--- a/convert/ob_convert.xml	Tue May 14 17:01:10 2013 -0400
+++ b/convert/ob_convert.xml	Thu May 23 17:29:11 2013 -0400
@@ -48,6 +48,8 @@
         $oformat.cml_omit
         $oformat.cml_continuous
         $oformat.cml_properties
+        $oformat.cml_gen2d
+        $oformat.cml_gen3d
     #elif $format == 'inchi':
         ##ignore less import warnings
         -w
@@ -82,6 +84,8 @@
         $oformat.sdf_no_prop
         $oformat.sdf_wedge_bonds
         $oformat.sdf_alias_out
+        $oformat.sdf_gen2d
+        $oformat.sdf_gen3d
     #elif $format == 'fpt':
         $oformat.fpt_fptype
         #if int($oformat.fpt_fold) > 0:
@@ -93,6 +97,8 @@
         $oformat.fpt_unset
     #elif $format == 'mol2':
         $oformat.mol2_ignore_res
+        $oformat.mol2_gen2d
+        $oformat.mol2_gen3d
     #end if
 
     ## Uniqueness according to stripped InChI's or canonical SMILES
@@ -233,6 +239,8 @@
                 <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" />
                 <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" />
                 <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
+                <param name="cml_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
+                <param name="cml_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
             </when>
             <when value="cmlr" />
             <when value="com" />
@@ -319,6 +327,8 @@
             <when value="mmod" />
             <when value="mol2">
                 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands (-xl)" truevalue="-xl" falsevalue="" checked="false" />
+                <param name="mol2_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
+                <param name="mol2_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
             </when>
             <when value="molreport" />
             <when value="mop" />
@@ -340,6 +350,8 @@
                 <param name="sdf_no_prop" type="boolean" label="write no properties (-xm)" truevalue="-xm" falsevalue="" checked="false" />
                 <param name="sdf_wedge_bonds" type="boolean" label="use wedge and hash bonds from input (2D structures only) (-xw)" truevalue="-xw" falsevalue="" checked="false" />
                 <param name="sdf_alias_out" type="boolean" label="output in Alias form, e.g. Ph (-xA)" truevalue="-xA" falsevalue="" checked="false" />
+                <param name="sdf_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
+                <param name="sdf_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
             </when>
             <when value="smi">
                 <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" />