Editing Lisica (section)

==  Usage == 

The plugin window has four tabs. 

==== Inputs Tab ====


Both the reference and the target compound files need to be in the Tripos mol2 format. The reference file should contain only one (reference) compound; 
the target file may contain many compounds. If the reference file contains more than one compound, the first molecule is used as a reference. The molecules
in the target file having the same name are considered as different conformers of the same molecule. By default only the best-scoring (by Tanimoto coefficient) 
conformer will be shown in the final output for the 3D screening option.

In the mol2 input files, the name of the molecule (ZINC ID) must be specified under the line for @<TRIPOS>MOLECULE tag. For example,

   @<TRIPOS>MOLECULE
   '''ZINC73655097'''
   46    48     0     0     0
   SMALL
   USER_CHARGES
   
   @<TRIPOS>ATOM
   ...

LiSiCA checks similarities based on the mol2 atom types. Hence '''SYBYL''' atom types have to be specified in the mol2 files. For example, under the @<TRIPOS>ATOM tag, each atom specification should include the SYBYL atom type, as in:

   1 C1         -0.0647    1.4496   -0.0592   '''C.3'''       1 <0>        -0.167

In the above line from a mol2 file, in bold, in column 5, the SYBYL atom type is specified.


In 2D screening, the  option '''Maximum Allowed Shortest path Difference''' corresponds to the maximum allowed difference in shortest-path length between 
atoms of the two compared product graph vertices. Lesser values correspond to a more rigorous screening. By default this value is unit bond.

In 3D screening, the  option '''Maximum Allowed Spatial Distance Difference''' corresponds to the maximum allowed difference in distances between atoms of 
the two compared product graph vertices. Lesser values correspond to a more rigorous screening. By default this value is 1 Å.
The '''Number of Conformations'''  option corresponds to the maximum number of outputted files of one molecule in different conformations and is to be used only for 3D screening.


[[File: InputTab2DLiSiCALinuxv1.0.0.png|550 px]] [[File: InputTab3DLiSiCALinuxv1.0.0.png|520 px]]


According to the value of '''Number of highest ranked molecules to be written to the output (say W)''', LiSiCA will create mol2 files of that many (W) highest scoring 
target molecules with a comment section at the end of the file where the matching atom pairs are displayed. This value is by default 100. The resulting mol2 files 
are written into a time-stamp directory in the folder specified in '''Save results in:'''. By default this folder is the user's home directory. Also, a text file named 
lisica_results.txt with the target molecules with (in the descending order of) Tanimoto coefficients is written to the time-stamp folder. 

The '''Number of CPU cores to be used''' allows selection of CPU threads used for LiSiCA. By default, it tries to detect the number of CPUs available.
The '''Consider Hydrogen''' options lets the user to choose if the hydrogen atoms are to be considered for the calculation of the similarity using the maximum clique algorithm. 
By default, hydrogen atoms are not considered in finding the largest substructure common to the reference and target molecules, so as to obtain faster results.

==== Load Project Tab ==== 

The plugin also has a feature to load saved results. On the '''Load Project''' tab, the user can choose the directory with the saved results (mol2 files of each target 
and the reference) and the lisica_results.txt file. 
When the load button is clicked, the results will be loaded onto the output tab and the PyMOL Viewer window.

==== Output Tab ==== 

In the output tab, there are two listboxes:
* One contains ZINC ID and Tanimoto Coefficients of target molecules in the decreasing order of the Tanimoto coefficient values. 
Any single target molecule can be selected on this listbox using a mouse click or using up/down arrow keys. 
The selected target molecule is displayed with the reference molecule on the PyMOL viewer window.
* Depending on the target molecule chosen on the first listbox, the corresponding atoms from reference and the target molecules are displayed on the other listbox. 
Any single pair of corresponding atoms can be selected on this listbox using a mouse click or using up/down arrow keys. 
The selected pair is highlighted on the PyMOL viewer window.


For '''2D Screening''', the two molecules (the reference and the selected target) are visualized side by side on the PyMOL viewer screen.
 
[[File: 2DResultOutputtabPyMOLViewerLinux1.png|700 px|2D LiSiCA output- Note the reference and target molecules are aligned side by side]] 

For '''3D Screening''', the 3D structures of the two molecules (the reference and the selected target) are superimposed on one another to visualize the similarity on the PyMOL viewer screen.

[[File: 3DResultsOutputtabPyMOLViewer1.png|700 px|3D LiSiCA output-Note that the reference and target molecules are superimposed]]

==== About Tab ==== 

The users can get information on new updates if available on the About tab.