Index

A

abs() (proteindf_bridge.vector.Vector method) add() (proteindf_bridge.matrix.Matrix method) add_bond() (proteindf_bridge.atomgroup.AtomGroup method) add_methyl() (proteindf_bridge.modeling.Modeling method) add_spaces() (proteindf_bridge.str_processing.StrUtils class method) AmberPrmtop (class in proteindf_bridge.amber_prmtop) AmberToolsVer (proteindf_bridge.biopdb.Pdb attribute) AminoAcid (class in proteindf_bridge.aminoacid) arbitary_rotate_matrix() (proteindf_bridge.modeling.Modeling method)

argsort() (proteindf_bridge.vector.Vector method) assign_charges() (proteindf_bridge.atomgroup.AtomGroup method) Atom (class in proteindf_bridge.atom) atom_names (proteindf_bridge.amber_prmtop.AmberPrmtop property) AtomGroup (class in proteindf_bridge.atomgroup) atomic_number (proteindf_bridge.atom.Atom property) atomic_numbers (proteindf_bridge.amber_prmtop.AmberPrmtop property) atomic_weight() (proteindf_bridge.periodictable.PeriodicTable static method) atoms() (proteindf_bridge.atomgroup.AtomGroup method)

B

Bond (class in proteindf_bridge.bond) box() (proteindf_bridge.atomgroup.AtomGroup method)

BrError BrInputError BrValueError

C

calc() (proteindf_bridge.superposer_quaternion.Superposer_quaternion method) center() (proteindf_bridge.atomgroup.AtomGroup method) center1 (proteindf_bridge.superposer.Superposer property) (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) center2 (proteindf_bridge.superposer.Superposer property) (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) charge (proteindf_bridge.atom.Atom property) (proteindf_bridge.atomgroup.AtomGroup property)

charges (proteindf_bridge.amber_prmtop.AmberPrmtop property) charset (proteindf_bridge.mail.Mail property) check_pickled() (proteindf_bridge.str_processing.StrUtils class method) clear() (proteindf_bridge.matrix.Matrix method) cols (proteindf_bridge.matrix.Matrix property) copy() (proteindf_bridge.matrix.Matrix method) create_table() (proteindf_bridge.dbmanager.DbManager method) cross() (proteindf_bridge.position.Position method)

D

data (proteindf_bridge.matrix.Matrix property) (proteindf_bridge.vector.Vector property) DbManager (class in proteindf_bridge.dbmanager) debug (proteindf_bridge.biopdb.Pdb property) del_spaces() (proteindf_bridge.str_processing.StrUtils class method)

delete() (proteindf_bridge.dbmanager.DbManager method) dim (proteindf_bridge.matrix.SymmetricMatrix property) distance_from() (proteindf_bridge.position.Position method) divide_path() (proteindf_bridge.atomgroup.AtomGroup static method) dot() (proteindf_bridge.position.Position method)

E

eig() (proteindf_bridge.matrix.SymmetricMatrix method) eigval (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) eigvec (proteindf_bridge.superposer_quaternion.Superposer_quaternion property)

erase_atom() (proteindf_bridge.atomgroup.AtomGroup method) erase_group() (proteindf_bridge.atomgroup.AtomGroup method) execute() (proteindf_bridge.dbmanager.DbManager method)

F

flip() (proteindf_bridge.vector.Vector method) force (proteindf_bridge.atom.Atom property)

Format (class in proteindf_bridge.format) formula() (proteindf_bridge.atomgroup.AtomGroup method) from_address (proteindf_bridge.mail.Mail property)

G

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

get_last_index() (proteindf_bridge.modeling.Modeling method) get_modpdb_atomgroup() (proteindf_bridge.biopdb.Pdb method) get_molecule_names() (proteindf_bridge.mmcif.SimpleMmcif method) get_ndarray() (proteindf_bridge.matrix.Matrix method) (proteindf_bridge.vector.Vector method) get_NH3() (proteindf_bridge.modeling.Modeling method) get_NME() (proteindf_bridge.modeling.Modeling method) get_NME_simple() (proteindf_bridge.modeling.Modeling method) get_num_of_atoms() (proteindf_bridge.periodictable.PeriodicTable static method) get_number_of_all_atoms() (proteindf_bridge.atomgroup.AtomGroup method) get_number_of_atoms() (proteindf_bridge.atomgroup.AtomGroup method) get_number_of_bonds() (proteindf_bridge.atomgroup.AtomGroup method) get_number_of_groups() (proteindf_bridge.atomgroup.AtomGroup method) get_path_list() (proteindf_bridge.atomgroup.AtomGroup method) get_primary_keys() (proteindf_bridge.dbmanager.DbManager method) get_raw_data() (proteindf_bridge.atom.Atom method) (proteindf_bridge.atomgroup.AtomGroup method) (proteindf_bridge.matrix.Matrix method) (proteindf_bridge.matrix.SymmetricMatrix method) (proteindf_bridge.position.Position method) get_res_id() (proteindf_bridge.path.Path class method) get_results() (proteindf_bridge.dbmanager.DbManager method) get_row_vector() (proteindf_bridge.matrix.Matrix method) get_sequential_residue_id() (proteindf_bridge.utils.Utils class method) get_symbol() (proteindf_bridge.periodictable.PeriodicTable static method) get_symmetric_matrix() (proteindf_bridge.matrix.Matrix method) get_table_names() (proteindf_bridge.dbmanager.DbManager method) get_text() (proteindf_bridge.xyz.Xyz method) get_user_version() (proteindf_bridge.dbmanager.DbManager method) get_xyz() (proteindf_bridge.atomgroup.AtomGroup method) get_yaml() (in module proteindf_bridge.functions) groups() (proteindf_bridge.atomgroup.AtomGroup method)

H

has_atom() (proteindf_bridge.atomgroup.AtomGroup method) has_atomkey() (proteindf_bridge.atomgroup.AtomGroup method) has_atomname() (proteindf_bridge.atomgroup.AtomGroup method)

has_group() (proteindf_bridge.atomgroup.AtomGroup method) has_groupkey() (proteindf_bridge.atomgroup.AtomGroup method) has_groupname() (proteindf_bridge.atomgroup.AtomGroup method) has_table() (proteindf_bridge.dbmanager.DbManager method)

I

identity_matrix() (in module proteindf_bridge.matrix) insert() (proteindf_bridge.dbmanager.DbManager method) inverse() (proteindf_bridge.matrix.Matrix method) IonPair (class in proteindf_bridge.ionpair) is_aminoacid() (proteindf_bridge.aminoacid.AminoAcid class method) is_chain() (proteindf_bridge.format.Format class method) is_match() (proteindf_bridge.select.Select method) (proteindf_bridge.select.Select_Atom method) (proteindf_bridge.select.Select_AtomGroup method) (proteindf_bridge.select.Select_Name method) (proteindf_bridge.select.Select_Path method) (proteindf_bridge.select.Select_Path_simple method) (proteindf_bridge.select.Select_Path_wildcard method) (proteindf_bridge.select.Select_PathRegex method) (proteindf_bridge.select.Select_Range method) (proteindf_bridge.select.Select_Symbol method)

is_models() (proteindf_bridge.format.Format class method) is_protein() (proteindf_bridge.format.Format class method) is_real (proteindf_bridge.atom.Atom property) is_residue() (proteindf_bridge.format.Format class method)

L

label (proteindf_bridge.atom.Atom property) load() (proteindf_bridge.biopdb.Pdb method) (proteindf_bridge.gro.SimpleGro method) (proteindf_bridge.mmcif.SimpleMmcif method) (proteindf_bridge.xyz.Xyz method)

load_atomgroup() (in module proteindf_bridge.functions) load_config() (proteindf_bridge.mail.Mail method) load_msgpack() (in module proteindf_bridge.functions) (proteindf_bridge.mmcif.SimpleMmcif method) load_yaml() (in module proteindf_bridge.functions) locate() (in module proteindf_bridge.functions)

M

Mail (class in proteindf_bridge.mail) main() (in module proteindf_bridge.biopdb) matB (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) matR (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) Matrix (class in proteindf_bridge.matrix) max (proteindf_bridge.vector.Vector property) max() (proteindf_bridge.matrix.Matrix method) merge() (proteindf_bridge.atomgroup.AtomGroup method) min (proteindf_bridge.vector.Vector property) min() (proteindf_bridge.matrix.Matrix method) Modeling (class in proteindf_bridge.modeling) 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 method) (proteindf_bridge.position.Position method)

N

name (proteindf_bridge.atom.Atom property) (proteindf_bridge.atomgroup.AtomGroup property) Neutralize (class in proteindf_bridge.neutralize) neutralize_ARG() (proteindf_bridge.modeling.Modeling method) neutralize_ASP() (proteindf_bridge.modeling.Modeling method) neutralize_Cterm() (proteindf_bridge.modeling.Modeling method) neutralize_FAD() (proteindf_bridge.modeling.Modeling method)

neutralize_GLU() (proteindf_bridge.modeling.Modeling method) neutralize_LYS() (proteindf_bridge.modeling.Modeling method) neutralize_Nterm() (proteindf_bridge.modeling.Modeling method) neutralized (proteindf_bridge.neutralize.Neutralize property) norm() (proteindf_bridge.position.Position method) nuclei_charge (proteindf_bridge.atomgroup.AtomGroup property) num_of_positions (proteindf_bridge.superposer.Superposer property) num_spaces() (proteindf_bridge.str_processing.StrUtils class method)

P

parent (proteindf_bridge.atomgroup.AtomGroup property) parse_yaml() (in module proteindf_bridge.functions) Path (class in proteindf_bridge.path) path (proteindf_bridge.atom.Atom property) (proteindf_bridge.atomgroup.AtomGroup property) Pdb (class in proteindf_bridge.biopdb) PeriodicTable (class in proteindf_bridge.periodictable) pickup_atoms() (proteindf_bridge.atomgroup.AtomGroup method) Position (class in proteindf_bridge.position) position (proteindf_bridge.atom.Atom property) positions1 (proteindf_bridge.superposer.Superposer property) positions2 (proteindf_bridge.superposer.Superposer property) pp() (proteindf_bridge.dbmanager.DbManager method) pp_table() (proteindf_bridge.dbmanager.DbManager method) 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 method)

R

r_A (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) r_B (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) real_nuclei_charge (proteindf_bridge.atomgroup.AtomGroup property) remove_atom() (proteindf_bridge.atomgroup.AtomGroup method) remove_group() (proteindf_bridge.atomgroup.AtomGroup method) remove_WAT() (proteindf_bridge.utils.Utils class method) renumber() (proteindf_bridge.biopdb.Pdb method) resize() (proteindf_bridge.matrix.Matrix method) (proteindf_bridge.matrix.SymmetricMatrix method) (proteindf_bridge.vector.Vector method)

restructure() (proteindf_bridge.atomgroup.AtomGroup method) rmsd (proteindf_bridge.superposer.Superposer property) (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) rotate() (proteindf_bridge.atom.Atom method) (proteindf_bridge.atomgroup.AtomGroup method) (proteindf_bridge.position.Position method) rotation_mat (proteindf_bridge.superposer.Superposer property) (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) rows (proteindf_bridge.matrix.Matrix property)

S

save() (proteindf_bridge.mol2.SimpleMol2 method) (proteindf_bridge.xyz.Xyz method) save_atomgroup() (in module proteindf_bridge.functions) save_config() (proteindf_bridge.mail.Mail method) save_csv() (proteindf_bridge.atomgroup.AtomGroup method) save_msgpack() (in module proteindf_bridge.functions) (proteindf_bridge.mmcif.SimpleMmcif method) save_yaml() (in module proteindf_bridge.functions) Select (class in proteindf_bridge.select) select() (proteindf_bridge.atomgroup.AtomGroup method) (proteindf_bridge.dbmanager.DbManager method) (proteindf_bridge.matrix.Matrix method) Select_Atom (class in proteindf_bridge.select) Select_AtomGroup (class in proteindf_bridge.select) Select_Name (class in proteindf_bridge.select) Select_Path (class in proteindf_bridge.select) Select_Path_simple (class in proteindf_bridge.select) Select_Path_wildcard (class in proteindf_bridge.select) Select_PathRegex (class in proteindf_bridge.select) Select_Range (class in proteindf_bridge.select) select_residues() (proteindf_bridge.modeling.Modeling method) Select_Symbol (class in proteindf_bridge.select) send() (proteindf_bridge.mail.Mail method) set() (proteindf_bridge.matrix.Matrix method) (proteindf_bridge.matrix.SymmetricMatrix method) (proteindf_bridge.vector.Vector method) set_atom() (proteindf_bridge.atomgroup.AtomGroup method) set_buffer() (proteindf_bridge.matrix.Matrix method) (proteindf_bridge.vector.Vector method) set_by_atomgroup() (proteindf_bridge.biopdb.Pdb method) (proteindf_bridge.gro.SimpleGro method) (proteindf_bridge.mol2.SimpleMol2 method) (proteindf_bridge.xyz.Xyz method)

set_by_dict_data() (proteindf_bridge.atomgroup.AtomGroup method) set_by_raw_data() (proteindf_bridge.atom.Atom method) set_group() (proteindf_bridge.atomgroup.AtomGroup method) set_user_version() (proteindf_bridge.dbmanager.DbManager method) setup() (proteindf_bridge.bond.Bond method) shift_by() (proteindf_bridge.atom.Atom method) (proteindf_bridge.atomgroup.AtomGroup method) shift_positions1 (proteindf_bridge.superposer.Superposer property) shift_positions2 (proteindf_bridge.superposer.Superposer property) SimpleGro (class in proteindf_bridge.gro) SimpleMmcif (class in proteindf_bridge.mmcif) SimpleMol2 (class in proteindf_bridge.mol2) size() (proteindf_bridge.vector.Vector method) smtp_account (proteindf_bridge.mail.Mail property) smtp_password (proteindf_bridge.mail.Mail property) smtp_port (proteindf_bridge.mail.Mail property) smtp_server (proteindf_bridge.mail.Mail property) sort_atoms (proteindf_bridge.atomgroup.AtomGroup property) sort_groups (proteindf_bridge.atomgroup.AtomGroup property) sort_nicely() (proteindf_bridge.str_processing.StrUtils class method) split_path() (proteindf_bridge.path.Path class method) square_distance_from() (proteindf_bridge.position.Position method) SSBond (class in proteindf_bridge.ssbond) str_to_bool() (proteindf_bridge.str_processing.StrUtils class method) StrUtils (class in proteindf_bridge.str_processing) subject (proteindf_bridge.mail.Mail property) sum_of_atomic_number() (proteindf_bridge.atomgroup.AtomGroup method) superimpose() (proteindf_bridge.superposer.Superposer method) (proteindf_bridge.superposer_quaternion.Superposer_quaternion method) Superposer (class in proteindf_bridge.superposer) Superposer_quaternion (class in proteindf_bridge.superposer_quaternion) symbol (proteindf_bridge.atom.Atom property) SymmetricMatrix (class in proteindf_bridge.matrix)

T

text (proteindf_bridge.mail.Mail property) to_address (proteindf_bridge.mail.Mail property) to_bytes() (proteindf_bridge.str_processing.StrUtils class method) to_list() (proteindf_bridge.vector.Vector method)

to_unicode() (proteindf_bridge.str_processing.StrUtils class method) to_unicode_dict() (proteindf_bridge.str_processing.StrUtils class method) to_unicode_list() (proteindf_bridge.str_processing.StrUtils class method) transpose() (proteindf_bridge.matrix.Matrix method) type (proteindf_bridge.matrix.Matrix property)

U

unindent_block() (proteindf_bridge.str_processing.StrUtils class method) update() (proteindf_bridge.dbmanager.DbManager method) update_positions1 (proteindf_bridge.superposer.Superposer property)

update_positions2 (proteindf_bridge.superposer.Superposer property) use_SSL (proteindf_bridge.mail.Mail property) Utils (class in proteindf_bridge.utils)

V

va (proteindf_bridge.superposer_quaternion.Superposer_quaternion property) vb (proteindf_bridge.superposer_quaternion.Superposer_quaternion property)

vdw (proteindf_bridge.atom.Atom property) vdw() (proteindf_bridge.periodictable.PeriodicTable static method) Vector (class in proteindf_bridge.vector)

W

weight (proteindf_bridge.atomgroup.AtomGroup property)

weight() (proteindf_bridge.atom.Atom method)

X

x (proteindf_bridge.position.Position property) Xyz (class in proteindf_bridge.xyz)

xyz (proteindf_bridge.amber_prmtop.AmberPrmtop property) (proteindf_bridge.atom.Atom property) (proteindf_bridge.position.Position property)

Y

y (proteindf_bridge.position.Position property)

Z

z (proteindf_bridge.position.Position property)