The szmap_report utility reads an OEBinary file (.oeb or .oeb.gz) generated by using the -at_coords flag with szmap and produces a .pdf file containing one or more 2-dimensional renderings of the results. The calculated values for a given property are shown as colored patches around each coordinate position. (You can also visualize these properties in 3D using Color By Atom Properties VIDA Extension). Atoms at coordinates with no calculated property because the probe clashed when placed there are grayed out.
If a concatenated series of molecules are used as input to szmap -at_coords, szmap_report will produce a figure for each molecule. You can control the formatting to either place the output for each molecule on a separate page, or align the output for different molecules on the same page.
By default option -surface is true, meaning a 2D surface boundary for the molecule is shown with different line types depending on how loose or tight the binding site is around each atom. Boundary styles are: simple black lines for close contacts, lines with short radial lines indicate a small gap, and outward reaching fingers indicate a cavity, a place with enough space to place a water or other atoms. Thin gray lines indicate a solvent exposed region.
If hydrogens are in the output, they are usually suppressed from the display. If you want to display data calculated at hydrogen positions, use -keep_hydrogens, but because surfaces are rendered only for heavy atoms, -surface must also set to false.
The output is rendered by OpenEye’s OEDepict and Grapheme toolkits (additional licenses not required). See figure SZMAP report output.
A description of the basic command line interface can be obtained by executing szmap_report with no arguments.
will generate output similar to the following:
szmap_report, Copyright (c) 2010-2015 OpenEye Scientific Software, Inc. Version: 1.2.1 Release: 20150305 OEChem version: 1.9.2 20150305 Platform: redhat-RHEL5-g++4.1-x64 Licensed for the exclusive use of Company Name. Licensed for use only in Site. License expires on August 15, 2015. No arguments specified on the command line Required parameters: -input : Input .oeb or .oeb.gz format file containing SZMAP -at_coords results For more help type: szmap_report --help
[keyless parameter 2]
Output .pdf file containing one or more 2D renderings.
[default = szmap_report.pdf]
[keyless parameter 3]
Atom property used to generate color patches around each atom:
The szmap_neut_diff_free_energy property is one of the most useful. It describes the hydrophilicity/hydrophobicity at each coordinate.
If no tag is specified, an array of properties will be displayed for each input molecule.
Aromatic ring display style: Kekule, Circle, Dash.
[default = Kekule]
Atom coloring style: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome, cow, cob, bow, wob.
|cow||(color on white) same as WhiteCPK|
|cob||(color on black) same as BlackCPK|
|bow||(black on white) same as WhiteMonochrome|
|wob||(white on black) same as BlackMonochrome|
[default = WhiteCPK]
Atom stereo display style: Hidden, AtomStereo, StandardStyle, FancyStyle. Combined expressions: Created by combining primitive tokens with “|”.
[default = AtomStereo|FancyStyle]
Bond coloring style: ByElement, Monochrome.
[default = ByElement]
Title for each page.
[default = “SZMAP Report”]
Quality of color maps representing properties. The level will influence the size of the output—high produces output several times larger than medium produces.
|low||chunky (grain size: 5 x 5)|
|medium||smooth (grain size: 2 x 2)|
|high||very smooth (grain size: 1 x 1)|
[default = medium]
Show property legend.
[default = true]
Show 2D molecular surface outline.
[default = true]
Show all the explicit hydrogens in depictions. Requires -surface to be set to false.
[default = false]
Tag set used when no explicit tag is specified. The set ‘v1’ is provided for backwards compatibility with SZMAP version 1 results.
|min||szmap_neut_diff_free_energy, szmap_vdw, szmap_order|
|max||szmap_neut_diff_free_energy, szmap_neut_diff_entropy, szmap_interaction, szmap_vdw, szmap_psolv, szmap_wsolv|
[default = min]