#
#     Copyright (C) 1999-2004  Liz Potterton, Peter Briggs
#
#     This code is distributed under the terms and conditions of the
#     CCP4 Program Suite Licence Agreement as a CCP4 Library.
#     A copy of the CCP4 licence can be obtained by writing to the
#     CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
#
#CCP4i_cvs_Id $Id$
#===========================================================================
#
# oasis.script
#
#===========================================================================
source [SearchPath TOP src CCP4_utils.tcl]

set job_id [GetJobid]
set cpath  [GetCurrentDir]
set dpath [GetDefaultDirPath]

set NAME [split $HKLOUT .]
set HKL_T [lindex $NAME 0]

set oasis_script "{TIT $TITLE}"

##################################################
#MODE
##################################################
if { [regexp SAD $OASIS_MODE] } {
append oasis_script " {SAD }"
}

if { [regexp SIR $OASIS_MODE] } {
append oasis_script " {SIR }"
}

if { [regexp DMR $OASIS_MODE] } {
	if { $MR_SAD } {
append oasis_script " {DMR }"
} else {
append oasis_script " {DMR 1 }"
}
}



if { $RES } {
append oasis_script " {LIM $RES_L $RES_H}" 
}

if { [regexp DMR $OASIS_MODE] } {
append oasis_script " {NHA $NHA}"
append oasis_script " {SED $SED}"
}

################################
#LABIN
################################
append oasis_script " {LABIN "

if { [regexp SAD $OASIS_MODE] }  {
  if { $MAP_FM }  { 
append oasis_script "FP=$FP SIGFP=$SIGFP DANO=$DANO SIGDANO=$SIGDANO"
}  else  {
append oasis_script "F(+)=$FP SIGF(+)=$FP F(-)=$DANO SIGF(-)=$SIGDANO"
}
}


if { [regexp SIR $OASIS_MODE] } {
append oasis_script "FP=$FP SIGFP=$SIGFP FPH=$FPH SIGFPH=$SIGFPH"
}

if { [regexp DMR $OASIS_MODE] } {
append oasis_script "FP=$FP SIGFP=$SIGFP"

}

if { $COMPARE_PHI } {
append oasis_script " PHIC=$PHIC"
}
append oasis_script "}"


##################################################
#DUM
##################################################
set OASIS_NS_S 0
  if { [regexp P_PDB $PAR_MODE] && $PAR } {  

      set par_tmp_pdb_file [GetTmpFileName -ext pdb]
      
      WriteFile [set par_tmp_script [GetTmpFileName -ext _com]]\
      "input PDB -
                orth 1
       output HA
       cell $CELL_A $CELL_B $CELL_C $CELL_ALPHA $CELL_BETA $CELL_GAMMA
       end
      "

      set Coordconv_cmd "[BinPath coordconv] XYZOUT $par_tmp_pdb_file XYZIN $PAR_PDB_FILE "
      set status [Execute $Coordconv_cmd $par_tmp_script program_status report -nolog]



if { [ReadFile $par_tmp_pdb_file file_list -split] }  {
set par_input_file $HKL_T
append par_input_file "_partial.frc"
if [file exists $par_input_file] { DeleteFile $par_input_file }
set n 0
	foreach line0 $file_list {

      	 set line [string trim $line0]
	 set par_tmp   [lindex $line 1]
       set par_type  [string toupper [string range $par_tmp 0 0]]
	if { $par_type != "" } {		
	    set xpar      [format "%.4f" [lindex $line 2]]
	    set ypar      [format "%.4f" [lindex $line 3]]
	    set zpar      [format "%.4f" [lindex $line 4]]
	    set hatom_occ [format "%.4f" [lindex $line 5]]
	    set hatom_b   [format "%.4f" [lindex $line 8]]
           }    
       if { $par_type=="C"}   {
       set par_type "C "      
}

       if { $par_type=="D"}   {
       set par_type "C "      
}
       if { $par_type=="O" }   {
       set  par_type "O "       
}
 
       if { $par_type=="N" }   {      
		 set par_type "N "
}

       if { $par_type=="S"  }   {
       set par_type "S "
       incr OASIS_NS_S       

}
if {$par_type!=""}  {
	incr n
      WriteFile $par_input_file\
      "$par_type       $n        $xpar       $ypar       $zpar      $hatom_occ       $hatom_b"

}	 
}
}

	DeleteFile $par_tmp_pdb_file
}

  if { [regexp P_OAS $PAR_MODE] && $PAR }  {
if { [ReadFile $PAR_OAS_FILE file_list -split] }  {
	foreach line0 $file_list {
          
      	  set line [string trim $line0]
          
          set par_tmp   [lindex $line 1]
          set par_type  [string toupper [string range $par_tmp 0 0]] 

       if { $par_type=="S"  }   {
       incr OASIS_NS_S       
}
}
}
set par_input_file $PAR_OAS_FILE
}

##################################################
# CELL CONTENTS
##################################################
append oasis_script " {CON"

if { [regexp NUM $CELL_CON] }  {
    set OASIS_NS_C [expr $CELL_CON_NUM*5]
    set OASIS_NS_N [expr $CELL_CON_NUM*1.2]
    set OASIS_NS_O [expr $CELL_CON_NUM*1.5]
    set OASIS_NS_H [expr $CELL_CON_NUM*8]
append oasis_script " C $OASIS_NS_C N $OASIS_NS_N O $OASIS_NS_O H $OASIS_NS_H "
 
    for {set i 1} { $i <= $C_NUM} {incr i} {
    if { $C_TYPE($i) == "S" } {
       if { $C_TYPE_NUM($i) > $OASIS_NS_S }  {
		set  OASIS_NS_S $C_TYPE_NUM($i)
}	
	continue
}
append oasis_script "$C_TYPE($i) $C_TYPE_NUM($i) "
}



if { [regexp SAD $OASIS_MODE] || [regexp SIR $OASIS_MODE] }  {


    for {set i 1} { $i <= $HA_T_NUM } {incr i} {

    if { $HA_T_TYPE($i) == "S" }  {
       if { $HA_T_TYPE_NUM($i) > $OASIS_NS_S }  {
		set  OASIS_NS_S $HA_T_TYPE_NUM($i)
}
	continue	
}	
append oasis_script "$HA_T_TYPE($i) $HA_T_TYPE_NUM($i) "
}
}

if { $OASIS_NS_S != 0 } {
	append oasis_script "S $OASIS_NS_S"
}

}  else  {

set seq_C(A) 3
set seq_N(A) 1
set seq_O(A) 1
set seq_S(A) 0

set seq_C(R) 6
set seq_N(R) 4
set seq_O(R) 1
set seq_S(R) 0

set seq_C(N) 4
set seq_N(N) 2
set seq_O(N) 2
set seq_S(N) 0

set seq_C(D) 4
set seq_N(D) 1
set seq_O(D) 3
set seq_S(D) 0

set seq_C(C) 3
set seq_N(C) 1
set seq_O(C) 1
set seq_S(C) 1

set seq_C(E) 5
set seq_N(E) 1
set seq_O(E) 3
set seq_S(E) 0

set seq_C(Q) 5
set seq_N(Q) 2
set seq_O(Q) 2
set seq_S(Q) 0

set seq_C(G) 2
set seq_N(G) 1
set seq_O(G) 1
set seq_S(G) 0

set seq_C(H) 6
set seq_N(H) 3
set seq_O(H) 1
set seq_S(H) 0

set seq_C(I) 6
set seq_N(I) 1
set seq_O(I) 1
set seq_S(I) 0

set seq_C(L) 6
set seq_N(L) 1
set seq_O(L) 1
set seq_S(L) 0

set seq_C(K) 6
set seq_N(K) 2
set seq_O(K) 1
set seq_S(K) 0

set seq_C(M) 5
set seq_N(M) 1
set seq_O(M) 1
set seq_S(M) 1

set seq_C(F) 9
set seq_N(F) 1
set seq_O(F) 1
set seq_S(F) 0

set seq_C(P) 5
set seq_N(P) 1
set seq_O(P) 1
set seq_S(P) 0

set seq_C(S) 3
set seq_N(S) 1
set seq_O(S) 2
set seq_S(S) 0

set seq_C(T) 4
set seq_N(T) 1
set seq_O(T) 2
set seq_S(T) 0

set seq_C(W) 11
set seq_N(W) 2
set seq_O(W) 1
set seq_S(W) 0

set seq_C(Y) 9
set seq_N(Y) 1
set seq_O(Y) 2
set seq_S(Y) 0

set seq_C(V) 5
set seq_N(V) 1
set seq_O(V) 1
set seq_S(V) 0

    set OASIS_NS_C 0
    set OASIS_NS_N 0
    set OASIS_NS_O 0
    set OASIS_NS_S 0

      if { [ReadFile $SEQIN file_list -split] } {

	foreach line0 $file_list {
      set line [string trim $line0]
	set len [string length $line]
	set c [string range $line 0 0]
	if { $c == ">" } {
	continue
}
	for {set i 1} { $i <= $len } { incr i } {
	set t [expr $i - 1]	

	set c [string range $line $t $t]
	set OASIS_NS_C [expr $seq_C($c) + $OASIS_NS_C]
	set OASIS_NS_N [expr $seq_N($c) + $OASIS_NS_N]
	set OASIS_NS_O [expr $seq_O($c) + $OASIS_NS_O]
	set OASIS_NS_S [expr $seq_S($c) + $OASIS_NS_S]
}

}
}


append oasis_script " C $OASIS_NS_C N $OASIS_NS_N O $OASIS_NS_O "

    for {set i 1} { $i <= $HA_T_NUM } {incr i} {
    if { $HA_T_TYPE($i) == "S" } {
       if { $HA_T_TYPE_NUM($i) > $OASIS_NS_S }  {
		set  OASIS_NS_S $HA_T_TYPE_NUM($i)
}
	continue	
}	
append oasis_script "$HA_T_TYPE($i) $HA_T_TYPE_NUM($i) "
}

if { $OASIS_NS_S != 0 } {
	append oasis_script "S $OASIS_NS_S"
}
}

append oasis_script "} "
##################################################
# SPACE GROUP
##################################################

##################################################
# GENERAL OPTIONS
##################################################

##################################################
if { $COS } {
append oasis_script " {COS } "
}

if { $CYC != "2" } {
append oasis_script " {CYC $CYC}"
}

if { $FOM } {
append oasis_script " {FOM } "
}

append oasis_script " {KMI $KMI}"
# ANO
##################################################
if { [regexp SAD $OASIS_MODE] }  {
    for {set i 1} { $i <= $HA_T_NUM } {incr i} {

	if { $X_F($i) != "" }  {
	set ano_tem $X_F($i)

}  else  {
      set ha_ano_tem [GetTmpFileName -ext _log]
       WriteFile [set f_tmp_script [GetTmpFileName -ext _com]]\
      "ATOM $HA_T_TYPE($i)
       NWAV 1 $X_WLENGTH
       END  
       "

      set Cro_cmd "[BinPath crossec] "
      set status [Execute $Cro_cmd $f_tmp_script program_status report -copy_log $ha_ano_tem ]

      if { [ReadFile $ha_ano_tem file_list -split] } {

      foreach line0 $file_list {
      set line [string trim $line0]

      if { [regexp ^$HA_T_TYPE($i) $line] } {
      set ano_tem [lindex $line 3]
      break
      }
      }
      }
	DeleteFile $ha_ano_tem
}


if { $i == 1} {
append oasis_script " {ANO $HA_T_TYPE($i) $ano_tem}"
} else {
append oasis_script " {   $HA_T_TYPE($i) $ano_tem}"
}
}
}
##################################################
# HEAVY ATOM DATA
##################################################

if { [regexp SAD $OASIS_MODE] || [regexp SIR $OASIS_MODE] }  {

if { [regexp HA_PDB $HA] }  {
      set ha_tmp_file [GetTmpFileName -ext pdb]
      WriteFile [set ha_tmp_script [GetTmpFileName -ext _com]]\
      "input PDB -
                orth 1
       output HA
       cell $CELL_A $CELL_B $CELL_C $CELL_ALPHA $CELL_BETA $CELL_GAMMA
       end
      "

      set Coordconv_cmd "[BinPath coordconv] XYZOUT \"$ha_tmp_file\" XYZIN \"$HA_FILE_PDB\" "
      set status [Execute $Coordconv_cmd $ha_tmp_script program_status report -nolog]

} 

if { [regexp HA_OAS $HA] } {
       if { [ReadFile $HA_FILE_OAS file_list -split] } {
	set n 0
	foreach line0 $file_list {
       set line [string trim $line0]
	    set h_tem [lindex $line 0]
	if { $h_tem != "" }  {
	    incr n
	    set HA_TYPE($n) [lindex $line 0]
	    set HA_X($n)    [lindex $line 2]
	    set HA_Y($n)    [lindex $line 3]
	    set HA_Z($n)    [lindex $line 4]
	    set HA_OCC($n)  [lindex $line 5]
	    set HA_B($n)    [lindex $line 6] 
		}
	}
      }
set HA_NUM $n   
} 
if { [regexp HA_PDB $HA] } {

      if { [ReadFile $ha_tmp_file file_list -split] } {
	set n 0
	foreach line0 $file_list {
       set line [string trim $line0]
       set hatom_type [lindex $line 1]
       if { [regexp ^ATOM $line] } {
	    incr n
	    set HA_TYPE($n) $hatom_type
	    set HA_X($n)    [lindex $line 2]
	    set HA_Y($n)    [lindex $line 3]
	    set HA_Z($n)   [lindex $line 4]
	    set HA_OCC($n)  [lindex $line 5]
	    set HA_B($n)    [lindex $line 8]
	  } 

	}
      }
set HA_NUM $n
}

append oasis_script " {POS}"
    for {set i 1} { $i <= $HA_NUM } {incr i} {
     append oasis_script " {   $HA_TYPE($i) $i $HA_X($i) $HA_Y($i) $HA_Z($i) $HA_OCC($i) $HA_B($i)}"
}
}



append oasis_script " {END }"
##################################################
#EXECUTE OASIS
##################################################

set oasis_script_file [GetTmpFileName -ext _com]

	foreach line0 $oasis_script {
       set line [string trim $line0]
      WriteFile $oasis_script_file\
      "$line"
	}

set cmd "[BinPath oasis]"
append cmd " HKLIN \"$HKLIN\""
append cmd " HKLOUT \"$HKLOUT\""
set C_LOG $HKL_T
append C_LOG ".log"
set LOG $dpath
append LOG "/"
append LOG $job_id
append LOG "_oasis.log"


if { $PAR } {
append cmd " FRCIN \"$par_input_file\""
set status [Execute $cmd $oasis_script_file program_status report ]
if [file exists $C_LOG] { DeleteFile $C_LOG }
CopyFile $LOG $C_LOG
} else {
set status [Execute $cmd $oasis_script_file program_status report ]
if [file exists $C_LOG] { DeleteFile $C_LOG }
CopyFile $LOG $C_LOG
} 



set name_script $HKL_T
append name_script ".csh"

if [file exists $name_script] { DeleteFile $name_script }
      WriteFile $name_script \
      "oasis \\
hklin \"$HKLIN\"  \\"


if { $PAR } {
      WriteFile $name_script \
      "frcin \"$par_input_file\" \\"
}
      WriteFile $name_script \
	"hklout \"$HKLOUT\" << +"
	foreach line0 $oasis_script {
       set line [string trim $line0]
      WriteFile $name_script\
      "$line"
	}
	WriteFile $name_script "+"


##################################################
#EXECUTE merge
##################################################
set fof_sig "F"
if { [regexp DMR $OASIS_MODE] }  {
#	if { [ regexp M_MER $MOD_MOD ] } {
#         set M_HKLOUT $HKL_T
#	  append M_HKLOUT "_MER.mtz"
#     WriteFile [set merge_tmp_script [GetTmpFileName -ext _com]]\
#      "LABIN FOM=$M_FOM   PHIB=$M_PHIC
#      "
#	set mcmd "[BinPath combinereslv]"
#	append mcmd " HKLIN1 \"$HKLOUT\" HKLIN2 \"$M_HKLIN\" HKLOUT \"$M_HKLOUT\" "
#	set status [Execute $mcmd $merge_tmp_script program_status report ]
#       if { $KEEP_MOD }  {
#
#	 } else {
#	DeleteFile $HKLOUT
#      MoveFile $M_HKLOUT $HKLOUT
#}
#}

	if { [ regexp M_FOM $MOD_MOD ]  } {
	set cadcmd "[BinPath cad]"
	set CAD_HKLOUT $HKL_T
	append CAD_HKLOUT "_CAD.mtz"

if { [ regexp DMR $OASIS_MODE ] } {
set lab_list [GetMtzAllCols $M_HKLIN]
	foreach i $lab_list {
	if { $i == "2FOFCWT" } {
			set fof_sig "T"	
			break
		}	
	}

}



append cadcmd " HKLIN1 \"$HKLOUT\" HKLIN2 \"$M_HKLIN\"  HKLOUT \"$CAD_HKLOUT\" "
if { $fof_sig == "F" } {
  WriteFile [set cad_tmp_script [GetTmpFileName -ext _com]]\
          "monitor BRIEF
	labin file 1 -
	    E1 = PHIB 
	labout file 1 -
	    E1 = PHIB 
	ctypin file 1 -
	    E1 = P 
	labin file 2 -
	    E1 = $FP -
	    E2 = $SIGFP -
	    E3 = $FOMM 
	labout file 2 -
	    E1 = $FP -
	    E2 = $SIGFP -
	    E3 = FOM 
	ctypin file 2 -
	    E1 = F -
	    E2 = Q -
	    E3 = W 
          "
} else {
  WriteFile [set cad_tmp_script [GetTmpFileName -ext _com]]\
	"monitor BRIEF
	labin file 1 -
	    E1 = PHIB 
	labout file 1 -
	    E1 = PHIB 
	ctypin file 1 -
	    E1 = P 
	labin file 2 -
	    E1 = $FP -
	    E2 = $SIGFP -
	    E3 = $FOMM -
	    E4 = 2FOFCWT
	labout file 2 -
	    E1 = $FP -
	    E2 = $SIGFP -
	    E3 = FOM -
	    E4 = 2FOFCWT
	ctypin file 2 -
	    E1 = F -
	    E2 = Q -
	    E3 = W -
	    E4 = F
	"
}
set status [Execute $cadcmd $cad_tmp_script program_status report ]
       if { $KEEP_MOD }  {

	 } else {
	DeleteFile $HKLOUT
      MoveFile $CAD_HKLOUT $HKLOUT
}

}
}

##################################################
#EXECUTE DM
##################################################

if { $DM } {
	set DM_T [GetTmpFileName -ext _mtz]
	set DM_FP "FP"	
	set DM_SFP "SIGFP"
	if { [ regexp DMR $OASIS_MODE ] } {
	set DM_FP $FP	
	set DM_SFP $SIGFP
		if { $fof_sig == "T" } {
		set DM_FP "2FOFCWT"
		}
}
	set dmcmd "[BinPath dm]"
	if { $KEEP_MOD && $MOD } {
	if { [ regexp M_MER $MOD_MOD ] } {
	append dmcmd " HKLIN \"$M_HKLOUT\" HKLOUT \"$DM_T\" "
}	
	if { [ regexp M_FOM $MOD_MOD ] } {
	append dmcmd " HKLIN \"$CAD_HKLOUT\" HKLOUT \"$DM_T\" "
}	
	} else {
	append dmcmd " HKLIN \"$HKLOUT\" HKLOUT \"$DM_T\" "
}
	WriteFile [set dm_tmp_script [GetTmpFileName -ext _com]]\
	"mode -
	SOLV
	combine PERT
	scheme ALL
	ncycles -
    	AUTO
	solc $solc
	ncsmask
	LABIN  FP=$DM_FP SIGFP=$DM_SFP PHIO=PHIB FOMO=FOM
	LABOUT  FDM=FDM PHIDM=PHIDM FOMDM=FOMDM
	RSIZE 80
	END
	"
	set status [Execute $dmcmd $dm_tmp_script program_status report ]
	set rfree "[BinPath freerflag]"
	append rfree " HKLIN \"$DM_T\" HKLOUT \"$DM_HKLOUT\""
	WriteFile [set dm_t_script [GetTmpFileName]]\
	"FREERFRAC 0.05"
	set status [Execute $rfree $dm_t_script program_status report ]
	DeleteFile $dm_t_script
	DeleteFile $DM_T
}