# Purpose : align a single sequence with several structures
#
# Input   : SEGFILE, KNOWNS, SEQUENCE
#
# Output  : alignment in file ALNFILE


SUBROUTINE ROUTINE = 'align_strs_seq'

# SET OUTPUT = 'SHORT'

# Read the sequences of structures from the specs in SEGFILE:
READ_ALIGNMENT FILE = SEGFILE, ALIGN_CODES = KNOWNS

# Only align structures if there's more than one:
IF ARGUMENTS = NUMB_OF_SEQUENCES 1, OPERATION = 'GT'

  # do a multiple sequence alignment of structures:
  # SET MATRIX_FILE = '${LIB}/as1.sim.mat'
  MALIGN GAP_PENALTIES_1D = -600 -400

  # do a multiple structural alignment of structures:
  MALIGN3D GAP_PENALTIES_3D = 0.0 2.0, FIT_ATOMS = 'CA'

END_IF

# remember the number of structures
SET ALIGN_BLOCK = NUMB_OF_SEQUENCES

# add the sequence of the unknown to the sequence/alignment arrays containing
# the aligned structures:
READ_ALIGNMENT FILE = SEGFILE, ALIGN_CODES = ALIGN_CODES SEQUENCE, ADD_SEQUENCE = on
SET ADD_SEQUENCE = off

# align the last sequence with the fixed alignment of structures:
ALIGN GAP_PENALTIES_1D = -600 -400

# write the alignment to a file ALNFILE
WRITE_ALIGNMENT FILE = ALNFILE

# do some sequence comparisons:
ID_TABLE

RETURN
END_SUBROUTINE