<name> = library ( <input form><modifier>* )
| <input form> | = | file_pdb (" <Cformat>") | ||
| = | file_bin (" <Cformat>") | |||
| = | file_rnaml (" <File name>") | |||
| = | socket_bin (" <address>" <port> " <Cformat>") | |||
| <modifier> | = | strip( <residue>+ ) | change_id( " <char1>" , " <char2>" ) |
Before using a library object, one must specify the files constituting the library. For now, only one type of files is available: the PDB format. All input files must be named exactly the same way, i.e. a name that works as a C format string. A filename may be given followed by a ``counter'' so that increasing the counter will produce a new filename, i.e. "anticodon-%04d.pdb" where "%04d" (the counter) means that the number will be four digits long and padded with ``0''. File numbers must begin at 1 and must be consecutive.
Example:
antic_lib = library (file_pdb ("/home/foo/ANTI/anticodon-%04d.pdb"))
will lead to these filenames:
/home/foo/ANTI/anticodon-0001.pdb /home/foo/ANTI/anticodon-0002.pdb /home/foo/ANTI/anticodon-0003.pdb /home/foo/ANTI/anticodon-0004.pdb ... |
As the libraries are usally constructed independently of the main modeling project, it is frequent that chain IDs of loaded residues do not correspond to the chain IDs of the main project's residues. It is possible to specify new chain IDs with chain_id for the loaded residues (if you don't, the program will not recognize the library).
It is possible to ignore some residues that are present in the library files by using the strip option. The user is responsible to properly handle those residues with some other fragment generators. This is for example useful when careful handling of a ``joint'' between two or more fragments is required.
Example:
kiss = library
(
file_pdb ("/home/foo/PDB/kiss-%05d.pdb")
change_id (" ", "B")
strip (A37)
strip (A51)
strip (A60)
)
|