Sequence.pm Show Source

The Sequence package manages protein sequence information (residue type and secondary structure). It allows reading and writing of MONSSTER sequence files and methods are available to set secondary structure information from prediction output or DSSP. 

new([seqstring|molecule][,fraglist])
creates a new Sequence object. An abbreviated sequence string or a Molecule object can be given as arguments to extract the sequence. A fragment list can be given as a second argument to complete fragments missing in a molecule structure from abbreviated sequence strings. 
readMONSSTER(file)
read a sequence from a MONSSTER sequence file
 
writeMONSSTER(file)
write the current sequence to a MONSSTER sequence file
 
$string = abbrevSeq()
generates an abbreviated sequence string
 
$string = abbrevSec()
generates an abbreviated string for the secondary structure information
 
modifyResidueName(newreslist)
sets residue names to new names in the argument
 
setSecondary(index,type)
sets the secondary structure information for a specific residue
 
secFromOneFile(file)
extracts secondary structure information from a file containing single letter abbreviations
 
secFromPredict(filelist)
extracts secondary structure information from a list of file names containing output from common prediction servers
 
secFromDSSP(molecule)
sets secondary structure information from the output of the external DSSP program for the protein structure given as Molecule object argument
 
number = firstResNum()
number of first residue
 
number = lastResNum()
number of last residue
 
setValidResidues(fraglist)
sets the valid flag to 1 for residues in the fragment list and to 0 for residues outside the list
 
resetValidResidues([value])
sets the valid flag of all residues to the given value (default: 1)
 
$list = listFromValid(force)
returns a list of residues from the residues previously set with setValidResidues.
 
$index = getResidue(resnum)
returns the residue index for a residue number. A reference to a chain structure may be given as additional argument for multi-domain structures
 
readMoleculeChain(file)
read a sequence from a molecule chain 
sequence[] -> { residue secondary index valid }
sequence data
 
resinx[]
lookup table for residue index
GenUtil.pm  Molecule.pm
Michael Feig, Brooks group, TSRI