m.dx: m.in m.pqr
	apbs $<

t.dx: t.in t.pqr
	apbs $<

m-outer.dx: m-outer.in m.pqr
	apbs $<

t-outer.dx: t-outer.in t.pqr
	apbs $<

t-atoms.xml: t.pqr
	cat $< | pqr2xml > $@

m-atoms.xml: m.pqr
	cat $< | pqr2xml > $@

t-m-rxn-pairs.xml: t-atoms.xml m-atoms.xml protein-protein-contacts.xml
	make_rxn_pairs -nonred -mol0 t-atoms.xml -mol1 m-atoms.xml -ctypes protein-protein-contacts.xml -dist 5.5 > $@

t-m-rxns.xml: t-m-rxn-pairs.xml
	make_rxn_file -pairs $< -distance 4.9 -nneeded 3 > $@

protein-protein-contacts.xml: protein-protein-contacts.xml.bak
	cp $< $@

input.xml: input.xml.bak
	cp $< $@


all: protein-protein-contacts.xml t-atoms.xml m-atoms.xml t-m-rxns.xml m.dx t.dx input.xml

clean: 
	rm -f *.dx *.xml io.mc