SimData.pm Show Source

The SimData package is the base class for the Ensemble package and manages common data elements. File names and options can be set as parameters for the native PDB structure, sequence file, fragment list and template structure for loop/fragment modeling. The package automatically creates and maintains objects associated with these parameters for use in ensemble based simulation and minimization runs. 

new(dir)
creates a new SimData object with the working directory given as argument. The default configuration file is read automatically if present. 
set(parameters)
sets new parameters or modifies existing ones
 
save()
saves all parameters to the default configuration file if new parameters have been set or changed
 
readConfig([file])
reads a configuration file. If no argument is given it reads the default configuration file.
 
writeConfig([file])
writes all parameters to a configuration file. If no argument is given the parameters are written to the default configuration file
 
$fraglist = getFragList()
returns a fragment list object generated from the fragment list parameter fraglist in string format
 
$mol = getFragRef()
returns a Molecule object created from the fragref parameter containing a PDB file name for the reference template structure used in fragment/loop modeling
 
$seq = getSeq()
returns a Sequence object created from the parameter seq describing a MONSSTER sequence file
 
$mol = getNatPDB()
returns a Molecule object created from the natpdb parameter containing a file name for the native structure. 
dir
ensemble working directory
 
par -> { fraglist fragref hsdlist hselist 
         seq natpdb }
parameters in text string form that are used to create corresponding objects when requested
 
obj -> { fraglist fragref seq natpdb }
object references for objects created from the corresponding parameter values
GenUtil.pm  Molecule.pm  MONSSTER.pm
Michael Feig, Brooks group, TSRI