#!/usr/bin/env ccp4-python

import sys
from CCP4pipeline import Control

keywords = """
<key name="title"        text default="nautilus auto-build"></key>
<key name="mtzin"        text compulsory>Input MTZ (post density mod)</key>
<key name="seqin"        text compulsory>Input sequence file</key>
<key name="pdbin"        text>Initial model to extend</key>
<key name="pdbout"       text default="nautilus.pdb"></key>
<key name="colin-fo"     text list compulsory>Observed F/sigma</key>
<key name="colin-hl"     text list>HL coeffs</key>
<key name="colin-phifom" text list>PHI/FOM</key>
<key name="colin-fc"     text list>Initial map coeffs scaled to F</key>
<key name="colin-free"   text list>Free-R flag</key>
<key name="cycles"       int default="5">Number of build/refine cycles</key>
<key name="nautilus-anisotropy-correction"     bool></key>
<key name="nautilus-resolution"                float default="2.0" ></key>
<key name="pdbin-ref"     text list>Reference data</key>
<key name="refmac-twin"   bool default="false"></key>
<key name="refmac-mlhl"   bool default="true" ></key>
<key name="refmac-weight" float></key>
<key name="refmac-colin-hl"     text list>HL coeffs</key>
<key name="prefix"        text default="nautilus/"></key>
<key name="verbose"       int></key>
<key name="nautilus-keyword" text multiple></key>
<key name="refmac-keyword"   text multiple></key>
"""

#
# Nautilus script template (1st cycle)
#

nautilus_1st = ( 'cnautilus', '-stdin', '''
title  <=title>

<if pdbin-ref>pdbin-ref <=pdbin-ref></if>

seqin <=seqin>

mtzin <=mtzin>
colin-fo <=colin-fo>
<if colin-hl    >colin-hl     <=colin-hl    ></if>
<if colin-phifom>colin-phifom <=colin-phifom></if>
<if colin-fc    >colin-fc     <=colin-fc    ></if>
<if colin-free  >colin-free   <=colin-free  ></if>

<if pdbin>pdbin <=pdbin></if>

pdbout <=build-pdbout>

<if nautilus-anisotropy-correction>anisotropy-correction</if>

resolution <=nautilus-resolution>

<if verbose>verbose <=verbose></if>

<foreach nautilus-keyword><=.>
</foreach>
''' )

#
# Nautilus script template (nth cycle)
#

nautilus_nth = ( 'cnautilus', '-stdin', '''
title  <=title>

<if pdbin-ref>pdbin-ref <=pdbin-ref></if>

seqin <=seqin>

mtzin <=refine-mtzout>
colin-fo <=colin-fo>
colin-fc FWT,PHWT
<if colin-free  >colin-free   <=colin-free  ></if>

pdbin <=refine-pdbout>

pdbout <=build-pdbout>

<if nautilus-anisotropy-correction>anisotropy-correction</if>

resolution <=nautilus-resolution>

<if verbose>verbose <=verbose></if>

<foreach nautilus-keyword><=.>
</foreach>
''' )

#
# Refmac script template
#

refmac_all = ( 'refmac5', '''
HKLIN  <=mtzin>         XYZIN  <=build-pdbout>
HKLOUT <=refine-mtzout> XYZOUT <=refine-pdbout>
''', '''
title  <=title>
ncyc 10
labin -
  <if refmac-mlhl="1"> -
    <if colin-hl> -
      HLA=<=colin-hl/list[1]> HLB=<=colin-hl/list[2]> -
      HLC=<=colin-hl/list[3]> HLD=<=colin-hl/list[4]> -
    </if> -
    <if colin-phifom> -
      PHIB=<=colin-phifom/list[1]> FOM=<=colin-phifom/list[2]> -
    </if> -
    <if refmac-colin-hl> -
      HLA=<=refmac-colin-hl/list[1]> HLB=<=refmac-colin-hl/list[2]> -
      HLC=<=refmac-colin-hl/list[3]> HLD=<=refmac-colin-hl/list[4]> -
    </if> -
  </if> -
  <if colin-free>FREE=<=colin-free/list[1]></if> -
  FP=<=colin-fo/list[1]> SIGFP=<=colin-fo/list[2]>
<if    (refmac-weight)>weight MATRIX <=refmac-weight></if>
<if not(refmac-weight)>weight AUTO            </if>
<if refmac-twin="1">twin</if>
make check NONE
PNAME nautilus
DNAME nautilus
<foreach refmac-keyword><=.>
</foreach>
END
''' )

#
# Pipeline control program
#

control = Control()
control.parse_input( keywords )
print control.display_params( "nautilus-pipeline v0.3" )

prefix = control.xml.get( "prefix" )
if ( prefix[-1:] == "/" ): control.mkdir( prefix )
control.xml.set( "build-pdbout", prefix+"build.pdb" )
control.xml.set( "refine-pdbout", prefix+"refine.pdb" )
control.xml.set( "refine-mtzout", prefix+"refine.mtz" )

control.run_program_template( nautilus_1st )
control.run_program_template( refmac_all )
for i in range( 1, int(control.xml.get("cycles")) ):
  control.run_program_template( nautilus_nth )
  control.run_program_template( refmac_all )
control.copy( control.xml.get("refine-pdbout"), control.xml.get("pdbout") )