path: root/sci-chemistry/cns/files/1.2.1-aria.patch

diff -arNu aria2.2/cns/src/cns.f aria2.2.new/cns/src/cns.f
--- aria2.2/cns/src/cns.f	2007-08-22 17:25:51.000000000 +0200
+++ aria2.2.new/cns/src/cns.f	2009-06-14 15:28:39.907685273 +0200
@@ -12,7 +12,7 @@
 C  +          J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,          +
 C  +          L.M.Rice, T.Simonson, G.L.Warren                     +
 C  +===============================================================+
-C  + Copyright 1997-2007 Yale University                           +
+C  + Copyright 1997-2008 Yale University                           +
 C  +===============================================================+
 C  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 C
@@ -470,6 +470,7 @@
       INTEGER      HNLEN, TMP, PTRSZ, STLEN
       CHARACTER*(1) CNSPTMP
       CHARACTER*(4) ST
+!$    integer omp_get_max_threads
 C
 C write header
       WRITE(6,'(10X,A)')
@@ -511,7 +512,7 @@
      &'             J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,',
      &'             L.M.Rice, T.Simonson, G.L.Warren.'
       WRITE(6,'(10X,A)')
-     &' Copyright (c) 1997-2007 Yale University'
+     &' Copyright (c) 1997-2008 Yale University'
       WRITE(6,'(10X,A)')
      &'============================================================'
 C
@@ -526,6 +527,9 @@
       WRITE(6,'(10X,7A)')
      & ' Running on machine: ',HOSTNM(1:HNLEN),
      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
+!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
+!$   &  ' threads'
+!$C (to change use setenv OMP_NUM_THREADS x)
 C
       CALL GETNAM(USERNM,12,TMP)
       WRITE(6,'(10X,2A)')
diff -arNu aria2.2/cns/src/energy.f aria2.2.new/cns/src/energy.f
--- aria2.2/cns/src/energy.f	2006-12-18 16:26:49.000000000 +0100
+++ aria2.2.new/cns/src/energy.f	2009-06-14 14:47:57.421262637 +0200
@@ -23,7 +23,8 @@
       INTEGER I, NDIM, N
       DOUBLE PRECISION TOTAL
       DOUBLE COMPLEX DCVAL
-      DOUBLE COMPLEX EDUMMY
+CCC modifcation ATB 4/27/08
+      DOUBLE PRECISION EDUMMY
 C parameters
       DOUBLE PRECISION ZERO, ONE
       PARAMETER (ZERO=0.0D0, ONE=1.0D0)
diff -arNu aria2.2/cns/src/noe.f aria2.2.new/cns/src/noe.f
--- aria2.2/cns/src/noe.f	2007-08-22 17:25:51.000000000 +0200
+++ aria2.2.new/cns/src/noe.f	2009-06-14 15:03:30.001587922 +0200
@@ -36,8 +36,8 @@
       INTEGER ISLCT(*), JSLCT(*)
 C local
       INTEGER I, II, NISLCT, NJSLCT, ICL1, ICL2, NN, ITEMP, IEMODE
-      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET
-      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH
+      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET, DENMODE
+      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH, GAMMA, KAPPA
       LOGICAL MATCH
 C parameter
       DOUBLE PRECISION ZERO, ONE, SIX
@@ -140,7 +140,7 @@
      &     NPEAKI,HEAP(HPNPID),HEAP(HPNSPC),
      &     HEAP(HPNPP1),HEAP(HPNPP2),HEAP(HPNHP1),HEAP(HPNHP2),
      &     HEAP(HPNVOL),HEAP(HPCDIS),HEAP(HPCVOL),NATOM,ISLCT,NISLCT,
-     &     JSLCT,NJSLCT,X,Y,Z)
+     &     JSLCT,NJSLCT,X,Y,Z,HEAP(HPDENINIT))
 C===================================================================
       ELSE IF (WD(1:4).EQ.'?   ') THEN
       WRITE(6,'(A,I6,A,I6,A,/,A,F8.3,A,I6)')
@@ -167,7 +167,8 @@
 C
 C get the class name:
       CALL NEXTA4('class-name=',CLASS)
-      CALL NEXTF('AVERaging=',RTEMP)
+CCC modification ATB 4/27/08
+      CALL NEXTF('AVEXponent=',RTEMP)
       DO I=1,NOECCN
       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
       IF (MATCH) THEN
@@ -179,7 +180,8 @@
 C
 C get the class name:
       CALL NEXTA4('class-name=',CLASS)
-      CALL NEXTF('AVERaging=',RTEMP)
+CCC modification ATB 4/27/08
+      CALL NEXTF('OREXponent=',RTEMP)
       DO I=1,NOECCN
       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
       IF (MATCH) THEN
@@ -585,6 +587,38 @@
       IF (NOEICV.GT.0) CALL NOEPRI(THRESH,1)
       END IF
 C====================================================================
+CCC modification ATB 5/02/08
+      ELSE IF (WD(1:4).EQ.'OUTD') THEN
+      CALL NOEOUT(0)
+      IF (NOEICV.GT.0) CALL NOEOUT(1)
+C====================================================================
+CCC modification ATB 4/25/08
+      ELSE IF (WD(1:3).EQ.'DEN') THEN
+      CALL NEXTWD('DEN>')
+      IF (WD(1:4).NE.'INIT'.AND.WD(1:4).NE.'UPDA') THEN
+      WRITE(6,'(A)') ' %NOE-ERR: DEN expects INIT or UPDAte'
+      ELSE
+      DENMODE=WD(1:4)
+      GAMMA=0.0D0
+      KAPPA=0.0D0
+      IF (DENMODE.EQ.'UPDA') THEN
+      CALL NEXTWD('DEN>')
+      IF (WD(1:4).NE.'GAMM') THEN
+      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects GAMMa parameter'
+      ELSE
+      CALL NEXTF('GAMMa=',GAMMA)
+      CALL NEXTWD('DEN>')
+      IF (WD(1:4).NE.'KAPP') THEN
+      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects KAPPa parameter'
+      ELSE
+      CALL NEXTF('KAPPa=',KAPPA)
+      END IF
+      END IF
+      END IF 
+      CALL NOEDEN(DENMODE,GAMMA,KAPPA,0)
+      IF (NOEICV.GT.0) CALL NOEDEN(DENMODE,GAMMA,KAPPA,1)
+      END IF
+C====================================================================
       ELSE IF (WD(1:4).EQ.'ANAL') THEN
       CALL NEXTA4('ANALyse=',RANA)
 C====================================================================
@@ -683,7 +717,7 @@
      &           NOEXCL,NPEAKI,NOEPID,NOESPC,NOEPP1,NOEPP2,NOEHP1,
      $           NOEHP2,NOEVOL,NOECDI,
      &           NOECVO,NATOM,ISLCT,NISLCT,
-     &           JSLCT,NJSLCT,X,Y,Z)
+     &           JSLCT,NJSLCT,X,Y,Z,NOEDENINIT)
 C
 C Subroutine parses an NOE ASSIgn statement and
 C puts the information into the NOE restraints list
@@ -706,7 +740,7 @@
       DOUBLE PRECISION NOEPP1(*),NOEPP2(*),NOEHP1(*),NOEHP2(*)
       DOUBLE PRECISION NOEVOL(*), NOECDI(*),NOECVO(*)
       INTEGER NATOM, ISLCT(*), NISLCT, JSLCT(*), NJSLCT
-      DOUBLE PRECISION X(*), Y(*), Z(*)
+      DOUBLE PRECISION X(*), Y(*), Z(*), NOEDENINIT(*)
 C local
       INTEGER I, II, JJ, J, TISLCT, TJSLCT, PEAKID
       LOGICAL SUCCES,OK
@@ -737,6 +771,10 @@
       CALL NEXTF('lower-average-distance=',NOELOW(NOENUM))
       CALL NEXTF('higher-average-distance=',NOEHIG(NOENUM))
 C
+C initialize initial DEN distance
+      NOEDENINIT(NOENUM)=ZERO
+
+C
 C initialize time-average and running average stuff
 C
 C set the time-averaged distance and
@@ -1732,6 +1770,232 @@
       RETURN
       END
 C====================================================================
+      SUBROUTINE NOEOUT(ITEST)
+C
+C print a list of current NOE restraints
+C as assign statements
+C Front-end for NOEPR3
+      IMPLICIT NONE
+C I/O
+      INCLUDE 'cns.inc'
+      INCLUDE 'heap.inc'
+      INCLUDE 'noe.inc'
+      INTEGER ITEST
+C begin
+      CALL NOEPR3(ITEST,
+     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
+     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
+     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
+     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID))
+
+      RETURN
+      END
+C====================================================================
+      SUBROUTINE NOEPR3(ITEST,
+     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
+     &           NOEJLS,NOECND,NOERAV,NOERRV,
+     &           NOEDIS,NOELOW,NOEHIG,
+     &           NOEVIO,NOECV,NOEPID)
+      IMPLICIT NONE
+C I/O
+      INCLUDE 'cns.inc'
+      INCLUDE 'noe.inc'
+      INCLUDE 'mtf.inc'
+      INCLUDE 'pick.inc'
+      INCLUDE 'comand.inc'
+      INCLUDE 'numbers.inc'
+      INTEGER ITEST
+C
+C global NOE arrays on HEAP
+C restraint and atom pointers
+      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
+C classes
+      INTEGER NOECND(*)
+C averages
+      DOUBLE PRECISION NOERAV(*),NOERRV(*)
+C target distance and errors
+      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
+C number of violations
+      INTEGER NOEVIO(*)
+C time average pointer, test set, restraint number
+      INTEGER NOECV(*), NOEPID(*)
+C
+C local
+      INTEGER N, K, I, J, CLASS, NORR
+      INTEGER I1, I2
+C begin
+      IF (NOENUM.GT.0) THEN
+C
+C loop over all classes
+      DO CLASS=1,NOECCN
+      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
+     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
+     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
+      CALL WRNDIE(-5,'NOEPRI',
+     & 'DENOut not possible with POTEntial set to SYMM, HIGH, or 3DPO')
+      ELSE
+C
+C loop over all NOE's belonging to this class
+      DO N=1,NOENUM
+      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
+     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
+      IF (NOECND(N).EQ.CLASS) THEN
+C
+C     WE ONLY TAKE THE FIRST FROM EACH SET
+      NORR=NOEORR(N)+1
+C
+C     DO I=NOEIPR(NORR)+1,NOEIPR(NORR+1)
+C
+C     WE ONLY TAKE THE FIRST FROM EACH SET
+      I=NOEIPR(NORR)+1
+      K=NOEILS(I)
+      I1=K
+C
+C     WE ONLY TAKE THE FIRST FROM EACH SET
+      J=NOEJPR(NORR)+1
+      K=NOEJLS(J)
+      I2=K
+C
+      WRITE(PUNIT,'(A,I6,A,I6,A,F6.3,A,F6.3,A,F6.3)') 
+     & 'ASSIGn (id ',
+     & I1, ' ) (id ', I2, ' ) ', NOEDIS(N), 
+     & ' ', NOELOW(N), ' ', NOEHIG(N)
+C
+      END IF
+      END IF
+      END DO
+      END IF
+      END DO
+      END IF
+      RETURN
+      END
+C====================================================================
+      SUBROUTINE NOEDEN(DENMODE,GAMMA,KAPPA,ITEST)
+C
+C print a list of current NOE restraints
+C Front-end for NOEPR2
+      IMPLICIT NONE
+C I/O
+      INCLUDE 'cns.inc'
+      INCLUDE 'heap.inc'
+      INCLUDE 'noe.inc'
+      CHARACTER*4 DENMODE
+      DOUBLE PRECISION GAMMA, KAPPA
+      INTEGER ITEST
+C begin
+      CALL NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
+     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
+     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
+     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
+     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID),
+     &           HEAP(HPDENINIT))
+
+      RETURN
+      END
+C====================================================================
+      SUBROUTINE NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
+     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
+     &           NOEJLS,NOECND,NOERAV,NOERRV,
+     &           NOEDIS,NOELOW,NOEHIG,
+     &           NOEVIO,NOECV,NOEPID,NOEDENINIT)
+      IMPLICIT NONE
+C I/O
+      INCLUDE 'cns.inc'
+      INCLUDE 'noe.inc'
+      INCLUDE 'mtf.inc'
+      INCLUDE 'pick.inc'
+      INCLUDE 'comand.inc'
+      INCLUDE 'numbers.inc'
+      CHARACTER*4 DENMODE
+      DOUBLE PRECISION GAMMA,KAPPA
+      INTEGER ITEST
+C
+C global NOE arrays on HEAP
+C restraint and atom pointers
+      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
+C classes
+      INTEGER NOECND(*)
+C averages
+      DOUBLE PRECISION NOERAV(*),NOERRV(*)
+C target distance and errors
+      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
+C number of violations
+      INTEGER NOEVIO(*)
+C time average pointer, test set, restraint number
+      INTEGER NOECV(*), NOEPID(*)
+C initial den distance
+      DOUBLE PRECISION NOEDENINIT(*)
+C
+C local
+      DOUBLE PRECISION EN, NOERMS, NOERM2(NOECMX), THRESH
+      DOUBLE COMPLEX DBCOMP
+      DOUBLE PRECISION DBPREC
+      INTEGER NOENU2(NOECMX)
+      INTEGER NOEVIT
+      INTEGER N, K, I, J, CLASS, NOENUML, NORR
+      CHARACTER*6 SSAVE
+      CHARACTER*11 SSPOT
+      LOGICAL QHEAD
+C begin
+      THRESH=-0.1
+      NOERMS=ZERO
+      NOEVIT=0
+      NOENUML=0
+      IF (NOENUM.GT.0) THEN
+C
+C
+C loop over all classes
+      DO CLASS=1,NOECCN
+      NOENU2(CLASS)=0
+      NOERM2(CLASS)=ZERO
+      NOEVIO(CLASS)=0
+      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
+     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
+     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
+      CALL WRNDIE(-5,'NOEPRI',
+     & 'DEN not possible with POTEntial set to SYMM, HIGH, or 3DPO')
+      ELSE
+C
+C loop over all NOE's belonging to this class
+      QHEAD=.TRUE.
+      DO N=1,NOENUM
+      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
+     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
+      IF (NOECND(N).EQ.CLASS) THEN
+      NOENUML=NOENUML+1
+C
+C get NOE energy, current distance (in PCDATA(PCGEOM), and other results
+      CALL ENOE(EN,'ANAL',N)
+      NOERMS=NOERMS+PCDATA(PCDEVI)**2
+      NOERM2(CLASS)=NOERM2(CLASS)+PCDATA(PCDEVI)**2
+      NOENU2(CLASS)=NOENU2(CLASS)+1
+      IF (ABS(PCDATA(PCDEVI)).GT.THRESH) THEN
+      NOEVIO(CLASS)=NOEVIO(CLASS)+1
+      NOEVIT=NOEVIT+1
+      END IF
+C
+      IF (DENMODE.EQ.'INIT') THEN
+C
+C initialization
+      NOEDENINIT(N)=PCDATA(PCGEOM)
+CCCCxxx      NOEDIS(N)=PCDATA(PCGEOM)
+      ELSE
+C
+C update step
+      NOEDIS(N)=NOEDIS(N)+KAPPA*(GAMMA*(PCDATA(PCGEOM)-NOEDIS(N))+ 
+     &          (ONE-GAMMA)*(NOEDENINIT(N)-NOEDIS(N)) )       
+      END IF
+C
+      END IF      
+      END IF
+      END DO
+      END IF
+      END DO
+C
+      END IF
+      RETURN
+      END
+C====================================================================
       SUBROUTINE ENOE(EN,ANALYS,NA)
 C
 C Routine computes force field for NOE restraints
@@ -3357,6 +3621,7 @@
       HPNRRV=0
       HPNNSP=0
       HPNDIS=0
+      HPDENINIT=0
       HPNLOW=0
       HPNHIG=0
       HPNWGH=0
@@ -3373,7 +3638,6 @@
       HPNVOL=0
       HPCVOL=0
       HPCDIS=0
-      HPNPRD=0
 C
 C
 C reset other variables
@@ -3463,6 +3727,7 @@
       IF (HPNRRV.NE.0) CALL FREHP(HPNRRV,IREAL8(NOEMAX))
       IF (HPNNSP.NE.0) CALL FREHP(HPNNSP,INTEG4(NOEMAX))
       IF (HPNDIS.NE.0) CALL FREHP(HPNDIS,IREAL8(NOEMAX))
+      IF (HPDENINIT.NE.0) CALL FREHP(HPDENINIT,IREAL8(NOEMAX))
       IF (HPNLOW.NE.0) CALL FREHP(HPNLOW,IREAL8(NOEMAX))
       IF (HPNHIG.NE.0) CALL FREHP(HPNHIG,IREAL8(NOEMAX))
       IF (HPNWGH.NE.0) CALL FREHP(HPNWGH,IREAL8(NOEMAX))
@@ -3495,6 +3760,7 @@
       HPNRRV=0
       HPNNSP=0
       HPNDIS=0
+      HPDENINIT=0
       HPNLOW=0
       HPNHIG=0
       HPNWGH=0
@@ -3511,7 +3777,6 @@
       HPNVOL=0
       HPCVOL=0
       HPCDIS=0
-      HPNPRD=0
 C
 C now allocate new space
       IF (NOENEW.GT.0) THEN
@@ -3536,6 +3801,7 @@
       HPNRRV=ALLHP(IREAL8(NOENEW))
       HPNNSP=ALLHP(INTEG4(NOENEW))
       HPNDIS=ALLHP(IREAL8(NOENEW))
+      HPDENINIT=ALLHP(IREAL8(NOENEW))
       HPNCND=ALLHP(INTEG4(NOENEW))
       HPNJLS=ALLHP(INTEG4(NOENEW))
       HPNJPR=ALLHP(INTEG4(NOENEW))
diff -arNu aria2.2/cns/src/noe.inc aria2.2.new/cns/src/noe.inc
--- aria2.2/cns/src/noe.inc	2007-08-22 17:25:51.000000000 +0200
+++ aria2.2.new/cns/src/noe.inc	2009-06-14 15:24:50.995208687 +0200
@@ -29,6 +29,9 @@
 C list for distances and +/- error estimates (heap pointers)
       INTEGER HPNDIS, HPNLOW, HPNHIG
 C
+C list for initial DEN distances
+      INTEGER HPDENINIT
+C
 C individual weights on restraints
       INTEGER HPNWGH
 C
@@ -119,7 +122,7 @@
       INTEGER HPNVIO, HPNEXC, HPNNUM
 
 C peak identifier
-      INTEGER NPEAKI, HPNPID, HPNPRD
+      INTEGER NPEAKI, HPNPID
 C
 C
 C
@@ -142,7 +145,7 @@
      &              NMONO,  RAVEXP, NOECOR, NOEICV, 
      &              HPNVIO, HPNEXC, HPNNUM,
      &              NPEAKI, HPNPID, IDIMER, HPNPP1, HPNPP2, 
-     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPNPRD
+     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPDENINIT
 C
 C     character string block
 C