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Packages that use PolymerSet | |
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org.strbio.local | These classes are for running or exchanging data with local programs (other programs installed on your computer). |
org.strbio.mol | These classes represent objects or concepts useful to structural biologists. |
org.strbio.mol.lib | These classes represent conceptual objects used in structural biology algorithms. |
org.strbio.mol.lib.pred2ary | These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes. |
Uses of PolymerSet in org.strbio.local |
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Methods in org.strbio.local that return PolymerSet | |
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PolymerSet |
Muscle.runOnPolymerSet(PolymerSet p)
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PolymerSet |
Muscle.runOnPolymerSet(PolymerSet p,
java.lang.String options)
return a protein set resulting from running muscle on a protein set, with optional options to Muscle |
Methods in org.strbio.local with parameters of type PolymerSet | |
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PolymerSet |
Muscle.runOnPolymerSet(PolymerSet p)
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PolymerSet |
Muscle.runOnPolymerSet(PolymerSet p,
java.lang.String options)
return a protein set resulting from running muscle on a protein set, with optional options to Muscle |
Uses of PolymerSet in org.strbio.mol |
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Subclasses of PolymerSet in org.strbio.mol | |
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class |
ProfilePSISet
Class to represent a set of profiles with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential. |
class |
ProfileSet
Class to represent a set of proteins with profile information. |
class |
ProteinSet
Class to represent a set of proteins to be acted on in a group. |
Fields in org.strbio.mol declared as PolymerSet | |
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PolymerSet |
ThreadSet.folds
Folds being threaded. |
PolymerSet |
ThreadSet.seqs
Sequences being threaded. |
Methods in org.strbio.mol with parameters of type PolymerSet | |
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void |
PolymerSet.add(PolymerSet q)
add in another set of Polymers, without duplicating them. |
boolean |
PolymerSet.isEqual(PolymerSet y)
do 2 sets of Polymers contain the same Polymers? |
void |
AlignmentSet.load(java.io.BufferedReader infile,
PolymerSet seqs,
PolymerSet folds)
Load alignment out of new format file. |
void |
AlignmentSet.load(java.lang.String in_file,
PolymerSet seqs,
PolymerSet folds)
Load alignment out of new format file. |
Constructors in org.strbio.mol with parameters of type PolymerSet | |
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PolymerSet.PolymerEnumeration(java.io.BufferedReader inf,
Printf outf,
PolymerSet ps)
create an enumeration on a given file, with a given polymer set. |
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PolymerSet(PolymerSet y)
Create a set by copying another set, but not the polymers in it. |
Uses of PolymerSet in org.strbio.mol.lib |
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Subclasses of PolymerSet in org.strbio.mol.lib | |
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class |
FoldLibrary
A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library. |
class |
TOMFoldLibrary
The TOM fold library. |
class |
UserFoldLibrary
A standard fold library for threading, loaded in by the user. |
Uses of PolymerSet in org.strbio.mol.lib.pred2ary |
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Subclasses of PolymerSet in org.strbio.mol.lib.pred2ary | |
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class |
PCPSet
Class to represent a set of profiles with information for 2ary structure prediction. |
class |
PredictionSet
Class to represent a set of profiles being used in 2ary structure prediction as a prediction set. |
class |
TPSet
Class to represent a set of profiles being used in 2ary structure prediction; this might be either a training or prediction set. |
class |
TrainingSet
Class to represent a set of profiles being used in 2ary structure prediction as a training set. |
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