REINDEX_RESTRAINTS -- renumber MODEL2 restraints for MODEL

Requirements:

restraints & MODEL & MODEL2

Description:

This command renumbers atom indices in all restraints in memory. It is expected that the input restraints refer to MODEL2; the re-indexed restraints will correspond to MODEL. Both MODEL and MODEL2 have to be in memory. Only those restraints that have all atoms in MODEL will be selected. You can remove the others by CONDENSE_RESTRAINTS. This command is useful when the old restraints have to be used while changing from one topology model to another.

Example:

# Example for: REINDEX_RESTRAINTS

# This will reindex restraints obtained previously for a simpler topology so 
# that they will now apply to a more complicated topology.

# Generate the model for the simpler topology (CA only in this case):
READ_TOPOLOGY   FILE = '$(LIB)/top_ca.lib'
READ_PARAMETERS FILE = '$(LIB)/par_ca.lib'
SET TOPOLOGY_MODEL = 7
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ca', ;
                ALIGN_CODES = ALIGN_CODES '1fas-ca'
GENERATE_TOPOLOGY SEQUENCE = '1fas-ca'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
WRITE_MODEL FILE = '1fas.ca'

# Generate the restraints for the simpler topology:
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
WRITE_RESTRAINTS FILE = '1fas-ca.rsr'
ENERGY

# Generate the model for the more complicated topology:
READ_TOPOLOGY   FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
SET TOPOLOGY_MODEL = 3
READ_MODEL FILE = '1fas'
SET ADD_SEQUENCE = off
SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ;
                ALIGN_CODES = ALIGN_CODES '1fas-ini'
GENERATE_TOPOLOGY SEQUENCE = '1fas-ini'
TRANSFER_XYZ
WRITE_MODEL FILE = '1fas.ini'

READ_MODEL2 FILE = '1fas.ca'
REINDEX_RESTRAINTS
WRITE_RESTRAINTS FILE = '1fas.rsr'
ENERGY