
; ariaproject_template          : For backward compatibility with different
;                                 versions of ARIA since there is several
;                                 differences between aria templates.This package
;                                 can switch between 6 version actually:
;                                   - 2.3.0 with ramachandran potential tag
;                                   - 2.3.2 with exponent tag
;                                   - 2.3.3 with clustering tag
;                                   - 2.3.4 with scoring tag
;                                   - 2.3.5 with avg_exponent field in ambiguous
;                                   restraint tag
;                                   - 2.3.6 with method field in clustering tag
ss_dist_file:
scsc_min_file:
interlowerbounds_pdbstat:
intertarget_pdbstat:
interupperbounds_pdbstat:
intralowerbounds_pdbstat:
intratarget_pdbstat:
intraupperbounds_pdbstat:
ariaproject_template:                       2.3.6
procheck_executable:
prosa_executable:
whatif_executable:
clashlist_executable:
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[contactdef]
; Contact definition section used to define maplot from pdb file.
; Decrease this threshold if using other cutoff (e.g. 5.0)
default_cutoff:                             8.0
; Add contact cutoff folowwing the syntax atm1_atm2
;ca_ca:                                      7.0
;cb_cb:                                      7.0
;sc_sc:                                      5.0

[setup]
; ------------------------------ TBL parameters ------------------------------ #
; longrange_hb                  : True, False [False]
;                                 use long range hbond restraints. If there is
;                                 no hbond map given, use the naive method from
;                                 METAPSICOV (Take the top nf_longrange_hb * seq
;                                 length predicted contacts from the contactlist
;                                 and set those who are in a beta sheet as hb
; nf_longrange_hb               : Float [0.1]
;                                 Number hbond generated = nf * seq length
; longrange_hbtype              : main, all [main]
;                                 Consider short range hbond only as main chain
;                                 hydrogen bond or for all donor/acceptor
; hb_dminus/dplus               : Float [0.0, 0.5]
;                                 distance bound in tbl restraints
longrange_hb:                               False
nf_longrange_hb:                            0.1
longrange_hbtype:                           main
hb_dminus:                                  0.0
hb_dplus:                                   0.5
; ---------------------- Distance restraint parameters ----------------------- #
; native_reliable               : True, False [False]
;                                 Define native contact map as reliable in aria
;                                 iterative protocol. Those contacts will not be
;                                 filtered.
; evfold_weight                 : True, False [False]
;                                 use EVFold weight -> 10/i (i:contact rank) for
;                                 contact map derived distance restraints in
;                                 aria protocol
; neighborhood_contact          : True, False [False]
;                                 Generate restraints for neighbors foreach
;                                 contact in the contact map
; pair_list                     : all, heavy, min [min]
;                                 use all, heavy atms or from a minimized
;                                 list (CA, CB, SC) for contribution list for
;                                 each distance restraint
; atoms_type                    : all, heavy, min [min]
;                                 use all, heavy atms or from a minimized
;                                 list (CA, CB, SC) for contribution list for
;                                 each distance restraint
; contributions_type            : same, allvsall, onevsall [same]
;                                 By default contributions list will be a
;                                 simple list between atoms of the same type
;                                 (CA-CA, CB-CB, ...). Otherwise, compute
;                                 pairwise product between contribution
;                                 lists of the 2 residues (onevsall and
;                                 allvsall). In the case of ADR, onevsall will
;                                 generate one ADR for all contribution pairs
;                                 between an atom of the first residue against
;                                 all the other atoms in the second residue
; distance_type                 : fixed, pdbstat, distfile [fixed]
;                                 Define distance use for target distance. By
;                                 default the target distance is fixed by
;                                 parameters listed below. Otherwise a distance
;                                 map derived from pdb distance distribution
;                                 (not yet implemented) or given by the user can
;                                 be used.
; pdbdistance_level             : ss, res,
; groupby_method                : mean, min, deff [min]
;                                 If a distance map is used for setting distance
;                                 target, define if we use min, mean or deff
;                                 distance on all the possible values.
; ambiguous_distance_restraint  : True, False [False]
;                                 Generate Ambiguous Distance Restraints.
;                                 Otherwise, each distance restraints will have
;                                 only one contribution (unambiguous distance
;                                 restraints)
native_reliable:                            False
evfold_weight:                              False
neighborhood_contact:                       False
atoms_type:                                 min
contributions_type:                         same
distance_type:                              fixed
groupby_method:                             min
deffpow:                                    6
pdbdistance_level:                          ss
ambiguous_distance_restraint:               False
; Parameters below used only when distance_type is set to "fixed"
restraint_distance:                         2.5
lower_bound:                                1.0
def_upper_bound:                            5.0
; Specific tresholds only for unambig restraints
ca_upper_bound:                             7.0
cb_upper_bound:                             7.0
; ---------------------------- Filter parameters ----------------------------- #
; n_factor      : float [1.0]
;                 Factor used for selection of contacts according to their score
;                 (n * n_factor with n as sequence length)
; contactfilter : all or combination of pos, cons, cys, ssclash separated by "+"
;                 character [pos]
;                 If empty, use only position filter (avoid short range
;                 restraints)
n_factor:                                   1.0
contactfilter:                              all
; conservation_treshold :   Float [95]
;                           Remove contact with highly conservated residues
; position_treshold     :   Int [5]
;                           Remove short range contacts
conservation_treshold:                      95
position_treshold:                          5
; seed          : If no scoremap to select top n contacts, choose a subset wit
;                 random.sample method. For reproductibility, the seed used for
;                 the sampling is provided here
seed:                                       89764443
; net_deconv    : use network deconvolution to filter contact map
; nd_beta       : eigenvalue scaling parameter for network deconvolution.
;                 Corresponding to propagation of indirect effects over
;                 longer indirect paths.
; nd_alpha      : Network density parameter corresponding to the use of the
;                 full mutual information and direct information matrices
net_deconv:                                 False
nd_beta:                                    0.99
nd_alpha:                                   1.0
; --------------------------- ARIA XML parameters ---------------------------- #
runid:                                      1
cpus:                                       100
host_command:                               "sbatch -t 02:00:00"
host_executable:                            bin/cns1.21_aria_logn_linux_x86_64_intel.exe
temp_root:                                  examples/tmp
parameter_definition:                       automatic
ss_dist_format:                             tbl
ss_dist_enabled:                            yes
ss_dist_add_to_network:                     no
ss_dist_calibrate:                          no
ss_dist_run_network_anchoring:              no
ss_dist_filter_contributions:               no
dist_format:                                xml
dist_enabled:                               yes
dist_add_to_network:                        no
dist_calibrate:                             no
dist_run_network_anchoring:                 no
dist_filter_contributions:                  yes
dist_avg_exponent:                          6
cns_executable:                             bin/cns1.21.exe
cns_keep_output:                            no
unambiguous_restraints_k_cool1_initial:     10.0
unambiguous_restraints_k_cool1_final:       50.0
unambiguous_restraints_k_cool2:             50.0
hbond_restraints_k_cool1_initial:           10.0
hbond_restraints_k_cool1_final:             50.0
hbond_restraints_k_cool2:                   50.0
dihedral_restraints_k_cool1:                25.0
dihedral_restraints_k_cool2:                200.0
logharmonic_potential_enabled:              no
logharmonic_potential_use_auto_weight:      no
logharmonic_potential_weight_unambig:       25.0
logharmonic_potential_weight_ambig:         10.0
logharmonic_potential_weight_hbond:         25.0
rama_potential_enabled:                     yes
hbdb_potential_enabled:                     no
scoring_method:                             standard
md_parameters_random_seed:                  89764443
md_parameters_steps_high:                   10000
md_parameters_steps_cool1:                  5000
md_parameters_steps_cool2:                  4000
water_refinement_solvent:                   water
water_refinement_n_structures:              10
water_refinement_enabled:                   no
water_refinement_write_solvent_molecules:   no
procheck_executable:
procheck_enabled:                           yes
prosa_executable:
prosa_enabled:                              yes
whatif_executable:
whatif_enabled:                             yes
clashlist_executable:
clahlist_enabled:                           no
pickle_output:                              no
; --------------------------- Iteration parameters --------------------------- #
; /!\ Parameters below can be formatted as a list if we want different values
; foreach iteration. Actually, only 2 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
viol_sigma_mode:                            fix
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
clustering_enabled:                         no
clustering_mask:                            CA
clustering_nclusters:                       2
clustering_method:                          kmeans

[maplot]
; -------------------------- Contactmap parameters --------------------------- #
; Report settings
; n_factors:            Number of EC tested: n * n_factor (n: sequence length)
n_factors:                                  0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0
; Plot settings
save_fig:                                   True
heatmap_linewidths:                         0.0
size_fig:                                   10
plot_ext:                                   pdf
plot_dpi:                                   200
alpha:                                      1.0

[bbconv]
; -------------------------- bbconverter parameters -------------------------- #
couplingmatrix:
start:
end:
outputprefix:
PSIPREDfile:
diversityvalue:
L:

[pdbqual]
trash_directory:                            /tmp
prosa:                                      False
skip_prefix:                                fitted
csh_executable:                             csh

[pdbdist]
; ----------------------- PDB distribution parameters ------------------------ #
; contact_cutoff:                           float [4.5]
;                                           Cutoff used to search neighbor atoms
; dssp_exec:                                path
;                                           Path of DSSP executable
contact_cutoff:                             4.5
dssp_exec:                                  /c6/shared/bin/dssp
download_pdbs:                              True
obsolete_directory:                         /tmp/obsolete
remove_pdbs:                                False
pair_list:                                  min

[pdbstat]
; mode:                                     simple [simple]
;       Extract minimal distance, mean of minimal mode, maximal distance from
;       distance distribution to define bounds in serialized dictionaries
; groups:                                   {ss,res,atm} [ss+res+atm]
;       Group levels in serialized dictionaries
mode:                                       simple
groups:                                     ss+atm+res
sample_minsize:                             20

[analysis]
atmask:                                     CA
violation_treshold:                         0.5
nbest_structures:                           15
sort_criterion:                             total_energy
```


## Setup
Translate contact maps into distance restraints and setup ARIA infrastructure
```
usage: ariaec setup [-h] [-d DISTFILE] -t
                    {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
                    [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
                    [-r REF] [--hb HB] [--ssidx] [--no-filter]
                    seq sspred infile [infile ...]

optional arguments:
  -h, --help            show this help message and exit

required arguments:
  seq                   sequence file [FASTA]
  sspred                secondary structure prediction file
  infile                contact or pdb file(s) used to build aria distance
                        restraints
  -d DISTFILE, --distfile DISTFILE
                        Pdb or distance matrix iif distance_type set to
                        distfile in conf file, use distances in the given file
                        as target distance to build distance restraints
  -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...], --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
                        Infile(s) contact type(s)
  -r REF, --ref REF     Native pdb. Allow TP/FP detection.
  --hb HB               H-bonds contact file (eg: metapsicov.hb)
  --ssidx               Use secondary structure index
  --no-filter           Do not filter contact map.
```

## Contactmap
Contactmap analysis and visualisation
```
usage: ariaec maplot [-h] -t
                     {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
                     [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
                     [--merge {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]]
                     [--filter] [--onlyreport] [--ssidx]
                     [--prefix PREFIX [PREFIX ...]]
                     seq sspred infile [infile ...]

positional arguments:
  seq                   sequence file [FASTA]
  sspred                secondary structure prediction file
  infile                contact or pdb file(s) used to build aria distance
                        restraints

optional arguments:
  -h, --help            show this help message and exit
  -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...], --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
                        Infile(s) contact type(s)
  --merge {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} [{evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist} ...]
                        Merge given contact types with other maps
  --filter              Use contact list filter and top n contacts selection
  --onlyreport          Generate only report file
  --ssidx               Use secondary structure index
  --prefix PREFIX [PREFIX ...]
                        Contact map name

```
## Pdbqual
Quality tool for pdb file(s)
```
usage: ariaec pdbqual [-h] infile [infile ...]

positional arguments:
  infile      PDB file(s) used to run quality tools with aria API

optional arguments:
  -h, --help  show this help message and exit
```
## Tbl2xml
ARIA XML converter for tbl distance restraint
```
usage: ariaec tbl2xml [-h] molecule.xml list_name infile.tbl [infile.tbl ...]

positional arguments:
  molecule.xml  ARIA XML molecule file
  list_name     Restraint list name in the tbl file
  infile.tbl    TBL distance restraint file(s)

optional arguments:
  -h, --help    show this help message and exit

```

## Bbconv
Convert contacts in bbcontact format
```
usage: ariaec bbconv [-h] -t
                     {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
                     contactfile sspred seq [msa]

positional arguments:
  contactfile           contacts file (pconsc, plm)
  sspred                psipred file
  seq                   sequence file [FASTA]
  msa                   MSA [FASTA] for diversityvalueused with bbcontacts

optional arguments:
  -h, --help            show this help message and exit
  -t {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}, --type {evfold,plmev,plm,plmdca,plmc,bbcontacts,pconsc,pconsc1,pconsc2,psicov,metapsicovhb,metapsicov_stg1,metapsicov_stg2,gremlin,pdb,native,native_full,contactlist}
                        Infile contact type

```