diff --git a/aria/conbox/conf/config.ini b/aria/conbox/conf/config.ini index 05251f68fdd98df5c4de827440049b94aba8e911..74f24c0bb5c9016f23f132a84b26842835a52daf 100644 --- a/aria/conbox/conf/config.ini +++ b/aria/conbox/conf/config.ini @@ -36,7 +36,7 @@ default_cutoff: 8.0 ;ca_ca: ;cb_cb: ;sc_sc: - +bool [setup] ; ------------------------------ TBL parameters ------------------------------ # ; longrange_hb : True, False [False] @@ -150,7 +150,7 @@ nd_alpha: 1.0 runid: 1 cpus: 100 host_command: "sbatch -t 02:00:00" -host_executable: bin/cns1.21_aria_logn_linux_x86_64_intel.exe +host_executable: temp_root: examples/tmp parameter_definition: automatic ss_dist_format: tbl @@ -166,7 +166,7 @@ dist_calibrate: no dist_run_network_anchoring: no dist_filter_contributions: yes dist_avg_exponent: 6 -cns_executable: bin/cns1.21.exe +cns_executable: cns_keep_output: no unambiguous_restraints_k_cool1_initial: 10.0 unambiguous_restraints_k_cool1_final: 50.0 diff --git a/aria/conbox/protmap.py b/aria/conbox/protmap.py index d78299837971022b01ed98e0eaf38eef649ecc9d..37b7b7212162f1f7ad7e3098f10c339bfd411264 100644 --- a/aria/conbox/protmap.py +++ b/aria/conbox/protmap.py @@ -1017,7 +1017,6 @@ class ResAtmMap(ProteinMap): Returns ------- - """ if self._sequence: # If non empty string @@ -1128,14 +1127,14 @@ class ResAtmMap(ProteinMap): def contact_map(self, contactdef, scsc_min=None, def_cut=5.0): """ Contact map generator from all atoms distance map. There's a contact - with 2 residues iff dist between 2 atoms are below the given treshold + with 2 residues iff distance between 2 atoms are below the given treshold Parameters ---------- - def_cut : - (Default value = 5.0) + def_cut : float + Default cutoff (Default value = 5.0) contactdef : - for all atom pair + Contact definition for all atom pair scsc_min : (Default value = None) diff --git a/docs/configuration.rst b/docs/configuration.rst index 7862df5985d6254c85b4bb5a20245dbda8e72566..7f57e85af769a40eede92a52c4ca1959ee0c3dbe 100644 --- a/docs/configuration.rst +++ b/docs/configuration.rst @@ -18,11 +18,16 @@ configuration file should follow the `INI <https://en.wikipedia.org/wiki/INI_fil main ---- +.. note:: + + Leave these fields empty in order to use default files. + + .. rst-class:: table-hover +--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Name | Type | Default | Description | -+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ ++==========================+======+==========================================================================================+=================================================================================================================================================================+ | ss_dist_file | path | :download:`ss_dist.txt <../aria/conbox/data/ss_dist.txt>` | Distances between stable secondary structures. Those distances are used to make supplementary distance restraints related to secondary structure predictions. | +--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+ | scsc_min_file | path | :download:`scsc_min.p <../aria/conbox/data/scsc_min.p>` | | @@ -54,23 +59,358 @@ main contactdef ---------- +Contact definition section used to define maplot from pdb file. More specific +contact definitions can be added by following ``atomname_atomname`` syntax +(e.g. ca_ca, cb_cb, ...) or ``sc_sc`` if we want to use a single treshold for +side chain contacts defined in ``scsc_min_file``. + +.. rst-class:: table-hover + ++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+ +| Name | Type | Default | Description | ++==================================+=======+=========+=======================================================================================================+ +| default_cutoff | float | 8.0 | Default cutoff used for all type of contact. Decrease this threshold if using other cutoff (e.g. 5.0) | ++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+ +| atm1_atm2 (ca_ca, cb_cb, ...) | float | None | Specific treshold for a contact defined between atoms of two residues | ++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+ +| sc_sc | float | None | Default side chain atom treshold | ++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+ + setup ----- +All the configuration parameters related to the ``setup`` command. + +.. rst-class:: table-hover + ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Name | Type | Default | Description | ++==============================================+========================================================================+==============================================+=========================================================================================================================================================================================================================================================================================================================================================================================+ +| longrange_hb | bool | 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 | float | 0.0 | distance lower bound in tbl hbond restraints | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| hb_dplus | float | 0.5 | distance upper bound in tbl hbond restraints | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| native_reliable | bool | False | Define native contact map as reliable in aria iterative protocol. Those contacts will not be filtered | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| evfold_weight | bool | False | use EVFold weight -> 10/i (i:contact rank) for contact map derived distance restraints in aria protocol | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| neighborhood_contact | bool | False | Generate restraints for neighbors foreach contact in the contact map | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| atom_groups | {all, heavy, min} | min | use all, heavy atms or from a minimizedlist (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 or given by the user can be used. | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| 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. | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| deffpow | int | 6 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| pdbdistance_level | {ss, res} | ss | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ambiguous_distance_restraint | bool | False | Generate Ambiguous Distance Restraints. Otherwise, each distance restraints will have only one contribution (unambiguous distance restraints) | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| restraint_distance | float | 2.5 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| lower_bound | float | 1.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| def_upper_bound | float | 5.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ca_upper_bound | float | 7.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| cb_upper_bound | float | 7.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| n_factor | float | 1.0 | Factor used for selection of contacts according to their score (n * factor with n as sequence length) | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| contactfilter | all or combination of pos, cons, cys, ssclash separated by + character | all | If empty, use only position filter (avoid short range restraints) | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| conservation_treshold | int | 95 | Remove contact with highly conservated residues | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| position_treshold | int | 5 | Remove short range contacts | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| seed | int | 89764443 | If no scoremap to select top n contacts, choose a subset with random.sample method. For reproductibility, the seed used for the sampling is provided here | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| net_deconv | bool | False | use network deconvolution to filter contact map | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| nd_beta | float | 0.99 | eigenvalue scaling parameter for network deconvolution. Corresponding to propagation of indirect effects over longer indirect paths. | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| nd_alpha | float | 1.0 | Network density parameter corresponding to the use of the full mutual information and direct information matrices | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| runid | int | 1 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| cpus | int | 100 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| host_command | str | "sbatch -t 02:00:00" | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| host_executable | path | | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| temp_root | path | examples/tmp | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| parameter_definition | {} | automatic | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ss_dist_format | {} | tbl | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ss_dist_enabled | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ss_dist_add_to_network | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ss_dist_calibrate | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ss_dist_run_network_anchoring | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| ss_dist_filter_contributions | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_format | {} | xml | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_enabled | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_add_to_network | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_calibrate | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_run_network_anchoring | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_filter_contributions | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dist_avg_exponent | int | 6 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| cns_executable | path | | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| cns_keep_output | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| unambiguous_restraints_k_cool1_initial | float | 10.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| unambiguous_restraints_k_cool1_final | float | 50.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| unambiguous_restraints_k_cool2 | float | 50.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| hbond_restraints_k_cool1_initial | float | 10.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| hbond_restraints_k_cool1_final | float | 50.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| hbond_restraints_k_cool2 | float | 50.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dihedral_restraints_k_cool1 | float | 25.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| dihedral_restraints_k_cool2 | float | 200.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| logharmonic_potential_enabled | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| logharmonic_potential_use_auto_weight | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| logharmonic_potential_weight_unambig | float | 25.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| logharmonic_potential_weight_ambig | float | 10.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| logharmonic_potential_weight_hbond | float | 25.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| rama_potential_enabled | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| hbdb_potential_enabled | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| scoring_method | {} | standard | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| md_parameters_random_seed | int | 89764443 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| md_parameters_steps_high | int | 10000 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| md_parameters_steps_cool1 | int | 5000 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| md_parameters_steps_cool2 | int | 4000 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| water_refinement_solvent | {} | water | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| water_refinement_n_structures | int | 10 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| water_refinement_enabled | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| water_refinement_write_solvent_molecules | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| procheck_executable | path | | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| procheck_enabled | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| prosa_executable | path | | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| prosa_enabled | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| whatif_executable | path | | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| whatif_enabled | {yes, no} | yes | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| clashlist_executable | path | | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| clahlist_enabled | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| pickle_output | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| iterations | int | 8 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| iteration_n_structures | int | 100 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| iteration_sort_criterion | {} | total_energy | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| iteration_n_best_structures | int | 15 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| iteration_n_kept_structures | int | 0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| merging_method | {} | standard | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| calib_relaxation_matrix | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| calib_distance_cutoff | float | 6.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| calib_estimator | {} | ratio_of_averages | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| calib_error_estimator | {} | distance | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| viol_violation_tolerance | list of float | 1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| viol_violation_threshold | float | 0.5 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| viol_sigma_mode | {} | fix | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| partassign_weight_threshold | list of float | 1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| partassign_max_contributions | int | 1000 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| partassign_exponent | int | 6 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| netanch_high_residue_threshold | float | 4.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| netanch_enabled | {yes, no} | no | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| netanch_min_residue_threshold | float | 1.0 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| netanch_min_atom_threshold | float | 0.25 | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| clustering_enabled | {yes, no} | no | Clustering step group generated structures into clusters. Cluster ensemble with the lowest energy will then be selected at the end of each iteration | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| clustering_mask | {CA, CB} | CA | Atom coordinate mask | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| clustering_nclusters | int | 2 | Number of clusters | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| clustering_method | {kmeans, hclust, hdbscan} | kmeans | | ++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ + maplot ------ +.. rst-class:: table-hover + ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| Name | Type | Default | Description | ++=====================+===============+=================================================+=========================================================+ +| n_factors | list of float | 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0 | Number of EC tested: n * n_factor (n: sequence length) | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| save_fig | bool | True | | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| heatmap_linewidths | float | 0.0 | | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| size_fig | int | 10 | | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| plot_ext | {} | pdf | | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| plot_dpi | int | 200 | | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ +| alpha | float | 1.0 | | ++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+ + bbconv ------ +.. rst-class:: table-hover + ++----------------+------+---------+-------------+ +| Name | Type | Default | Description | ++================+======+=========+=============+ +| couplingmatrix | | | | ++----------------+------+---------+-------------+ +| start | | | | ++----------------+------+---------+-------------+ +| end | | | | ++----------------+------+---------+-------------+ +| outputprefix | | | | ++----------------+------+---------+-------------+ +| PSIPREDfile | | | | ++----------------+------+---------+-------------+ +| diversityvalue | | | | ++----------------+------+---------+-------------+ +| L | | | | ++----------------+------+---------+-------------+ + pdbqual ------- +.. rst-class:: table-hover + ++------------------+------+---------+-------------+ +| Name | Type | Default | Description | ++==================+======+=========+=============+ +| trash_directory | path | /tmp | | ++------------------+------+---------+-------------+ +| prosa | bool | False | | ++------------------+------+---------+-------------+ +| skip_prefix | str | fitted | | ++------------------+------+---------+-------------+ +| csh_executable | path | | | ++------------------+------+---------+-------------+ + pdbdist ------- +.. rst-class:: table-hover + ++---------------------+-------+---------------------+--------------------------------------+ +| Name | Type | Default | Description | ++=====================+=======+=====================+======================================+ +| contact_cutoff | float | 4.5 | Cutoff used to search neighbor atoms | ++---------------------+-------+---------------------+--------------------------------------+ +| dssp_exec | path | /c6/shared/bin/dssp | Path of DSSP executable | ++---------------------+-------+---------------------+--------------------------------------+ +| download_pdbs | bool | True | | ++---------------------+-------+---------------------+--------------------------------------+ +| obsolete_directory | path | /tmp/obsolete | | ++---------------------+-------+---------------------+--------------------------------------+ +| remove_pdbs | bool | False | | ++---------------------+-------+---------------------+--------------------------------------+ +| pair_list | {} | min | | ++---------------------+-------+---------------------+--------------------------------------+ + pdbstat ------- +.. rst-class:: table-hover + ++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+ +| Name | Type | Default | Description | ++=================+================+============+=========================================================================================================================================+ +| 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+atm+res | Group levels in serialized dictionaries | ++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+ +| sample_minsize | int | 20 | | ++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+ + analysis -------- + +.. rst-class:: table-hover + ++---------------------+------------+---------------+-------------+ +| Name | Type | Default | Description | ++=====================+============+===============+=============+ +| atmask | {CA, CB} | CA | | ++---------------------+------------+---------------+-------------+ +| violation_treshold | float | 0.5 | | ++---------------------+------------+---------------+-------------+ +| nbest_structures | int | 15 | | ++---------------------+------------+---------------+-------------+ +| sort_criterion | {} | total_energy | | ++---------------------+------------+---------------+-------------+ \ No newline at end of file diff --git a/docs/examples/bpt1/bpt1.rst b/docs/examples/bpt1/bpt1.rst index 21acce0b14bf070b3513ba645ba1269f841668b9..203341f562ced8d2d0b1fcfd1051042776ecad85 100644 --- a/docs/examples/bpt1/bpt1.rst +++ b/docs/examples/bpt1/bpt1.rst @@ -1,2 +1,75 @@ BPT1_BOVIN structure prediction with EC map =========================================== + +Setup +----- + +Here we show an example of setup with GREMLIN contacts with secondary structure +prediction + +.. code-block:: console + + ariaec -o examples/bpt1/out -c examples/bpt1/data/config.ini setup examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out -t gremlin -s examples/bpt1/data/BPT1_BOVIN.indextableplus + +The output should look like this + +.. code-block:: console + + ================================================================================ + + ARIA Evolutive Contact toolbox + + ================================================================================ + + INFO Initialize settings + INFO Updating settings according to config file + INFO Making output directories + reading FASTA file examples/bpt1/data/BPT1_BOVIN.fa + INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG + INFO Checking if file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format + INFO Format type correct (indextableplus) + INFO Reading secondary structure file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus] + INFO Loading ss dist file + INFO Reading distance file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/aria/conbox/data/ss_dist.txt + INFO Align secondary structure sequence with protein sequence + INFO Reader focused on file(s) ['/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['gremlin'] + INFO Reading /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file + INFO Filtering gremlin contact map + INFO ...Position filter + INFO Removed 21 contacts. + INFO ...Conservation filter + INFO Conservation filter only works with indextableplus files ! + INFO ...Secondary structure clash filter + INFO Removed 1 contacts. + INFO ...Disulfure bridge unicity filter + INFO Removed 11 contacts. + INFO Setting contact number with treshold 1.0 + INFO Update gremlin maplot + INFO Update gremlin scoremap + INFO Select top 53 contacts according to scoremap + writing to the file: /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.seq + INFO Load molecule file and convert it into xml format + MESSAGE [SequenceList]: reading sequence /baycells/home/fallain/Projects/ariaec/ + bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN. + seq + reading /baycells/home/fallain/Projects/ariaec/bin/ + python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.seq + INFO Writing tbl files ... + INFO Dihedral restraints for secondary structures (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_dihed.tbl) + INFO Secondary structure restraints (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_ssdist.tbl) + INFO Helix bond restraints (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_hbond.tbl) + INFO Writing gremlin ARIA XML distance restraints + INFO Using contact scores as selection criteria + INFO Selecting 53 contacts + INFO 0%| | 0/53 [00:00<?, ?it/s] + INFO 100%|##########| 53/53 [00:00<00:00, 1485.97it/s] + INFO Write 53 xml distance restraints in /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/xml/BPT1_BOVIN_gremlin.xml + INFO Loading aria template file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/aria/conbox/templates/aria_project_v2.3.4.xml + INFO Directory /tmp/BPT1_BOVIN/gremlin doesn't exist. + INFO Create new directory /tmp/BPT1_BOVIN/gremlin + INFO Writing ARIA project file (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/ariaproject.xml) + INFO Generate contact file (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN_gremlin_filtered.contact.txt) + +Run +--- + diff --git a/docs/examples/bpt1/data/BPT1_BOVIN.fa b/docs/examples/bpt1/data/BPT1_BOVIN.fa new file mode 100644 index 0000000000000000000000000000000000000000..4259b24e02af6e580c01c52c6409f37c018eb974 --- /dev/null +++ b/docs/examples/bpt1/data/BPT1_BOVIN.fa @@ -0,0 +1,2 @@ +>sp|P00974|BPT1_BOVIN Pancreatic trypsin inhibitor OS=Bos taurus PE=1 SV=2 +FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG diff --git a/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus b/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus new file mode 100644 index 0000000000000000000000000000000000000000..05a4ba779870ed0ec4c6698ae15986e8d2ad3d80 --- /dev/null +++ b/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus @@ -0,0 +1,101 @@ +up_index up_residue ss_pred ss_conf msa_index msa_cons% msa_cons in_const pdb_atom pdb_chain pdb_index pdb_residue pdb_x_pos pdb_y_pos pdb_z_pos +1 M C 9 - - - - - - - - - - - +2 K C 3 - - - - - - - - - - - +3 M H 2 - - - - - - - - - - - +4 S H 6 - - - - - - - - - - - +5 R H 7 - - - - - - - - - - - +6 L H 9 - - - - - - - - - - - +7 C H 9 - - - - - - - - - - - +8 L H 9 - - - - - - - - - - - +9 S H 9 - - - - - - - - - - - +10 V H 9 - - - - - - - - - - - +11 A H 9 - - - - - - - - - - - +12 L H 9 - - - - - - - - - - - +13 L H 9 - - - - - - - - - - - +14 V H 9 - - - - - - - - - - - +15 L H 9 - - - - - - - - - - - +16 L H 8 - - - - - - - - - - - +17 G H 6 - - - - - - - - - - - +18 T H 5 - - - - - - - - - - - +19 L H 1 - - - - - - - - - - - +20 A C 2 - - - - - - - - - - - +21 A C 7 - - - - - - - - - - - +22 S C 9 - - - - - - - - - - - +23 T C 9 - - - - - - - - - - - +24 P C 8 - - - - - - - - - - - +25 G C 9 - - - - - - - - - - - +26 C C 8 - - - - - - - - - - - +27 D C 7 - - - - - - - - - - - +28 T C 7 - - - - - - - - - - - +29 S C 6 - - - - - - - - - - - +30 N C 6 - - - - - - - - - - - +31 Q C 4 - - - - - - - - - - - +32 A C 1 - - - - - - - - - - - +33 K C 1 - - - - - - - - - - - +34 A C 4 - - - * - - - - - - - +35 Q C 9 - - - * - - - - - - - +36 R C 9 - - - * 2 A 1 R 32.184 14.697 -11.772 +37 P C 9 - - - * 28 A 2 P 34.897 13.603 -9.390 +38 D C 9 - - - * 42 A 3 D 35.837 10.014 -9.507 +39 F C 7 35 12 * * 54 A 4 F 34.975 9.704 -5.855 +40 C C 7 36 86 * * 74 A 5 C 31.286 10.029 -6.794 +41 L C 6 37 13 * * 84 A 6 L 31.467 6.583 -8.351 +42 E C 8 38 34 * * 103 A 7 E 32.663 4.924 -5.112 +43 P C 9 39 52 * * 127 A 8 P 30.224 2.852 -3.086 +44 P C 8 40 19 * * 141 A 9 P 29.160 4.238 0.321 +45 Y C 7 44 29 * * 155 A 10 Y 31.512 3.320 3.156 +46 T C 5 45 15 * * 176 A 11 T 30.045 2.720 6.641 +47 G C 6 46 82 * * 190 A 12 G 33.523 2.128 8.130 +48 P C 8 52 30 * * 197 A 13 P 34.519 0.168 11.227 +49 C C 7 56 85 * * 211 A 14 C 32.817 2.337 13.956 +50 K C 5 57 23 * * 221 A 15 K 29.455 1.371 15.454 +51 A C 3 63 30 * * 243 A 16 A 27.519 4.598 15.454 +52 R C 1 82 13 * * 253 A 17 R 24.373 4.865 13.248 +53 I E 5 83 15 * * 277 A 18 I 24.709 8.341 11.537 +54 I E 6 91 19 * * 296 A 19 I 22.472 8.852 8.467 +55 R E 5 92 54 * * 315 A 20 R 24.442 10.455 5.670 +56 Y E 4 93 45 * * 339 A 21 Y 23.980 10.950 1.898 +57 F E 5 96 49 * * 360 A 22 F 25.997 9.344 -0.804 +58 Y E 5 97 61 * * 380 A 23 Y 25.779 9.725 -4.634 +59 N E 5 98 44 * * 401 A 24 N 24.473 6.511 -6.126 +60 A C 4 111 17 * * 415 A 25 A 25.937 6.771 -9.710 +61 K C 9 112 12 * * 425 A 26 K 23.844 3.843 -10.944 +62 A C 9 113 28 * * 447 A 27 A 20.576 5.701 -10.043 +63 G C 9 114 25 * * 457 A 28 G 21.970 9.249 -10.618 +64 L C 1 115 18 * * 464 A 29 L 20.589 10.458 -7.271 +65 C E 5 116 99 * * 483 A 30 C 21.875 11.033 -3.734 +66 Q E 4 117 24 * * 493 A 31 Q 20.508 8.474 -1.259 +67 T E 7 121 15 * * 510 A 32 T 20.941 7.836 2.490 +68 F E 8 122 85 * * 524 A 33 F 23.207 5.275 4.060 +69 V E 7 125 19 * * 544 A 34 V 24.349 4.496 7.646 +70 Y E 2 127 73 * * 560 A 35 Y 27.814 5.860 8.458 +71 G C 4 131 54 * * 581 A 36 G 29.544 4.252 11.487 +72 G C 6 149 86 * * 588 A 37 G 31.172 7.377 12.736 +73 C C 7 151 86 * * 595 A 38 C 34.813 7.212 11.868 +74 R C 9 155 37 * * 605 A 39 R 37.025 7.056 8.805 +75 A C 9 157 80 * * 629 A 40 A 34.631 8.632 6.385 +76 K C 9 161 80 * * 639 A 41 K 35.456 8.549 2.638 +77 R C 8 165 14 * * 661 A 42 R 34.659 11.372 0.167 +78 N C 9 173 95 * * 685 A 43 N 31.235 10.157 -1.075 +79 N C 9 174 49 * * 699 A 44 N 29.680 10.998 2.281 +80 F C 3 175 90 * * 713 A 45 F 27.732 14.188 2.696 +81 K C 0 176 18 * * 733 A 46 K 25.670 15.810 5.399 +82 S C 3 177 48 * * 755 A 47 S 23.068 17.191 3.061 +83 A H 9 178 20 * * 766 A 48 A 21.452 16.202 -0.192 +84 E H 9 179 35 * * 776 A 49 E 22.235 19.620 -1.652 +85 D H 9 180 37 * * 791 A 50 D 25.961 19.288 -1.082 +86 C H 9 185 98 * * 803 A 51 C 25.822 15.753 -2.493 +87 M H 9 186 27 * * 813 A 52 M 23.975 16.860 -5.592 +88 R H 9 187 13 * * 838 A 53 R 26.111 19.970 -6.044 +89 T H 7 188 24 * * 862 A 54 T 29.317 17.889 -5.933 +90 C C 0 189 97 * * 876 A 55 C 28.337 14.779 -7.839 +91 G C 7 190 10 * * 886 A 56 G 25.221 15.180 -9.791 +92 G C 7 - - - * 893 A 57 G 23.532 16.179 -13.038 +93 A C 9 - - - * 900 A 58 A 20.058 15.148 -14.143 +94 I C 9 - - - * - - - - - - - +95 G C 9 - - - * - - - - - - - +96 P C 9 - - - * - - - - - - - +97 W C 9 - - - - - - - - - - - +98 E C 8 - - - - - - - - - - - +99 N C 9 - - - - - - - - - - - +100 L C 9 - - - - - - - - - - - diff --git a/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out b/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out new file mode 100644 index 0000000000000000000000000000000000000000..7f5016ed7a885bbbe5fa7f8815554eddab91b459 --- /dev/null +++ b/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out @@ -0,0 +1,81 @@ +i j i_id j_id r_sco s_sco prob +11 35 11_C 35_C 1.8751 4.951 1.000 +17 41 17_R 41_N 1.2690 3.351 1.000 +21 28 21_N 28_Q 1.2309 3.250 1.000 +45 49 45_A 49_M 1.0435 2.755 1.000 +24 28 24_A 28_Q 0.8186 2.161 1.000 +14 31 14_R 31_V 0.8011 2.115 1.000 +6 19 6_P 19_F 0.7280 1.922 1.000 +18 45 18_Y 45_A 0.6058 1.600 0.998 +17 43 17_R 43_K 0.6022 1.590 0.998 +4 42 4_E 42_F 0.5441 1.437 0.995 +10 33 10_P 33_G 0.5022 1.326 0.991 +44 47 44_S 47_D 0.4921 1.299 0.990 +4 39 4_E 39_R 0.4679 1.235 0.985 +48 52 48_C 52_C 0.4673 1.234 0.985 +49 53 49_M 53_G 0.4665 1.232 0.984 +43 47 43_K 47_D 0.4617 1.219 0.983 +1 39 1_F 39_R 0.4528 1.196 0.981 +34 37 34_G 37_A 0.4515 1.192 0.980 +8 33 8_T 33_G 0.4497 1.188 0.980 +37 41 37_A 41_N 0.4362 1.152 0.975 +16 29 16_I 29_T 0.4345 1.147 0.974 +38 41 38_K 41_N 0.4193 1.107 0.968 +7 37 7_Y 37_A 0.4172 1.102 0.967 +19 28 19_F 28_Q 0.4127 1.090 0.964 +32 37 32_Y 37_A 0.4055 1.071 0.960 +46 50 46_E 50_R 0.3972 1.049 0.955 +10 36 10_P 36_R 0.3778 0.998 0.939 +47 51 47_D 51_T 0.3735 0.986 0.935 +9 37 9_G 37_A 0.3652 0.964 0.926 +9 41 9_G 41_N 0.3635 0.960 0.925 +25 53 25_G 53_G 0.3470 0.916 0.904 +30 38 30_F 38_K 0.3295 0.870 0.878 +1 51 1_F 51_T 0.3260 0.861 0.872 +16 31 16_I 31_V 0.3187 0.842 0.859 +1 42 1_F 42_F 0.3148 0.831 0.850 +15 31 15_I 31_V 0.3107 0.820 0.842 +3 22 3_L 22_A 0.3057 0.807 0.831 +3 45 3_L 45_A 0.2994 0.791 0.818 +11 33 11_C 33_G 0.2955 0.780 0.808 +32 40 32_Y 40_N 0.2914 0.769 0.797 +20 25 20_Y 25_G 0.2876 0.759 0.787 +13 34 13_A 34_G 0.2867 0.757 0.785 +8 12 8_T 12_K 0.2854 0.754 0.782 +14 33 14_R 33_G 0.2763 0.730 0.757 +32 41 32_Y 41_N 0.2761 0.729 0.756 +3 51 3_L 51_T 0.2701 0.713 0.738 +46 49 46_E 49_M 0.2698 0.712 0.737 +18 28 18_Y 28_Q 0.2615 0.691 0.713 +32 38 32_Y 38_K 0.2612 0.690 0.711 +5 23 5_P 23_K 0.2551 0.674 0.692 +18 29 18_Y 29_T 0.2549 0.673 0.691 +50 53 50_R 53_G 0.2540 0.671 0.688 +36 39 36_R 39_R 0.2507 0.662 0.677 +12 33 12_K 33_G 0.2468 0.652 0.664 +22 28 22_A 28_Q 0.2353 0.621 0.623 +25 28 25_G 28_Q 0.2341 0.618 0.618 +13 33 13_A 33_G 0.2299 0.607 0.603 +9 19 9_G 19_F 0.2286 0.604 0.599 +14 36 14_R 36_R 0.2260 0.597 0.590 +9 34 9_G 34_G 0.2240 0.592 0.583 +3 25 3_L 25_G 0.2200 0.581 0.567 +12 20 12_K 20_Y 0.2184 0.577 0.562 +23 29 23_K 29_T 0.2132 0.563 0.542 +20 27 20_Y 27_C 0.2089 0.552 0.526 +23 26 23_K 26_L 0.2037 0.538 0.507 +27 52 27_C 52_C 0.2036 0.538 0.507 +4 23 4_E 23_K 0.2036 0.538 0.507 +12 31 12_K 31_V 0.2023 0.534 0.501 +25 46 25_G 46_E 0.1989 0.525 0.488 +30 37 30_F 37_A 0.1986 0.524 0.487 +23 43 23_K 43_K 0.1985 0.524 0.487 +22 25 22_A 25_G 0.1900 0.502 0.456 +27 48 27_C 48_C 0.1895 0.500 0.454 +4 49 4_E 49_M 0.1872 0.494 0.445 +19 29 19_F 29_T 0.1832 0.484 0.432 +36 50 36_R 50_R 0.1802 0.476 0.421 +4 38 4_E 38_K 0.1800 0.475 0.420 +3 47 3_L 47_D 0.1798 0.475 0.420 +8 31 8_T 31_V 0.1765 0.466 0.408 +30 33 30_F 33_G 0.1755 0.463 0.404 diff --git a/docs/examples/bpt1/data/config.ini b/docs/examples/bpt1/data/config.ini index 24ad5a6944b251d2ec59dc4315ee8ec7dd1e225c..d44c73e864e8bd02fd7001d889628e9bd9f5766b 100644 --- a/docs/examples/bpt1/data/config.ini +++ b/docs/examples/bpt1/data/config.ini @@ -10,7 +10,7 @@ n_factor: 1.0 host_command: sbatch -t 06:00:00 host_executable: /path/to/cns1.21.exe cns_executable: /path/to/cns1.21.exe -temp_root: /path/to/tempdir +temp_root: /tmp # Protocol parameters # ------------------- rama_potential_enabled: yes diff --git a/docs/tutorial/analysis.rst b/docs/tutorial/analysis.rst index 88282d21fc2b40e731a05588ca110daed03ecc8a..63fb6b45e3be6e75b174ee383aa66685bae6a787 100644 --- a/docs/tutorial/analysis.rst +++ b/docs/tutorial/analysis.rst @@ -1,2 +1,5 @@ Analysis ======== + +Analyse des cartes de contacts via la commande maplot +Analyse de structures au format PDB via la commande pdbqual (en ayant précisé les chemins des programmes dans le fichier de configuration) diff --git a/docs/tutorial/run.rst b/docs/tutorial/run.rst index 332cd5431a5c529606b8b9fed71dd902dd719b5b..5d3a1e5f23f6be0c03760d5b38560524b49a5e4e 100644 --- a/docs/tutorial/run.rst +++ b/docs/tutorial/run.rst @@ -1,2 +1,7 @@ Run === + +Cette étape se résume en deux partie, +L'initialisation du projet ARIA généré durant le setup +L'exécution du projet +=> NB vérifier la commande utilisée pour exécuter le projet si elle correspond au gestionnaire de job utilisé par votre cluster diff --git a/docs/tutorial/setup.rst b/docs/tutorial/setup.rst index 1f6b43aa54305580689fa0edca64ae3b559808ce..5d0934b1e21803b131e789547a6ac957e4bdb10c 100644 --- a/docs/tutorial/setup.rst +++ b/docs/tutorial/setup.rst @@ -1,3 +1,7 @@ Setup ===== +Modifier les paramètres indiquant le chemin de CNS et du ou des programmes d'analyse qu'on souhaite utiliser +Lancer la commande setup en prenant en compte l'ensemble des fichiers qu'on souhaite convertir +Lister les différents fichiers générés +Verifier dans les log si les étapes se sont correctement déroulé diff --git a/docs/usage.rst b/docs/usage.rst index ea6aae38bd8d9124eaec25efb5d1248af6c80761..005043b4ea1d20c75b0b28409b4b4e46e7d8fb78 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -27,7 +27,7 @@ ARIAEC +-------------------------+-----------------------------------------------------+ | Name | Short description | -+-------------------------+-----------------------------------------------------+ ++=========================+=====================================================+ | `setup <Setup_>`_ | Setup ARIA project with EC data | +-------------------------+-----------------------------------------------------+ | `bbconv <BBconv_>`_ | Translate BBcontacts as distance restraints | @@ -56,7 +56,7 @@ ARIAEC +--------------------------------------------------------+-----------------------------------------------------+ | Name | Description | -+--------------------------------------------------------+-----------------------------------------------------+ ++========================================================+=====================================================+ | ``-h``, ``--help`` | show help message and exit | +--------------------------------------------------------+-----------------------------------------------------+ | ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) | @@ -86,7 +86,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure. +-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Name | Short description | -+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ ++=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+ | ``seq`` | Sequence file [``FASTA``] | +-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | ``infile`` | Contact or pdb file(s) used to build aria distance restraints | @@ -107,7 +107,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure. +--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+ | Name | Description | -+--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+ ++========================================================+========================================================================================================================================================+ | ``-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 | +--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+ | ``-s SSPRED``, ``--ssfile SSPRED`` | Secondary structure prediction file |