Index

A

add_atom() (python_pdb.entities.Residue method) add_chain() (python_pdb.entities.Model method) add_child() (python_pdb.entities.Atom method) (python_pdb.entities.Entity method) add_model() (python_pdb.entities.Structure method) add_residue() (python_pdb.entities.Chain method) align_entities() (in module python_pdb.aligners) align_pandas_structure() (in module python_pdb.aligners) align_sequences() (in module python_pdb.aligners)

alt_loc (python_pdb.entities.Atom attribute) (python_pdb.records.ParticleRecord attribute) ALT_LOC_RANGE (in module python_pdb.formats.pdb) AMINO_ACIDS (in module python_pdb.formats.residue) Atom (class in python_pdb.entities) atom_name (python_pdb.records.ParticleRecord attribute) ATOM_NAME_RANGE (in module python_pdb.formats.pdb) atom_num (python_pdb.records.ParticleRecord attribute) ATOM_NUMBER_RANGE (in module python_pdb.formats.pdb) AtomRecord (class in python_pdb.records)

B

b_factor (python_pdb.entities.Atom attribute) (python_pdb.records.ParticleRecord attribute)

B_FACTOR_RANGE (in module python_pdb.formats.pdb)

C

Chain (class in python_pdb.entities) chain_id (python_pdb.records.ParticleRecord attribute) CHAIN_ID_RANGE (in module python_pdb.formats.pdb) charge (python_pdb.entities.Atom attribute) (python_pdb.records.ParticleRecord attribute) CHARGE_RANGE (in module python_pdb.formats.pdb) children (python_pdb.entities.Entity attribute)

children_equal() (python_pdb.entities.Atom method) (python_pdb.entities.Entity method) copy() (python_pdb.entities.Atom method) (python_pdb.entities.Chain method) (python_pdb.entities.Model method) (python_pdb.entities.Residue method) (python_pdb.entities.Structure method)

D

dehydrate() (python_pdb.entities.Structure method)

E

element (python_pdb.entities.Atom attribute) (python_pdb.records.ParticleRecord attribute)

ELEMENT_RANGE (in module python_pdb.formats.pdb) EndModelRecord (class in python_pdb.records) Entity (class in python_pdb.entities)

F

format_atom_record() (in module python_pdb.formats.pdb) format_model_record() (in module python_pdb.formats.pdb)

from_pandas() (python_pdb.entities.Structure class method) from_pdb() (python_pdb.entities.Structure class method)

G

generate_records_from_pandas() (in module python_pdb.formats.pandas) generate_records_from_pdb() (in module python_pdb.formats.pdb) get_atoms() (python_pdb.entities.Residue method) get_chains() (python_pdb.entities.Model method)

get_children() (python_pdb.entities.Atom method) (python_pdb.entities.Entity method) get_coordinates() (python_pdb.entities.Entity method) get_models() (python_pdb.entities.Structure method) get_residues() (python_pdb.entities.Chain method)

H

het_atom (python_pdb.entities.Atom attribute)

HetAtomRecord (class in python_pdb.records)

I

insert_code (python_pdb.entities.Residue attribute) (python_pdb.records.ParticleRecord attribute)

INSERT_CODE_RANGE (in module python_pdb.formats.pdb)

M

Model (class in python_pdb.entities) MODEL_SERIAL_RANGE (in module python_pdb.formats.pdb) ModelRecord (class in python_pdb.records) module python_pdb python_pdb.aligners python_pdb.chemistry python_pdb.comparisons python_pdb.entities python_pdb.formats python_pdb.formats.pandas python_pdb.formats.pdb python_pdb.formats.residue python_pdb.parsers python_pdb.records

MOLECULAR_WEIGHTS (in module python_pdb.chemistry)

N

name (python_pdb.entities.Atom attribute) (python_pdb.entities.Chain attribute) (python_pdb.entities.Residue attribute)

number (python_pdb.entities.Atom attribute)

O

occupancy (python_pdb.entities.Atom attribute) (python_pdb.records.ParticleRecord attribute)

OCCUPANCY_RANGE (in module python_pdb.formats.pdb) olc (python_pdb.entities.Residue property) ONE_TO_THREE_CODE (in module python_pdb.formats.residue)

P

parent (python_pdb.entities.Entity attribute) parse_pdb() (in module python_pdb.parsers) parse_pdb_to_pandas() (in module python_pdb.parsers) ParticleRecord (class in python_pdb.records) pos_x (python_pdb.entities.Atom attribute) pos_y (python_pdb.entities.Atom attribute) pos_z (python_pdb.entities.Atom attribute) position (python_pdb.entities.Atom property) python_pdb module python_pdb.aligners module python_pdb.chemistry module python_pdb.comparisons module

python_pdb.entities module python_pdb.formats module python_pdb.formats.pandas module python_pdb.formats.pdb module python_pdb.formats.residue module python_pdb.parsers module python_pdb.records module

R

Record (class in python_pdb.records) record_type (python_pdb.records.AtomRecord property) (python_pdb.records.EndModelRecord property) (python_pdb.records.HetAtomRecord property) (python_pdb.records.ModelRecord property) RECORD_TYPE_RANGE (in module python_pdb.formats.pdb) remove_atom() (python_pdb.entities.Residue method) remove_chain() (python_pdb.entities.Model method)

remove_child() (python_pdb.entities.Atom method) (python_pdb.entities.Entity method) remove_model() (python_pdb.entities.Structure method) remove_non_amino_acids() (python_pdb.entities.Structure method) remove_residue() (python_pdb.entities.Chain method) res_name (python_pdb.records.ParticleRecord attribute) Residue (class in python_pdb.entities) RESIDUE_NAME_RANGE (in module python_pdb.formats.pdb) rmsd() (in module python_pdb.comparisons)

S

seq_id (python_pdb.entities.Residue attribute) (python_pdb.records.ParticleRecord attribute) SEQ_ID_RANGE (in module python_pdb.formats.pdb) serial_number (python_pdb.entities.Model attribute) (python_pdb.records.ModelRecord attribute), [1]

split_states() (python_pdb.entities.Structure method) stringify_structure() (in module python_pdb.parsers) Structure (class in python_pdb.entities) StructureConstructionWarning

T

THREE_TO_ONE_CODE (in module python_pdb.formats.residue)

tlc (python_pdb.entities.Residue property) to_pandas() (python_pdb.entities.Structure method)

U

UnknownResidueError

X

x_pos (python_pdb.records.ParticleRecord attribute)

X_POS_RANGE (in module python_pdb.formats.pdb)

Y

y_pos (python_pdb.records.ParticleRecord attribute)

Y_POS_RANGE (in module python_pdb.formats.pdb)

Z

z_pos (python_pdb.records.ParticleRecord attribute)

Z_POS_RANGE (in module python_pdb.formats.pdb)