Depicting Molecules in Multi-Page¶
A program that converts molecular structures into a multi-page PDF
image.
Command Line Interface¶
A description of the command line interface can be obtained by executing the program with the –help argument.
prompt> python mols2pdf.py --help
will generate the following output:
Simple parameter list
input/output options :
-in : Input filename
-out : Output filename
-ringdict : User-defined 2D ring dictionary
molecule display options :
-aromstyle : Aromatic ring display style
-atomcolor : Atom coloring style
-atomlabelfontscale : Atom label font scale
-atomprop : Atom property display
-atomstereostyle : Atom stereo display style
-bondcolor : Bond coloring style
-bondprop : Bond property display
-bondstereostyle : Bond stereo display style
-hydrstyle : Hydrogen display style
-linewidth : Default bond line width
-protgroupdisp : Protective group display style
-scale : Scaling of the depicted molecule
-superdisp : Super atom display style
-titleloc : Location of the molecule title
prepare depiction options :
-clearcoords : Clear and regenerate 2D coordinates of molecule(s)
-orientation : Set the preferred orientation of 2D coordinates
-suppressH : Suppress explicit hydrogens of molecule(s)
report options :
-colsperpage : Number of columns per page
-pageheight : Page height
-pageorientation : Page orientation
-pagesize : Page size
-pagewidth : Page width
-rowsperpage : Number of rows per page
See also
Multi Page Reports chapter
Note
The above program can generate 2D coordinates with user-defined 2D ring layouts when using the -ringdict parameter.
See also the 2D coordinate generation examples section of the OEChem TK manual that shows examples about how to generate and utilize user-defined ring dictionaries.
Code¶
Download code
See also
Multi Page Images chapter
OEConfigureReportOptions
functionOEConfigurePrepareDepictionOptions
functionOEConfigure2DMolDisplayOptions
functionOEReportOptions
classOESetupReportOptions
functionOEReport
classOESetupPrepareDepictionOptions
functionOE2DMolDisplayOptions
classOESetup2DMolDisplayOptions
functionOEPrepareDepiction
functionOE2DMolDisplay
classOERenderMolecule
functionOEFont
classOEDrawTextToCenter
functionOEWriteReport
function