Molconn-Z 4.00 Manual: Chapter 2S

The Graphical Interface

Molconn-Z Menubar

Found as MolconnZ under eslc. The MolconnZ command allows you to calculate and display a large variety of molecular shape, topology, and information indices. Selection of MolconnZ reveals three submenus: Output, EState Map, and MolconnZ QSAR. The first presents dialogs that enable calculation and storage of ASCII files of Molconn-Z parameters; the EState Map submenu lists commands associated with calculating and displaying EState 3D maps; while the MolconnZ QSAR submenu contains some utilities for use with the SYBYL Molecular Spreadsheet.

Output

The Output commands set up and performs the MolconnZ computation for a single molecule, i.e., a current SYBYL molecule. The outputs are either a MolconnZ "S" file, consistent with previous versions of MolconnZ, or a human-readable ASCII Structure Report.

S File Dialog

The MolconnZ S File dialog sets up the MolconnZ calculation and outputs a formatted dump of descriptors in a record format described in Appendix II.

View MolconnZ S File Output Dialog Box

Algorithm Options Dialog

The MolconnZ Algorithm Options dialog sets a few calculational options for the MolconnZ calculation.

View MolconnZ Algorithm Options Dialog Box

Structure Report Dialog

The Structure Report dialog sets up and performs the MolconnZ computation for a single molecule. The user can choose which of the Report Sections he wants written: the output is a human-readable ASCII file.

View MolconnZ Structure Report Dialog Box

EState Map

The EState Map submenu contains the commands to execute the EState map creation for Molecules and to calculate difference maps from two input maps. It also contains the Contour command for contouring MolconnZ EState (or other) 3D maps. The three options on this submenu are: Molecule..., Difference..., and Contour...

Map Molecule Dialog Box

The Map Molecule dialog box defines the parameters and molecule necessary for creation of an EState field grid that maps the 3D electrotopology of the molecule.

View EState Map Molecule Dialog Box

Map Difference Dialog Box

The Map Difference Dialog Box enables you to calculate the difference (or sum) of two separate MolconnZ EState (or other) contour files. The Difference between two EState Molecule maps for two related molecules can be used to determine the areas where electrotopology is enhanced, etc. Note that the validity and interpretability of a map difference result is enhanced when the two input maps match closely in terms of region spanned and grid spacing.

View Map Difference Dialog Box

Contour Dialog Box

The Map Contour Dialog Box is a convenience utility for contouring and displaying SYBYL (.cnt) contour files.

View Map Contour Dialog Box

Region Definition Dialog Box

The Region Definition Dialog Box assists in describing the region in 3D cartesian space that the map calculation should span.

View Region Definition Dialog Box

EState Distance Function Dialog Box

Parameters in the EState Distance Function Dialog Box control the functional form of the EState calculation with respect to distance between atoms and grid points (for Map calculations).

View EState Distance Function Dialog Box

MolconnZ QSAR

The MolconnZ QSAR submenu contains some utility functions to aid in the use of MolconnZ with the SYBYL QSAR module. Most of the MolconnZ QSAR functionality is associated with the SYBYL Molecular Spreadsheet. This will be discussed in the next section.

The two options available in the MolconnZ QSAR submenu are Graph MolconnZ QSAR... and Fill MSS Cells with EState CoMFA Field.

Retrieve MolconnZ QSAR Dialog Box

The Retrieve MolconnZ QSAR Dialog Box is a convenience function to facilitate creation (for graphing) of the CoMFA coefficients*standard deviation contour maps for PLS runs where the MolconnZ EState fields were included. The dialog box enables selection of the desired field information and writes the selected CoMFA fields to scratch disk files. Then these fields are sequentially contoured.

View Retrieve MolconnZ QSAR Dialog Box

Fill MSS Cells with EState CoMFA Field Dialog Box

This command allows you to fill specified MSS cells with the EState CoMFA field. You may wish to use this option if you are attempting to predict activity of a new compound with a CoMFA model that includes the EState field.

View Fill MSS Cells with EState CoMFA Field Dialog Box

MolconnZ and the Molecular Spreadsheet

MolconnZ provides added functionality to the molecular spreadsheet. Two additional column types are defined by MolconnZ: MCONNIDX and MCONNCOMFA. These are available through the Spreadsheet "Autofill" button in the list of column types.

MolconnZ MSS Dialog Box

The MolconnZ MSS Dialog Box sets the parameters for filling the cells in a spreadsheet column with the topological, shape, and/or information indices of each molecule (row) in the table.

View MolconnZ MSS Dialog Box

MolconnZ MSS (Chi Indices) Dialog Box

The MolconnZ MSS (Chi Indices) Dialog Box allows the user to select the particular Chi Indices he/she wishes to place in the Molecular Spreadsheet. Each chosen Index from the menu will represent a column to be added to the MSS and filled for each molecule (row) in the table.

View MolconnZ MSS (Chi Indices) Dialog Box

MolconnZ MSS (Kappa Indices) Dialog Box

The MolconnZ MSS (Kappa Indices) Dialog Box allows the user to select the particular Kappa Indices he/she wishes to place in the Molecular Spreadsheet. Each chosen Index from the menu will represent a column to be added to the MSS and filled for each molecule (row) in the table.

View MolconnZ MSS (Kappa Indices) Dialog Box

MolconnZ MSS (Counts and complexity Indices) Dialog Box

The MolconnZ MSS (Counts and complexity Indices) Dialog Box allows the user to select the particular counts and/or molecule complexity Indices he/she wishes to place in the Molecular Spreadsheet. Each chosen Index from the menu will represent a column to be added to the MSS and filled for each molecule (row) in the table.

View MolconnZ MSS (Counts and complexity Indices) Dialog Box

MolconnZ MSS (Topological State, Shape, Wiener and Shannon Indices) Dialog Box

The MolconnZ MSS (Topological State, Shape, Wiener and Shannon Indices) Dialog Box allows the user to select the particular Topological State, Shape, etc. Indices he/she wishes to place in the Molecular Spreadsheet. Each chosen Index from the menu will represent a column to be added to the MSS and filled for each molecule (row) in the table.

View MolconnZ MSS (Topological State, Shape, Wiener and Shannon Indices) Dialog Box

MolconnZ MSS (Hydrogen Bond-related counts and EState Indices) Dialog Box

The MolconnZ MSS (Hydrogen Bond-related counts and EState Indices) Dialog Box allows the user to select the particular H-Bond Indices he/she wishes to place in the Molecular Spreadsheet. Each chosen Index from the menu will represent a column to be added to the MSS and filled for each molecule (row) in the table.

View MolconnZ MSS (Hydrogen Bond-related counts and EState Indices) Dialog Box

MolconnZ MSS (Vertex and Edge-type Counts) Dialog Box

The MolconnZ MSS (Vertex and Edge-type Counts) Dialog Box allows the user to select the particular Vertex Count Indices to be placed in the Molecular Spreadsheet. Each chosen Index from the menu will represent a column to be added to the MSS and filled for each molecule (row) in the table.

View MolconnZ MSS (Vertex and Edge-type Counts) Dialog Box

MolconnZ Select Atom Types Dialog Box

The MolconnZ Select Atom Types Dialog Box presents a menu of MolconnZ atom types that can be chosen for either Atom-Type Sum EState or Atom-type Count Indices.

View MolconnZ Select Atom Types Dialog Box

MolconnZ Select Group Types Dialog Box

The MolconnZ Select Group Types Dialog Box presents a menu of MolconnZ functional group types that can be chosen for either Group-Type Sum EState or Group-type Count Indices.

View MolconnZ Select Group Types Dialog Box

MCONNCOMFA: Add Column (EState CoMFA) Dialog Box

The Add Column (EState CoMFA) Dialog Box sets the parameters for filling each cell in a spreadsheet with the EState or H EState field. This Dialog Box contains parameters related to the initial MolconnZ calculation of each molecule and parameters related to the map creation for each molecule (row) in the table.

View Add Column (EState CoMFA) Dialog Box

Calculate CoMFA Region Automatically Dialog Box

This dialog box is called from the MolconnZ COMFA routine and is used to set the parameters for defining the CoMFA region based on the union space spanned by the entire molecule set. The routine determines the spatial extents of each molecule and creates a region that encompasses all molecules.

View Calculate CoMFA Region Automatically Dialog Box

Define CoMFA Region Dialog Box

The Define CoMFA Region Dialog Box is used if the cartesian coordinate set defining the region (Lower Box Corner, Upper Box Corner) is known, or if a custom region that includes more than one Box is needed. This latter case may be a useful option for some CoMFA experiments where much of the molecular structures are identical and a "closeup" on the areas of difference is appropriate.