##### HYDROPHOBIC
# PROTEIN
# hfprot =  all S or C that are not conneced with polar atoms
define hfa  ala.cb
define hfr  arg.cb, arg.cg
define hfnd asn.cb, asp.cb 
define hfc  cys.cb, cys.sg
define hfqe gln.cb, gln.cg, glu.cb, glu.cg
define hfh  his.cb 
define hfi  ile.cb, ile.cg1, ile.cg2, ile.cd1 
define hfl  leu.cb, leu.cg, leu.cd1, leu.cd2 
define hfk lys.cb, lys.cg, lys.cd
define hfm  met.cb, met.cg, met.sd, met.ce
define hff  phe.cb, phe.cg, phe.cd2, phe.ce2, phe.cz, phe.ce1, phe.cd1
define hfp  pro.cb, pro.cg
define hft  thr.cg2
define hfw  trp.cb, trp.cg, trp.cd2, trp.ce3, trp.cz3, trp.ch2, trp.cz2
define hfy  tyr.cb, tyr.cg, tyr.cd2, tyr.ce2, tyr.ce1, tyr.cd1
define hfv  val.cb, val.cg1, val.cg2


define hfailmv hfa, hfi, hfl, hfv, hfm
define hfrk    hfr, hfk
define hfndqe  hfnd, hfqe
define hffywh  hff, hfy, hfw, hfh
define hfcp    hfc, hfp 

define hfprot  hfailmv, hfrk, hfndqe, hffywh, hfcp    


# DNA
define hfmjg t.c5m,t.c6,c.c5,c.c6,g.c5,g.c8,a.c5,a.c8
define hfall  hfprot,hfmjg

##### HBONDS
# PROTEIN

define hbnegative asp.od1, asp.od2, glu.oe1, glu.oe2
define hbpositive arg.ne, arg.nh1, arg.nh2, lys.nz
define haprot  hbnegative, asn.od1, gln.oe1, *.o 
define hdprot hbpositive, asn.nd2, gln.ne2, trp.ne1, cys.sg, *.n 
define hbdaprot ser.og, thr.og1, tyr.oh, his.nd1, his.ne2

define hbprot hdprot,haprot,hdaprot

#define hdprot *.n,arg.ne, arg.nh1, arg.nh2,  asn.nd2,cys.sg,gln.ne2,trp.ne1,tyr.oh,lys.nz
#define haprot *.o,asn.od1,gln.oe1
#define hdaprot arg.nh1,arg.nh2,asp.od1,asp.od2,glu.oe1,glu.oe2,his.nd1,his.ne2,ser.og,thr.og1


# DNA
define hdmjg  c.n4,a.n6
define hamjg  t.o4,g.o6,g.n7,a.n7
define hdmig  g.n2
define hamig  a.n3,g.n3,c.o2,t.o2
define hadnabb *.o1p,*.o2p
define hddna hdmjg,hdmig
define hadna hamjg,hamig,hadnabb
define hbdna hddna, hadna
#
define hbmjg hdmjg,hamjg
define hbmig hdmig,hamig
define hbdnabb hadnabb

define hdall hdprot,hdaprot,hddna
define haall haprot,hdaprot,hadna
define hball hdall,haall