proteindf_bridge package

Submodules

• proteindf_bridge.amber_prmtop module
  • AmberPrmtop
    • AmberPrmtop.atom_names
    • AmberPrmtop.atomic_numbers
    • AmberPrmtop.charges
    • AmberPrmtop.get_atomgroup()
    • AmberPrmtop.xyz
• proteindf_bridge.aminoacid module
  • AminoAcid
    • AminoAcid.is_aminoacid()
• proteindf_bridge.atom module
  • Atom
    • Atom.atomic_number
    • Atom.charge
    • Atom.force
    • Atom.get_raw_data()
    • Atom.is_real
    • Atom.label
    • Atom.move_to()
    • Atom.name
    • Atom.path
    • Atom.position
    • Atom.rotate()
    • Atom.set_by_raw_data()
    • Atom.shift_by()
    • Atom.symbol
    • Atom.vdw
    • Atom.weight()
    • Atom.xyz
• proteindf_bridge.atomgroup module
  • AtomGroup
    • AtomGroup.add_bond()
    • AtomGroup.assign_charges()
    • AtomGroup.atoms()
    • AtomGroup.box()
    • AtomGroup.center()
    • AtomGroup.charge
    • AtomGroup.divide_path()
    • AtomGroup.erase_atom()
    • AtomGroup.erase_group()
    • AtomGroup.formula()
    • AtomGroup.get_atom()
    • AtomGroup.get_atom_keys()
    • AtomGroup.get_atom_kinds()
    • AtomGroup.get_atom_kinds_count()
    • AtomGroup.get_atom_list()
    • AtomGroup.get_bond_list()
    • AtomGroup.get_family()
    • AtomGroup.get_formula()
    • AtomGroup.get_group()
    • AtomGroup.get_group_list()
    • AtomGroup.get_number_of_all_atoms()
    • AtomGroup.get_number_of_atoms()
    • AtomGroup.get_number_of_bonds()
    • AtomGroup.get_number_of_groups()
    • AtomGroup.get_path_list()
    • AtomGroup.get_raw_data()
    • AtomGroup.get_xyz()
    • AtomGroup.groups()
    • AtomGroup.has_atom()
    • AtomGroup.has_atomkey()
    • AtomGroup.has_atomname()
    • AtomGroup.has_group()
    • AtomGroup.has_groupkey()
    • AtomGroup.has_groupname()
    • AtomGroup.merge()
    • AtomGroup.name
    • AtomGroup.nuclei_charge
    • AtomGroup.parent
    • AtomGroup.path
    • AtomGroup.pickup_atoms()
    • AtomGroup.real_nuclei_charge
    • AtomGroup.remove_atom()
    • AtomGroup.remove_group()
    • AtomGroup.restructure()
    • AtomGroup.rotate()
    • AtomGroup.save_csv()
    • AtomGroup.select()
    • AtomGroup.set_atom()
    • AtomGroup.set_by_dict_data()
    • AtomGroup.set_group()
    • AtomGroup.shift_by()
    • AtomGroup.sort_atoms
    • AtomGroup.sort_groups
    • AtomGroup.sum_of_atomic_number()
    • AtomGroup.weight
• proteindf_bridge.biopdb module
  • Pdb
    • Pdb.AmberToolsVer
    • Pdb.debug
    • Pdb.get_atomgroup()
    • Pdb.get_modpdb_atomgroup()
    • Pdb.load()
    • Pdb.renumber()
    • Pdb.set_by_atomgroup()
  • main()
• proteindf_bridge.bond module
  • Bond
    • Bond.setup()
• proteindf_bridge.common module
• proteindf_bridge.dbmanager module
  • DbManager
    • DbManager.create_table()
    • DbManager.delete()
    • DbManager.execute()
    • DbManager.get_field_names()
    • DbManager.get_primary_keys()
    • DbManager.get_results()
    • DbManager.get_table_names()
    • DbManager.get_user_version()
    • DbManager.has_table()
    • DbManager.insert()
    • DbManager.pp()
    • DbManager.pp_table()
    • DbManager.select()
    • DbManager.set_user_version()
    • DbManager.update()
• proteindf_bridge.error module
  • BrError
  • BrInputError
  • BrValueError
• proteindf_bridge.format module
  • Format
    • Format.is_chain()
    • Format.is_models()
    • Format.is_protein()
    • Format.is_residue()
• proteindf_bridge.functions module
  • get_yaml()
  • load_atomgroup()
  • load_msgpack()
  • load_yaml()
  • locate()
  • parse_yaml()
  • save_atomgroup()
  • save_msgpack()
  • save_yaml()
• proteindf_bridge.gro module
  • SimpleGro
    • SimpleGro.get_atomgroup()
    • SimpleGro.load()
    • SimpleGro.set_by_atomgroup()
• proteindf_bridge.ionpair module
  • IonPair
    • IonPair.get_ion_pairs()
• proteindf_bridge.mail module
  • Mail
    • Mail.charset
    • Mail.from_address
    • Mail.load_config()
    • Mail.save_config()
    • Mail.send()
    • Mail.smtp_account
    • Mail.smtp_password
    • Mail.smtp_port
    • Mail.smtp_server
    • Mail.subject
    • Mail.text
    • Mail.to_address
    • Mail.use_SSL
• proteindf_bridge.matrix module
  • Matrix
    • Matrix.add()
    • Matrix.clear()
    • Matrix.cols
    • Matrix.copy()
    • Matrix.data
    • Matrix.get()
    • Matrix.get_buffer()
    • Matrix.get_col_vector()
    • Matrix.get_ndarray()
    • Matrix.get_raw_data()
    • Matrix.get_row_vector()
    • Matrix.get_symmetric_matrix()
    • Matrix.inverse()
    • Matrix.max()
    • Matrix.min()
    • Matrix.pseudo_inverse()
    • Matrix.resize()
    • Matrix.rows
    • Matrix.select()
    • Matrix.set()
    • Matrix.set_buffer()
    • Matrix.transpose()
    • Matrix.type
  • SymmetricMatrix
    • SymmetricMatrix.dim
    • SymmetricMatrix.eig()
    • SymmetricMatrix.get()
    • SymmetricMatrix.get_general_matrix()
    • SymmetricMatrix.get_raw_data()
    • SymmetricMatrix.resize()
    • SymmetricMatrix.set()
  • identity_matrix()
• proteindf_bridge.mmcif module
  • SimpleMmcif
    • SimpleMmcif.get_atomgroup()
    • SimpleMmcif.get_molecule_names()
    • SimpleMmcif.load()
    • SimpleMmcif.load_msgpack()
    • SimpleMmcif.save_msgpack()
• proteindf_bridge.modeling module
  • Modeling
    • Modeling.add_methyl()
    • Modeling.arbitary_rotate_matrix()
    • Modeling.get_ACE()
    • Modeling.get_ACE_simple()
    • Modeling.get_NH3()
    • Modeling.get_NME()
    • Modeling.get_NME_simple()
    • Modeling.get_last_index()
    • Modeling.neutralize_ARG()
    • Modeling.neutralize_ASP()
    • Modeling.neutralize_Cterm()
    • Modeling.neutralize_FAD()
    • Modeling.neutralize_GLU()
    • Modeling.neutralize_LYS()
    • Modeling.neutralize_Nterm()
    • Modeling.select_residues()
• proteindf_bridge.mol2 module
  • SimpleMol2
    • SimpleMol2.save()
    • SimpleMol2.set_by_atomgroup()
• proteindf_bridge.neutralize module
  • Neutralize
    • Neutralize.neutralized
• proteindf_bridge.path module
  • Path
    • Path.get_chain_id()
    • Path.get_res_id()
    • Path.split_path()
• proteindf_bridge.periodictable module
  • PeriodicTable
    • PeriodicTable.atomic_weight()
    • PeriodicTable.get_atomic_number()
    • PeriodicTable.get_num_of_atoms()
    • PeriodicTable.get_symbol()
    • PeriodicTable.vdw()
• proteindf_bridge.position module
  • Position
    • Position.cross()
    • Position.distance_from()
    • Position.dot()
    • Position.get_raw_data()
    • Position.move_to()
    • Position.norm()
    • Position.rotate()
    • Position.square_distance_from()
    • Position.x
    • Position.xyz
    • Position.y
    • Position.z
• proteindf_bridge.select module
  • Select
    • Select.is_match()
  • Select_Atom
    • Select_Atom.is_match()
  • Select_AtomGroup
    • Select_AtomGroup.is_match()
  • Select_Name
    • Select_Name.is_match()
  • Select_Path
    • Select_Path.is_match()
  • Select_PathRegex
    • Select_PathRegex.is_match()
  • Select_Path_simple
    • Select_Path_simple.is_match()
  • Select_Path_wildcard
    • Select_Path_wildcard.is_match()
  • Select_Range
    • Select_Range.is_match()
  • Select_Symbol
    • Select_Symbol.is_match()
• proteindf_bridge.ssbond module
  • SSBond
    • SSBond.get_bonds()
• proteindf_bridge.str_processing module
  • StrUtils
    • StrUtils.add_spaces()
    • StrUtils.check_pickled()
    • StrUtils.del_spaces()
    • StrUtils.get_common_str()
    • StrUtils.num_spaces()
    • StrUtils.sort_nicely()
    • StrUtils.str_to_bool()
    • StrUtils.to_bytes()
    • StrUtils.to_unicode()
    • StrUtils.to_unicode_dict()
    • StrUtils.to_unicode_list()
    • StrUtils.unindent_block()
• proteindf_bridge.superposer module
  • Superposer
    • Superposer.center1
    • Superposer.center2
    • Superposer.get_center()
    • Superposer.num_of_positions
    • Superposer.positions1
    • Superposer.positions2
    • Superposer.rmsd
    • Superposer.rotation_mat
    • Superposer.shift_positions1
    • Superposer.shift_positions2
    • Superposer.superimpose()
    • Superposer.update_positions1
    • Superposer.update_positions2
• proteindf_bridge.superposer_quaternion module
  • Superposer_quaternion
    • Superposer_quaternion.calc()
    • Superposer_quaternion.center1
    • Superposer_quaternion.center2
    • Superposer_quaternion.eigval
    • Superposer_quaternion.eigvec
    • Superposer_quaternion.matB
    • Superposer_quaternion.matR
    • Superposer_quaternion.r_A
    • Superposer_quaternion.r_B
    • Superposer_quaternion.rmsd
    • Superposer_quaternion.rotation_mat
    • Superposer_quaternion.superimpose()
    • Superposer_quaternion.va
    • Superposer_quaternion.vb
• proteindf_bridge.utils module
  • Utils
    • Utils.get_sequential_residue_id()
    • Utils.remove_WAT()
• proteindf_bridge.vector module
  • Vector
    • Vector.abs()
    • Vector.argsort()
    • Vector.data
    • Vector.flip()
    • Vector.get()
    • Vector.get_buffer()
    • Vector.get_ndarray()
    • Vector.max
    • Vector.min
    • Vector.resize()
    • Vector.set()
    • Vector.set_buffer()
    • Vector.size()
    • Vector.to_list()
• proteindf_bridge.xyz module
  • Xyz
    • Xyz.get_atom_group()
    • Xyz.get_text()
    • Xyz.load()
    • Xyz.save()
    • Xyz.set_by_atomgroup()