# <plugin name>=<plugin class name>$<plugin JAR URL>$<plugin group name>$<parameters>$<default tag name>$<description>$<helptext>$<exampletext>
# important: plugins cannot have -c options because it is in conflict with the
# general option -c --config.
# separate parameter description items by ';' (will be separated by newline
# characters) in <helptext>
# do not use $ characters except for field separation
# <exampletext> is optional

bemismurcko=$BemisMurckoPlugin\
	$BemisMurckoPlugin.jar\
	$-\
	$t=type:structure;i=lfin:false;o=lfout:false;s=keepsingleatom:true;f=format:smiles\
	$BEMISMURCKO\
	$Calculates Bemis-Murcko framework of the molecule\
	$-i, --lfin=[true|false] Process only the largest fragment\n\of input structure (default: false);-o, --lfout=[true|false] Return only the largest fragment of\nthe result (default: false);-s, --keepsingleatom=[true|false] Return a single atom for non-empty\nacyclic input structures (default: true);-f, --format=<output format> (default: smiles)\
	$cxcalc bemismurcko test.mol

bemismurckoatomcount=$BemisMurckoPlugin\
	$BemisMurckoPlugin.jar\
	$-\
	$t=type:atomcount;i=lfin:false;o=lfout:false;s=keepsingleatom:true\
	$BEMISMURCKO_ATOM_COUNT\
	$Calculates the number of atoms in the Bemis-Murcko framework\
	$-i, --lfin=[true|false] Process only the largest fragment\n\of input structure (default: false);-o, --lfout=[true|false] Return only the largest fragment of\nthe result (default: false);-s, --keepsingleatom=[true|false] Return a single atom for non-empty\nacyclic input structures (default: true)\
	$cxcalc bemismurckoatomcount test.mol

bemismurckobondcount=$BemisMurckoPlugin\
	$BemisMurckoPlugin.jar\
	$-\
	$t=type:bondcount;i=lfin:false;o=lfout:false;s=keepsingleatom:true\
	$BEMISMURCKO_BOND_COUNT\
	$Calculates the number of bonds in the Bemis-Murcko framework\
	$-i, --lfin=[true|false] Process only the largest fragment\n\of input structure (default: false);-o, --lfout=[true|false] Return only the largest fragment of\nthe result (default: false);-s, --keepsingleatom=[true|false] Return a single atom for non-empty\nacyclic input structures (default: true)\
	$cxcalc bemismurckobondcount test.mol

