# Purpose: calculate model(s) using some restraints, possibly obtained
#          from the alignment of a sequence with related structure(s).
#
# Input  : ALNFILE, KNOWNS, SEQUENCE, DATABASE_DIRECTORY,
#           DEVIATION, TOPLIB, PARLIB, GENERATE_METHOD, RAND_METHOD, 
#           MD_LEVEL
#
# Output : stereochemical and homology restraints in file CSRFILE
#          schedule in file SCHFILE, final model in file FINAL_MODEL,
#          debugging output in .D
#          MODEL, CSRFILE, SCHFILE, FINAL_MODEL, REFINED_MODEL

SUBROUTINE ROUTINE = 'model'

  # get the filenames from SEQUENCE:
  CALL ROUTINE = 'getnames'

  # getting restraints and the initial model from the alignment:
  CALL ROUTINE = 'homcsr'

  # exit early?
  IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE'
    RETURN
  END_IF

  # Read all restraints once for the whole job (except when loops are
  # done when restraints are read for each *.B9999???? model):
  CALL ROUTINE = 'rd_restraints'

  # getting model(s) (topology library must be in memory; ensured
  # now by one of the three GENERATE_METHOD routines):
  CALL ROUTINE = 'multiple_models'

  IF ARGUMENTS=FINAL_MALIGN3D 1, OPERATION='EQ'

      SET FILE_EXT = PDB_EXT
      SET EDIT_FILE_EXT = PDB_EXT '_fit.pdb'
# --- MALIGN3D on all templates and all .B models:
      CALL ROUTINE = 'fit_models_on_template'
      IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'EQ'
        DO ID2 = STARTING_MODEL ENDING_MODEL 1
          CALL ROUTINE = 'fit_loop_models'
        END_DO
      END_IF

  END_IF

RETURN
END_SUBROUTINE

#
# _fit.pdb extension for the output whole models, superposed on the template
#
# Input: ALNFILE, KNOWNS, SEQUENCE, ROOT_NAME, FILE_EXT
#
SUBROUTINE ROUTINE = 'fit_models_on_template'
      SET ADD_SEQUENCE = OFF
      READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE
      SET FILE_ID = '.B'
      EXPAND_ALIGNMENT EXPAND_CONTROL = 9999 9999 STARTING_MODEL ENDING_MODEL 0
      # To take care of the '.' in segment specs:
      WRITE_ALIGNMENT FILE = '.tmp.ali', ALIGNMENT_FORMAT = 'PIR'
      READ_ALIGNMENT FILE = '.tmp.ali'
      DELETE_FILE FILE = '.tmp.ali'
      # superpose all on the first structure in the alignment:
      COMPARE FIT = on, OUTPUT = 'SHORT'
      MALIGN3D GAP_PENALTIES_3D = 0 3, WRITE_WHOLE_PDB = off, WRITE_FIT = on, ;
               FIT = off, CURRENT_DIRECTORY = on
RETURN
END_SUBROUTINE

#
# _fit.pdb extension for the output loop models, superposed on their whole .B*_fit.pdb structure
#
# Input: ID2
#
SUBROUTINE ROUTINE = 'fit_loop_models'
    READ_MODEL FILE = 'default', FILE_EXT = '_fit.pdb', FILE_ID = '.B', ROOT_NAME = SEQUENCE, ID1 = 9999
    SEQUENCE_TO_ALI ALIGN_CODES = SEQUENCE, ATOM_FILES = LOOP_MODEL, ADD_SEQUENCE = off
    SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES SEQUENCE, ATOM_FILES = ATOM_FILES LOOP_MODEL
    DO ID1 = LOOP_STARTING_MODEL,LOOP_ENDING_MODEL,1
      READ_MODEL2 FILE = 'default' , FILE_EXT = '', FILE_ID = '.BL'
      PICK_ATOMS PICK_ATOMS_SET = 1, ATOM_TYPES = 'CA'
      SUPERPOSE FIT = 'ON'
      WRITE_MODEL2 FILE = 'default', FILE_EXT = '_fit.pdb', FILE_ID = '.BL'
    END_DO
    RETURN
END_SUBROUTINE