==============
Documentation
==============

.. toctree::
   :maxdepth: 2

Before starting, take into account that only the Basic parameters are mandatory. Otherwise, Optional parameters have
predefined default values. You can find and modify them in ``constants.py``.

Basic parameters
----------------

- **-cp**, **---complex_pdb**: Path to the PDB file which must contain a protein-ligand complex. Its ligand will be used
  as the core structure. Remember to rename the ligand chain with a different character in order to detect it.
- **-sef**, **---serie_file**:  Name of the tabular file which must contain the instructions required to perform several
  successive growings, using different fragments or different growing positions.

Optional parameters
-------------------

Protocol
----------

- **-HT**: High throughput protocol

- **default option**: Sp protocol

For more information refer to the protocol tab

FrAG configuration
``````````````````
This are the options directly related to FrAG itself.

- **-x**, **---growing_steps**: Number of Growing Steps (GS). By default: 10. Set 6 for small ligands and 2 to perform HT mode.
- **-cr**, **---criteria**: Name of the column of the report file to select the structures that will spawn in the
  next GS. Additionally, this parameter will be the selection criteria to extract the best structure after completing
  the growing. By default: 'Binding Energy'.
- **-rst**, **---restart**: If set FrAG will continue from the last GS detected. If all GS are finished it will restart
  in the equilibration phase.
- **-cc**, **---c_chain**: Chain name of the core. By default: 'L'.
- **-fc**, **---f_chain**: Chain name of the fragment. By default: 'L'.
- **-docon**, **---docontrolsim**: When it is set, FrAG runs a negative-control simulation (without growing). By default: None.

PELE configuration
``````````````````
Most of the following arguments are only focused in localize PELE's directories in the user machine. If you want to
modify parameters directly related to PELE configuration (control_file) it is highly recommendable to read PELE's
documentation.

- **-d**, **---pele_dir**: Complete path to Pele_serial.
- **-c**, **---contrl**: Path to PELE's control file templatized.
- **-l**, **---license**: Absolute path to PELE's licenses folder.
- **-r**, **---resfold**: Name for PELE's results folder. By default: 'growing_output'.
- **-rp**, **---report**: Suffix name of the report file from PELE.  By default: 'report'
- **-tj**, **---traject**: Suffix name of the trajectory file from PELE. By default: 'trajectory'
- **-cs**, **---cpus**: Number of cores (computational power) to paralellize PELE's simulations. By default: 48.
- **-stp**, **---steps**: Number of simulation steps inside each GS. By default: 6.
- **-es**, **---pele_eq_steps**: Number of PELE steps in equilibration. By default: 20.
- **-miov**, **---min_overlap**: Minimum value of overlapping factor used in the control_file of PELE. By default: 0'5.
- **-maov**, **---max_overlap**: Maximum value of overlapping factor used in the control_file of PELE. By default: 0'7.
- **-tmp**, **---temperature**: Temperature value to add in the control file. If the temperature is high more steps of
  PELE will be accepted when applying the Metropolis Criteria. By default: 1000.

Clustering and spawning configuration
`````````````````````````````````````
The following parameters are extracted from `AdaptivePELE <https://github.com/AdaptivePELE/AdaptivePELE/>`_. It is not
recommendable to modify default parameters.

- **-dis**, **---distcont**: Distance used to determine which amino acids are in contact with the ligand to generate
  different clusters of structures to initialize the next GS. By default: 4.
- **-ct**, **---threshold***: Threshold distance used in the clustering. By default: 0'3.
- **-e**, **---epsilon**: An epsilon fraction of processors are distributed proportionally to the value of a metric,
  and the rest are inverselyProportional distributed. A param n can be specified to only consider the n clusters with
  best metric. By default: 0'5.
- **-cn**, **--condition**: Selects whether to take into account maximum or minimum values in epsilon related spawning,
  values are min or max. By default: min.
- **-mw**, **---metricweights**: Selects how to distribute the weights of the cluster according to its metric, two
  options: linear (proportional to metric) or Boltzmann weigths (proportional to exp(-metric/T). Needs to define the
  temperature T. By default: 'linear'.
- **-ncl**, **--nclusters**: Number of initial structures that we want to use in each new GS. By default: 5.
- **-pdbf**, **--pdbout**: Folder where PDBs selected to spawn in the next GS will be stored. By default: 'PDBs_growing'.

Output configuration
``````````````````````
- **--mae**: Output mae files with binding energy trajectory as property inside the file

Others
``````
- **-pl**, **--plop_path**: Absolute path to PlopRotTemp.py.
- **-sp**, **--sch_python**: Absolute path to Schrödinger's python.