Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv19863
Modified Files:
refmac.info
Added Files:
refmac.patch
Log Message:
refmac revision to permit building of makecif program
--- NEW FILE: refmac.patch ---
diff -ruN refmac-orig/make_unix.f refmac/make_unix.f
--- refmac-orig/make_unix.f 2006-11-23 19:29:38.000000000 -0800
+++ refmac/make_unix.f 2006-11-23 19:30:03.000000000 -0800
@@ -98,16 +98,16 @@
CMS IH(1)=I100H/2
CDP
- CALL ITIME(ID)
+C CALL ITIME(ID)
IH(4)=ID(1)
IH(3)=ID(2)
IH(2)=ID(3)
- CALL IDATE(IMON,IDAY,IYR)
- IF(IYR.GE.99) THEN
- IYR=IYR+1900
- ELSE
- IYR=IYR+2000
- ENDIF
+C CALL IDATE(IMON,IDAY,IYR)
+C IF(IYR.GE.99) THEN
+C IYR=IYR+1900
+C ELSE
+C IYR=IYR+2000
+C ENDIF
IH(5)=IDAY
IH(6)=IMON
IH(7)=IYR
diff -ruN refmac-orig/makefile refmac/makefile
--- refmac-orig/makefile 2006-11-23 19:29:38.000000000 -0800
+++ refmac/makefile 2006-11-23 19:34:38.000000000 -0800
@@ -1,305 +1,155 @@
-
-#--------------------------------------------------------------------------------
-
-i386-linux = linux
-alpha = alpha
-iris4d = sgin
-sun4 = sun
-
-u = $($(HOSTTYPE))
-
-#--------------------------------------------------------------------------------
-
-refmac = refmac_$(u)_5
-libcheck = libcheck_$(u)_5
-
-tar = $(refmac).tar
-
-#--------------------------------------------------------------------------------
-
-f_alpha = f77 -O2 -fpe0 -assume dummy_aliases -non_shared -check overflow
-check bounds
-f_linux = g77 -O1 -fno-second-underscore -fno-globals -fno-automatic
-unroll-loops -static
-f_sgin = f77 -O1 -n32 -OPT:Olimit=7000 -nocpp -w -c
-f_sun = /opt/SUNWspro/bin/f77 -xlang=f77 -ftrap=%none -Xlist -xcheck=%all -O3
-w -KPIC -fpover=yes
-f = $(f_$(u))
-
-#--------------------------------------------------------------------------------
-
-s_alpha = ALPHA
-s_linux = LINUX
-s_sgin = SGIn32
-s_sun = SunOS
-s = $(s_$(u))
-
-l = $(CLIB)/
-
-t = tmp_$(u)/
-
-SUBR = \
-$(t)refmac_newdic.o \
-$(t)solvent_contr_mask.o \
-$(t)hkon_secder_tch.o \
-$(t)fast_hessian_tabulation.o \
-$(t)subvag.o \
-$(t)lsq_symm_atoms.o \
-$(t)oppro_tor1.o \
-$(t)rcard_tor1.o \
-$(t)subcf_scale1.o \
-$(t)subag_scale_hessian.o \
-$(t)extra_eigen.o \
-$(t)rigid_body_newdic.o \
-$(t)aniso_ref_eigen.o \
-$(t)linalgebra.o \
-$(t)make_CIF.o \
-$(t)make_subr.o \
-$(t)make_subr_refmac.o \
-$(t)tls_newdic_non.o \
-$(t)vdw_symmetry.o \
-$(t)make_lib.o \
-$(t)make_crd.o \
-$(t)make_new.o \
-$(t)make_rst.o \
-$(t)make_PDB.o \
-$(t)makecif.o \
-$(t)make_refmac_dummy.o \
-$(t)ls_scaling_double.o \
-$(t)interpolate_mod.o \
-$(t)rharvest.o \
-$(t)newentry_idealise.o \
-$(t)ml_scaling_double.o \
-$(t)ncs_const.o \
-$(t)gaussian_int.o \
-$(t)subnumrec.o
-
-LIBR = \
-$(SUBR) \
-$(l)libccp4f.a \
-$(l)libccp4c.a \
-$(l)libccif.a
-
-SUBL = \
-$(t)main_libcheck.o \
-$(t)make_subr_2.o \
-$(t)make_subr.o \
-$(t)make_lib.o \
-$(t)libcheck.o \
-$(t)make_PDB.o \
-$(t)make_CIF.o \
-$(t)make_new.o \
-$(t)make_crd.o \
-$(t)make_unix_ccp4.o \
-$(t)emin.o \
-$(t)libcheck_min.o
-
-LIBL = \
-$(SUBL) \
-$(l)libccp4f.a \
-$(l)libccp4c.a
-
-#--------------------------------------------------------------------------------
-
-ed = echo 'g/^CMDW-4.2/s// /@[EMAIL PROTECTED]@' | tr "@" "\012" | ed -s
-
-#--------------------------------------------------------------------------------
-
-all: $(refmac) $(libcheck)
-
-gz: $(tar).gz
-
-$(tar).gz: $(refmac) $(libcheck)
- tar -cvf $(tar) $(refmac) $(libcheck)
- gzip --best $(tar)
-
-$(refmac): $(t) $(LIBR)
- $(f) -o $(refmac) $(LIBR)
-
-$(libcheck): $(t) $(LIBL)
- $(f) -o $(libcheck) $(LIBL)
-
-$(t):
- mkdir $(t)
-
-#--------------------------------------------------------------------------------
-
-clean:
- /bin/rm -f $(SUBR) $(SUBL) oppro_tor1.f
rcard_tor1.f
-
-cleanall:
- /bin/rm -f $(SUBR) $(SUBL) $(refmac)
$(libcheck) $(tar) $(tar).gz
-
-vars:
- echo ' ' ; echo u ; echo $(u)
- echo ' ' ; echo refmac ; echo $(refmac)
- echo ' ' ; echo libcheck ; echo $(libcheck)
- echo ' ' ; echo f ; echo $(f)
- echo ' ' ; echo l ; echo $(l)
- echo ' ' ; echo s ; echo $(s)
- echo ' ' ; echo t ; echo $(t)
- echo ' ' ; echo SUBR ; echo $(SUBR)
- echo ' ' ; echo LIBR ; echo $(LIBR)
- echo ' ' ; echo SUBL ; echo $(SUBL)
- echo ' ' ; echo LIBL ; echo $(LIBL)
-
-#--------------------------------------------------------------------------------
-
-$(t)aniso_ref_eigen.o: aniso_ref_eigen.f atom_com.fh celsym_aniso.fh
celsym.fh const.fh pls_incl.fh refi_flags.fh vitals.fh
- $(f) -o $(t)aniso_ref_eigen.o \
- -c aniso_ref_eigen.f
-
-$(t)emin.o: emin.f atom_com.fh atom_com_str.fh crd_com.fh
emin_version.fh ener_com.fh ref_com.fh ref_com_str.fh rstr_com.fh
- $(f) -o $(t)emin.o \
- -c emin.f
-
-$(t)extra_eigen.o: extra_eigen.f agreem.fh atom_com.fh
celsym_aniso.fh celsym.fh const.fh expcost.fh files.fh gaussian.fh
refi_flags.fh vitals.fh
- $(f) -o $(t)extra_eigen.o \
- -c extra_eigen.f
-
-$(t)fast_hessian_tabulation.o: fast_hessian_tabulation.f atom_com.fh
celsym_aniso.fh celsym.fh hessian_impl.fh pls_incl.fh vitals.fh weights.fh
- $(f) -o $(t)fast_hessian_tabulation.o \
- -c fast_hessian_tabulation.f
-
-$(t)gaussian_int.o: gaussian_int.f
- $(f) -o $(t)gaussian_int.o \
- -c gaussian_int.f
-
-$(t)hkon_secder_tch.o: hkon_secder_tch.f agreem.fh atom_com.fh
celsym_aniso.fh celsym.fh cif_incl.fh const.fh hessian_impl.fh monitor.fh
ncs_rest.fh occupancy_params.fh pls_incl.fh refi_flags.fh restr_files.fh
rharvest.fh save_all_params.fh solvent.fh tls.fh vitals.fh weights.fh
- $(f) -o $(t)hkon_secder_tch.o \
- -c hkon_secder_tch.f
-
-$(t)interpolate_mod.o: interpolate_mod.f
- $(f) -o $(t)interpolate_mod.o \
- -c interpolate_mod.f
-
-$(t)libcheck_min.o: libcheck_min.f atom_com.fh atom_com_str.fh
crd_com.fh ener_com.fh lib_com.fh ref_com.fh ref_com_str.fh rstr_com.fh
- $(f) -o $(t)libcheck_min.o \
- -c libcheck_min.f
-
-$(t)libcheck.o: libcheck.f atom_com.fh crd_com.fh
libcheck_version.fh lib_com.fh
- $(f) -o $(t)libcheck.o \
- -c libcheck.f
-
-$(t)linalgebra.o: linalgebra.f atom_com.fh pls_incl.fh
- $(f) -o $(t)linalgebra.o \
- -c linalgebra.f
-
-$(t)lsq_symm_atoms.o: lsq_symm_atoms.f atom_com.fh celsym_aniso.fh
celsym.fh cif_incl.fh const.fh monitor.fh ncs_rest.fh pls_incl.fh refi_flags.fh
restr_files.fh rharvest.fh vitals.fh weights.fh
- $(f) -o $(t)lsq_symm_atoms.o \
- -c lsq_symm_atoms.f
-
-$(t)ls_scaling_double.o: ls_scaling_double.f agreem.fh celsym_aniso.fh
celsym.fh const.fh monitor.fh refi_flags.fh weights.fh
- $(f) -o $(t)ls_scaling_double.o \
- -c ls_scaling_double.f
-
-$(t)main_libcheck.o: main_libcheck.f libcheck_version.fh
- $(f) -o $(t)main_libcheck.o \
- -c main_libcheck.f
-
-$(t)makecif.o: makecif.f crd_com.fh lib_com.fh
makecif_version.fh
- $(f) -o $(t)makecif.o \
- -c makecif.f
-
-$(t)make_CIF.o: make_CIF.f atom_com.fh atom_com_str.fh
CIF_items_crd.fh crd_com.fh metal.fh
- $(f) -o $(t)make_CIF.o \
- -c make_CIF.f
-
-$(t)make_crd.o: make_crd.f atom_com.fh crd_com.fh lib_com.fh
link_com.fh metal.fh
- $(f) -o $(t)make_crd.o \
- -c make_crd.f
-
-$(t)make_lib.o: make_lib.f CIF_items_lib.fh crd_com.fh
lib_com.fh
- $(f) -o $(t)make_lib.o \
- -c make_lib.f
-
-$(t)make_new.o: make_new.f atom_com.fh CIF_items_crd.fh
crd_com.fh lib_com.fh metal.fh
- $(f) -o $(t)make_new.o \
- -c make_new.f
-
-$(t)make_PDB.o: make_PDB.f atom_com.fh crd_com.fh link_com.fh
metal.fh
- $(f) -o $(t)make_PDB.o \
- -c make_PDB.f
-
-$(t)make_refmac_dummy.o: make_refmac_dummy.f agreem.fh atom_com.fh
const.fh makecif.fh makecif_version.fh ncs_rest.fh refi_flags.fh rharvest.fh
solvent.fh tls.fh vitals.fh weights.fh
- $(f) -o $(t)make_refmac_dummy.o \
- -c make_refmac_dummy.f
-
-$(t)make_rst.o: make_rst.f atom_com.fh atom_com_str.fh
crd_com.fh lib_com.fh
- $(f) -o $(t)make_rst.o \
- -c make_rst.f
-
-$(t)make_subr_2.o: make_subr_2.f atom_com.fh crd_com.fh
- $(f) -o $(t)make_subr_2.o \
- -c make_subr_2.f
-
-$(t)make_subr.o: make_subr.f atom_com.fh crd_com.fh metal.fh
- $(f) -o $(t)make_subr.o \
- -c make_subr.f
-
-$(t)make_subr_refmac.o: make_subr_refmac.f
- $(f) -o $(t)make_subr_refmac.o \
- -c make_subr_refmac.f
-
-$(t)make_unix_ccp4.o: make_unix_ccp4.f
- $(f) -o $(t)make_unix_ccp4.o \
- -c make_unix_ccp4.f
-
-$(t)ml_scaling_double.o: ml_scaling_double.f agreem.fh celsym.fh
const.fh expcost.fh monitor.fh refi_flags.fh rharvest.fh weights.fh
- $(f) -o $(t)ml_scaling_double.o \
- -c ml_scaling_double.f
-
-$(t)ncs_const.o: ncs_const.f atom_com.fh const.fh monitor.fh
ncs_rest.fh pls_incl.fh restr_files.fh rharvest.fh vitals.fh weights.fh
- $(f) -o $(t)ncs_const.o \
- -c ncs_const.f
-
-$(t)newentry_idealise.o: newentry_idealise.f agreem.fh atom_com.fh
celsym.fh const.fh makecif.fh pls_incl.fh refi_flags.fh tls.fh vitals.fh
weights.fh
- $(f) -o $(t)newentry_idealise.o \
- -c newentry_idealise.f
-
-$(t)oppro_tor1.o: oppro_tor1.f agreem.fh atom_com.fh
atom_com_str.fh celsym.fh const.fh crd_com.fh expcost.fh makecif.fh
map_params.fh monitor.fh ncs_rest.fh pls_incl.fh ref_com_str.fh refi_flags.fh
restr_files.fh restr_params.fh weights.fh
- $(f) -o $(t)oppro_tor1.o \
- -c oppro_tor1.f
-
-$(t)rcard_tor1.o: rcard_tor1.f agreem.fh atom_com.fh celsym.fh
cif_incl.fh const.fh expcost.fh makecif.fh map_params.fh monitor.fh ncs_rest.fh
occupancy_params.fh pls_incl.fh refi_flags.fh restr_files.fh restr_params.fh
rharvest.fh rigid_body.fh solvent.fh tls.fh vitals.fh weights.fh
- $(f) -o $(t)rcard_tor1.o \
- -c rcard_tor1.f
-
-$(t)refmac_newdic.o: refmac_newdic.f agreem.fh atom_com.fh
celsym_aniso.fh celsym.fh cif_incl.fh const.fh expcost.fh makecif.fh
makecif_version.fh monitor.fh pls_incl.fh refi_flags.fh restr_files.fh
rharvest.fh vitals.fh weights.fh
- $(f) -o $(t)refmac_newdic.o \
- -c refmac_newdic.f
-
-$(t)rharvest.o: rharvest.f agreem.fh atom_com.fh celsym.fh
const.fh makecif.fh makecif_version.fh ncs_rest.fh pls_incl.fh refi_flags.fh
rharvest.fh solvent.fh tls.fh weights.fh
- $(f) -o $(t)rharvest.o \
- -c rharvest.f
-
-$(t)rigid_body_newdic.o: rigid_body_newdic.f agreem.fh atom_com.fh
celsym.fh const.fh monitor.fh pls_incl.fh refi_flags.fh restr_files.fh
rigid_body.fh vitals.fh
- $(f) -o $(t)rigid_body_newdic.o \
- -c rigid_body_newdic.f
-
-$(t)solvent_contr_mask.o: solvent_contr_mask.f agreem.fh atom_com.fh
atom_com_str.fh celsym_aniso.fh celsym.fh const.fh monitor.fh pls_incl.fh
refi_flags.fh rharvest.fh solvent.fh vitals.fh weights.fh
- $(f) -o $(t)solvent_contr_mask.o \
- -c solvent_contr_mask.f
-
-$(t)subag_scale_hessian.o: subag_scale_hessian.f agreem.fh atom_com.fh
celsym_aniso.fh celsym.fh const.fh monitor.fh pls_incl.fh refi_flags.fh
rharvest.fh solvent.fh tls.fh vitals.fh weights.fh
- $(f) -o $(t)subag_scale_hessian.o \
- -c subag_scale_hessian.f
-
-$(t)subcf_scale1.o: subcf_scale1.f agreem.fh atom_com.fh
celsym.fh const.fh gaussian.fh pls_incl.fh refi_flags.fh rharvest.fh vitals.fh
weights.fh
- $(f) -o $(t)subcf_scale1.o \
- -c subcf_scale1.f
-
-$(t)subvag.o: subvag.f celsym.fh const.fh
- $(f) -o $(t)subvag.o \
- -c subvag.f
-
-$(t)tls_newdic_non.o: tls_newdic_non.f agreem.fh atom_com.fh
celsym_aniso.fh celsym.fh const.fh monitor.fh pls_incl.fh refi_flags.fh
restr_files.fh save_all_params.fh tls.fh vitals.fh weights.fh
- $(f) -o $(t)tls_newdic_non.o \
- -c tls_newdic_non.f
-
-$(t)vdw_symmetry.o: vdw_symmetry.f atom_com.fh atom_com_str.fh
celsym.fh pls_incl.fh restr_files.fh vitals.fh weights.fh
- $(f) -o $(t)vdw_symmetry.o \
- -c vdw_symmetry.f
-
-$(t)subnumrec.o: subnumrec.f
- $(f) -o $(t)subnumrec.o \
- -c subnumrec.f
-#--------------------------------------------------------------------------------
-
+VERSION = 5.3.0021
+FC = gfortran
+FOPTIM = -O3
+COPTIM = -O
+XFFLAGS = -fno-second-underscore
+
+XCFLAGS = -DGFORTRAN -DPROTOTYPE
+FFLAGS = $(FOPTIM) $(XFFLAGS)
+CFLAGS = $(COPTIM) $(XCFLAGS)
+
+LLIBCIF = $(CLIB)/libccif.a
+LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a
+
+
+
+SUBR = \
+refmac_newdic.o \
+solvent_contr_mask.o \
+hkon_secder_tch.o \
+fast_hessian_tabulation.o \
+subvag.o \
+lsq_symm_atoms.o \
+oppro_tor1.o \
+rcard_tor1.o \
+subcf_scale1.o \
+subag_scale_hessian.o \
+extra_eigen.o \
+rigid_body_newdic.o \
+aniso_ref_eigen.o \
+linalgebra.o \
+make_CIF.o \
+make_subr.o \
+make_subr_refmac.o \
+tls_newdic_non.o \
+vdw_symmetry.o \
+make_lib11.o \
+make_lib12.o \
+make_lib2.o \
+make_crd1.o \
+make_crd2.o \
+make_new1.o \
+make_new2.o \
+set_num.o \
+make_rst1.o \
+make_rst2.o \
+make_PDB.o \
+makecif.o \
+make_refmac_dummy.o \
+ls_scaling_double.o \
+interpolate_mod.o \
+rharvest.o \
+newentry_idealise.o \
+ml_scaling_double.o \
+ncs_const.o \
+gaussian_int.o \
+subnumrec.o \
+read_extra_restraints.o \
+inout_routines.o \
+ncs_rest.o \
+occupancy_only_refine.o \
+iheap_sort.o \
+$(LLIBCCP) \
+$(LLIBCIF)
+
+SUBL = \
+main_libcheck.o \
+make_subr_2.o \
+make_subr.o \
+make_lib11.o \
+make_lib12.o \
+make_lib2.o \
+make_crd1.o \
+make_crd2.o \
+libcheck.o \
+make_PDB.o \
+make_CIF.o \
+make_new1.o \
+make_new2.o \
+set_num.o \
+make_unix_ccp4.o \
+emin.o \
+libcheck_min.o \
+mol2_file.o \
+sdf_files.o \
+$(LLIBCCP)
+
+SUBM = \
+main_makecif.o \
+make_CIF.o \
+make_subr.o \
+make_subr_2.o \
+make_lib11.o \
+make_lib12.o \
+make_lib2.o \
+make_crd1.o \
+make_crd2.o \
+make_new1.o \
+make_new2.o \
+set_num.o \
+make_rst1.o \
+make_rst2.o \
+make_PDB.o \
+makecif.o \
+make_vdw.o \
+make_unix.o \
+$(LLIBCCP) \
+$(LLIBCIF)
+
+
+SUBT = \
+tlsgroups.o \
+make_CIF.o \
+make_subr.o \
+make_subr_refmac.o \
+make_lib11.o \
+make_lib12.o \
+make_lib2.o \
+make_crd1.o \
+make_crd2.o \
+make_new1.o \
+make_new2.o \
+set_num.o \
+make_rst1.o \
+make_rst2.o \
+make_PDB.o \
+makecif.o \
+make_unix_ccp4.o \
+make_refmac_dummy.o \
+inout_routines.o \
+subnumrec.o \
+linalgebra.o \
+$(LLIBCCP) \
+$(LLIBCIF)
+#--------------------------------------------------------------------------------
+
+ed = echo 'g/^CMDW-5.0/s// /@[EMAIL PROTECTED]@' | tr "@" "\012" | ed -s
+
+#--------------------------------------------------------------------------------
+
+all: refmac libcheck makecif tlsgroups
+
+refmac: $(SUBR)
+ $(FC) $(FFLAGS) -o refmac${VERSION} $(SUBR)
+
+libcheck: $(SUBL)
+ $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
+
+makecif: $(SUBM)
+ $(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM)
+tlsgroups: $(SUBT)
+ $(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT)
+
+clean:
+ /bin/rm *.o
+
Index: refmac.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- refmac.info 22 Nov 2006 14:21:22 -0000 1.5
+++ refmac.info 24 Nov 2006 04:12:16 -0000 1.6
@@ -1,6 +1,6 @@
Package: refmac
Version: 5.3.0021
-Revision: 2
+Revision: 3
Source: http://www.ysbl.york.ac.uk/refmac/data/refmac5.3_source.tar.gz
Source-MD5: 378a4963ce5eb00d931483a327807e67
SourceRename: %n-%v.tar.gz
@@ -11,15 +11,11 @@
BuildDepends: ccp4-dev (>= 6.0.2-1) | ccp4-g77-dev, gcc4, ccp4 (>= 6.0.2-1) |
ccp4-g77
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
-#Patch: refmac.patch
+Patch: refmac.patch
CompileScript: <<
#!/bin/bash -efv
source %p/bin/init.sh
-touch makefile
-rm -f makefile
-cp makefile_gfortran Makefile
-perl -pi -e 's|5.3.0014|%v|g' Makefile
-make refmac libcheck tlsgroups
+make
<<
InstallScript: <<
#!/bin/bash -efv
@@ -27,12 +23,17 @@
cp refmac%v %i/share/xtal/ccp4-6.0.2/bin/.
cp libcheck%v %i/share/xtal/ccp4-6.0.2/bin/.
cp tlsgroups%v %i/share/xtal/ccp4-6.0.2/bin/.
+cp makecif%v %i/share/xtal/ccp4-6.0.2/bin/.
#
mkdir -p %i/share/xtal/ccp4-6.0.2/refmac_%v_monomers
cp -R dic %i/share/xtal/ccp4-6.0.2/refmac_%v_monomers/.
#
mkdir -p %i/bin
ln -s %p/share/xtal/ccp4-6.0.2/bin/refmac%v %i/bin/refmac5
+ln -s %p/share/xtal/ccp4-6.0.2/bin/refmac%v %i/bin/refmac
+ln -s %p/share/xtal/ccp4-6.0.2/bin/libcheck%v %i/bin/libcheck
+ln -s %p/share/xtal/ccp4-6.0.2/bin/tlsgroups%v %i/bin/tlsgroups
+ln -s %p/share/xtal/ccp4-6.0.2/bin/makecif%v %i/bin/makecif
<<
RunTimeVars: CLIBD_MON: %p/share/xtal/ccp4-6.0.2/refmac_%v_monomers/dic/
Description: CCP4 refmac5 update
@@ -40,7 +41,8 @@
This is a drop-in update replacement for refmac5. As long as you have
sourced %p/bin/init.(c)sh and %p is at the head of your path, no further
configuration is required. Binaries for the programs refmac libcheck
-and tlsgroupsreside in $CBIN with %v suffix.
+makecif and tlsgroups reside in $CBIN with %v suffix and are symbolically
+linked to suffixless commands in %p/bin.
<<
License: Restrictive
Homepage: http://www.ysbl.york.ac.uk/refmac
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