Index

_

__add__() (Trajectory method) __check_pbc__() (BoxWriter method) __contains__() (Trajectory method) __eq__() (Angle method) (Atom method) (AtomicSystem method) (BaseEnumFormat method) (Bond method) (Cell method) (Dihedral method) (Element method) (InputDictionary method) (OutputFileFormat method) (Residue method) (Topology method) (Trajectory method) __getitem__() (AtomicSystem method) (InputDictionary method) (Topology method) (Trajectory method)

__info_file_found__() (EnergyFileReader method) __iter__() (Trajectory method) __len__() (Trajectory method) __repr__() (Atom method) (AtomicSystem method) (Cell method) (Element method) (Residue method) (Selection method) (Topology method) (Trajectory method) __setitem__() (InputDictionary method) __str__() (Atom method) (AtomicSystem method) (Cell method) (Element method) (Residue method) (Selection method) (Topology method) (Trajectory method)

A

add_arguments() (AddMoleculesCLI class method) (BuildNEPTrajCLI class method) (ContinueInputCLI class method) (GEN2XYZCLI class method) (RDFCLI class method) (Rst2XYZCLI class method) (Traj2BoxCLI class method) (Traj2QMCFCCLI class method) (XYZ2GENCLI class method) add_comments() (ShakeTopologyGenerator method) add_molecule() (in module PQAnalysis.tools.add_molecule) add_molecules() (AddMolecule method) AddMolecule (class in PQAnalysis.tools.add_molecule) AddMoleculesCLI (class in PQAnalysis.cli.add_molecules) all() (SelectionTransformer method) allclose_vectorized() (in module PQAnalysis.utils.math) alpha (Cell property) and_statement() (SelectionTransformer method) Angle (class in PQAnalysis.topology.bonded_topology.angle) angle_linkers (BondedTopology property) APPEND (FileWritingMode attribute) append() (Trajectory method)

array() (ComposedDatatypesTransformer method) assign() (InputFileVisitor method) Atom (class in PQAnalysis.core.atom.atom) atom() (SelectionTransformer method) atom_types (Residue property) AtomError atomic_masses (AtomicSystem property) atomic_number (Atom property) (Element property) AtomicSystem (class in PQAnalysis.atomic_system.atomic_system) AtomicSystemError AtomicSystemMassError AtomicSystemPositionsError atoms (AtomicSystem property) Atoms (class in PQAnalysis.core.atom.atom) atoms (Topology property) atomtype() (SelectionTransformer method) atomtype_names (Topology property) AUTO (OutputFileFormat attribute) (TrajectoryFormat attribute) average_equivalents() (ShakeTopologyGenerator method) average_volume (RDF property)

B

BaseEnumFormat (class in PQAnalysis.formats) BaseEnumFormatError BaseReader (class in PQAnalysis.io.base) BaseWriter (class in PQAnalysis.io.base) beta (Cell property) bold_cyan (CustomColorFormatter attribute) bold_green (CustomColorFormatter attribute) bold_orange (CustomColorFormatter attribute) bold_red (CustomColorFormatter attribute) bold_yellow (CustomColorFormatter attribute) Bond (class in PQAnalysis.topology.bonded_topology.bond) bond_linkers (BondedTopology property) BondedTopology (class in PQAnalysis.topology.bonded_topology.bonded_topology)

boolean() (PrimitiveTransformer method) bounding_edges (Cell property) box_angles (Cell property) box_lengths (Cell property) (Trajectory property) box_matrix (Cell property) box_volumes (Trajectory property) BoxFileFormat (class in PQAnalysis.io.formats) BoxFileFormatError BoxWriter (class in PQAnalysis.io.box_writer) BoxWriterError build_custom_element (AtomicSystem property) BuildNEPTrajCLI (class in PQAnalysis.cli.build_nep_traj)

C

calculate_frame_size() (TrajectoryReader method) calculate_frames_of_trajectory_file() (in module PQAnalysis.io.traj_file.api) calculate_number_of_frames_per_file() (TrajectoryReader method) cell (AtomicSystem property) Cell (class in PQAnalysis.core.cell.cell) Cells (class in PQAnalysis.core.cell.cell) cells (Trajectory property) (TrajectoryReader property) center() (AtomicSystem method) center_of_mass (AtomicSystem property) center_of_mass_residues (AtomicSystem property) CHARGE (OutputFileFormat attribute) (TrajectoryFormat attribute) charge_file (PQInputFileReader property) charges (AtomicSystem property) check_known_keys() (PQAnalysisInputFileReader method) check_pbc() (Trajectory method) check_required_keys() (PQAnalysisInputFileReader method) check_residues (Topology property) check_trajectory_pbc() (in module PQAnalysis.traj.api)

check_trajectory_vacuum() (in module PQAnalysis.traj.api) check_vacuum() (Trajectory method) close() (BaseWriter method) com_residue_traj (Trajectory property) combined_name (AtomicSystem property) ComposedDatatypesTransformer (class in PQAnalysis.io.input_file_reader.input_file_parser) compute_com_atomic_system() (AtomicSystem method) continue_input_file() (in module PQAnalysis.io.api) (PQInputFileReader method) ContinueInputCLI (class in PQAnalysis.cli.continue_input) copy() (Angle method) (AtomicSystem method) (Bond method) (Dihedral method) (Trajectory method) count_decorator() (in module PQAnalysis.utils.decorators) critical() (CustomLogger method) CustomColorFormatter (class in PQAnalysis.utils.custom_logging) CustomElement (class in PQAnalysis.core.atom.element) CustomFormatter (class in PQAnalysis.utils.custom_logging) CustomLogger (class in PQAnalysis.utils.custom_logging)

D

DATA (BoxFileFormat attribute) delta_r (PQAnalysisInputFileReader property) delta_r_key (PQAnalysisInputFileReader attribute)

Dihedral (class in PQAnalysis.topology.bonded_topology.dihedral) dihedral_linkers (BondedTopology property) distance() (in module PQAnalysis.core.api)

E

element (Atom property) Element (class in PQAnalysis.core.atom.element) element() (SelectionTransformer method) element_name (Atom property) ElementNotFoundError Elements (class in PQAnalysis.core.atom.element) elements (Residue property) energy (AtomicSystem property)

Energy (class in PQAnalysis.physical_data.energy) ENERGY (OutputFileFormat attribute) energy_file (PQInputFileReader property) EnergyError EnergyFileReader (class in PQAnalysis.io.energy_file_reader) error() (CustomLogger method) expression() (SelectionVisitor method) extend_shake_bonds() (BondedTopology method) extend_topology_file() (AddMolecule method)

F

file_extensions() (OutputFileFormat class method) file_prefix (PQInputFileReader property) FileWritingMode (class in PQAnalysis.io.formats) FileWritingModeError find_files_with_prefix() (in module PQAnalysis.utils.files) find_matching_files() (OutputFileFormat class method) fit_atomic_system() (AtomicSystem method) fitting_logger (AtomicSystem attribute) float() (PrimitiveTransformer method) FORCE (OutputFileFormat attribute) (TrajectoryFormat attribute)

force_file (PQInputFileReader property) forces (AtomicSystem property) format (TrajectoryWriter property) format() (CustomFormatter method) format_level() (CustomColorFormatter method) (CustomFormatter method) FORMATS (CustomColorFormatter attribute) frame_generator() (TrajectoryReader method) FrameReaderError frames (Trajectory property)

G

gamma (Cell property) gen2xyz() (in module PQAnalysis.io.conversion_api) GEN2XYZCLI (class in PQAnalysis.cli.gen2xyz) generate_shake_topology_file() (in module PQAnalysis.topology.api) generate_topology() (ShakeTopologyGenerator method) GenFileReader (class in PQAnalysis.io.gen_file.gen_file_reader) GenFileReaderError GenFileWriter (class in PQAnalysis.io.gen_file.gen_file_writer) get_arg_var_by_name() (in module PQAnalysis.utils.decorators)

get_atom_indices_from_residue_names() (Topology method) get_atom_indices_from_residue_numbers() (Topology method) get_file_extensions() (OutputFileFormat class method) get_line() (InputDictionary method) get_random_seed() (in module PQAnalysis.utils.random) get_type() (InputDictionary method) get_type_error_message() (in module PQAnalysis.type_checking) get_value() (InputDictionary method) glob() (ComposedDatatypesTransformer method)

H

handler (AtomicSystem attribute) has_charges (AtomicSystem property) has_energy (AtomicSystem property) has_forces (AtomicSystem property)

has_pos (AtomicSystem property) has_stress (AtomicSystem property) has_vel (AtomicSystem property) has_virial (AtomicSystem property) header (CustomColorFormatter attribute)

I

id (Residue property) image() (AtomicSystem method) (Cell method) improper_linkers (BondedTopology property) index() (SelectionTransformer method) indices() (SelectionTransformer method) infer_format_from_extension() (OutputFileFormat class method) (TrajectoryFormat class method) INFO (OutputFileFormat attribute) info_file (PQInputFileReader property) InfoFileReader (class in PQAnalysis.io.info_file_reader) init_from_box_matrix() (Cell class method) InputDictionary (class in PQAnalysis.io.input_file_reader.input_file_parser) InputFileError InputFileFormat (class in PQAnalysis.io.input_file_reader.formats) InputFileFormatError

InputFileParser (class in PQAnalysis.io.input_file_reader.input_file_parser) InputFileVisitor (class in PQAnalysis.io.input_file_reader.input_file_parser) InputFileWarning INSTANTANEOUS_ENERGY (OutputFileFormat attribute) INT() (SelectionTransformer method) integer() (PrimitiveTransformer method) (SelectionTransformer method) inverse_box_matrix (Cell property) is_comment_line() (in module PQAnalysis.utils.string) is_qmcf_type() (InputFileFormat class method) is_qmcfc_type() (MDEngineFormat class method) is_rpmd_start_file_defined (PQInputFileReader property) is_start_file_defined (PQInputFileReader property) is_vacuum (Cell property) isclose() (AtomicSystem method) (Cell method) (Trajectory method)

K

key() (ComposedDatatypesTransformer method)

keys() (InputDictionary method) known_keys (PQAnalysisInputFileReader attribute)

L

letters() (SelectionTransformer method) level_keys (CustomFormatter attribute) log_file (PQAnalysisInputFileReader property) log_file_key (PQAnalysisInputFileReader attribute) logger (AddMolecule attribute) (Atom attribute) (AtomicSystem attribute) (BaseReader attribute) (BaseWriter attribute) (BondedTopology attribute) (BoxWriter attribute) (Element attribute) (Energy attribute) (EnergyFileReader attribute) (GenFileReader attribute) (GenFileWriter attribute) (InfoFileReader attribute) (InputDictionary attribute) (MoldescriptorReader attribute) (NEPWriter attribute) (PQAnalysisInputFileReader attribute) (PQInputFileReader attribute) (RDF attribute) (RDFInputFileReader attribute) (Residue attribute) (RestartFileReader attribute) (RestartFileWriter attribute) (Selection attribute) (ShakeTopologyGenerator attribute) (Topology attribute) (TopologyFileReader attribute) (TopologyFileWriter attribute) (Trajectory attribute) (TrajectoryReader attribute)

longest_level (CustomFormatter attribute) lower() (OutputFileFormat method) (TrajectoryFormat method)

M

main() (in module PQAnalysis.cli.add_molecules) (in module PQAnalysis.cli.build_nep_traj) (in module PQAnalysis.cli.continue_input) (in module PQAnalysis.cli.gen2xyz) (in module PQAnalysis.cli.main) (in module PQAnalysis.cli.rdf) (in module PQAnalysis.cli.rst2xyz) (in module PQAnalysis.cli.traj2box) (in module PQAnalysis.cli.traj2qmcfc) (in module PQAnalysis.cli.xyz2gen) mass (Atom property) (AtomicSystem property) (Element property) MDEngineFormat (class in PQAnalysis.traj.formats) MDEngineFormatError member_repr() (BaseEnumFormat class method) message (AtomicSystemMassError attribute) (AtomicSystemPositionsError attribute) mode (BaseWriter property) module PQAnalysis PQAnalysis.analysis PQAnalysis.analysis.rdf PQAnalysis.analysis.rdf.api PQAnalysis.analysis.rdf.exceptions PQAnalysis.analysis.rdf.rdf PQAnalysis.analysis.rdf.rdf_input_file_reader PQAnalysis.analysis.rdf.rdf_output_file_writer PQAnalysis.atomic_system PQAnalysis.atomic_system.atomic_system PQAnalysis.atomic_system.exceptions PQAnalysis.cli PQAnalysis.cli.add_molecules PQAnalysis.cli.build_nep_traj PQAnalysis.cli.continue_input PQAnalysis.cli.gen2xyz PQAnalysis.cli.main PQAnalysis.cli.rdf PQAnalysis.cli.rst2xyz PQAnalysis.cli.traj2box PQAnalysis.cli.traj2qmcfc PQAnalysis.cli.xyz2gen PQAnalysis.config PQAnalysis.core PQAnalysis.core.api PQAnalysis.core.atom PQAnalysis.core.atom.atom PQAnalysis.core.atom.element PQAnalysis.core.cell PQAnalysis.core.cell.cell PQAnalysis.core.exceptions PQAnalysis.core.residue PQAnalysis.exceptions PQAnalysis.formats PQAnalysis.io PQAnalysis.io.api PQAnalysis.io.base PQAnalysis.io.box_writer PQAnalysis.io.conversion_api PQAnalysis.io.energy_file_reader PQAnalysis.io.exceptions PQAnalysis.io.formats PQAnalysis.io.gen_file PQAnalysis.io.gen_file.api PQAnalysis.io.gen_file.exceptions PQAnalysis.io.gen_file.gen_file_reader PQAnalysis.io.gen_file.gen_file_writer PQAnalysis.io.info_file_reader PQAnalysis.io.input_file_reader PQAnalysis.io.input_file_reader.exceptions PQAnalysis.io.input_file_reader.formats PQAnalysis.io.input_file_reader.input_file_parser PQAnalysis.io.input_file_reader.pq PQAnalysis.io.input_file_reader.pq.output_files PQAnalysis.io.input_file_reader.pq.pq_input_file_reader PQAnalysis.io.input_file_reader.pq_analysis PQAnalysis.io.input_file_reader.pq_analysis.pqanalysis_input_file_reader PQAnalysis.io.moldescriptor_reader PQAnalysis.io.nep PQAnalysis.io.nep.exceptions PQAnalysis.io.nep.nep_writer PQAnalysis.io.restart_file PQAnalysis.io.restart_file.api PQAnalysis.io.restart_file.exceptions PQAnalysis.io.restart_file.restart_reader PQAnalysis.io.restart_file.restart_writer PQAnalysis.io.topology_file PQAnalysis.io.topology_file.api PQAnalysis.io.topology_file.exceptions PQAnalysis.io.topology_file.topology_file_reader PQAnalysis.io.topology_file.topology_file_writer PQAnalysis.io.traj_file PQAnalysis.io.traj_file.api PQAnalysis.io.traj_file.exceptions PQAnalysis.io.traj_file.frame_reader PQAnalysis.io.traj_file.process_lines PQAnalysis.io.traj_file.trajectory_reader PQAnalysis.io.traj_file.trajectory_writer PQAnalysis.io.virial PQAnalysis.io.virial.api PQAnalysis.io.virial.virial_reader PQAnalysis.io.write_api PQAnalysis.physical_data PQAnalysis.physical_data.energy PQAnalysis.physical_data.exceptions PQAnalysis.tools PQAnalysis.tools.add_molecule PQAnalysis.tools.traj_to_com_traj PQAnalysis.topology PQAnalysis.topology.api PQAnalysis.topology.bonded_topology PQAnalysis.topology.bonded_topology.angle PQAnalysis.topology.bonded_topology.bond PQAnalysis.topology.bonded_topology.bonded_topology PQAnalysis.topology.bonded_topology.dihedral PQAnalysis.topology.exceptions PQAnalysis.topology.selection PQAnalysis.topology.shake_topology PQAnalysis.topology.topology PQAnalysis.traj PQAnalysis.traj.api PQAnalysis.traj.exceptions PQAnalysis.traj.formats PQAnalysis.traj.trajectory PQAnalysis.type_checking PQAnalysis.types PQAnalysis.utils PQAnalysis.utils.common PQAnalysis.utils.custom_logging PQAnalysis.utils.decorators PQAnalysis.utils.files PQAnalysis.utils.math PQAnalysis.utils.random PQAnalysis.utils.string PQAnalysis.utils.units

moldescriptor_file (PQAnalysisInputFileReader property) moldescriptor_file_key (PQAnalysisInputFileReader attribute) MoldescriptorReader (class in PQAnalysis.io.moldescriptor_reader) MoldescriptorReaderError multiline_statement() (InputFileVisitor method)

N

n_atoms (AtomicSystem property) (RDF property) (Residue property) (Topology property) n_atoms_per_residue (Topology property) n_bins (PQAnalysisInputFileReader property) n_bins_key (PQAnalysisInputFileReader attribute) n_frames (RDF property) n_mm_residues (Topology property) n_qm_residues (Topology property) n_residues (Topology property) n_unique_residues (Topology property)

name (Atom property) (Residue property) nearest_neighbours() (AtomicSystem method) NEPError NEPWriter (class in PQAnalysis.io.nep.nep_writer) no_intra_molecular (PQAnalysisInputFileReader property) no_intra_molecular_key (PQAnalysisInputFileReader attribute) Np1DIntArray (class in PQAnalysis.types) Np1DNumberArray (class in PQAnalysis.types) Np2DIntArray (class in PQAnalysis.types) Np2DNumberArray (class in PQAnalysis.types) Np3x3NumberArray (in module PQAnalysis.types) NpnDNumberArray (class in PQAnalysis.types)

O

open() (BaseWriter method) optional_keys (RDFInputFileReader attribute) or_statement() (SelectionTransformer method) original_critical() (CustomLogger method) original_error() (CustomLogger method) out_file (PQAnalysisInputFileReader property)

out_file_key (PQAnalysisInputFileReader attribute) output_file (PQInputFileReader property) output_file_keys (PQInputFileReader attribute) output_format (BoxWriter property) OutputFileFormat (class in PQAnalysis.io.formats) OutputFileFormatError OVERWRITE (FileWritingMode attribute)

P

parse() (InputFileParser method) partial_charges (Residue property) pbc (AtomicSystem property) pop() (Trajectory method) pos (AtomicSystem property) PositiveInt (class in PQAnalysis.types) PQ (InputFileFormat attribute) (MDEngineFormat attribute) PQAnalysis module PQANALYSIS (InputFileFormat attribute) PQAnalysis.analysis module PQAnalysis.analysis.rdf module PQAnalysis.analysis.rdf.api module PQAnalysis.analysis.rdf.exceptions module PQAnalysis.analysis.rdf.rdf module PQAnalysis.analysis.rdf.rdf_input_file_reader module PQAnalysis.analysis.rdf.rdf_output_file_writer module PQAnalysis.atomic_system module PQAnalysis.atomic_system.atomic_system module PQAnalysis.atomic_system.exceptions module PQAnalysis.cli module PQAnalysis.cli.add_molecules module PQAnalysis.cli.build_nep_traj module PQAnalysis.cli.continue_input module PQAnalysis.cli.gen2xyz module PQAnalysis.cli.main module PQAnalysis.cli.rdf module PQAnalysis.cli.rst2xyz module PQAnalysis.cli.traj2box module PQAnalysis.cli.traj2qmcfc module PQAnalysis.cli.xyz2gen module PQAnalysis.config module PQAnalysis.core module PQAnalysis.core.api module PQAnalysis.core.atom module PQAnalysis.core.atom.atom module PQAnalysis.core.atom.element module PQAnalysis.core.cell module PQAnalysis.core.cell.cell module PQAnalysis.core.exceptions module PQAnalysis.core.residue module PQAnalysis.exceptions module PQAnalysis.formats module PQAnalysis.io module PQAnalysis.io.api module PQAnalysis.io.base module PQAnalysis.io.box_writer module PQAnalysis.io.conversion_api module PQAnalysis.io.energy_file_reader module PQAnalysis.io.exceptions module PQAnalysis.io.formats module PQAnalysis.io.gen_file module PQAnalysis.io.gen_file.api module PQAnalysis.io.gen_file.exceptions module PQAnalysis.io.gen_file.gen_file_reader module PQAnalysis.io.gen_file.gen_file_writer module PQAnalysis.io.info_file_reader module PQAnalysis.io.input_file_reader module PQAnalysis.io.input_file_reader.exceptions module PQAnalysis.io.input_file_reader.formats module PQAnalysis.io.input_file_reader.input_file_parser module PQAnalysis.io.input_file_reader.pq module PQAnalysis.io.input_file_reader.pq.output_files module PQAnalysis.io.input_file_reader.pq.pq_input_file_reader module PQAnalysis.io.input_file_reader.pq_analysis module PQAnalysis.io.input_file_reader.pq_analysis.pqanalysis_input_file_reader module PQAnalysis.io.moldescriptor_reader module PQAnalysis.io.nep module PQAnalysis.io.nep.exceptions module PQAnalysis.io.nep.nep_writer module

PQAnalysis.io.restart_file module PQAnalysis.io.restart_file.api module PQAnalysis.io.restart_file.exceptions module PQAnalysis.io.restart_file.restart_reader module PQAnalysis.io.restart_file.restart_writer module PQAnalysis.io.topology_file module PQAnalysis.io.topology_file.api module PQAnalysis.io.topology_file.exceptions module PQAnalysis.io.topology_file.topology_file_reader module PQAnalysis.io.topology_file.topology_file_writer module PQAnalysis.io.traj_file module PQAnalysis.io.traj_file.api module PQAnalysis.io.traj_file.exceptions module PQAnalysis.io.traj_file.frame_reader module PQAnalysis.io.traj_file.process_lines module PQAnalysis.io.traj_file.trajectory_reader module PQAnalysis.io.traj_file.trajectory_writer module PQAnalysis.io.virial module PQAnalysis.io.virial.api module PQAnalysis.io.virial.virial_reader module PQAnalysis.io.write_api module PQAnalysis.physical_data module PQAnalysis.physical_data.energy module PQAnalysis.physical_data.exceptions module PQAnalysis.tools module PQAnalysis.tools.add_molecule module PQAnalysis.tools.traj_to_com_traj module PQAnalysis.topology module PQAnalysis.topology.api module PQAnalysis.topology.bonded_topology module PQAnalysis.topology.bonded_topology.angle module PQAnalysis.topology.bonded_topology.bond module PQAnalysis.topology.bonded_topology.bonded_topology module PQAnalysis.topology.bonded_topology.dihedral module PQAnalysis.topology.exceptions module PQAnalysis.topology.selection module PQAnalysis.topology.shake_topology module PQAnalysis.topology.topology module PQAnalysis.traj module PQAnalysis.traj.api module PQAnalysis.traj.exceptions module PQAnalysis.traj.formats module PQAnalysis.traj.trajectory module PQAnalysis.type_checking module PQAnalysis.types module PQAnalysis.utils module PQAnalysis.utils.common module PQAnalysis.utils.custom_logging module PQAnalysis.utils.decorators module PQAnalysis.utils.files module PQAnalysis.utils.math module PQAnalysis.utils.random module PQAnalysis.utils.string module PQAnalysis.utils.units module PQAnalysisInputFileReader (class in PQAnalysis.io.input_file_reader.pq_analysis.pqanalysis_input_file_reader) PQException PQFileNotFoundError PQIndexError PQInputFileReader (class in PQAnalysis.io.input_file_reader.pq.pq_input_file_reader) PQKeyError PQNotImplementedError PQTypeError PQValueError PQWarning primitive_types (ComposedDatatypesTransformer attribute) PrimitiveTransformer (class in PQAnalysis.io.input_file_reader.input_file_parser) print_header() (in module PQAnalysis.utils.common) process_lines() (in module PQAnalysis.io.traj_file.process_lines) process_lines_with_atoms() (in module PQAnalysis.io.traj_file.process_lines) program_name() (AddMoleculesCLI class method) (BuildNEPTrajCLI class method) (ContinueInputCLI class method) (GEN2XYZCLI class method) (RDFCLI class method) (Rst2XYZCLI class method) (Traj2BoxCLI class method) (Traj2QMCFCCLI class method) (XYZ2GENCLI class method)

Q

QMCFC (InputFileFormat attribute) (MDEngineFormat attribute)

QMResidue (class in PQAnalysis.core.residue)

R

r_max (PQAnalysisInputFileReader property) r_max_key (PQAnalysisInputFileReader attribute) r_min (PQAnalysisInputFileReader property) r_min_key (PQAnalysisInputFileReader attribute) Range (class in PQAnalysis.types) range() (ComposedDatatypesTransformer method) RDF (class in PQAnalysis.analysis.rdf.rdf) rdf() (in module PQAnalysis.analysis.rdf.api) RDFCLI (class in PQAnalysis.cli.rdf) RDFDataWriter (class in PQAnalysis.analysis.rdf.rdf_output_file_writer) RDFError RDFInputFileReader (class in PQAnalysis.analysis.rdf.rdf_input_file_reader) RDFLogWriter (class in PQAnalysis.analysis.rdf.rdf_output_file_writer) RDFWarning read() (EnergyFileReader method) (GenFileReader method) (InfoFileReader method) (MoldescriptorReader method) (PQAnalysisInputFileReader method) (PQInputFileReader method) (RDFInputFileReader method) (RestartFileReader method) (TopologyFileReader method) (TrajectoryReader method) read_gen_file() (in module PQAnalysis.io.gen_file.api) read_restart_file() (in module PQAnalysis.io.restart_file.api) read_stress_file() (in module PQAnalysis.io.virial.api) read_topology_file() (in module PQAnalysis.io.topology_file.api) read_trajectory() (in module PQAnalysis.io.traj_file.api) read_trajectory_generator() (in module PQAnalysis.io.traj_file.api) read_virial_file() (in module PQAnalysis.io.virial.api) red (CustomColorFormatter attribute) reference_residue_ids (Topology property) reference_residues (Topology property) reference_selection (PQAnalysisInputFileReader property) reference_selection_key (PQAnalysisInputFileReader attribute) required_keys (RDFInputFileReader attribute) reset (CustomColorFormatter attribute)

Residue (class in PQAnalysis.core.residue) residue() (SelectionTransformer method) residue_atom_indices (Topology property) residue_ids (Topology property) residue_ids_per_residue (Topology property) residue_number() (SelectionTransformer method) residue_numbers (Topology property) ResidueError Residues (class in PQAnalysis.core.residue) residues (Topology property) ResidueWarning RESTART (OutputFileFormat attribute) restart_file (PQAnalysisInputFileReader property) (PQInputFileReader property) restart_file_key (PQAnalysisInputFileReader attribute) RestartFileReader (class in PQAnalysis.io.restart_file.restart_reader) RestartFileReaderError RestartFileWriter (class in PQAnalysis.io.restart_file.restart_writer) RestartFileWriterError rpmd_charge_file (PQInputFileReader property) rpmd_energy_file (PQInputFileReader property) rpmd_force_file (PQInputFileReader property) rpmd_restart_file (PQInputFileReader property) rpmd_start_file (PQInputFileReader property) rpmd_trajectory_file (PQInputFileReader property) rpmd_velocity_file (PQInputFileReader property) rst2xyz() (in module PQAnalysis.io.conversion_api) Rst2XYZCLI (class in PQAnalysis.cli.rst2xyz) run() (AddMoleculesCLI class method) (BuildNEPTrajCLI class method) (ContinueInputCLI class method) (GEN2XYZCLI class method) (RDF method) (RDFCLI class method) (Rst2XYZCLI class method) (Traj2BoxCLI class method) (Traj2QMCFCCLI class method) (XYZ2GENCLI class method)

S

select() (Selection method) select_from_restart_file() (in module PQAnalysis.topology.api) Selection (class in PQAnalysis.topology.selection) selection (PQAnalysisInputFileReader property) selection_from_restart_file_as_list() (in module PQAnalysis.topology.api) selection_key (PQAnalysisInputFileReader attribute) selection_object (ShakeTopologyGenerator property) SelectionCompatible (class in PQAnalysis.topology.selection) SelectionTransformer (class in PQAnalysis.topology.selection) SelectionVisitor (class in PQAnalysis.topology.selection) set_charges_no_checks() (AtomicSystem method) set_forces_no_checks() (AtomicSystem method) set_pos_no_checks() (AtomicSystem method)

set_vel_no_checks() (AtomicSystem method) setup_box_matrix() (Cell method) setup_logger() (in module PQAnalysis.utils.custom_logging) setup_residues() (Topology method) shake_linkers (BondedTopology property) ShakeTopologyGenerator (class in PQAnalysis.topology.shake_topology) start_file (PQInputFileReader property) start_file_keys (PQInputFileReader attribute) stress (AtomicSystem property) STRESS (OutputFileFormat attribute) StressFileReader (class in PQAnalysis.io.virial.virial_reader) symbol (Atom property) (CustomElement property) (Element property)

T

target_selection (PQAnalysisInputFileReader property) target_selection_key (PQAnalysisInputFileReader attribute) topology (AtomicSystem property) Topology (class in PQAnalysis.topology.topology) topology (Trajectory property) TopologyError TopologyFileError TopologyFileReader (class in PQAnalysis.io.topology_file.topology_file_reader) TopologyFileWriter (class in PQAnalysis.io.topology_file.topology_file_writer) total_charge (Residue property) traj2box() (in module PQAnalysis.io.conversion_api) Traj2BoxCLI (class in PQAnalysis.cli.traj2box) traj2qmcfc() (in module PQAnalysis.io.conversion_api)

Traj2QMCFCCLI (class in PQAnalysis.cli.traj2qmcfc) traj_files (PQAnalysisInputFileReader property) traj_files_key (PQAnalysisInputFileReader attribute) traj_to_com_traj() (in module PQAnalysis.tools.traj_to_com_traj) Trajectory (class in PQAnalysis.traj.trajectory) trajectory_file (PQInputFileReader property) TrajectoryError TrajectoryFormat (class in PQAnalysis.traj.formats) TrajectoryFormatError TrajectoryReader (class in PQAnalysis.io.traj_file.trajectory_reader) TrajectoryReaderError TrajectoryWriter (class in PQAnalysis.io.traj_file.trajectory_writer) type (TrajectoryWriter property)

U

unique_angle1_indices (BondedTopology property) unique_angle2_indices (BondedTopology property) unique_angle3_indices (BondedTopology property) unique_bond1_indices (BondedTopology property) unique_bond2_indices (BondedTopology property) unique_dihedral1_indices (BondedTopology property) unique_dihedral2_indices (BondedTopology property) unique_dihedral3_indices (BondedTopology property) unique_dihedral4_indices (BondedTopology property) unique_element_names (AtomicSystem property)

unique_improper1_indices (BondedTopology property) unique_improper2_indices (BondedTopology property) unique_improper3_indices (BondedTopology property) unique_improper4_indices (BondedTopology property) unique_shake_indices (BondedTopology property) unique_shake_target_indices (BondedTopology property) UNSIGNED_INT() (SelectionTransformer method) unsigned_integer() (SelectionTransformer method) use_full_atom_info (PQAnalysisInputFileReader property) use_full_atom_info_key (PQAnalysisInputFileReader attribute)

V

value() (ComposedDatatypesTransformer method) value_repr() (BaseEnumFormat class method) values() (BaseEnumFormat class method) vel (AtomicSystem property) VEL (OutputFileFormat attribute) (TrajectoryFormat attribute) velocity_file (PQInputFileReader property)

virial (AtomicSystem property) VIRIAL (OutputFileFormat attribute) VirialFileReader (class in PQAnalysis.io.virial.virial_reader) visit() (InputFileVisitor method) (SelectionVisitor method) VMD (BoxFileFormat attribute) volume (Cell property)

W

window() (Trajectory method) window_generator() (TrajectoryReader method) without_statement() (SelectionTransformer method) word() (PrimitiveTransformer method) (SelectionTransformer method) WRITE (FileWritingMode attribute) write() (BoxWriter method) (GenFileWriter method) (in module PQAnalysis.io.write_api) (RDFDataWriter method) (RestartFileWriter method) (TopologyFileWriter method) (TrajectoryWriter method)

write_after_run() (RDFLogWriter method) write_before_run() (RDFLogWriter method) write_box() (in module PQAnalysis.io.write_api) write_box_file() (BoxWriter method) write_from_atomic_system() (NEPWriter method) write_from_files() (NEPWriter method) write_from_trajectory() (NEPWriter method) write_gen_file() (in module PQAnalysis.io.gen_file.api) write_restart_file() (AddMolecule method) write_topology() (ShakeTopologyGenerator method) write_topology_file() (in module PQAnalysis.io.topology_file.api) write_trajectory() (in module PQAnalysis.io.traj_file.api) write_vmd() (BoxWriter method)

X

x (Cell property) XYZ (OutputFileFormat attribute) (TrajectoryFormat attribute)

xyz2gen() (in module PQAnalysis.io.conversion_api) XYZ2GENCLI (class in PQAnalysis.cli.xyz2gen)

Y

y (Cell property)

Z

z (Cell property)