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). 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.
prompt> szmap_report 4std_lig_coords.oeb.gz 4std_lig_coords.pdf
This executes SzmapReport with the default parameters. The file 4std_lig_coords.oeb.gz containing SZMAP -at_coords results is used as input, and the output is written to the file 4std_lig_coords.pdf,
Command Line Help¶
A description of the command line interface can be obtained by executing SzmapReport with the --help option.
> szmap_report --help
will generate the following output:
Help functions: szmap_report --help simple : Get a list of simple parameters szmap_report --help all : Get a complete list of parameters szmap_report --help defaults : List the defaults for all parameters szmap_report --help <parameter> : Get detailed help on a parameter szmap_report --help html : Create an html help file for this program szmap_report --help versions : List the toolkits and versions used in the application
- -output <filename>¶
- -o <filename>¶
[keyless parameter 2]
Output .pdf file containing one or more 2D renderings.
[default = szmap_report.pdf]
- -tagname <prop>¶
- -t <prop>¶
[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.
Molecule Display Options¶
- -aromstyle <style>¶
- -astl <style>¶
Aromatic ring display style: Kekule, Circle, Dash.
[default = Kekule]
- -atomcolor <color>¶
- -acolor <color>¶
Atom coloring style: WhiteCPK, BlackCPK, WhiteMonochrome, BlackMonochrome, cow, cob, bow, wob.
Style Meaning 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]
- -atomstereostyle <style>¶
- -atomsstl <style>¶
Atom stereo display style: Hidden, AtomStereo, StandardStyle, FancyStyle. Combined expressions: Created by combining primitive tokens with “|”.
[default = AtomStereo|FancyStyle]
- -bondcolor <color>¶
- -bcolor <color>¶
Bond coloring style: ByElement, Monochrome.
[default = ByElement]
- -title <text>¶
Title for each page.
[default = “SZMAP Report”]
- -rows <number>¶
Number of rows on a page [1-10].
- -cols <number>¶
Number of columns on a page [1-10].
- -resolution <level>¶
Quality of color maps representing properties. The level will influence the size of the output—high produces output several times larger than medium produces.
Level Meaning low chunky (grain size: 5 x 5) medium smooth (grain size: 2 x 2) high very smooth (grain size: 1 x 1)
[default = medium]
- -legend <bool>¶
Show property legend.
[default = true]
- -surface <bool>¶
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 <set>¶
Tag set used when no explicit tag is specified. The set ‘v1’ is provided for backwards compatibility with SZMAP version 1 results.
Set Meaning 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 v1 szmap_neut_diff_free_energy, szmap_probe_burial
[default = min]