Index

_

_constructor (moldf.pdb_dataframe.PDBDataFrame property) _count_n_lines() (in module moldf.read_jcsv) _filter_num_col() (moldf.pdb_dataframe.PDBDataFrame method) _get_header_df() (in module moldf.read_mol2) _get_molecule_df() (in module moldf.read_mol2)

_metadata (moldf.pdb_dataframe.PDBDataFrame attribute) _pdbx_to_pdb() (moldf.pdb_dataframe.PDBDataFrame method) _read_jcsv_by_line() (in module moldf.read_jcsv) _set_atom_df_dtypes() (in module moldf.read_mol2) _set_bond_df_dtypes() (in module moldf.read_mol2) _split_atom_line() (in module moldf.read_pdb)

A

AF2_MODEL (in module moldf.read_pdb) (in module moldf.read_pdbx) alt_locs() (moldf.pdb_dataframe.PDBDataFrame method) ATOM_COL_NAMES (in module moldf.read_mol2)

atom_names() (moldf.pdb_dataframe.PDBDataFrame method) atom_numbers() (moldf.pdb_dataframe.PDBDataFrame method) ATOM_SITE (in module moldf.read_pdb) atoms (moldf.pdb_dataframe.PDBDataFrame property)

B

b_factors() (moldf.pdb_dataframe.PDBDataFrame method) backbone (moldf.pdb_dataframe.PDBDataFrame property)

BOND_COL_NAMES (in module moldf.read_mol2) bonds (moldf.pdb_dataframe.PDBDataFrame property)

C

ca_atoms (moldf.pdb_dataframe.PDBDataFrame property) center_of_geometry (moldf.pdb_dataframe.PDBDataFrame property) center_of_mass (moldf.pdb_dataframe.PDBDataFrame property) chain_ids() (moldf.pdb_dataframe.PDBDataFrame method)

chain_list (moldf.pdb_dataframe.PDBDataFrame property) charges() (moldf.pdb_dataframe.PDBDataFrame method) CHEM_COMP (in module moldf.read_pdb) coords (moldf.pdb_dataframe.PDBDataFrame property)

D

distance_matrix (moldf.pdb_dataframe.PDBDataFrame property)

distances() (moldf.pdb_dataframe.PDBDataFrame method)

E

ELEMENT_MASSES (moldf.pdb_dataframe.PDBDataFrame property)

element_set (moldf.pdb_dataframe.PDBDataFrame property) element_symbols() (moldf.pdb_dataframe.PDBDataFrame method)

G

get_bonds_by_distance() (moldf.pdb_dataframe.PDBDataFrame method) get_bonds_by_template() (moldf.pdb_dataframe.PDBDataFrame method) get_chain_list() (moldf.pdb_dataframe.PDBDataFrame class method) get_covalent_bond_cutoffs() (in module moldf.covalent_bond)

get_distance_matrix() (moldf.pdb_dataframe.PDBDataFrame class method) get_masses() (moldf.pdb_dataframe.PDBDataFrame method) get_residue_list() (moldf.pdb_dataframe.PDBDataFrame class method) get_residue_template() (in module moldf.covalent_bond)

H

hash_random_state (moldf.pdb_dataframe.PDBDataFrame property)

heavy_atoms (moldf.pdb_dataframe.PDBDataFrame property) hetero_atoms (moldf.pdb_dataframe.PDBDataFrame property)

I

IMPLEMENTED_MOL2_CATS (in module moldf.read_mol2) (in module moldf.write_mol2) IMPLEMENTED_PDB_CATS (in module moldf.read_pdb) (in module moldf.write_pdb)

insertions() (moldf.pdb_dataframe.PDBDataFrame method) is_chimera (moldf.pdb_dataframe.PDBDataFrame property)

M

module moldf.covalent_bond moldf.pdb_dataframe moldf.read_jcsv moldf.read_mol2 moldf.read_pdb moldf.read_pdbx moldf.write_jcsv moldf.write_mol2 moldf.write_pdb moldf.write_pdbx moldf.covalent_bond module moldf.pdb_dataframe module

moldf.read_jcsv module moldf.read_mol2 module moldf.read_pdb module moldf.read_pdbx module moldf.write_jcsv module moldf.write_mol2 module moldf.write_pdb module moldf.write_pdbx module

N

n_atoms (moldf.pdb_dataframe.PDBDataFrame property) n_chains (moldf.pdb_dataframe.PDBDataFrame property) n_models (moldf.pdb_dataframe.PDBDataFrame property)

n_residues (moldf.pdb_dataframe.PDBDataFrame property) n_segments (moldf.pdb_dataframe.PDBDataFrame property) NMR_MDL (in module moldf.read_pdb) nmr_models() (moldf.pdb_dataframe.PDBDataFrame method)

O

occupancies() (moldf.pdb_dataframe.PDBDataFrame method)

P

pdb_format (moldf.pdb_dataframe.PDBDataFrame property)

PDBDataFrame (class in moldf.pdb_dataframe) PDBX_COLS (in module moldf.pdb_dataframe)

R

radius_of_gyration (moldf.pdb_dataframe.PDBDataFrame property) read_jcsv() (in module moldf.read_jcsv) read_mol2() (in module moldf.read_mol2) read_pdb() (in module moldf.read_pdb) read_pdbx() (in module moldf.read_pdbx) record_names() (moldf.pdb_dataframe.PDBDataFrame method)

RESIDUE_CODES (in module moldf.pdb_dataframe) (moldf.pdb_dataframe.PDBDataFrame property) residue_list (moldf.pdb_dataframe.PDBDataFrame property) residue_names() (moldf.pdb_dataframe.PDBDataFrame method) residue_numbers() (moldf.pdb_dataframe.PDBDataFrame method) residues (moldf.pdb_dataframe.PDBDataFrame property) rmsd() (moldf.pdb_dataframe.PDBDataFrame method)

S

segment_ids() (moldf.pdb_dataframe.PDBDataFrame method) sequences (moldf.pdb_dataframe.PDBDataFrame property)

side_chain (moldf.pdb_dataframe.PDBDataFrame property) split_line() (in module moldf)

U

use_square_form (moldf.pdb_dataframe.PDBDataFrame property)

use_squared_distance (moldf.pdb_dataframe.PDBDataFrame property)

W

water (moldf.pdb_dataframe.PDBDataFrame property) write_jcsv() (in module moldf.write_jcsv)

write_mol2() (in module moldf.write_mol2) write_pdb() (in module moldf.write_pdb) write_pdbx() (in module moldf.write_pdbx)

X

x_coords() (moldf.pdb_dataframe.PDBDataFrame method)

Y

y_coords() (moldf.pdb_dataframe.PDBDataFrame method)

Z

z_coords() (moldf.pdb_dataframe.PDBDataFrame method)