ProteinInteraction [version 1.0.0.0]

Module AssemblyName: file:///G:/GCModeller/manual/bin/pitr.exe
Root namespace: ProteinTools.Interactions.CLI

All of the command that available in this program has been list below:

Function API Info
–align.LDM
–Contacts
–CrossTalks.Probability
–Db.From.Exists
–domain.Interactions
–interact.TCS
–Merge.Pfam
–predicts.TCS
–Profiles.Create
–ProtFasta.Downloads
–ProtFasta.Downloads.Batch
–signature
–SwissTCS.Downloads

Commands


Help for command ‘–align.LDM’:

Prototype: ProteinTools.Interactions.CLI::Int32 GenerateModel(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --align.LDM /in <source.fasta>
Example: pitr --align.LDM
Help for command ‘–Contacts’:

Prototype: ProteinTools.Interactions.CLI::Int32 Contacts(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --Contacts /in <in.DIR>
Example: pitr --Contacts
Help for command ‘–CrossTalks.Probability’:

Prototype: ProteinTools.Interactions.CLI::Int32 CrossTalksCal(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --CrossTalks.Probability /query <pfam-string.csv> /swiss <swissTCS_pfam-string.csv> [/out <out.CrossTalks.csv> /test <queryName>]
Example: pitr --CrossTalks.Probability
Help for command ‘–Db.From.Exists’:

Prototype: ProteinTools.Interactions.CLI::Int32 DbMergeFromExists(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --Db.From.Exists /aln <clustal-aln.DIR> /pfam <pfam-string.csv>
Example: pitr --Db.From.Exists
Help for command ‘–domain.Interactions’:

Prototype: ProteinTools.Interactions.CLI::Int32 DomainInteractions(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --domain.Interactions /pfam <pfam-string.csv> /swissTCS <swissTCS.DIR>
Example: pitr --domain.Interactions
Help for command ‘–interact.TCS’:

Prototype: ProteinTools.Interactions.CLI::Int32 TCSParser(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --interact.TCS /door <door.opr> /MiST2 <mist2.xml> /swiss <tcs.csv.DIR> /out <out.DIR>
Example: pitr --interact.TCS
Help for command ‘–Merge.Pfam’:

Prototype: ProteinTools.Interactions.CLI::Int32 MergePfam(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --Merge.Pfam /in <in.DIR>
Example: pitr --Merge.Pfam
Help for command ‘–predicts.TCS’:

Prototype: ProteinTools.Interactions.CLI::Int32 Predicts(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --predicts.TCS /pfam <pfam-string.csv> /prot <prot.fasta> /Db <interaction.xml>
Example: pitr --predicts.TCS
Help for command ‘–Profiles.Create’:

Prototype: ProteinTools.Interactions.CLI::Int32 CreateProfiles(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --Profiles.Create /MiST2 <MiST2.xml> /pfam <pfam-string.csv> [/out <out.csv>]
Example: pitr --Profiles.Create
Help for command ‘–ProtFasta.Downloads’:

Prototype: ProteinTools.Interactions.CLI::Int32 ProtFastaDownloads(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --ProtFasta.Downloads /in <sp.DIR>
Example: pitr --ProtFasta.Downloads
Help for command ‘–ProtFasta.Downloads.Batch’:

Prototype: ProteinTools.Interactions.CLI::Int32 ProtFastaDownloadsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --ProtFasta.Downloads.Batch /in <sp.DIR.Source>
Example: pitr --ProtFasta.Downloads.Batch
Help for command ‘–signature’:

Prototype: ProteinTools.Interactions.CLI::Int32 SignatureGenerates(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --signature /in <aln.fasta> [/p-cut <0.95>]
Example: pitr --signature
Help for command ‘–SwissTCS.Downloads’:

Prototype: ProteinTools.Interactions.CLI::Int32 DownloadEntireDb(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\pitr.exe --SwissTCS.Downloads /out <out.DIR>
Example: pitr --SwissTCS.Downloads