add_subdirectory(source/lib/xdrf)
-add_subdirectory(source/unres/src_MD)
+#add_subdirectory(source/unres/src_MD)
if(UNRES_WITH_MPI)
- add_subdirectory(source/unres/src_MD-M)
- add_subdirectory(source/unres/src_MD_DFA)
+# add_subdirectory(source/unres/src_MD-M)
+# add_subdirectory(source/unres/src_MD_DFA)
add_subdirectory(source/unres/src_CSA)
- add_subdirectory(source/unres/src_CSA_DiL)
- add_subdirectory(source/wham/src)
- add_subdirectory(source/wham/src-M)
- add_subdirectory(source/cluster/wham/src)
- add_subdirectory(source/cluster/wham/src-M)
+# add_subdirectory(source/unres/src_CSA_DiL)
+# add_subdirectory(source/wham/src)
+# add_subdirectory(source/wham/src-M)
+# add_subdirectory(source/cluster/wham/src)
+# add_subdirectory(source/cluster/wham/src-M)
endif(UNRES_WITH_MPI)
-add_subdirectory(source/unres/src_MIN)
+#add_subdirectory(source/unres/src_MIN)
add_subdirectory(source/cluster/unres/src)
-add_subdirectory(source/xdrfpdb/src)
+#add_subdirectory(source/xdrfpdb/src)
add_subdirectory(source/xdrfpdb/src-M)
-add_subdirectory(source/maxlik/src_CSA)
-add_subdirectory(source/unres-dock)
+#add_subdirectory(source/maxlik/src_CSA)
+#add_subdirectory(source/unres-dock)
#
# 9/23/2010 A. Liwo
#
-# CMake file by D. Jagieła
+# CMake file by D. Jagie?a
#
set(UNRES_XDRF_XDRF2PDB_SRC-M
#=========================================
add_executable(UNRES_XDRF2PDB_BIN-M ${UNRES_XDRF_XDRF2PDB_SRC-M} )
target_link_libraries(UNRES_XDRF2PDB_BIN-M xdrf )
-set_target_properties(UNRES_XDRF2PDB_BIN-M PROPERTIES OUTPUT_NAME xdrf-M2pdb )
+set_target_properties(UNRES_XDRF2PDB_BIN-M PROPERTIES OUTPUT_NAME xdrf2pdb )
set_property(TARGET UNRES_XDRF2PDB_BIN-M PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
add_executable(UNRES_XDRF2PDBM_BIN-M ${UNRES_XDRF_XDRF2PDB-M_SRC-M} )
target_link_libraries( UNRES_XDRF2PDBM_BIN-M xdrf )
-set_target_properties(UNRES_XDRF2PDBM_BIN-M PROPERTIES OUTPUT_NAME xdrf-M2pdb-m )
+set_target_properties(UNRES_XDRF2PDBM_BIN-M PROPERTIES OUTPUT_NAME xdrf2pdb-m )
set_property(TARGET UNRES_XDRF2PDBM_BIN-M PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin )
install(TARGETS UNRES_XDRF2PDB_BIN-M DESTINATION ${CMAKE_INSTALL_PREFIX}/xdrfpdb)
install(TARGETS UNRES_XDRF2PDBM_BIN-M DESTINATION ${CMAKE_INSTALL_PREFIX}/xdrfpdb)
+
+#=========================================
+# TESTS
+#=========================================
+
+
+# Create files needed for tests
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/ala10one.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/ala10three.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Yone.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Ythree.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/ala10MD.cx
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Y_MREMD_MD000.cx
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+
+# Test xdrf2pdb
+add_test(NAME XDRF2PDB-one COMMAND ${CMAKE_BINARY_DIR}/bin/xdrf2pdb one ala10one.seq ala10MD.cx )
+add_test(NAME XDRF2PDB-three COMMAND ${CMAKE_BINARY_DIR}/bin/xdrf2pdb three ala10three.seq ala10MD.cx )
+
+# Test xdrf2pdb-m
+add_test(NAME XDRF2PDB-M-one COMMAND ${CMAKE_BINARY_DIR}/bin/xdrf2pdb-m one 1L2Yone.seq 1L2Y_MREMD_MD000.cx 32 30 )
+add_test(NAME XDRF2PDB-M-three COMMAND ${CMAKE_BINARY_DIR}/bin/xdrf2pdb-m three 1L2Ythree.seq 1L2Y_MREMD_MD000.cx 32 30 )
+
+# Test xdrf2ang
+#add_test(NAME XDRF2ANG-one COMMAND ${CMAKE_BINARY_DIR}/bin/xdrf2ang one ala10one.seq ala10MD.cx )
+#add_test(NAME XDRF2ANG-three COMMAND ${CMAKE_BINARY_DIR}/bin/xdrf2ang three ala10three.seq ala10MD.cx )
+
+
+
c include 'COMMON.DISTFIT'
c include 'COMMON.MD'
character*50 tytul
- character*1 chainid(10) /'A','B','C','D','E','F','G','H','I','J'/
+ character*1 chainid(26) /'A','B','C','D','E','F','G','H','I','J',
+ & 'K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'/
dimension ica(maxres)
write (iunit,'(3a,1pe15.5)') 'REMARK ',tytul,' ENERGY ',etot
cmodel write (iunit,'(a5,i6)') 'MODEL',1
iatom=iatom+1
ica(i)=iatom
iti=itype(i)
- if (iti.eq.21) then
+ if (iti.eq.ntyp1) then
ichain=ichain+1
ires=0
write (iunit,'(a)') 'TER'
ires=ires+1
iatom=iatom+1
ica(i)=iatom
- write (iunit,10) iatom,restyp(iti),chainid(ichain),
+ write (iunit,10) iatom,restyp(iti),chainid(1+mod(ichain/2,26)),
& ires,(c(j,i),j=1,3)!,vtot(i)
if (iti.ne.10) then
iatom=iatom+1
- write (iunit,20) iatom,restyp(iti),chainid(ichain),
- & ires,(c(j,nres+i),j=1,3)!,
+ write (iunit,20) iatom,restyp(iti),
+ & chainid(1+mod(ichain/2,26)),ires,(c(j,nres+i),j=1,3)
+!,
! & vtot(i+nres)
endif
endif
enddo
write (iunit,'(a)') 'TER'
do i=nnt,nct-1
- if (itype(i).eq.21) cycle
- if (itype(i).eq.10 .and. itype(i+1).ne.21) then
+ if (itype(i).eq.ntyp1) cycle
+ if (itype(i).eq.10 .and. itype(i+1).ne.ntyp1) then
write (iunit,30) ica(i),ica(i+1)
- else if (itype(i).ne.10 .and. itype(i+1).ne.21) then
+ else if (itype(i).ne.10 .and. itype(i+1).ne.ntyp1) then
write (iunit,30) ica(i),ica(i+1),ica(i)+1
- else if (itype(i).ne.10 .and. itype(i+1).eq.21) then
+ else if (itype(i).ne.10 .and. itype(i+1).eq.ntyp1) then
write (iunit,30) ica(i),ica(i)+1
endif
enddo
c print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
open(9,file=pdbfile)
nnt = 1
- if (itype(1).eq.21) nnt = 2
+ if (itype(1).eq.ntyp1) nnt = 2
nct=nres
- if (itype(nres).eq.21) nct = nres-1
+ if (itype(nres).eq.ntyp1) nct = nres-1
print *,"nnt",nnt," nct",nct
call xdrfopen(ixdrf,arg, "r", iret)
kk = 0
kk = kk + 1
call xdrffloat(ixdrf, potE, iret)
call xdrffloat(ixdrf, uconst, iret)
-#ifdef NEWUNRES
- call xdrffloat(ixdrf, uconst_back, iret)
-#endif
+c#ifdef NEWUNRES
+c call xdrffloat(ixdrf, uconst_back, iret)
+c#endif
call xdrffloat(ixdrf, t_bath, iret)
call xdrfint(ixdrf, nss, iret)
do j=1,nss
call xdrfint(ixdrf, jhpb(j), iret)
enddo
call xdrfint(ixdrf, nfrag, iret)
+ call xdrfint(ixdrf, iset, iret)
do i=1,nfrag
call xdrffloat(ixdrf, qfrag(i), iret)
enddo
prec=10000.0
-
+c print *,'nss=',nss,'nfrag=',nfrag,'iset=',iset
isize=0
call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
enddo
enddo
etot=potE
- write (tytul,'(a,i6)') "Structure",kk
+ write (tytul,'(a1,i6,a8,f6.1,a6,f10.1)') "#",kk," t_bath ",
+ & t_bath, " time ",time
call pdbout(etot,tytul,9)
endif
enddo
endif
open(9,file=pdbfile)
nnt = 1
- if (itype(1).eq.21) nnt = 2
+ if (itype(1).eq.ntyp1) nnt = 2
nct=nres
- if (itype(nres).eq.21) nct = nres-1
+ if (itype(nres).eq.ntyp1) nct = nres-1
print *,"nnt",nnt," nct",nct
print *,"file",arg
call xdrfopen(ixdrf,arg, "r", iret)
--- /dev/null
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ include 'COMMON.INTERACT'
+ include 'COMMON.SBRIDGE'
+ real*4 coord(3,1000)
+ real*4 prec,potE,efree,rmsdev
+ real*8 etot
+ character*80 arg,seqfile,pdbfile
+ character*3 sequenc(maxres)
+ character*50 tytul
+ character*8 onethree,cfreq
+ character*8 ucase
+ external ucase
+ logical oneletter
+ integer rescode
+ external rescode
+ logical ilen,iblnk
+
+ ifreq=1
+ if (iargc().lt.4) then
+ print '(a)',
+ & "Usage: xdrf2pdb one/three seqfile cxfile conf [pdbfile]"
+ stop
+ endif
+ call getarg(1,onethree)
+ onethree = ucase(onethree)
+ if (onethree.eq.'ONE') then
+ oneletter = .true.
+ else if (onethree.eq.'THREE') then
+ oneletter = .false.
+ else
+ print *,"ONE or THREE must be specified"
+ endif
+ call getarg(2,seqfile)
+ open (1,file=seqfile,status='old')
+ if (oneletter) then
+ read(1,'(80a1)',end=10,err=10) (sequenc(i)(1:1),i=1,maxres)
+ 10 continue
+ nres=i
+ i=0
+ do while (.not.iblnk(sequenc(i+1)(1:1)))
+ i=i+1
+ enddo
+ nres=i
+ do i=1,nres
+ itype(i)=rescode(i,sequenc(i),1)
+ enddo
+ else
+ read(1,'(20(a3,1x))',end=11,err=11) (sequenc(i),i=1,maxres)
+ 11 continue
+ nres=i
+ print *,"nres",nres
+ do i=1,nres
+ print *,i," ",sequenc(i)
+ enddo
+ print *
+ i=0
+ do while (.not.iblnk(sequenc(i+1)(1:1)))
+ print *,i+1," ",sequenc(i+1)," ",sequenc(i+1)(1:1)
+ i=i+1
+ enddo
+ nres=i
+ print *,"nres",nres
+ do i=1,nres
+ itype(i)=rescode(i,sequenc(i),0)
+ enddo
+ print *,(itype(i),i=1,nres)
+ endif
+ call getarg(3,arg)
+ iext = index(arg,'.cx') - 1
+ if (iext.lt.0) then
+ print *,"Error - not a cx file"
+ stop
+ endif
+ print *,"arg ",arg
+ call getarg(4,cfreq)
+ read (cfreq,*) iconf
+ print *,"iconf",iconf
+ if (iargc().gt.4) then
+ call getarg(5,pdbfile)
+ else
+ pdbfile=arg(:iext)//'.pdb'
+ endif
+ open(9,file=pdbfile)
+ nnt = 1
+ if (itype(1).eq.21) nnt = 2
+ nct=nres
+ if (itype(nres).eq.21) nct = nres-1
+c if (nct.eq.nres-1) nres=nres-1
+c if (nnt.eq.2) nres=nres-1
+
+ print *,"nres",nres," nnt",nnt," nct",nct
+
+ call xdrfopen(ixdrf,arg, "r", iret)
+ print *,"iret",iret
+ kk = 0
+ do while(.true.)
+ prec=10000.0
+ isize=0
+ call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf, potE, iret)
+ if(iret.eq.0) exit
+ kk = kk + 1
+ call xdrffloat(ixdrf, efree, iret)
+ call xdrffloat(ixdrf, rmsdev, iret)
+ call xdrfint(ixdrf, iscor, iret)
+ if (kk.eq.iconf) then
+ print *,"pote",pote," efree",efree," rmsdev",rmsdev
+
+ print *,"isize",isize
+
+ if (isize .ne. nres+nct-nnt+1) then
+ print *,"Error: inconsistent sizes",isize,nres+nct-nnt+1
+ endif
+ do i=1,nres
+ do j=1,3
+ c(j,i)=coord(j,i)
+ enddo
+ enddo
+ ii = 0
+ do i=nnt,nct
+ ii = ii + 1
+ do j=1,3
+ c(j,i+nres)=coord(j,ii+nres)
+ enddo
+ enddo
+ etot=potE
+ write (tytul,'(a,i6)') "Structure",kk
+ call pdbout(etot,tytul,9)
+ stop
+ endif
+ enddo
+
+ end
--- /dev/null
+ implicit real*8 (a-h,o-z)
+ integer ihpb(100),jhpb(100)
+ real*4 coord(3,1000)
+ real*4 prec,potE,efree,rmsdev,qfrag(100)
+ real*8 etot
+ character*80 arg,xfile
+ character*8 ucase,cfreq
+ external ucase
+ logical oneletter
+ integer rescode
+ external rescode
+
+ ifreq=1
+ if (iargc().lt.2) then
+ print '(a)',
+ & "Usage: xdrf2x1 cxfile conf [pdbfile]"
+ stop
+ endif
+ call getarg(1,arg)
+ iext = index(arg,'.cx') - 1
+ if (iext.lt.0) then
+ print *,"Error - not a cx file"
+ stop
+ endif
+ print *,"arg ",arg
+ call getarg(2,cfreq)
+ read (cfreq,*) iconf
+ print *,"iconf",iconf
+ if (iargc().gt.2) then
+ call getarg(3,pdbfile)
+ else
+ xfile=arg(:iext)//'.x'
+ endif
+ open(9,file=xfile)
+
+ call xdrfopen(ixdrf,arg, "r", iret)
+ print *,"iret",iret
+ kk = 0
+ do while(.true.)
+ prec=10000.0
+ isize=0
+ call xdrf3dfcoord(ixdrf, coord, isize, prec, iret)
+ call xdrfint(ixdrf, nss, iret)
+ do j=1,nss
+ call xdrfint(ixdrf, ihpb(j), iret)
+ call xdrfint(ixdrf, jhpb(j), iret)
+ enddo
+ call xdrffloat(ixdrf, potE, iret)
+ if(iret.eq.0) exit
+ kk = kk + 1
+ call xdrffloat(ixdrf, efree, iret)
+ call xdrffloat(ixdrf, rmsdev, iret)
+ call xdrfint(ixdrf, iscor, iret)
+ if (kk.eq.iconf) then
+ print *,"pote",pote," efree",efree," rmsdev",rmsdev
+
+ print *,"isize",isize
+
+ write (9,'(e15.8,2e15.5,f12.5,$)') time,potE,uconst,t_bath
+ write (9,'(i4,$)') nss,(ihpb(j),jhpb(j),j=1,nss)
+ write (9,'(i4,20f7.4)') nfrag,(qfrag(i),i=1,nfrag)
+ write (9,'(8f10.5)') ((coord(k,j),k=1,3),j=1,isize)
+ stop
+ endif
+ enddo
+
+ end
projects / unres.git / commitdiff