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> java Mols2PDF --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


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.