ssbio
  • Getting Started
    • Introduction
    • The basics
      • From a systems perspective
      • From a structures perspective
    • Modules & submodules
    • References
  • The GEM-PRO Pipeline
    • Introduction
    • Tutorials
      • GEM-PRO - Calculating Protein Properties
        • Imports
        • Initialization
        • Mapping gene ID –> sequence
        • Mapping representative sequence –> structure
        • Downloading and ranking structures
        • Computing and storing protein properties
        • Additional annotations
        • Global protein properties
        • Local protein properties
      • GEM-PRO - Genes & Sequences
        • Imports
        • Initialization of the project
        • Mapping sequence –> structure
        • Downloading and ranking structures
        • Creating homology models
        • Saving your GEM-PRO
      • GEM-PRO - List of Gene IDs
        • Imports
        • Initialization of the project
        • Mapping gene ID –> sequence
        • Mapping representative sequence –> structure
        • Downloading and ranking structures
        • Saving your GEM-PRO
      • GEM-PRO - SBML Model
        • Imports
        • Initialization of the project
        • Mapping gene ID –> sequence
        • Mapping representative sequence –> structure
        • Downloading and ranking structures
        • Creating homology models
        • Saving your GEM-PRO
        • Loading a saved GEM-PRO
    • Features
    • COBRApy model additions
      • COBRApy
      • ssbio
    • Use cases
      • From the “top-down”:
      • From the “bottom-up”
    • File organization
    • API
      • GEMPRO
    • Further reading
    • References
  • The Protein Class
    • Introduction
    • Tutorials
      • Protein - Structure Mapping, Alignments, and Visualization
        • Imports
        • Initialization of the project
        • Mapping sequence –> structure
        • Downloading and ranking structures
        • Loading and aligning new sequences
        • Some additional methods
        • Mapping sequence residue numbers to structure residue numbers
        • Viewing structures
        • Saving
    • Features
    • API
      • Protein
    • Further reading
  • The StructProp Class
    • Introduction
    • Tutorials
      • PDBProp - Working With a Single PDB Structure
        • Imports
        • Basic methods
      • FATCAT - Structure Similarity
        • Pairwise
        • All-by-all
    • Available functions
      • Sequence & structure-based predictions
      • Structure-based calculations or functions
    • API
      • StructProp
  • The SeqProp Class
    • Introduction
    • Tutorials
      • SeqProp - Protein Sequence Properties
        • Imports
        • Initialization of the project
        • Computing and storing protein properties
    • Available functions
      • Sequence-based predictions
      • Sequence-based calculations
    • API
      • SeqProp
  • Index: Software
    • Protein structure predictions
      • Homology modeling
        • I-TASSER
      • Transmembrane orientations
        • OPM
      • Kinetic folding rate
        • FOLD-RATE
    • Protein structure calculations
      • Secondary structure
        • DSSP
        • STRIDE
      • Solvent accessibilities
        • DSSP
        • FreeSASA
      • Residue depths
        • MSMS
      • Structural similarity
        • FATCAT
      • Various structure properties
      • Quality
      • Structure cleaning, mutating
    • Protein sequence predictions
      • Secondary structure
        • SCRATCH
      • Solvent accessibilities
        • SCRATCH
      • Thermostability
      • Transmembrane domains
        • TMHMM
      • Aggregation propensity
        • AMYLPRED2
    • Protein sequence calculations
      • Various sequence properties
        • EMBOSS pepstats
      • Sequence alignment
        • EMBOSS needle
  • Index: Tutorials
    • Testing
    • The GEM-PRO Pipeline
    • The Protein Class
    • The StructProp Class
    • The SeqProp Class
    • Other tutorials
  • Python API
    • ssbio.pipeline.gempro
      • GEMPRO
    • ssbio.databases
      • PDBProp
      • PISA
      • SWISSMODEL
      • UniProtProp
      • KEGGProp
    • ssbio.protein.structure.utils
      • CleanPDB
      • MutatePDB
      • DOCK
    • ssbio.protein.structure.properties
      • Structure Residues
    • ssbio.protein.sequence.utils
      • Sequence Alignment
      • Sequence BLAST
    • ssbio.protein.sequence.properties
      • Thermostability
ssbio
  • Docs »
  • Overview: module code
  • Edit on GitHub

All modules for which code is available

  • ssbio.core.object
  • ssbio.core.protein
  • ssbio.databases.kegg
  • ssbio.databases.pdb
  • ssbio.databases.pisa
  • ssbio.databases.swissmodel
  • ssbio.databases.uniprot
  • ssbio.pipeline.gempro
  • ssbio.protein.sequence.properties.aggregation_propensity
  • ssbio.protein.sequence.properties.kinetic_folding_rate
  • ssbio.protein.sequence.properties.residues
  • ssbio.protein.sequence.properties.scratch
  • ssbio.protein.sequence.properties.thermostability
  • ssbio.protein.sequence.properties.tmhmm
  • ssbio.protein.sequence.seqprop
  • ssbio.protein.sequence.utils.alignment
  • ssbio.protein.sequence.utils.blast
  • ssbio.protein.structure.homology.itasser.itasserprep
  • ssbio.protein.structure.homology.itasser.itasserprop
  • ssbio.protein.structure.properties.dssp
  • ssbio.protein.structure.properties.fatcat
  • ssbio.protein.structure.properties.freesasa
  • ssbio.protein.structure.properties.msms
  • ssbio.protein.structure.properties.opm
  • ssbio.protein.structure.properties.residues
  • ssbio.protein.structure.structprop
  • ssbio.protein.structure.utils.cleanpdb
  • ssbio.protein.structure.utils.dock

© Copyright 2017, Nathan Mih. Revision d367e283.

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