#!/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

#
# run bp3
#

bp3 HKLIN $CEXAM/rnase/rnase25.mtz HKLOUT $CCP4_SCR/rnase_bp3_$$.mtz <<+

# native crystal

Xtal NATIVE
  DName NATIVE
    COLUmn F=FNAT SF=SIGFNAT

# platinum derivative

Xtal Platinum
  ATOM Pt
    XYZ 0.566  0.828  0.018
    OCCU 0.2
    BISO 25.0
  ATOM Pt
    XYZ 0.842  0.944  0.469
    OCCU 0.2
    BISO 25.0
  ATOM Pt
    XYZ 0.103  0.941  0.189
    OCCU 0.2
    BISO 25.0
  ATOM Pt
    XYZ 0.190  0.005  0.742
    OCCU 0.2
    BISO 25.0
  ATOM Pt
    XYZ 0.047  0.848  0.273
    OCCU 0.2
    BISO 25.0

  DNAME Plat
    COLUmn F=FPTNCD25 SF=SIGFPTNCD25

ALLIn

+

#
# run dm 
#

dm hklin $CCP4_SCR/rnase_bp3_$$.mtz hklout $CCP4_SCR/rnase_bp3_dm_$$.mtz <<+ 
solc 0.45
mode solv hist aver
COMBINE PERT
NCYC 20
SCHEME ALL
AVER  REFI
ROTAT EULER 0 0 0
TRANS 0 0 0
AVER  REFI
ROTAT EULER  92.65556 -68.98311 -104.13478
TRANS -33.31073  21.15489  18.63655
LABIN FP=FNAT SIGFP=SIGFNAT 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_$$.log
%loop-cyc 3
%copy-pre $CCP4_SCR/rnase_bp3_dm_$$.mtz $CCP4_SCR/temporary_refmac_$$.mtz
%copy-post $CCP4_SCR/temporary_refmac_$$.pdb $CCP4_SCR/rnase_bp3_dm_buc_$$.pdb
%prgm-loop buccaneer cbuccaneer %exit
%prgm-loop refmac refmac5 %exit
buccaneer %arg -stdin
buccaneer title buccaneer_refmac_test
buccaneer pdbin-ref $CLIBD/reference_structures/reference-1tqw.pdb
buccaneer mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz
buccaneer seqin-wrk $CEXAM/rnase/rnase.seq
buccaneer mtzin-wrk $CCP4_SCR/temporary_refmac_$$.mtz
buccaneer colin-wrk-fo /*/*/[FNAT,SIGFNAT]
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/rnase_bp3_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=FNAT SIGFP=SIGFNAT
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

#
# csfcalc test
#
csfcalc -pdbin $CEXAM/rnase/rnase.pdb -mtzin $CCP4_SCR/rnase_bp3_dm_$$.mtz -colin-fo '/*/*/[FNAT,SIGFNAT]' -colin-free '/*/*/[FreeR_flag]' -mtzout $CCP4_SCR/rnase_csfcalc_$$.mtz | tee $CCP4_SCR/csfcalc_$$.log

#
# cphasematch/bp3 test
#
cphasematch -mtzin $CCP4_SCR/rnase_csfcalc_$$.mtz -colin-fo '/*/*/[FNAT,SIGFNAT]' -colin-hl-1 '/*/*/[HLA,HLB,HLC,HLD]' -colin-hl-2 '/*/*/sfcalc' | tee $CCP4_SCR/cphasematch_bp3_$$.log

#
# cphasematch/dm test
#
cphasematch -mtzin $CCP4_SCR/rnase_csfcalc_$$.mtz -colin-fo '/*/*/[FNAT,SIGFNAT]' -colin-hl-1 '/*/*/[HLADM,HLBDM,HLCDM,HLDDM]' -colin-hl-2 '/*/*/sfcalc' | tee $CCP4_SCR/cphasematch_dm_$$.log

#
# test the answers
#
csfc=`awk 'BEGIN{fr=99}/Free R-factor/{fr=int(100*$4)}END{print fr}' $CCP4_SCR/csfcalc_$$.log`
cpbp=`awk 'BEGIN{cr=0}/Qfom/{getline;cr=int(100*$7)}END{print cr}' $CCP4_SCR/cphasematch_bp3_$$.log`
cpdm=`awk 'BEGIN{cr=0}/Qfom/{getline;cr=int(100*$7)}END{print cr}' $CCP4_SCR/cphasematch_dm_$$.log`
seqr=`awk 'BEGIN{seq=0}/residues were seque/{seq=$1}END{print seq}' $CCP4_SCR/buccaneer_$$.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 "Sfcalc   - Free R factor     :\t $csfc \t(reference =  21, error >  22)"
echo -e "BP3      - Map correlation   :\t $cpbp \t(reference =  46, error <  45)"
echo -e "DM(ncs)  - Map correlation   :\t $cpdm \t(reference =  78, error <  75)"
echo -e "Buccaneer- Residues sequenced:\t $seqr \t(reference = 175, error < 150)"
echo -e "Refmac5  - Free R factor     :\t $free \t(reference =  44, error >  45)"

test $csfc -gt  22 && exit 1
test $cpbp -lt  45 && exit 1
test $cpdm -lt  75 && exit 1
test $seqr -lt 150 && exit 1
test $free -gt  50 && exit 1

echo "SUCCESS"