索引

A

abs() (proteindf_bridge.vector.Vector のメソッド) add() (proteindf_bridge.matrix.Matrix のメソッド) add_bond() (proteindf_bridge.atomgroup.AtomGroup のメソッド) add_methyl() (proteindf_bridge.modeling.Modeling のメソッド) add_spaces() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) AmberPrmtop (proteindf_bridge.amber_prmtop のクラス) AmberToolsVer (proteindf_bridge.biopdb.Pdb の属性) AminoAcid (proteindf_bridge.aminoacid のクラス) arbitary_rotate_matrix() (proteindf_bridge.modeling.Modeling のメソッド)

argsort() (proteindf_bridge.vector.Vector のメソッド) assign_charges() (proteindf_bridge.atomgroup.AtomGroup のメソッド) Atom (proteindf_bridge.atom のクラス) atom_names (proteindf_bridge.amber_prmtop.AmberPrmtop のプロパティ) AtomGroup (proteindf_bridge.atomgroup のクラス) atomic_number (proteindf_bridge.atom.Atom のプロパティ) atomic_numbers (proteindf_bridge.amber_prmtop.AmberPrmtop のプロパティ) atomic_weight() (proteindf_bridge.periodictable.PeriodicTable の静的メソッド) atoms() (proteindf_bridge.atomgroup.AtomGroup のメソッド)

B

Bond (proteindf_bridge.bond のクラス) box() (proteindf_bridge.atomgroup.AtomGroup のメソッド)

BrError BrInputError BrValueError

C

calc() (proteindf_bridge.superposer_quaternion.Superposer_quaternion のメソッド) center() (proteindf_bridge.atomgroup.AtomGroup のメソッド) center1 (proteindf_bridge.superposer.Superposer のプロパティ) (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) center2 (proteindf_bridge.superposer.Superposer のプロパティ) (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) charge (proteindf_bridge.atom.Atom のプロパティ) (proteindf_bridge.atomgroup.AtomGroup のプロパティ)

charges (proteindf_bridge.amber_prmtop.AmberPrmtop のプロパティ) charset (proteindf_bridge.mail.Mail のプロパティ) check_pickled() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) clear() (proteindf_bridge.matrix.Matrix のメソッド) cols (proteindf_bridge.matrix.Matrix のプロパティ) copy() (proteindf_bridge.matrix.Matrix のメソッド) create_table() (proteindf_bridge.dbmanager.DbManager のメソッド) cross() (proteindf_bridge.position.Position のメソッド)

D

data (proteindf_bridge.matrix.Matrix のプロパティ) (proteindf_bridge.vector.Vector のプロパティ) DbManager (proteindf_bridge.dbmanager のクラス) debug (proteindf_bridge.biopdb.Pdb のプロパティ) del_spaces() (proteindf_bridge.str_processing.StrUtils のクラスメソッド)

delete() (proteindf_bridge.dbmanager.DbManager のメソッド) dim (proteindf_bridge.matrix.SymmetricMatrix のプロパティ) distance_from() (proteindf_bridge.position.Position のメソッド) divide_path() (proteindf_bridge.atomgroup.AtomGroup の静的メソッド) dot() (proteindf_bridge.position.Position のメソッド)

E

eig() (proteindf_bridge.matrix.SymmetricMatrix のメソッド) eigval (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) eigvec (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ)

erase_atom() (proteindf_bridge.atomgroup.AtomGroup のメソッド) erase_group() (proteindf_bridge.atomgroup.AtomGroup のメソッド) execute() (proteindf_bridge.dbmanager.DbManager のメソッド)

F

flip() (proteindf_bridge.vector.Vector のメソッド) force (proteindf_bridge.atom.Atom のプロパティ)

Format (proteindf_bridge.format のクラス) formula() (proteindf_bridge.atomgroup.AtomGroup のメソッド) from_address (proteindf_bridge.mail.Mail のプロパティ)

G

get() (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.matrix.SymmetricMatrix のメソッド) (proteindf_bridge.vector.Vector のメソッド) get_ACE() (proteindf_bridge.modeling.Modeling のメソッド) get_ACE_simple() (proteindf_bridge.modeling.Modeling のメソッド) get_atom() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_atom_group() (proteindf_bridge.xyz.Xyz のメソッド) get_atom_keys() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_atom_kinds() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_atom_kinds_count() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_atom_list() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_atomgroup() (proteindf_bridge.amber_prmtop.AmberPrmtop のメソッド) (proteindf_bridge.biopdb.Pdb のメソッド) (proteindf_bridge.gro.SimpleGro のメソッド) (proteindf_bridge.mmcif.SimpleMmcif のメソッド) get_atomic_number() (proteindf_bridge.periodictable.PeriodicTable の静的メソッド) get_bond_list() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_bonds() (proteindf_bridge.ssbond.SSBond のメソッド) get_buffer() (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.vector.Vector のメソッド) get_center() (proteindf_bridge.superposer.Superposer のメソッド) get_chain_id() (proteindf_bridge.path.Path のクラスメソッド) get_col_vector() (proteindf_bridge.matrix.Matrix のメソッド) get_common_str() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) get_family() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_field_names() (proteindf_bridge.dbmanager.DbManager のメソッド) get_formula() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_general_matrix() (proteindf_bridge.matrix.SymmetricMatrix のメソッド) get_group() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_group_list() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_ion_pairs() (proteindf_bridge.ionpair.IonPair のメソッド)

get_last_index() (proteindf_bridge.modeling.Modeling のメソッド) get_modpdb_atomgroup() (proteindf_bridge.biopdb.Pdb のメソッド) get_molecule_names() (proteindf_bridge.mmcif.SimpleMmcif のメソッド) get_ndarray() (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.vector.Vector のメソッド) get_NH3() (proteindf_bridge.modeling.Modeling のメソッド) get_NME() (proteindf_bridge.modeling.Modeling のメソッド) get_NME_simple() (proteindf_bridge.modeling.Modeling のメソッド) get_num_of_atoms() (proteindf_bridge.periodictable.PeriodicTable の静的メソッド) get_number_of_all_atoms() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_number_of_atoms() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_number_of_bonds() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_number_of_groups() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_path_list() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_primary_keys() (proteindf_bridge.dbmanager.DbManager のメソッド) get_raw_data() (proteindf_bridge.atom.Atom のメソッド) (proteindf_bridge.atomgroup.AtomGroup のメソッド) (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.matrix.SymmetricMatrix のメソッド) (proteindf_bridge.position.Position のメソッド) get_res_id() (proteindf_bridge.path.Path のクラスメソッド) get_results() (proteindf_bridge.dbmanager.DbManager のメソッド) get_row_vector() (proteindf_bridge.matrix.Matrix のメソッド) get_sequential_residue_id() (proteindf_bridge.utils.Utils のクラスメソッド) get_symbol() (proteindf_bridge.periodictable.PeriodicTable の静的メソッド) get_symmetric_matrix() (proteindf_bridge.matrix.Matrix のメソッド) get_table_names() (proteindf_bridge.dbmanager.DbManager のメソッド) get_text() (proteindf_bridge.xyz.Xyz のメソッド) get_user_version() (proteindf_bridge.dbmanager.DbManager のメソッド) get_xyz() (proteindf_bridge.atomgroup.AtomGroup のメソッド) get_yaml() (proteindf_bridge.functions モジュール) groups() (proteindf_bridge.atomgroup.AtomGroup のメソッド)

H

has_atom() (proteindf_bridge.atomgroup.AtomGroup のメソッド) has_atomkey() (proteindf_bridge.atomgroup.AtomGroup のメソッド) has_atomname() (proteindf_bridge.atomgroup.AtomGroup のメソッド)

has_group() (proteindf_bridge.atomgroup.AtomGroup のメソッド) has_groupkey() (proteindf_bridge.atomgroup.AtomGroup のメソッド) has_groupname() (proteindf_bridge.atomgroup.AtomGroup のメソッド) has_table() (proteindf_bridge.dbmanager.DbManager のメソッド)

I

identity_matrix() (proteindf_bridge.matrix モジュール) insert() (proteindf_bridge.dbmanager.DbManager のメソッド) inverse() (proteindf_bridge.matrix.Matrix のメソッド) IonPair (proteindf_bridge.ionpair のクラス) is_aminoacid() (proteindf_bridge.aminoacid.AminoAcid のクラスメソッド) is_chain() (proteindf_bridge.format.Format のクラスメソッド) is_match() (proteindf_bridge.select.Select のメソッド) (proteindf_bridge.select.Select_Atom のメソッド) (proteindf_bridge.select.Select_AtomGroup のメソッド) (proteindf_bridge.select.Select_Name のメソッド) (proteindf_bridge.select.Select_Path のメソッド) (proteindf_bridge.select.Select_Path_simple のメソッド) (proteindf_bridge.select.Select_Path_wildcard のメソッド) (proteindf_bridge.select.Select_PathRegex のメソッド) (proteindf_bridge.select.Select_Range のメソッド) (proteindf_bridge.select.Select_Symbol のメソッド)

is_models() (proteindf_bridge.format.Format のクラスメソッド) is_protein() (proteindf_bridge.format.Format のクラスメソッド) is_real (proteindf_bridge.atom.Atom のプロパティ) is_residue() (proteindf_bridge.format.Format のクラスメソッド)

L

label (proteindf_bridge.atom.Atom のプロパティ) load() (proteindf_bridge.biopdb.Pdb のメソッド) (proteindf_bridge.gro.SimpleGro のメソッド) (proteindf_bridge.mmcif.SimpleMmcif のメソッド) (proteindf_bridge.xyz.Xyz のメソッド)

load_atomgroup() (proteindf_bridge.functions モジュール) load_config() (proteindf_bridge.mail.Mail のメソッド) load_msgpack() (proteindf_bridge.functions モジュール) (proteindf_bridge.mmcif.SimpleMmcif のメソッド) load_yaml() (proteindf_bridge.functions モジュール) locate() (proteindf_bridge.functions モジュール)

M

Mail (proteindf_bridge.mail のクラス) main() (proteindf_bridge.biopdb モジュール) matB (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) matR (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) Matrix (proteindf_bridge.matrix のクラス) max (proteindf_bridge.vector.Vector のプロパティ) max() (proteindf_bridge.matrix.Matrix のメソッド) merge() (proteindf_bridge.atomgroup.AtomGroup のメソッド) min (proteindf_bridge.vector.Vector のプロパティ) min() (proteindf_bridge.matrix.Matrix のメソッド) Modeling (proteindf_bridge.modeling のクラス) module proteindf_bridge proteindf_bridge.amber_prmtop proteindf_bridge.aminoacid proteindf_bridge.atom proteindf_bridge.atomgroup proteindf_bridge.biopdb proteindf_bridge.bond proteindf_bridge.common proteindf_bridge.dbmanager proteindf_bridge.error proteindf_bridge.format proteindf_bridge.functions proteindf_bridge.gro proteindf_bridge.ionpair proteindf_bridge.mail proteindf_bridge.matrix proteindf_bridge.mmcif proteindf_bridge.modeling proteindf_bridge.mol2 proteindf_bridge.neutralize proteindf_bridge.path proteindf_bridge.periodictable proteindf_bridge.position proteindf_bridge.select proteindf_bridge.ssbond proteindf_bridge.str_processing proteindf_bridge.superposer proteindf_bridge.superposer_quaternion proteindf_bridge.utils proteindf_bridge.vector proteindf_bridge.xyz

move_to() (proteindf_bridge.atom.Atom のメソッド) (proteindf_bridge.position.Position のメソッド)

N

name (proteindf_bridge.atom.Atom のプロパティ) (proteindf_bridge.atomgroup.AtomGroup のプロパティ) Neutralize (proteindf_bridge.neutralize のクラス) neutralize_ARG() (proteindf_bridge.modeling.Modeling のメソッド) neutralize_ASP() (proteindf_bridge.modeling.Modeling のメソッド) neutralize_Cterm() (proteindf_bridge.modeling.Modeling のメソッド) neutralize_FAD() (proteindf_bridge.modeling.Modeling のメソッド)

neutralize_GLU() (proteindf_bridge.modeling.Modeling のメソッド) neutralize_LYS() (proteindf_bridge.modeling.Modeling のメソッド) neutralize_Nterm() (proteindf_bridge.modeling.Modeling のメソッド) neutralized (proteindf_bridge.neutralize.Neutralize のプロパティ) norm() (proteindf_bridge.position.Position のメソッド) nuclei_charge (proteindf_bridge.atomgroup.AtomGroup のプロパティ) num_of_positions (proteindf_bridge.superposer.Superposer のプロパティ) num_spaces() (proteindf_bridge.str_processing.StrUtils のクラスメソッド)

P

parent (proteindf_bridge.atomgroup.AtomGroup のプロパティ) parse_yaml() (proteindf_bridge.functions モジュール) path (proteindf_bridge.atom.Atom のプロパティ) (proteindf_bridge.atomgroup.AtomGroup のプロパティ) Path (proteindf_bridge.path のクラス) Pdb (proteindf_bridge.biopdb のクラス) PeriodicTable (proteindf_bridge.periodictable のクラス) pickup_atoms() (proteindf_bridge.atomgroup.AtomGroup のメソッド) position (proteindf_bridge.atom.Atom のプロパティ) Position (proteindf_bridge.position のクラス) positions1 (proteindf_bridge.superposer.Superposer のプロパティ) positions2 (proteindf_bridge.superposer.Superposer のプロパティ) pp() (proteindf_bridge.dbmanager.DbManager のメソッド) pp_table() (proteindf_bridge.dbmanager.DbManager のメソッド) proteindf_bridge module proteindf_bridge.amber_prmtop module proteindf_bridge.aminoacid module proteindf_bridge.atom module proteindf_bridge.atomgroup module proteindf_bridge.biopdb module proteindf_bridge.bond module proteindf_bridge.common module proteindf_bridge.dbmanager module proteindf_bridge.error module proteindf_bridge.format module proteindf_bridge.functions module

proteindf_bridge.gro module proteindf_bridge.ionpair module proteindf_bridge.mail module proteindf_bridge.matrix module proteindf_bridge.mmcif module proteindf_bridge.modeling module proteindf_bridge.mol2 module proteindf_bridge.neutralize module proteindf_bridge.path module proteindf_bridge.periodictable module proteindf_bridge.position module proteindf_bridge.select module proteindf_bridge.ssbond module proteindf_bridge.str_processing module proteindf_bridge.superposer module proteindf_bridge.superposer_quaternion module proteindf_bridge.utils module proteindf_bridge.vector module proteindf_bridge.xyz module pseudo_inverse() (proteindf_bridge.matrix.Matrix のメソッド)

R

r_A (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) r_B (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) real_nuclei_charge (proteindf_bridge.atomgroup.AtomGroup のプロパティ) remove_atom() (proteindf_bridge.atomgroup.AtomGroup のメソッド) remove_group() (proteindf_bridge.atomgroup.AtomGroup のメソッド) remove_WAT() (proteindf_bridge.utils.Utils のクラスメソッド) renumber() (proteindf_bridge.biopdb.Pdb のメソッド) resize() (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.matrix.SymmetricMatrix のメソッド) (proteindf_bridge.vector.Vector のメソッド)

restructure() (proteindf_bridge.atomgroup.AtomGroup のメソッド) rmsd (proteindf_bridge.superposer.Superposer のプロパティ) (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) rotate() (proteindf_bridge.atom.Atom のメソッド) (proteindf_bridge.atomgroup.AtomGroup のメソッド) (proteindf_bridge.position.Position のメソッド) rotation_mat (proteindf_bridge.superposer.Superposer のプロパティ) (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) rows (proteindf_bridge.matrix.Matrix のプロパティ)

S

save() (proteindf_bridge.mol2.SimpleMol2 のメソッド) (proteindf_bridge.xyz.Xyz のメソッド) save_atomgroup() (proteindf_bridge.functions モジュール) save_config() (proteindf_bridge.mail.Mail のメソッド) save_csv() (proteindf_bridge.atomgroup.AtomGroup のメソッド) save_msgpack() (proteindf_bridge.functions モジュール) (proteindf_bridge.mmcif.SimpleMmcif のメソッド) save_yaml() (proteindf_bridge.functions モジュール) Select (proteindf_bridge.select のクラス) select() (proteindf_bridge.atomgroup.AtomGroup のメソッド) (proteindf_bridge.dbmanager.DbManager のメソッド) (proteindf_bridge.matrix.Matrix のメソッド) Select_Atom (proteindf_bridge.select のクラス) Select_AtomGroup (proteindf_bridge.select のクラス) Select_Name (proteindf_bridge.select のクラス) Select_Path (proteindf_bridge.select のクラス) Select_Path_simple (proteindf_bridge.select のクラス) Select_Path_wildcard (proteindf_bridge.select のクラス) Select_PathRegex (proteindf_bridge.select のクラス) Select_Range (proteindf_bridge.select のクラス) select_residues() (proteindf_bridge.modeling.Modeling のメソッド) Select_Symbol (proteindf_bridge.select のクラス) send() (proteindf_bridge.mail.Mail のメソッド) set() (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.matrix.SymmetricMatrix のメソッド) (proteindf_bridge.vector.Vector のメソッド) set_atom() (proteindf_bridge.atomgroup.AtomGroup のメソッド) set_buffer() (proteindf_bridge.matrix.Matrix のメソッド) (proteindf_bridge.vector.Vector のメソッド) set_by_atomgroup() (proteindf_bridge.biopdb.Pdb のメソッド) (proteindf_bridge.gro.SimpleGro のメソッド) (proteindf_bridge.mol2.SimpleMol2 のメソッド) (proteindf_bridge.xyz.Xyz のメソッド)

set_by_dict_data() (proteindf_bridge.atomgroup.AtomGroup のメソッド) set_by_raw_data() (proteindf_bridge.atom.Atom のメソッド) set_group() (proteindf_bridge.atomgroup.AtomGroup のメソッド) set_user_version() (proteindf_bridge.dbmanager.DbManager のメソッド) setup() (proteindf_bridge.bond.Bond のメソッド) shift_by() (proteindf_bridge.atom.Atom のメソッド) (proteindf_bridge.atomgroup.AtomGroup のメソッド) shift_positions1 (proteindf_bridge.superposer.Superposer のプロパティ) shift_positions2 (proteindf_bridge.superposer.Superposer のプロパティ) SimpleGro (proteindf_bridge.gro のクラス) SimpleMmcif (proteindf_bridge.mmcif のクラス) SimpleMol2 (proteindf_bridge.mol2 のクラス) size() (proteindf_bridge.vector.Vector のメソッド) smtp_account (proteindf_bridge.mail.Mail のプロパティ) smtp_password (proteindf_bridge.mail.Mail のプロパティ) smtp_port (proteindf_bridge.mail.Mail のプロパティ) smtp_server (proteindf_bridge.mail.Mail のプロパティ) sort_atoms (proteindf_bridge.atomgroup.AtomGroup のプロパティ) sort_groups (proteindf_bridge.atomgroup.AtomGroup のプロパティ) sort_nicely() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) split_path() (proteindf_bridge.path.Path のクラスメソッド) square_distance_from() (proteindf_bridge.position.Position のメソッド) SSBond (proteindf_bridge.ssbond のクラス) str_to_bool() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) StrUtils (proteindf_bridge.str_processing のクラス) subject (proteindf_bridge.mail.Mail のプロパティ) sum_of_atomic_number() (proteindf_bridge.atomgroup.AtomGroup のメソッド) superimpose() (proteindf_bridge.superposer.Superposer のメソッド) (proteindf_bridge.superposer_quaternion.Superposer_quaternion のメソッド) Superposer (proteindf_bridge.superposer のクラス) Superposer_quaternion (proteindf_bridge.superposer_quaternion のクラス) symbol (proteindf_bridge.atom.Atom のプロパティ) SymmetricMatrix (proteindf_bridge.matrix のクラス)

T

text (proteindf_bridge.mail.Mail のプロパティ) to_address (proteindf_bridge.mail.Mail のプロパティ) to_bytes() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) to_list() (proteindf_bridge.vector.Vector のメソッド)

to_unicode() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) to_unicode_dict() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) to_unicode_list() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) transpose() (proteindf_bridge.matrix.Matrix のメソッド) type (proteindf_bridge.matrix.Matrix のプロパティ)

U

unindent_block() (proteindf_bridge.str_processing.StrUtils のクラスメソッド) update() (proteindf_bridge.dbmanager.DbManager のメソッド) update_positions1 (proteindf_bridge.superposer.Superposer のプロパティ)

update_positions2 (proteindf_bridge.superposer.Superposer のプロパティ) use_SSL (proteindf_bridge.mail.Mail のプロパティ) Utils (proteindf_bridge.utils のクラス)

V

va (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ) vb (proteindf_bridge.superposer_quaternion.Superposer_quaternion のプロパティ)

vdw (proteindf_bridge.atom.Atom のプロパティ) vdw() (proteindf_bridge.periodictable.PeriodicTable の静的メソッド) Vector (proteindf_bridge.vector のクラス)

W

weight (proteindf_bridge.atomgroup.AtomGroup のプロパティ)

weight() (proteindf_bridge.atom.Atom のメソッド)

X

x (proteindf_bridge.position.Position のプロパティ) xyz (proteindf_bridge.amber_prmtop.AmberPrmtop のプロパティ) (proteindf_bridge.atom.Atom のプロパティ) (proteindf_bridge.position.Position のプロパティ)

Xyz (proteindf_bridge.xyz のクラス)

Y

y (proteindf_bridge.position.Position のプロパティ)

Z

z (proteindf_bridge.position.Position のプロパティ)