Editing SecStrAnnotator:OneToOne (section)

==Execution==

SecStrAnnotator is executed from command line:

 dotnet SecStrAnnotator.dll <span style=color:gray>[</span><span style=color:green>OPTIONS</span><span style=color:gray>]</span> <span style=color:green>DIRECTORY</span> <span style=color:green>TEMPLATE</span> <span style=color:green>QUERY</span>

Example of a call:

<source lang="bash">
 dotnet SecStrAnnotator.dll --help                                                                          # Show help

 dotnet SecStrAnnotator.dll --onlyssa my_data_directory 1tqn,A,7:478                                        # Only detect SSEs

 dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478                                           # Detect and annotate SSEs

 dotnet SecStrAnnotator.dll my_data_directory 2nnj,A 1tqn,A,7:478 --align cealign --matching mom --session  # Detect and annotate SSEs
</source>


===Arguments===

* <code><span style=color:green>DIRECTORY</span></code> is the directory containing all the input files. The output files will also be saved to this directory. 
* <code><span style=color:green>TEMPLATE</span></code> describes the template protein domain in one of the following formats: <code><span style=color:green>PDB</span></code> or <code><span style=color:green>PDB</span>,<span style=color:green>CHAIN</span></code> or <code><span style=color:green>PDB</span>,<span style=color:green>CHAIN</span>,<span style=color:green>RANGES</span></code>. The whole argument must be written without spaces. Examples: 
** <code>1og2</code> (structure 1og2, chain A by default)
** <code>1og2,B</code> (chain B)
** <code>1og2,B,100:400</code> (residues 100–400 of the chain B)
** <code>1og2,B,:400</code> (residues up to 400 of the chain B)
** <code>1h9r,A,123:183,252:261</code> (residues 123–183 and 252–261 of the chain A)
* <code><span style=color:green>QUERY</span></code> describes the query protein domain and uses the same format as <code><span style=color:green>TEMPLATE</span></code>.

Keep in mind that the chains and residues are numbered according to the label_* numbering scheme in mmCIF file format (i.e. chain identifier is <code>label_asym_id</code>, residue number is <code>label_seq_id</code>).

===Options===

There is a range of options which can be used to modify the behaviour of SecStrAnnotator.  The most important option is:
* <code>--help</code>  Prints the help message, which includes the description of all the other options.

===Input files===

* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>TEMPLATEPDB</span>.cif</code>  – structure of the template protein
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>TEMPLATEPDB</span>-template.sses.json</code>  – annotation of the template domain
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>.cif</code>  – structure of the query protein

===Output files===

* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-aligned.cif</code> – structure of the query protein after superimposition on the template protein
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-detected.sses.json</code> – secondary structure assignment of the query protein, i.e. all detected SSEs
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-annotated.sses.json</code> – annotated SSEs in the query protein
* <code><span style=color:green>DIRECTORY</span>/<span style=color:green>QUERYPDB</span>-annotated.pse</code> – PyMOL session with the visualization of the resulting annotation (only when executed with <code>--session</code> option)
* Additional output files and more detailed .sses.json files are produced when executed with <code>--verbose</code> option

===Auxiliary files and programs===

SecStrAnnotator has dependencies on other programs (PyMOL, optionally DSSP) and scripts. These auxiliary files need to be available in the system, and there location must be specified in the configuration file <code>SecStrAnnotator_config.json</code>. The configuration file itself must be in the same directory as <code>SecStrAnnotator.dll</code>. The default content of the configuration file is:
<source lang="json>
{
	"PymolExecutable":    "pymol",
	"PymolScriptAlign":   "./scripts/script_align.py",
	"PymolScriptSession": "./scripts/script_session.py",
	"DsspExecutable":     "mkdssp"
}    
</source>

which assumes that <code>pymol</code> is installed and can be run directly (from <code>$PATH</code>) and that the other files are present in subdirectory <code>scripts</code>. 

On Windows, you must find the location of PyMOL executable and insert it into the configuration file.

* It will be probably some impossible-to-find file like <code>C:\Program Files\PyMOL\PyMOL\PyMOL.exe</code> or <code>C:\ProgramData\PyMOL\Scripts\pymol.exe</code> (or <code>C:/Users/Adam/miniconda3/Scripts/pymol.exe</code> if you installed PyMOL via <code>conda</code>). 
* To make it more fun, <code>ProgramData</code> is a hidden directory, which is by default invisible in File Explorer. 
* We're looking for PyMOL.exe, not PyMOLWin.exe. PyMOLWin.exe will run asynchronously and it will probably not work.
* Note that <code>\</code> is a special escaping character in JSON. Therefore use <code>/</code> or <code>\\</code> instead of <code>\</code>.

<source lang="json>
{
	"PymolExecutable":    "C:/ProgramData/PyMOL/Scripts/pymol.exe",
	"PymolScriptAlign":   "./scripts/script_align.py",
	"PymolScriptSession": "./scripts/script_session.py",
	"DsspExecutable":     "./dssp.exe"
}    
</source>

===Annotation file format===

All files with extension <code>.sses.json</code> are in SecStrAnnotator annotation format. A short example of this  format:
<source lang="json>
{
  "1tqn": {
    "comment": "This is a demonstration of the annotation format. It shows a few SSEs selected from the real annotation of 1tqn.",
    "secondary_structure_elements": [
      { "label": "A", "chain_id": "A", "start": 36, "end": 47, "type": "H", "sequence": "FCMFDMECHKKY" },
      { "label": "B", "chain_id": "A", "start": 66, "end": 76, "type": "h", "sequence": "PDMIKTVLVKE" },
      { "label": "1-1", "chain_id": "A", "start": 50, "end": 55, "type": "E", "sheet_id": 1, "sequence": "VWGFYD" },
      { "label": "1-2", "chain_id": "A", "start": 58, "end": 63, "type": "E", "sheet_id": 1, "sequence": "QPVLAI" },
      { "label": "1-3", "chain_id": "A", "start": 372, "end": 375, "type": "E", "sheet_id": 1, "sequence": "VVMI" }
    ],
    "beta_connectivity": [
      [ "1-1", "1-2", -1 ],
      [ "1-2", "1-3", 1 ]
    ]
  }
}  
</source>

The example describes two helices, named A and B, and a β-sheet consisting of three strands, named 1-1, 1-2, and 1-3. Strands 1-1 and 1-2 are connected by an anti-parallel β-ladder, strands 1-2 and 1-3 by a parallel β-ladder. All the SSEs are located on chain A of structure 1tqn.


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