View source for pdb2SketchMacro

'''pdb2SketchMacro''' is [[Eos]]'s [[Command]].


== List of option ==
=== Main option ===
		<table border="1">
			<tr> 
				<th>Option</th> 
				<th>Essential/Optional</th> 
				<th>Description</th> 
				<th>Default</th> 
			</tr> 
			<tr> 
				<td>-i</td> 
				<td>Optional</td> 
				<td>Input: [[PDB]]</td> 
				<td>stdin</td> 
			</tr> 
			<tr> 
				<td>-o</td> 
				<td>Optional</td> 
				<td>Output: [[ASCII]]</td> 
				<td>stdout</td> 
			</tr> 
			<tr> 
				<td>-MolName</td> 
				<td>Optional</td> 
				<td>Molecule Name (recommend 2 words or less)</td> 
				<td>TS</td> 
			</tr> 
			<tr> 
				<td>-c</td> 
				<td>Optional</td> 
				<td>ConfigurationFile</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-m</td> 
				<td>Optional</td> 
				<td>Mode</td> 
				<td>15</td> 
			</tr> 
			<tr> 
				<td>-h</td> 
				<td>Optional</td> 
				<td>Help</td> 
				<td>　</td> 
			</tr> 
		</table>
<br> 

=== -m details ===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>Helix sketched with spirals </td> 
			</tr> 
			<tr> 
				<td>2</td> 
				<td>Sheet sketched with arrows </td> 
			</tr> 
			<tr> 
				<td>4</td> 
				<td>Turn  sketched with rattler</td> 
			</tr> 
			<tr> 
				<td>8</td> 
				<td>No structure sketched with rattler </td> 
			</tr> 
		</table> 
<br>

== Execution example ==
===[[:Media:Input-121P.pdb.zip|Input file]] image===
	<table> 
		<tr> 
			<td>[[File:Input-121P-PDB.png]]</td> 
			<td><p align="left">Gravity Centre(CA)<br> 
				Atom far from Centre(CA)<br> 
				Atom far from Centre(CA, Axis)<br> </p>
			</td> 
			<td><p align="left">6.053012e+00    2.519590e+01    1.189075e+01<br> 
				3.286664e+01 <br> 
				24.77      23.85      28.04<br></p>
			</td> 
		</tr> 
	</table> 
<br>

=== Example of options only essential ===
<pre>
sam_atom_in Input.pdb  TS
sketch_object TSH_A1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A16  A25  red
sketch_add    TS A16  A25 
end_object
sketch_object TSH_A2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A65  A74  red
sketch_add    TS A65  A74 
end_object
sketch_object TSH_A3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A87  A103 red
sketch_add    TS A87  A103
end_object
sketch_object TSH_A4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A127 A137 red
sketch_add    TS A127 A137
end_object
sketch_object TSH_A5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A152 A164 red
sketch_add    TS A152 A164
end_object
sketch_object TSS__S
sketch_setup  Arrow solid 2.5 0.5 3.75 2 7 3 2
sketch_type   Arrow 
paint_zone TS A37  A46  blue
sketch_add    TS A37  A46 
paint_zone TS A49  A58  blue
sketch_add    TS A49  A58 
paint_zone TS A2   A9   blue
sketch_add    TS A2   A9  
paint_zone TS A77  A83  blue
sketch_add    TS A77  A83 
paint_zone TS A111 A116 blue
sketch_add    TS A111 A116
paint_zone TS A141 A143 blue
sketch_add    TS A141 A143
end_oject
sketch_object TSN__1
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A1   A2   white
sketch_add    TS A1   A2  
end_object
sketch_object TSN__2
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A9   A16  white
sketch_add    TS A9   A16 
end_object

...

sketch_object TSN_11
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A143 A152 white
sketch_add    TS A143 A152
end_object
sketch_object TSN_12
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A164 0   white
sketch_add    TS A164 0  
end_object
</pre>
<br>

=== Option -m===
====Case: m=1==== 
<pre>
sam_atom_in Input.pdb  TS
sketch_object TSH_A1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A16  A25  red
sketch_add    TS A16  A25 
end_object
sketch_object TSH_A2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A65  A74  red
sketch_add    TS A65  A74 
end_object
sketch_object TSH_A3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A87  A103 red
sketch_add    TS A87  A103
end_object
sketch_object TSH_A4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A127 A137 red
sketch_add    TS A127 A137
end_object
sketch_object TSH_A5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A152 A164 red
sketch_add    TS A152 A164
end_object
</pre>
<br>

====Case: m=8==== 
<pre>
sam_atom_in Input.pdb  TS
sketch_object TSN__1
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A1   A2   white
sketch_add    TS A1   A2  
end_object
sketch_object TSN__2
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A9   A16  white
sketch_add    TS A9   A16 
end_object

...

sketch_object TSN_11
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A143 A152 white
sketch_add    TS A143 A152
end_object
sketch_object TSN_12
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A164 0   white
sketch_add    TS A164 0  
end_object
</pre>
<br>

=== Option -MolName===
====Case: MolName=XX, m=1==== 
<pre>
Input.pdb  XX
sketch_object XXH_A1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone XX A16  A25  red
sketch_add    XX A16  A25 
end_object
sketch_object XXH_A2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone XX A65  A74  red
sketch_add    XX A65  A74 
end_object
sketch_object XXH_A3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone XX A87  A103 red
sketch_add    XX A87  A103
end_object
sketch_object XXH_A4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone XX A127 A137 red
sketch_add    XX A127 A137
end_object
sketch_object XXH_A5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone XX A152 A164 red
sketch_add    XX A152 A164
end_object
</pre>
<br>