#!/bin/sh
set -e

# bug # 3192 - run-all examples produce harvest files - well to counteract
# this here set HARVESTHOME to somewhere in $CCP4_SCR

HARVESTHOME=$CCP4_SCR
export HARVESTHOME

cd $CCP4_SCR

#
# run freerflag
#
freerflag HKLIN $CEXAM/tutorial/data/gere_peak.mtz HKLOUT $CCP4_SCR/gere_peak_$$.mtz <<+
FREERFRAC  0.05
+

#
# run phaser
#

phaser <<+
TITLE [No title given]
MODE EP_AUTO
HKLIN $CCP4_SCR/gere_peak_$$.mtz
ROOT gere_phaser_$$
LLGCOMPLETE NCYC 50
LLGCOMPLETE COMPLETE ON
LLGCOMPLETE SCATTERER Se
ATOM CHANGE BFACTOR WILSON ON
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.567606 0.19651 0.117643 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.637982 0.0428475 0.217668 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.469871 0.255659 0.23827 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.49385 0.188126 0.41977 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.794401 0.401274 0.137605 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.716238 0.238362 0.0869784 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.259739 0.00855349 0.239787 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.343637 0.168551 0.319304 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.173773 0.928 0.391003 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.179076 0.0804735 0.520765 &
    OCC 1.0
ATOM CRYSTAL gere ELEMENT Se &
    FRAC 0.926494 0.231291 0.18954 &
    OCC 1.0
CRYSTAL gere DATASET peak &
    LABIN Fpos = F_peak(+) SIGFpos = SIGF_peak(+) &
    Fneg = F_peak(-) SIGFneg = SIGF_peak(-)
SCATTERING TYPE Se FP = -4.0 FDP = 4.0 FIX EDGE
COMPOSITION PROTEIN SEQUENCE $CEXAM/data/gere.seq NUMBER 6
WAVELENGTH 0.978
+

#
# run dm 
#

dm hklin $CCP4_SCR/gere_phaser_$$.1.mtz hklout $CCP4_SCR/gere_phaser_dm_$$.mtz <<+ 
mode SOLV HIST AVER
combine PERT
scheme ALL
ncycles AUTO
solc 0.31
average -
    REFI
rota EULER -
    0.0 0.0 0.0
tran 0.0 0.0 0.0
average -
    REFI
rota EULER -
    -60.0505 87.0344 -119.071
tran 96.3165 52.3549 -2.07883
average -
    REFI
rota EULER -
    -55.097 137.17 -33.3136
tran 124.957 8.70207 55.7661
average -
    REFI
rota EULER -
    123.504 48.8422 -41.4429
tran 22.9769 -51.2425 52.6721
average -
    REFI
rota EULER -
    34.5718 75.9769 -164.376
tran 4.35152 21.9137 -27.8829
average -
    REFI
rota EULER -
    -150.559 114.464 81.2349
tran 76.1239 73.4224 14.3897
LABIN FP=F_peak SIGFP=SIGF_peak PHIO=PHIB FOMO=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
LABOUT PHIDM=PHIDM FOMDM=WDM HLADM=HLADM HLBDM=HLBDM HLCDM=HLCDM HLDDM=HLDDM
+

#
# run buccaneer 
#

python $CBIN/ccp4_pipeline_simple << eof | tee $CCP4_SCR/buccaneer_$$.log
%loop-cyc 3
%copy-pre $CCP4_SCR/gere_phaser_dm_$$.mtz $CCP4_SCR/temporary_refmac_$$.mtz
%copy-post $CCP4_SCR/temporary_refmac_$$.pdb $CCP4_SCR/gere_phaser_dm_buc_$$.pdb
%prgm-loop buccaneer cbuccaneer %exit
%prgm-loop refmac refmac5 %exit
buccaneer %arg -stdin
buccaneer title buccaneer_refmac_test
buccaneer pdbin-ref $CLIBD/reference_structures/reference-1tqw.pdb
buccaneer mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz
buccaneer seqin-wrk $CEXAM/data/gere.seq
buccaneer mtzin-wrk $CCP4_SCR/temporary_refmac_$$.mtz
buccaneer colin-wrk-fo /*/*/[F_peak,SIGF_peak]
buccaneer colin-wrk-free /*/*/[FreeR_flag]
buccaneer:0 colin-wrk-hl /*/*/[HLADM,HLBDM,HLCDM,HLDDM]
buccaneer:1-* colin-wrk-phifom /*/*/[PHCOMB,FOM]
buccaneer:1-* pdbin-wrk $CCP4_SCR/temporary_refmac_$$.pdb
buccaneer pdbout-wrk $CCP4_SCR/temporary_buccaneer_$$.pdb
buccaneer find
buccaneer grow
buccaneer join
buccaneer link
buccaneer sequence
buccaneer correct
buccaneer filter
buccaneer ncsbuild
buccaneer prune
buccaneer rebuild
buccaneer:0 cycles 3
buccaneer:0 sequence-reliability 0.95
buccaneer:1-* cycles 1
buccaneer:1-* correlation-mode
buccaneer:1-* sequence-reliability 0.95
buccaneer new-residue-name UNK
buccaneer resolution 2.0
refmac %arg HKLIN $CCP4_SCR/gere_phaser_dm_$$.mtz
refmac %arg XYZIN $CCP4_SCR/temporary_buccaneer_$$.pdb
refmac %arg HKLOUT $CCP4_SCR/temporary_refmac_$$.mtz
refmac %arg XYZOUT $CCP4_SCR/temporary_refmac_$$.pdb
refmac title [No title given]
refmac weight MATRIX 0.1
refmac labin -
refmac HLA=HLADM HLB=HLBDM HLC=HLCDM HLD=HLDDM -
refmac FREE=FreeR_flag -
refmac FP=F_peak SIGFP=SIGF_peak
refmac make check NONE
refmac make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
refmac refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
refmac ncyc 10
refmac scal type SIMP LSSC ANISO EXPE
refmac solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
refmac monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0
refmac labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
refmac PNAME buccaneer
refmac DNAME buccaneer
refmac RSIZE 80
refmac END
eof

#
# test the answers
#
seqr=`awk 'BEGIN{seq=0}/residues were seque/{seq=$1}END{print seq}' $CCP4_SCR/buccaneer_$$.log`
free=`awk 'BEGIN{fr=0}/Free R factor/{fr=int(100*$5)}END{print fr}' $CCP4_SCR/buccaneer_$$.log`
echo
echo "Final result:"
echo -e "Buccaneer- Residues sequenced:\t $seqr \t(reference = 395, error < 275)"
echo -e "Refmac5  - Free R factor     :\t $free \t(reference =  43, error >  45)"

test $seqr -lt 275 && exit 1
test $free -gt  45 && exit 1

echo "SUCCESS"