Manual page for apps.BBQ program

BBQ reconstructs protein backbone atoms based on CA coordinates

-bbq.fix_r12=<T|F> Try to strech or shorten CA-CA virtual bonds to match 3.8A constraint
-bbq.hashing_class=<class name> class used to index quadrilaterals. Necessary only if you implemented your own indexing class in Java (in 99.9% you don’t need to use this option).
-bbq.library=<file name> an input file with a quadrilaterals library (optional). If not given, a standard library will be used.
-h print a brief summary of available options
-help=<name-part> print a help message on the screen - ANSI terminal version with visual enhancements. If <name-part> argumen is given, the program will print only these options that contains that substring
-help.dox=<name> print a help message in doxygen (*.dox) format on the screen for the BBQ program
-help.md=<name> print a help message in markdown (*.md) format on the screen
-help.option=<option-name> print a help message for a single option on the screen.
-help.plain=<name-part> print a help message on the screen - plain text version. If <name-part> argumen is given, the program will print only these options that contains that substring
-in.pdb=<file name> an input data in the PDB format. This option accepts the following types of input:
- file in PDB format (possibly gzip’ped)
- several files in PDB format (possibly gzip’ped) - in this case you must use -in.pdb.comma_separated option to let the program know to split the input string
- just PDB code, with -online option the data is downloaded from www.rcsb.org
- just PDB code, with -in.pdb.search_path option the program will look for the right file
-in.pdb.all_models=<T|F> forces PDB reader to take all the models from a PDB file.
-in.pdb.comma_separated forces -in.pdb option to look for several PDB file names, separated by a comma. In This case any of the file names may not contain a comma character.
Example:
-in.pdb.comma_separated -in.pdb=2gb1.pdb,2aza.pdb
-in.pdb.create_bu=<T|F> forces PDB reader to create biological unit for each structure. Biological unit creation is solely based on information stored in the PDB file header.Any error in the header will affect the resulting biological unit. This option fores PDB reading mechanism to create an array of structures for each structure (MODEL data) in the given PDB. Therefore (to avoid handling too many molecules) it is advised NOT to use -in.pdb.all_models combined with this option.
-in.pdb.dir=<dir name> provides directory with PDB files
-in.pdb.file_mask=<mask_regexp> provides a mask for directory-based input, e.g. for -input_pdb_dir option. Without file_mask, directory related options try to read all possible files in a directory. This is a way to change it and narrow the selection. In general a file mask should follow the rules of regular expression in Java. The only exceptions are >.< (dot character) and >*< (asterix) that should be given explicitly (with no escaping). Example masks are: *.pdb 1[ABC]*.pdb 1(MBA|;mba).pdb
-in.pdb.first_model_only=<T|F> forces PDB reader to take only the first model from a PDB file.
-in.pdb.online=<T|F> download a PDB file from www.rcsb.org rather than reading a file. In this case the parameter given to -ip must provide a valid four-character PDB code
-in.pdb.read_hydrogens=<T|F> forces PDB reader to read in all hydrogen atoms. This by default is switched off and all hydrogens are discarded
-in.pdb.search_path=<path string> provides a path where -ip and other PDB-reading options will look for a PDB data. In this case the parameter given to -ip must provide a valid four-character PDB code rather than a file name. Then, for the code (say, 1abc), several possible file locations will be tested, e.g:
PATH/1abc
PATH/1abc.pdb
PATH/1abc.pdb.gz
PATH/pdb1abc.ent
PATH/pdb1abc.ent.gz
PATH/1ABC
PATH/1ABC.PDB
PATH/ab/pdb1abc.ent
PATH/ab/pdb1abc.ent.gz
-in.pdb.skip_header=<T|F> skip a header when parsing a PDB file.
-mute suppress all messages from a given package or class, e.g. “-mute=jbcl.data.formats”, or “-mute=jbcl.calc.structural.Crmsd”. It is also possible to switch of a whole branch from the jbcl library, e.g. “-mute=jbcl.data” will mute all comming from jbcl.data.formats,jbcl.data.types, jbcl.data.dict and jbcl.data.basic. To switch all the messages, say: “-mute=jbcl” or simply “-mute” because the default behaviour is to mute everything. This option is executed AFTER -verbose, so user may increase verbosity level to a desired valueand then selectively switch off logging from some packages
-verbose=<integer> Sets up a verbosity level to a given value. The argument should be an integer from the rangefrom 0 (no messages at all, which is equivalent to -mute=jbcl) to 6 when everything is logged. See -mute for additional information.

EXAMPLES

      (1) Read a PDB file containing only CA atom, and rebuild a backbone.
    java BBQ -ip=8tlnE_ca.pdb