# Purpose: to construct typical comparative modelling restraints
#
# Input  : ALNFILE, SEQUENCE, MODEL, CSRFILE (necessary)
#
# Input  : KNOWNS, DATABASE_DIRECTORY (for homology restraints)
# 
# Input  : TOPLIB, PARLIB
#
# Output : stereochemical and homology restraints in file CSRFILE
#

SUBROUTINE ROUTINE = 'homcsr'
  # Check the alignment
  READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE

# Since in general we do not want to loose the original alignment file
# (which is usually not a temporary scratch file):

  STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPERATION = 'EQ'
    # Accelrys code here (Azat, you may want to add the .tmp.ali part so that
    # you do not change the input alignment file, unless you want to have it
    # changed here for some other use elsewhere):
    WRITE_ALIGNMENT # FILE = '.tmp.ali'
    READ_ALIGNMENT
    # DELETE_FILE FILE = '.tmp.ali'
  END_IF


  CHECK_ALIGNMENT

  # make topology and build/read the atom coordinates:
  CALL ROUTINE = GENERATE_METHOD

  # exit early?
  IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ'
    RETURN
  END_IF

  # make and write the stereochemical, homology, and special restraints?
  IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'NE'
    CALL ROUTINE = 'mkhomcsr'
  END_IF

  RETURN
END_SUBROUTINE




SUBROUTINE ROUTINE = 'mkhomcsr'

  MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS = OFF

  # go_to 'next'

  # SET ALIGNMENT_FORMAT = 'PIR'
  READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE

  MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_RESTRAINTS = ON

  SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINTS = 5

  MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RESTRAINTS = ON

  MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RESTRAINTS = ON

  MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RESTRAINTS = ON

  MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RESTRAINTS = ON
  
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RESTRAINTS = ON

  SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINTS = 5

  # Only do the standard residue types for CA, N, O, MNCH, SDCH dst rsrs
  # (no HET or BLK residue types):
  SET RES_TYPES = 'STD'

  SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_DISTANCE
  SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = on
  SET RESTRAINT_GROUP = 9
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'
  
  SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DISTANCE
  SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = off
  SET RESTRAINT_GROUP = 10
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'

  SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_DISTANCE
  SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = off
  SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'

  SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_DISTANCE
  SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = on
  SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH'
  MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAINTS = 'ON'

  # Generate intra-HETATM and HETATM-protein restraints:
  CALL ROUTINE = 'hetatm_restraints'

  # Generate intra-BLK and BLK-protein restraints:
  CALL ROUTINE = 'blk_restraints'

  # Special restraints have to be called last so that possible cis-proline
  # changes are reflected in the current restraints:
  CALL ROUTINE = 'special_restraints'

  # label 'next'

  CONDENSE_RESTRAINTS

  WRITE_RESTRAINTS FILE = CSRFILE

  SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = on

  RETURN
END_SUBROUTINE


SUBROUTINE ROUTINE = 'hetatm_restraints'

  # Select MODEL=7 where you can specify stand. dev. explicitly
  SET RESTRAINT_TYPE = 'distance'
  SET DISTANCE_RSR_MODEL = 7
  SET MAXIMAL_DISTANCE = 7.0
  SET ADD_RESTRAINTS = ON
  SET RESTRAINT_GROUP = 27

  # Inter- and intra- residue:
  SET RESTRAINT_STDEV = 0.2 0.0
  # Note: there are going to be duplicated HETATM-HETATM restraints:
  SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = off
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TYPES = 'ALL'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TYPES = 'HET'
  MAKE_RESTRAINTS

  RETURN
END_SUBROUTINE


# Re-define the auxillary restraints routine to include the restraints between
# the protein and the BLK residues. The BLK atoms will be restrained by their 
# distances to the protein CA atoms that are within MAXIMAL_DISTANCE angstroms 
# of the selected BLK atoms in the templates. Note: this only works because 
# the BLK atoms have unique atom names.
SUBROUTINE ROUTINE = 'blk_restraints'

  # To derive restraints from all (one) templates, comment out (uncomment):
  # READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = '3b5c' SEQUENCE

  # Select MODEL=7 where you can specify stand. dev. explicitly
  SET RESTRAINT_TYPE = 'distance'
  SET DISTANCE_RSR_MODEL = 7
  SET MAXIMAL_DISTANCE = 10.0
  SET ADD_RESTRAINTS = ON
  SET RESTRAINT_GROUP = 27

  # Intra-residue:
  SET RESTRAINT_STDEV = 0.05 0.0
  SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = on
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL',  RES_TYPES = 'BLK'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL',  RES_TYPES = 'BLK'
  MAKE_RESTRAINTS

  # Inter-residue:
  SET RESTRAINT_STDEV = 0.2 0.0
  SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = off
  # There may be some duplicated CA BLK - CA BLK restraints:
  PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA',  RES_TYPES = 'ALL'
  PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TYPES = 'BLK'
  MAKE_RESTRAINTS

  # Clean after yourself:
  DELETE_ALIGNMENT

  RETURN
END_SUBROUTINE