#################################
# Assume MOLNAME and PH are defined
# as environment variables 

all: clean pkout collected cleanup

# various executables and flags

clean: $(MOLNAME).clean

%.clean: %.pdb
	$(CLEAN_PATH)/clean.sh $* | tee -a master_warning_log 

pqr: $(MOLNAME).pqr

#right now, clean and pqr are all one block, to be separated soon
%.pqr: %.clean
	cp $*.clean $*.keepclean
	$(PDB_TO_PQR_PATH)/pdb2pqr.sh $* | tee -a master_warning_log

cleanpqr: $(MOLNAME).cleanpqr

%.cleanpqr: %.pqr
	# to stop execution of this step if pqr file not created (tee seems to hide exit code)
	cp $*.pqr temp.pqr
	rm temp.pqr
	$(PQR_CLEAN_PATH)/cleanpqr.sh $* | tee -a master_warning_log

pkout: $(MOLNAME).pkout

#likewise, MEAD and split are all one block, to be separated soon
%.pkout: %.cleanpqr
	cp $*.cleanpqr $*.pqr
	cp $*.cleanpqr $*.keeppqr
	$(COMPLETION_BIN_PATH)/pqr2pkout.sh $* $(PH) | tee -a master_warning_log
	#make clean >& /dev/null

collected: $(MOLNAME).collected

%.collected: %.pkout
	cp $*.pkout $*.keeppkout
	rm *.potat #remove potat files ~50% of hd usage
	$(COLLECT_PATH)/collect.sh $*   | tee -a master_warning_log
	touch $*.collected
	rm split* # clutter up the directory
cleanup:
	-rm -rf split*
	-rm -f tmp.*
	-rm -f leap.log
	-rm -f hipped.tmp
	-rm -f clean.tmp
	-rm -f tleap.err
	-rm -f res_no.tmp
	-rm -f *.g
	-rm -f *.pk_used
	-rm -f *.pkint
	-rm -f *.potat
	-rm -f *.out
	-rm -f *.st
	-rm -f *.dat
	-rm -f *.script