This module currently has limited function and no standalone capability, though this may be added with time. It is
designed for use with other modules. The disorder Class can be given a sequence and will run the appropriate
disorder prediction software and store disorder prediction results for use in other programs. The sequence will have
any gaps removed.
Currently six disorder prediction methods are implemented:
needs to be given as
IUPred2 : From V1.5.0, IUPred2 API calls can be made to https://iupred2a.elte.hu/iupred2a/. The IUPred method
redox. This can also be triggered by
iuanchor2 (or simply
locally. It is available on request from the IUPred website and any use of results should cite the method. (See
http://iupred.enzim.hu/index.html for more details.) IUPred returns a value for each residue, which by default,
is determined to be disordered if > 0.5. The IUPred method needs to be given as
IUPred: Dosztanyi Z, Csizmok V, Tompa P & Simon I (2005). J. Mol. Biol. 347, 827-839. This has to be installed
This can also be triggered by setting
returns a list of disordered regions. You must have a live web connection and
FoldIndex: This is run directly from the website (http://bioportal.weizmann.ac.il/fldbin/findex) and more simply
curl on your system to use this method!
locally. It is available on request from the ANCHOR website and any use of results should cite the method. (See
http://anchor.enzim.hu/ for more details.) ANCHOR returns a probability value for each residue, which by default,
is determined to be disordered if > 0.5.
ANCHOR: Meszaros B, Simon I & Dosztanyi Z (2009). PLoS Comput Biol 5(5): e1000376. This has to be installed
#X-Y = disordered region; &X-Y = ordered region [0.0]
Parse: Parsed disorder from protein sequence name, e.g. DisProt download.
IUScoreDir: From V1.2.0, pre-calculated disorder scores can be loaded from a file (see below). To activate this mode,
disorder=X setting should match the
<DISORDER> part of the filename (below). If this is one of the other
recognised disorder predictors above, missing files will be generated if possible. Otherwise, files must be present
for disorder prediction to occur.
For IUPred, the individual residue results are stored in Disorder.list['ResidueDisorder']. For all methods, the
disordered regions are stored in Disorder.list['RegionDisorder'] as (start,stop) tuples.
V1.2.0 introduced the optional use of
IUScoreDir/ to save and/or (re)load lists of disorder scores. These are files
named <ACC>.<DISORDER>.txt where <ACC> is the accession number of the protein. If
md5acc=T then an md5 hash of the
sequence is used instead:
disorder=X : Disorder method to use (iupred2/iupred/foldindex/anchor/anchor2/parse) [
strict=T/F : Whether to exit with error if disorder method not found [
iucut=X : Cut-off for score-based method (e.g. IUPred/ANCHOR) results [
iumethod=X : IUPred method to use (long/short/redox/anchor) [
sequence=X : Sequence to predict disorder for (autorun) 
name=X : Name of sequence to predict disorder for 
minregion=INT : Minimum length of an ordered/disordered region [
minorder=INT : Minimum length of an ordered region; over-rides minregion if >-1 [
smoothing=X : Smoothing mode for
minorder=X smoothing (foldfirst/sequence) [
iuscoredir=PATH : Path in which to save protein acc.DISORDER.txt score files for re-use 
discalculate=T/F: Whether to try to calculate disorder if existing score not loaded [
md5acc=T/F : Whether to use md5sum hexdigest hashing of sequence in place of accession numbers [
iupath=PATH : The full path to the IUPred executable [
anchor=PATH : Full path to ANCHOR executable 
filoop=INT : Number of times to try connecting to FoldIndex server [
fisleep=INT : Number of seconds to sleep between attempts [
iuchdir=T/F : Whether to change to IUPred directory and run (True) or rely on IUPred_PATH env variable [
History Module Version History
# 0.0 - Initial Compilation.
# 0.1 - Added parsing of disorder from name as an option instead of disorder prediction
# 0.2 - Added Folded tuple as well as disordered
# 0.3 - Added PrintLog opt attribute
# 0.4 - Added option for correct use of IUPred_PATH environment variable
# 0.5 - Added Minimum length of an ordered/disordered region
# 0.6 - Added ANCHOR prediction.
# 0.7 - Added globProportion calculation.
# 0.8 - Added makeRegions() method.
# 1.0.0 - Added random disorder function and elevated to v1.x as fully functional for SLiMSuite
# 1.1.0 - Added strict option for disorder method selection. Added minorder=X.
# 1.2.0 - Added saving and loading scores to IUScoreDir/.
# 1.3.0 - Switched default behaviour to be md5acc=T.
# 1.4.0 - Fixed up disorder=parse and disorder=foldindex.
# 1.5.0 - Added iupred2 and anchor2 parsing from URL using accnum. Made default disorder=iushort2.
# 1.5.1 - Fixed iupred2 URL generation error.