Recent changes to Usage

Usage modified by Igor

Igor — Fri, 25 Apr 2025 20:47:44 -0000

--- v23
+++ v24
@@ -138,20 +138,20 @@

 ## Files

-  * _/usr/local/share/spelling.txt_
+  * _/opt/local/osra/2.2.1spelling.txt_

 This is system-wide spelling corrections dictionary for atom labels and abbreviations that might not be correctly parsed by OCR engine. The default location of the file can be redefined with **-l** option. You can run with **-d** option for more debug output on OCR processing and spelling corrrection. 

-  * _/usr/local/share/superatom.txt_
+  * _/opt/local/osra/2.2.1//superatom.txt_

 This is system-wide translations of superatom labels to SMILES codes. The default location of the file can be redefined with **-a** option. 

 ## Diagnostics

-The following diagnostics may be issued on **stderr**: _Cannot open file "dummy.png"_ \- the given input file does not exist or is not readable. OSRA provides some return codes, that can be used in scripts. 
+The following diagnostics may be issued on **stdout**: _Cannot open file "dummy.png"_ \- the given input file does not exist or is not readable. OSRA provides some return codes, that can be used in scripts. 

   * Code 0: Program exited successfully. 
-  * Code 1: Some error occured. See above mentioned error messages. 
+  * Code 1 or other non-zero: Some error occured. See above mentioned error messages. 

 ## Bugs

Usage modified by Igor

Igor — Fri, 25 Apr 2025 20:45:14 -0000

--- v22
+++ v23
@@ -2,10 +2,23 @@

 ## Brief usage

-osra \[--learn\]\[-w <filename\>\]\[--preview  <filename\>\]\[-s <dimensions, 300x400\="">\] \[-o <filename prefix\="">\]\[-v\]\[-d\]
-\[--ocr   <ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\[-a <configfile\>\]\[-l <configfile\>\]\[-b\]\[-c\]\[-e\]\[-g\]\[-p\]
-\[--embedded-format <inchi smi="" can\="">\]\[-f <can smi="" sdf\="">\]\[-k\]\[-i\]\[-j\]\[-u  <default: 0="" rounds\="">\]\[-t <0.2..0.8\>\]\[-r  <default: auto\="">\]
-\[-n\]\[-R <0..360\>\]\[--\]\[--version\]\[-h\] <filename\>
+~~~
+
+osra [--learn] [-w <output file="" or="" folder="" name="">] [--preview
+                                   <filename>] [-s <dimensions, 300x400="">]
+                                   [-o <filename prefix="">] [-v] [-d] [--ocr
+                                   <ooccnnhfssbuugmeexyzrpp23456789amthdgq>
+                                   ] [-a <configfile>] [-l <configfile>]
+                                   [-b] [-c] [-e] [-g] [-p]
+                                   [--embedded-format <inchi smi="" can="">]
+                                   [--v3000] [-f <can smi="" sdf="">] [--timeout
+                                   <default: no="" timeout="">] [-k] [-i] [-j]
+                                   [-u <default: 0="" rounds="">] [-t <0.2..0.8>]
+                                   [--pdf <default: 300="">] [-r <default: +="" auto="">] [-n] [-R <0..360>] [--]
+                                   [--version] [-h] <input file="" or="" folder="" name=""> ...
+~~~
+



@@ -20,19 +33,20 @@
 ## Options

 The program follows the usual GNU command line syntax, with long options starting with two dashes (`-'). 
-       --learn
+~~~
+  --learn
      Print out all structure guesses with confidence parameters

-   -w <filename\>,  --write <filename\>
-     Write recognized structures to text file
+   -w <filename>,  --write <filename>
+     Write recognized structures to a file or folder

-   --preview <filename\>
+   --preview <filename>
      Preview Image

-   -s <dimensions, 300x400\="">,  --size <dimensions, 300x400\="">
+   -s <dimensions, 300x400="">,  --size <dimensions, 300x400="">
      Resize image on output

-   -o <filename prefix\="">,  --output <filename prefix\="">
+   -o <filename prefix="">,  --output <filename prefix="">
      Write recognized structures to image files with given prefix

    -v,  --verbose
@@ -41,13 +55,13 @@
    -d,  --debug
      Print out debug information on spelling corrections

-   --ocr <ooccnnhfssbuugmeexyzrpp23456789amthdgq\>
+   --ocr <ooccnnhfssbuugmeexyzrpp23456789amthdgq>
      OCR character filter

-   -a <configfile\>,  --superatom <configfile\>
+   -a <configfile>,  --superatom <configfile>
      Superatom label map to SMILES

-   -l <configfile\>,  --spelling <configfile\>
+   -l <configfile>,  --spelling <configfile>
      Spelling correction dictionary

    -b,  --bond
@@ -67,11 +81,17 @@
    -p,  --print
      Print out confidence estimate

-   --embedded-format <inchi smi="" can\="">
+   --embedded-format <inchi smi="" can="">
      Embedded format

-   -f <can smi="" sdf="">,  --format <can smi="" sdf\="">
+   --v3000
+     Use V3000 format for MDL MOL and SDF output
+
+   -f <can smi="" sdf="">,  --format <can smi="" sdf="">
      Output format
+
+   --timeout <default: no="" timeout="">
+     Timeout in seconds per file processing

    -k,  --keep
      Keep image unsegmented, do not separate molecules from text
@@ -83,19 +103,22 @@
    -j,  --jaggy
      Additional thinning/scaling down of low quality documents

-   -u <default: 0="" rounds="">,  --unpaper <default: 0="" rounds\="">
+   -u <default: 0="" rounds="">,  --unpaper <default: 0="" rounds="">
      Pre-process image with unpaper algorithm, rounds

-   -t <0.2..0.8>,  --threshold <0.2..0.8\>
+   -t <0.2..0.8>,  --threshold <0.2..0.8>
      Gray level threshold

-   -r <default: auto="">,  --resolution <default: auto\="">
+   --pdf <default: 300="">
+     Resolution in dots per inch for PDF rendering
+
+   -r <default: auto="">,  --resolution <default: auto="">
      Resolution in dots per inch

    -n,  --negate
      Invert color (white on black)

-   -R <0..360>,  --rotate <0..360\>
+   -R <0..360>,  --rotate <0..360>
      Rotate image clockwise by specified number of degrees

    --,  --ignore_rest
@@ -107,8 +130,10 @@
    -h,  --help
      Displays usage information and exits.

-   <filename\>
-     (required)  input file
+   <>  (accepted multiple times)
+     (required)  input file(s) or a single folder
+
+~~~


 ## Files
</filename\></default:></default:></default:></default:></default:></default:></default:></default:></default:></default:></can></can></can></can></inchi></inchi></configfile></configfile></configfile\></configfile\></configfile></configfile></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></filename></filename></filename></dimensions,></dimensions,></dimensions,></dimensions,></filename></filename\></filename></filename></filename\></filename\></default:></default:></default:></default:></can></inchi></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></dimensions,></filename></output></filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:23:12 -0000

--- v21
+++ v22
@@ -5,7 +5,7 @@
 osra \[--learn\]\[-w <filename\>\]\[--preview  <filename\>\]\[-s <dimensions, 300x400\="">\] \[-o <filename prefix\="">\]\[-v\]\[-d\]
 \[--ocr   <ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\[-a <configfile\>\]\[-l <configfile\>\]\[-b\]\[-c\]\[-e\]\[-g\]\[-p\]
 \[--embedded-format <inchi can\="" smi="">\]\[-f <can sdf\="" smi="">\]\[-k\]\[-i\]\[-j\]\[-u  <default: 0="" rounds\="">\]\[-t <0.2..0.8\>\]\[-r  <default: auto\="">\]
-\[-n\]\[-R <0..360\>\]\[--\]\[--version\]\ [-h\] <filename\>
+\[-n\]\[-R <0..360\>\]\[--\]\[--version\]\[-h\] <filename\>



@@ -23,16 +23,16 @@
        --learn
      Print out all structure guesses with confidence parameters

-   -w <filename>,  --write <filename>
+   -w <filename\>,  --write <filename\>
      Write recognized structures to text file

-   --preview <filename>
+   --preview <filename\>
      Preview Image

-   -s <dimensions, 300x400="">,  --size <dimensions, 300x400="">
+   -s <dimensions, 300x400\="">,  --size <dimensions, 300x400\="">
      Resize image on output

-   -o <filename prefix="">,  --output <filename prefix="">
+   -o <filename prefix\="">,  --output <filename prefix\="">
      Write recognized structures to image files with given prefix

    -v,  --verbose
@@ -41,13 +41,13 @@
    -d,  --debug
      Print out debug information on spelling corrections

-   --ocr <ooccnnhfssbuugmeexyzrpp23456789amthdgq>
+   --ocr <ooccnnhfssbuugmeexyzrpp23456789amthdgq\>
      OCR character filter

-   -a <configfile>,  --superatom <configfile>
+   -a <configfile\>,  --superatom <configfile\>
      Superatom label map to SMILES

-   -l <configfile>,  --spelling <configfile>
+   -l <configfile\>,  --spelling <configfile\>
      Spelling correction dictionary

    -b,  --bond
@@ -67,10 +67,10 @@
    -p,  --print
      Print out confidence estimate

-   --embedded-format <inchi can="" smi="">
+   --embedded-format <inchi can\="" smi="">
      Embedded format

-   -f <can sdf="" smi="">,  --format <can sdf="" smi="">
+   -f <can sdf="" smi="">,  --format <can sdf\="" smi="">
      Output format

    -k,  --keep
@@ -83,19 +83,19 @@
    -j,  --jaggy
      Additional thinning/scaling down of low quality documents

-   -u <default: 0="" rounds="">,  --unpaper <default: 0="" rounds="">
+   -u <default: 0="" rounds="">,  --unpaper <default: 0="" rounds\="">
      Pre-process image with unpaper algorithm, rounds

-   -t <0.2..0.8>,  --threshold <0.2..0.8>
+   -t <0.2..0.8>,  --threshold <0.2..0.8\>
      Gray level threshold

-   -r <default: auto="">,  --resolution <default: auto="">
+   -r <default: auto="">,  --resolution <default: auto\="">
      Resolution in dots per inch

    -n,  --negate
      Invert color (white on black)

-   -R <0..360>,  --rotate <0..360>
+   -R <0..360>,  --rotate <0..360\>
      Rotate image clockwise by specified number of degrees

    --,  --ignore_rest
@@ -107,7 +107,7 @@
    -h,  --help
      Displays usage information and exits.

-   <filename>
+   <filename\>
      (required)  input file


</filename\></filename></default:></default:></default:></default:></default:></default:></default:></default:></can></can></can></can></inchi></inchi></configfile\></configfile\></configfile></configfile></configfile\></configfile\></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></filename></filename></filename></dimensions,></dimensions,></dimensions,></dimensions,></filename\></filename></filename\></filename\></filename></filename></filename\></filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:21:41 -0000

--- v20
+++ v21
@@ -2,10 +2,10 @@

 ## Brief usage

-osra \[--learn\]\[-w \<filename\>\]\[--preview  \<filename\>\]\[-s \<dimensions, 300x400\="">\] \[-o \<filename prefix\="">\]\ [-v\]\ [-d\]
-\[--ocr    \<ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\ [-a \<configfile\>\]\ [-l \<configfile\>\]\ [-b\]\ [-c\]\ [-e\]\ [-g\]\ [-p\]
-\[--embedded-format \<inchi can\="" smi="">\]\[-f \<can sdf\="" smi="">\]\ [-k\]\ [-i\]\ [-j\]\ [-u  \<default: 0="" rounds\="">\]\[-t \<0.2..0.8\>\]\ [-r  \<default: auto\="">\]
-\[-n\]\ [-R \<0..360\>\]\ [--\]\[--version\]\ [-h\] \<filename\>
+osra \[--learn\]\[-w <filename\>\]\[--preview  <filename\>\]\[-s <dimensions, 300x400\="">\] \[-o <filename prefix\="">\]\[-v\]\[-d\]
+\[--ocr   <ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\[-a <configfile\>\]\[-l <configfile\>\]\[-b\]\[-c\]\[-e\]\[-g\]\[-p\]
+\[--embedded-format <inchi can\="" smi="">\]\[-f <can sdf\="" smi="">\]\[-k\]\[-i\]\[-j\]\[-u  <default: 0="" rounds\="">\]\[-t <0.2..0.8\>\]\[-r  <default: auto\="">\]
+\[-n\]\[-R <0..360\>\]\[--\]\[--version\]\ [-h\] <filename\>



</filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\></filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:14:46 -0000

--- v19
+++ v20
@@ -2,10 +2,10 @@

 ## Brief usage

-osra \[--learn\]\ [-w \<filename\>\]\ [--preview  \<filename\>\]\ [-s \<dimensions, 300x400\="">\] \ [-o \<filename prefix\="">\]\ [-v\]\ [-d\]
-\ [--ocr    \<ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\ [-a \<configfile\>\]\ [-l \<configfile\>\]\ [-b\]\ [-c\]\ [-e\]\ [-g\]\ [-p\]
-\[--embedded-format \<inchi can\="" smi="">\]\ [-f \<can sdf\="" smi="">\]\ [-k\]\ [-i\]\ [-j\]\ [-u  \<default: 0="" rounds\="">\]\ [-t \<0.2..0.8\>\]\ [-r  \<default: auto\="">\]
-\[-n\]\ [-R \<0..360\>\]\ [--\]\ [--version\]\ [-h\] \<filename\>
+osra \[--learn\]\[-w \<filename\>\]\[--preview  \<filename\>\]\[-s \<dimensions, 300x400\="">\] \[-o \<filename prefix\="">\]\ [-v\]\ [-d\]
+\[--ocr    \<ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\ [-a \<configfile\>\]\ [-l \<configfile\>\]\ [-b\]\ [-c\]\ [-e\]\ [-g\]\ [-p\]
+\[--embedded-format \<inchi can\="" smi="">\]\[-f \<can sdf\="" smi="">\]\ [-k\]\ [-i\]\ [-j\]\ [-u  \<default: 0="" rounds\="">\]\[-t \<0.2..0.8\>\]\ [-r  \<default: auto\="">\]
+\[-n\]\ [-R \<0..360\>\]\ [--\]\[--version\]\ [-h\] \<filename\>



</filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\></filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:13:41 -0000

--- v18
+++ v19
@@ -2,10 +2,10 @@

 ## Brief usage

-osra \[--learn\]\ [-w <filename>\]\ [--preview  <filename>\]\ [-s <dimensions, 300x400="">\] \ [-o <filename prefix="">\]\ [-v\]\ [-d\]
-\ [--ocr    <ooccnnhfssbuugmeexyzrpp23456789amthdgq>\]\ [-a <configfile>\]\ [-l <configfile>\]\ [-b\]\ [-c\]\ [-e\]\ [-g\]\ [-p\]
-\[--embedded-format <inchi can="" smi="">\]\ [-f  <can sdf="" smi="">\]\ [-k\]\ [-i\]\ [-j\]\ [-u  <default: 0="" rounds="">\]\ [-t <0.2..0.8>\]\ [-r  <default: auto="">\]
-\[-n\]\ [-R <0..360>\]\ [--\]\ [--version\]\ [-h\] <filename>
+osra \[--learn\]\ [-w \<filename\>\]\ [--preview  \<filename\>\]\ [-s \<dimensions, 300x400\="">\] \ [-o \<filename prefix\="">\]\ [-v\]\ [-d\]
+\ [--ocr    \<ooccnnhfssbuugmeexyzrpp23456789amthdgq\>\]\ [-a \<configfile\>\]\ [-l \<configfile\>\]\ [-b\]\ [-c\]\ [-e\]\ [-g\]\ [-p\]
+\[--embedded-format \<inchi can\="" smi="">\]\ [-f \<can sdf\="" smi="">\]\ [-k\]\ [-i\]\ [-j\]\ [-u  \<default: 0="" rounds\="">\]\ [-t \<0.2..0.8\>\]\ [-r  \<default: auto\="">\]
+\[-n\]\ [-R \<0..360\>\]\ [--\]\ [--version\]\ [-h\] \<filename\>



</filename\></default:></default:></can></inchi></configfile\></configfile\></ooccnnhfssbuugmeexyzrpp23456789amthdgq\></filename></dimensions,></filename\></filename\></filename></default:></default:></can></inchi></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></dimensions,></filename></filename>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:11:28 -0000

--- v17
+++ v18
@@ -2,17 +2,10 @@

 ## Brief usage

-osra --learn] [-w <filename>] [--preview
-                                   <filename>] [-s <dimensions, 300x400="">]
-                                   [-o <filename prefix="">] [-v] [-d] [--ocr
-                                   <ooccnnhfssbuugmeexyzrpp23456789amthdgq>
-                                   ] [-a <configfile>] [-l <configfile>]
-                                   [-b] [-c] [-e] [-g] [-p]
-                                   [--embedded-format <inchi can="" smi="">] [-f
-                                   <can sdf="" smi="">] [-k] [-i] [-j] [-u
-                                   <default: 0="" rounds="">] [-t <0.2..0.8>] [-r
-                                   <default: auto="">] [-n] [-R <0..360>] [--]
-                                   [--version] [-h] <filename>
+osra \[--learn\]\ [-w <filename>\]\ [--preview  <filename>\]\ [-s <dimensions, 300x400="">\] \ [-o <filename prefix="">\]\ [-v\]\ [-d\]
+\ [--ocr    <ooccnnhfssbuugmeexyzrpp23456789amthdgq>\]\ [-a <configfile>\]\ [-l <configfile>\]\ [-b\]\ [-c\]\ [-e\]\ [-g\]\ [-p\]
+\[--embedded-format <inchi can="" smi="">\]\ [-f  <can sdf="" smi="">\]\ [-k\]\ [-i\]\ [-j\]\ [-u  <default: 0="" rounds="">\]\ [-t <0.2..0.8>\]\ [-r  <default: auto="">\]
+\[-n\]\ [-R <0..360>\]\ [--\]\ [--version\]\ [-h\] <filename>



</filename></default:></default:></can></inchi></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></dimensions,></filename></filename></filename></default:></default:></can></inchi></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></dimensions,></filename></filename>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:07:42 -0000

--- v16
+++ v17
@@ -2,7 +2,18 @@

 ## Brief usage

-osra \[-c\] \[-i\] \[-j\] \[-b\] \[-w <filename\>\] \[-u <default: 0="" rounds\="">\] \[-R <0..360\>\] \[-e\] \[-d\] \[-a <configfile\>\] \[-l <configfile\>\] \[-f <can sdf\="" smi="">\] \[-g\] \[-p\] \[-s <dimensions, 300x400\="">\] \[-n\] \[-r <default: auto\="">\] \[-o <filename prefix\="">\] \[-t <0.2..0.8\>\] \[--embedded-format\] \[--\] \[--version\] \[-h\] <filename\>
+osra --learn] [-w <filename>] [--preview
+                                   <filename>] [-s <dimensions, 300x400="">]
+                                   [-o <filename prefix="">] [-v] [-d] [--ocr
+                                   <ooccnnhfssbuugmeexyzrpp23456789amthdgq>
+                                   ] [-a <configfile>] [-l <configfile>]
+                                   [-b] [-c] [-e] [-g] [-p]
+                                   [--embedded-format <inchi can="" smi="">] [-f
+                                   <can sdf="" smi="">] [-k] [-i] [-j] [-u
+                                   <default: 0="" rounds="">] [-t <0.2..0.8>] [-r
+                                   <default: auto="">] [-n] [-R <0..360>] [--]
+                                   [--version] [-h] <filename>
+


 Most common use: **osra** _filename_
</filename></default:></default:></can></inchi></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></dimensions,></filename></filename></filename\></filename></default:></dimensions,></can></configfile\></configfile\></default:></filename\>

Usage modified by Igor

Igor — Tue, 21 Jul 2020 18:05:37 -0000

--- v15
+++ v16
@@ -16,102 +16,96 @@
 ## Options

 The program follows the usual GNU command line syntax, with long options starting with two dashes (`-'). 
-    
-      -i, --adaptive
-         Adaptive thresholding pre-processing, useful for low light/low contrast images
-    
-    
-      -c, --coordinates
-        Show surrounding box coordinates (only for SDF/SMI/CAN output format)
-    
-    
-      --embedded-format "format"
-         Allows the user to have InChI or SMILES included in an SDF file as a molecular property 
-    
-    
-      -j,  --jaggy
-        Additional thinning/scaling down of low quality documents
-    
-    
-      -b,  --bond
-        Show average bond length in pixels
-    
-    
-      -w <filename>,  --write <filename>
-        Write output to file
-    
-    
-      -u <default: 0="" rounds="">,  --unpaper <default: 0="" rounds="">
-        Pre-process image with unpaper algorithm, rounds
-    
-    
-      -R <0..360>,  --rotate <0..360>
-        Rotate image clockwise by specified number of degrees
-    
-    
-      -e,  --page
-        Show page number for PDF/PS/TIFF documents
-    
-    
-      -d,  --debug
-        Print out debug information on spelling corrections
-    
-    
-      -a <configfile>,  --superatom <configfile>
-        Superatom label map to SMILES
-    
-    
-      -l <configfile>,  --spelling <configfile>
-        Spelling correction dictionary
-    
-    
-      -f <can sdf="" smi="">,  --format <can sdf="" smi="">
-        Output format
-    
-    
-      -g,  --guess
-        Print out resolution guess
-    
-    
-      -p,  --print
-        Print out confidence estimate
-    
-    
-      -s <dimensions, 300x400="">,  --size <dimensions, 300x400="">
-        Resize image on output
-    
-    
-      -n,  --negate
-        Invert color (white on black)
-    
-    
-      -r <default: auto="">,  --resolution <default: auto="">
-        Resolution in dots per inch
-    
-    
-      -o <filename prefix="">,  --output <filename prefix="">
-        Write out images to files
-    
-    
-      -t <0.2..0.8>,  --threshold <0.2..0.8>
-        Gray level threshold
-    
-    
-      --,  --ignore_rest
-        Ignores the rest of the labeled arguments following this flag.
-    
-    
-      --version
-        Displays version information and exits.
-    
-    
-      -h,  --help
-        Displays usage information and exits.
-    
-    
-      <filename>
-        (required)  input file
-    
+       --learn
+     Print out all structure guesses with confidence parameters
+
+   -w <filename>,  --write <filename>
+     Write recognized structures to text file
+
+   --preview <filename>
+     Preview Image
+
+   -s <dimensions, 300x400="">,  --size <dimensions, 300x400="">
+     Resize image on output
+
+   -o <filename prefix="">,  --output <filename prefix="">
+     Write recognized structures to image files with given prefix
+
+   -v,  --verbose
+     Be verbose and print the program flow
+
+   -d,  --debug
+     Print out debug information on spelling corrections
+
+   --ocr <ooccnnhfssbuugmeexyzrpp23456789amthdgq>
+     OCR character filter
+
+   -a <configfile>,  --superatom <configfile>
+     Superatom label map to SMILES
+
+   -l <configfile>,  --spelling <configfile>
+     Spelling correction dictionary
+
+   -b,  --bond
+     Show average bond length in pixels (only for SDF/SMI/CAN output
+     format)
+
+   -c,  --coordinates
+     Show surrounding box coordinates (only for SDF/SMI/CAN output format)
+
+   -e,  --page
+     Show page number for PDF/PS/TIFF documents (only for SDF/SMI/CAN
+     output format)
+
+   -g,  --guess
+     Print out resolution guess
+
+   -p,  --print
+     Print out confidence estimate
+
+   --embedded-format <inchi can="" smi="">
+     Embedded format
+
+   -f <can sdf="" smi="">,  --format <can sdf="" smi="">
+     Output format
+
+   -k,  --keep
+     Keep image unsegmented, do not separate molecules from text
+
+   -i,  --adaptive
+     Adaptive thresholding pre-processing, useful for low light/low
+     contrast images
+
+   -j,  --jaggy
+     Additional thinning/scaling down of low quality documents
+
+   -u <default: 0="" rounds="">,  --unpaper <default: 0="" rounds="">
+     Pre-process image with unpaper algorithm, rounds
+
+   -t <0.2..0.8>,  --threshold <0.2..0.8>
+     Gray level threshold
+
+   -r <default: auto="">,  --resolution <default: auto="">
+     Resolution in dots per inch
+
+   -n,  --negate
+     Invert color (white on black)
+
+   -R <0..360>,  --rotate <0..360>
+     Rotate image clockwise by specified number of degrees
+
+   --,  --ignore_rest
+     Ignores the rest of the labeled arguments following this flag.
+
+   --version
+     Displays version information and exits.
+
+   -h,  --help
+     Displays usage information and exits.
+
+   <filename>
+     (required)  input file
+

 ## Files

</filename></default:></default:></default:></default:></can></can></inchi></configfile></configfile></configfile></configfile></ooccnnhfssbuugmeexyzrpp23456789amthdgq></filename></filename></dimensions,></dimensions,></filename></filename></filename></filename></filename></filename></default:></default:></dimensions,></dimensions,></can></can></configfile></configfile></configfile></configfile></default:></default:></filename></filename>

Usage modified by Igor

Igor — Fri, 13 Jun 2014 11:59:07 -0000

--- v14
+++ v15
@@ -2,7 +2,7 @@

 ## Brief usage

-osra [-c] [-i] [-j] [-b] [-w <filename>] [-u <default: 0 rounds>] [-R <0..360>] [-e] [-d] [-a <configfile>] [-l <configfile>] [-f <can/smi/sdf>] [-g] [-p] [-s <dimensions, 300x400>] [-n] [-r <default: auto>] [-o <filename prefix>] [-t <0.2..0.8>] [--embedded-format] [--] [--version] [-h] <filename>
+osra \[-c\] \[-i\] \[-j\] \[-b\] \[-w \] \[-u \] \[-R <0..360\>\] \[-e\] \[-d\] \[-a \] \[-l \] \[-f smisdf\>\] \[-g\] \[-p\] \[-s \] \[-n\] \[-r \] \[-o \] \[-t <0.2..0.8\>\] \[--embedded-format\] \[--\] \[--version\] \[-h\] 

 Most common use: **osra** _filename_
@@ -37,15 +37,15 @@
         Show average bond length in pixels

-      -w <filename>,  --write <filename>
+      -w ,  --write 
         Write output to file

-      -u <default: 0 rounds>,  --unpaper <default: 0 rounds>
+      -u ,  --unpaper 
         Pre-process image with unpaper algorithm, rounds

-      -R <0..360>,  --rotate <0..360>
+      -R <0..360>,  --rotate <0..360>
         Rotate image clockwise by specified number of degrees

@@ -57,15 +57,15 @@
         Print out debug information on spelling corrections

-      -a <configfile>,  --superatom <configfile>
+      -a ,  --superatom 
         Superatom label map to SMILES

-      -l <configfile>,  --spelling <configfile>
+      -l ,  --spelling 
         Spelling correction dictionary

-      -f <can/smi/sdf>,  --format <can/smi/sdf>
+      -f smisdf>,  --format smisdf>
         Output format

@@ -77,7 +77,7 @@
         Print out confidence estimate

-      -s <dimensions, 300x400>,  --size <dimensions, 300x400>
+      -s ,  --size 
         Resize image on output

@@ -85,15 +85,15 @@
         Invert color (white on black)

-      -r <default: auto>,  --resolution <default: auto>
+      -r ,  --resolution 
         Resolution in dots per inch

-      -o <filename prefix>,  --output <filename prefix>
+      -o ,  --output 
         Write out images to files

-      -t <0.2..0.8>,  --threshold <0.2..0.8>
+      -t <0.2..0.8>,  --threshold <0.2..0.8>
         Gray level threshold

@@ -109,7 +109,7 @@
         Displays usage information and exits.

-      <filename>
+      
         (required)  input file