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VerMoUTH 0.15.1.dev77+gd0ec4df92 documentation
VerMoUTH 0.15.1.dev77+gd0ec4df92 documentation

Contents:

  • General Overview
  • Martinize 2 workflow
  • Technical background
    • Processor
    • Data
    • Graph algorithms
  • File formats
  • Tutorials
    • Basic usage
    • Elastic Networks
    • Gō models
    • Water biasing
    • Mutations and modifications
    • Adding new residues and links
    • Adding new modifications
  • vermouth
    • vermouth package
      • vermouth.bin package
        • vermouth.bin.martinize2 module
      • vermouth.data package
        • vermouth.data.data module
      • vermouth.dssp package
        • vermouth.dssp.dssp module
      • vermouth.gmx package
        • vermouth.gmx.gro module
        • vermouth.gmx.itp module
        • vermouth.gmx.itp_read module
        • vermouth.gmx.rtp module
        • vermouth.gmx.topology module
      • vermouth.pdb package
        • vermouth.pdb.cif module
        • vermouth.pdb.pdb module
      • vermouth.processors package
        • vermouth.processors.add_molecule_edges module
        • vermouth.processors.annotate_idrs module
        • vermouth.processors.annotate_mut_mod module
        • vermouth.processors.apply_posres module
        • vermouth.processors.apply_rubber_band module
        • vermouth.processors.attach_mass module
        • vermouth.processors.average_beads module
        • vermouth.processors.canonicalize_modifications module
        • vermouth.processors.cif_reader module
        • vermouth.processors.do_links module
        • vermouth.processors.do_mapping module
        • vermouth.processors.gro_reader module
        • vermouth.processors.idr_cross_domain_interaction_removal module
        • vermouth.processors.locate_charge_dummies module
        • vermouth.processors.make_bonds module
        • vermouth.processors.merge_all_molecules module
        • vermouth.processors.merge_chains module
        • vermouth.processors.name_moltype module
        • vermouth.processors.pdb_reader module
        • vermouth.processors.processor module
        • vermouth.processors.quote module
        • vermouth.processors.rename_modified_residues module
        • vermouth.processors.repair_graph module
        • vermouth.processors.rtp_polisher module
        • vermouth.processors.set_molecule_meta module
        • vermouth.processors.sort_molecule_atoms module
        • vermouth.processors.stash_attributes module
        • vermouth.processors.tune_cystein_bridges module
        • vermouth.processors.water_bias module
      • vermouth.rcsu package
        • vermouth.rcsu.contact_map module
        • vermouth.rcsu.go_pipeline module
        • vermouth.rcsu.go_structure_bias module
        • vermouth.rcsu.go_utils module
        • vermouth.rcsu.go_vs_includes module
      • vermouth.citation_parser module
      • vermouth.edge_tuning module
      • vermouth.ffinput module
      • vermouth.file_writer module
      • vermouth.forcefield module
      • vermouth.geometry module
      • vermouth.graph_utils module
      • vermouth.ismags module
      • vermouth.log_helpers module
      • vermouth.map_input module
      • vermouth.map_parser module
      • vermouth.molecule module
      • vermouth.parser_utils module
      • vermouth.selectors module
      • vermouth.system module
      • vermouth.truncating_formatter module
      • vermouth.utils module
  • Gromacs variables
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vermouth.bin package¶

Submodules¶

  • vermouth.bin.martinize2 module
    • entry()
    • martinize()
    • maxwarn()
    • pdb_to_universal()
    • read_system()

Module contents¶

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vermouth.bin.martinize2 module
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    • Submodules
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