The namespace for all functionality in the library. More...

Namespaces
	decorator
	See Decorators and Attributes for more information.

	HDF5
	The namespace for all HDF5 functionality in the library.

Classes
class	BufferConstHandle
	Manage a shared buffer for loading a RMF. More...

class	BufferHandle
	Manage a shared buffer for storing a RMF. More...

class	CoordinateTransformer
	Transform coordinates into the global reference frame. More...

class	Decorator
	The base class for decorators. More...

class	Enum
	A strong enum with an associated string name for each value. More...

class	Exception

class	Factory
	The base class for Factories. More...

class	FileConstHandle
	A handle for a read-only RMF file. More...

class	FileHandle
	A handle for an RMF file. More...

class	ID
	A general purpose ID in RMF used, with different tags, to identify things. More...

class	IndexException

class	InternalException

class	IOException

class	Label
	A decorator-like class to mark certain nodes (e.g. molecule boundaries) More...

class	NodeConstHandle
	A handle for a particular node in a read-only hierarchy. More...

class	NodeHandle
	A handle for a particular node in the hierarchy. More...

class	Nullable
	Return a possibly null value. More...

class	RestoreCurrentFrame
	Restore the frame that was current on creation upon destruction. More...

class	SetCurrentFrame
	Set the current frame to a value and then return it to the old value when this goes out of scope. More...

struct	Traits
	Traits classes describing how RMF uses types for storing data. More...

class	TraverseHelper
	Track common data that one needs to keep as one traverses the hierarchy. More...

class	UsageException

class	Vector
	Represent a point in some dimension. More...

Typedefs
typedef std::vector< Category >	Categories

typedef ID< CategoryTag >	Category

typedef std::vector < CoordinateTransformer >	CoordinateTransformers
	A list of them.

typedef std::vector < FileConstHandle >	FileConstHandles
	Pass a list of them.

typedef std::vector< FileHandle >	FileHandles
	Pass a list of them.

typedef float	Float

typedef std::vector< Float >	Floats

typedef std::vector< Floats >	FloatsList

typedef FloatsTraits	FloatsTag

typedef Traits< Floats >	FloatsTraits

typedef FloatTraits	FloatTag

typedef Traits< Float >	FloatTraits

typedef ID< FrameTag >	FrameID

typedef std::vector< FrameID >	FrameIDs

typedef Enum< FrameTypeTag >	FrameType

typedef int	Int

typedef std::array< int, 2 >	IntRange

typedef std::vector< Int >	Ints

typedef std::vector< Ints >	IntsList

typedef IntsTraits	IntsTag

typedef Traits< Ints >	IntsTraits

typedef IntTraits	IntTag

typedef Traits< Int >	IntTraits

typedef std::vector < NodeConstHandle >	NodeConstHandles
	Pass a list of them.

typedef std::vector< NodeHandle >	NodeHandles
	Pass a list of them.

typedef ID< NodeTag >	NodeID

typedef std::vector< NodeID >	NodeIDs

typedef Enum< NodeTypeTag >	NodeType

typedef Enum < RepresentationTypeTag >	RepresentationType

typedef std::string	String

typedef std::vector< String >	Strings

typedef std::vector< Strings >	StringsList

typedef StringsTraits	StringsTag

typedef Traits< Strings >	StringsTraits

typedef StringTraits	StringTag

typedef Traits< String >	StringTraits

typedef std::vector < TraverseHelper >	TraverseHelpers

typedef Vector< 3U >	Vector3

typedef std::vector< Vector3 >	Vector3s

typedef Vector3sTraits	Vector3sTag

typedef Traits< std::vector < Vector< 3 > > >	Vector3sTraits

typedef Vector3Traits	Vector3Tag

typedef Traits< Vector< 3 > >	Vector3Traits

typedef Vector< 4U >	Vector4

typedef std::vector< Vector4 >	Vector4s

typedef Vector4sTraits	Vector4sTag

typedef Traits< std::vector < Vector< 4 > > >	Vector4sTraits

typedef Vector4Traits	Vector4Tag

typedef Traits< Vector< 4 > >	Vector4Traits

typedef unsigned int	VectorDimension
	Work around clang issue.

Functions
FileHandle	create_rmf_buffer (BufferHandle buffer)
	Create an RMF in a buffer. More...

FileHandle	create_rmf_file (std::string path)
	Create an RMF from a file system path. More...

void	get_all_global_coordinates (FileConstHandle &fh, NodeConstHandle &nh, PyObject *coord)
	Get global XYZ coordinates for everything under the given node. More...

std::array< RMF::Vector3, 2 >	get_bounding_box (NodeConstHandle root)

float	get_diameter (NodeConstHandle root)

bool	get_equal_current_values (FileConstHandle input, FileConstHandle out)

bool	get_equal_static_values (FileConstHandle input, FileConstHandle out)

bool	get_equal_structure (FileConstHandle input, FileConstHandle output, bool print_diff=false)

log4cxx::LoggerPtr	get_logger ()

std::string	get_message (const Exception &e)

std::string	get_signature_string (FileConstHandle file)
	Return a string that captures information about the file. More...

std::size_t	hash_value (const BufferConstHandle &t)
	Produce hash values for boost hash tables.

template<class TagT >
std::size_t	hash_value (const Enum< TagT > &t)
	Produce hash values for boost hash tables.

template<class TagT >
std::size_t	hash_value (const ID< TagT > &t)
	Produce hash values for boost hash tables.

std::size_t	hash_value (const NodeConstHandle &t)
	Produce hash values for boost hash tables.

std::size_t	hash_value (const FileConstHandle &t)
	Produce hash values for boost hash tables.

FileConstHandle	open_rmf_buffer_read_only (BufferConstHandle buffer)

FileConstHandle	open_rmf_file_read_only (std::string path)

BufferConstHandle	read_buffer (std::string file_name)

void	set_log_level (std::string level)

void	show_info (RMF::FileConstHandle rh, std::ostream &out=std::cout)

void	test_throw_exception ()

void	validate (FileConstHandle fh)
	Validate the hierarchy, throwing an exception if any problems were found. More...

void	write_buffer (BufferConstHandle buffer, std::string file_name)

Variables
static const FrameID	ALL_FRAMES = FrameID(-1, FrameID::SpecialTag())

Node Types
The types nodes can take in an RMF file.
const NodeType	INVALID_NODE_TYPE

const NodeType	ROOT
	The root node.

const NodeType	REPRESENTATION
	Represent part of a molecule.

const NodeType	GEOMETRY
	Store a geometric object.

const NodeType	FEATURE
	Store information about some feature of the system. More...

const NodeType	ALIAS

const NodeType	CUSTOM
	Arbitrary data that is not standardized. More...

const NodeType	BOND
	A link between two atoms. More...

const NodeType	ORGANIZATIONAL
	A node that is purely there for organizational purposes. More...

const NodeType	PROVENANCE
	Represent the process by which a structure was created.

Frame Types
The types frames can take in an RMF file.
const FrameType	INVALID_FRAME_TYPE

const FrameType	STATIC
	The root frame.

const FrameType	FRAME
	A frame in a sequence of frames.

const FrameType	MODEL
	An independent model.

const FrameType	CENTER
	A cluster center.

const FrameType	FRAME_ALIAS
	An alias for another frame.

const FrameType	ALTERNATE
	An alternate state for a frame or model.

Representation Types
The types that representations used in the decorator::Alternatives decorator can take.
const RepresentationType	PARTICLE

const RepresentationType	GAUSSIAN_PARTICLE

Batch data access
These methods provide batch access to attribute data to try to reduce the overhead of repeated function calls. The missing_value argument is a placeholder that can fill in for values which are not found in the respective node. Note These methods are experimental and subject to change.
Floats	get_values (const NodeConstHandles &nodes, FloatKey k, Float missing_value=std::numeric_limits< float >::max())

Key types
RMF files support storing a variety of different types of data. These include IntKey: store an arbitrary integer as a 64 bit integer FloatKey: store an arbitrary floating point number as a `float` StringKey: store an arbitrary length string IndexKey: store non-negative indexes as 64 bit integers NodeIDKey: store the ID of a node in the hierarchy NodeIDsKey: store a list of NodeIDs DataSetKey: store a reference to an HDF5 data set via the path to the data set IntsKey: store a list of arbitrary integers
typedef ID< IntTag >	IntKey

typedef std::vector< IntKey >	IntKeys

typedef ID< FloatTag >	FloatKey

typedef std::vector< FloatKey >	FloatKeys

typedef ID< StringTag >	StringKey

typedef std::vector< StringKey >	StringKeys

typedef ID< IntsTag >	IntsKey

typedef std::vector< IntsKey >	IntsKeys

typedef ID< FloatsTag >	FloatsKey

typedef std::vector< FloatsKey >	FloatsKeys

typedef ID< StringsTag >	StringsKey

typedef std::vector< StringsKey >	StringsKeys

typedef ID< Vector3Tag >	Vector3Key

typedef std::vector< Vector3Key >	Vector3Keys

typedef ID< Vector4Tag >	Vector4Key

typedef std::vector< Vector4Key >	Vector4Keys

typedef ID< Vector3sTag >	Vector3sKey

typedef std::vector< Vector3sKey >	Vector3sKeys

Names
std::string	get_as_node_name (std::string input)
	Return a node name string that has been modified to obey the rules. More...

bool	get_is_valid_key_name (std::string name)
	Return true iff the string is a valid key name.

bool	get_is_valid_node_name (std::string name)
	Return true iff the string is a valid node name.

Showing the hierarchy
These functions print out the hierarchy with various extra information for each node. Each prints out an ASCII tree designed for human inspection.
void	show_hierarchy (NodeConstHandle root, std::ostream &out)

void	show_hierarchy (NodeConstHandle root)

void	show_hierarchy_with_values (NodeConstHandle root, std::ostream &out)

void	show_hierarchy_with_values (NodeConstHandle root)

void	show_hierarchy_with_decorators (NodeConstHandle root, bool verbose=false, std::ostream &out=std::cout)

void	show_frames (FileConstHandle fh, std::ostream &out=std::cout)

Copy functions
See the example cloning.py for a usage example.
void	clone_file_info (FileConstHandle input, FileHandle output)

void	clone_hierarchy (FileConstHandle input, FileHandle output)

void	clone_loaded_frame (FileConstHandle input, FileHandle output)

void	clone_static_frame (FileConstHandle input, FileHandle output)

Detailed Description

In python, the module is also called RMF.

Typedef Documentation

typedef std::vector<Category> RMF::Categories

List of categories.

Definition at line 117 of file ID.h.

typedef ID<CategoryTag> RMF::Category

Identify a category within a file.

Definition at line 110 of file ID.h.

typedef float RMF::Float

The type used to store lists of floating point values.

Definition at line 33 of file types.h.

typedef ID< FloatTag> RMF::FloatKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< FloatKey> RMF::FloatKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Float> RMF::Floats

The type used to store lists of floating point values.

Definition at line 35 of file types.h.

typedef ID< FloatsTag> RMF::FloatsKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< FloatsKey> RMF::FloatsKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Floats> RMF::FloatsList

The type used to store lists of floating point values.

Definition at line 37 of file types.h.

typedef ID<FrameTag> RMF::FrameID

Identify a frame within a file.

Definition at line 108 of file ID.h.

typedef std::vector<FrameID> RMF::FrameIDs

List of frame ids.

Definition at line 115 of file ID.h.

typedef Enum<FrameTypeTag> RMF::FrameType

The type for frames.

See Frame Types for a complete list of the possible values.

Definition at line 116 of file Enum.h.

typedef int RMF::Int

The type used to store integral values.

Definition at line 29 of file types.h.

typedef ID< IntTag> RMF::IntKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< IntKey> RMF::IntKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Int> RMF::Ints

The type used to store lists of integral values.

Definition at line 31 of file types.h.

typedef ID< IntsTag> RMF::IntsKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< IntsKey> RMF::IntsKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Ints> RMF::IntsList

The type used to store lists of lists of integers values.

Definition at line 45 of file types.h.

typedef ID<NodeTag> RMF::NodeID

Identify a node within a file.

Definition at line 106 of file ID.h.

typedef std::vector<NodeID> RMF::NodeIDs

List of node ids.

Definition at line 113 of file ID.h.

typedef Enum<NodeTypeTag> RMF::NodeType

The type for nodes.

See Node Types for a complete list of the possible values.

Definition at line 121 of file Enum.h.

typedef Enum<RepresentationTypeTag> RMF::RepresentationType

The type for representations used in decorator::Alternatives.

See Representation Types for a complete list of the possible values.

Definition at line 127 of file Enum.h.

typedef std::string RMF::String

The type used to store lists of string values.

Definition at line 39 of file types.h.

typedef ID< StringTag> RMF::StringKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< StringKey> RMF::StringKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<String> RMF::Strings

The type used to store lists of string values.

Definition at line 41 of file types.h.

typedef ID< StringsTag> RMF::StringsKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< StringsKey> RMF::StringsKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Strings> RMF::StringsList

The type used to store lists of strings values.

Definition at line 43 of file types.h.

typedef Vector<3U> RMF::Vector3

A Vector3

Definition at line 48 of file types.h.

typedef ID< Vector3Tag> RMF::Vector3Key

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< Vector3Key> RMF::Vector3Keys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Vector3> RMF::Vector3s

Many Vector3s

Definition at line 52 of file types.h.

typedef ID< Vector3sTag> RMF::Vector3sKey

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< Vector3sKey> RMF::Vector3sKeys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef Vector<4U> RMF::Vector4

A Vector3

Definition at line 50 of file types.h.

typedef ID< Vector4Tag> RMF::Vector4Key

Identify a value stored for a node.

Definition at line 41 of file keys.h.

typedef std::vector< Vector4Key> RMF::Vector4Keys

A list of identifiers.

Definition at line 41 of file keys.h.

typedef std::vector<Vector4> RMF::Vector4s

Many Vector4s

Definition at line 54 of file types.h.

Function Documentation

void RMF::clone_file_info	(	FileConstHandle	input,
		FileHandle	output
	)

Copy the hierarchy structure and set structure from one RMF file to another.

void RMF::clone_hierarchy	(	FileConstHandle	input,
		FileHandle	output
	)

Copy the hierarchy structure and set structure from one RMF file to another.

void RMF::clone_loaded_frame	(	FileConstHandle	input,
		FileHandle	output
	)

Copy the data of a single frame from between two files.

void RMF::clone_static_frame	(	FileConstHandle	input,
		FileHandle	output
	)

Copy the data of a single frame from between two files. Parts missing in the output file will be skipped.

FileHandle RMF::create_rmf_buffer ( BufferHandle buffer )

Parameters

buffer The buffer to place the contents in.

Examples:: benchmark/benchmark_rmf.cpp.

FileHandle RMF::create_rmf_file ( std::string path )

Parameters

path	the system path to the rmf file

Exceptions

RMF::IOException couldn't create file, or unsupported file format

Examples:: benchmark/benchmark_rmf.cpp.

void RMF::get_all_global_coordinates	(	FileConstHandle &	fh,
		NodeConstHandle &	nh,
		PyObject *	coord
	)

This will traverse the subset of the RMF file rooted at the given node in a depth first manner and put the XYZ coordinates for all appropriate nodes into the provided NumPy array, which must be an N*3 float array where N is the number of XYZ particles. The coordinates are global, i.e. they are transformed by any parent ReferenceFrame nodes.

This function is primarily intended to extract trajectory frames for visualization packages such as ChimeraX. It is only available to Python and if RMF is built with NumPy support.

std::string RMF::get_as_node_name ( std::string input )

Node and key names have to obey certain rules, such as no quotes in the name.

std::array<RMF::Vector3, 2> RMF::get_bounding_box ( NodeConstHandle root )

Return a lower bound/upper bound pair that bounds the data stored in the tree.

float RMF::get_diameter ( NodeConstHandle root )

Return the diameter of the system. Unlike bounding box, this one can be called from python.

bool RMF::get_equal_current_values	(	FileConstHandle	input,
		FileConstHandle	out
	)

Return true of the two have the same values in the current frame.

bool RMF::get_equal_static_values	(	FileConstHandle	input,
		FileConstHandle	out
	)

Return true if the two have the same values in the static frame.

bool RMF::get_equal_structure	(	FileConstHandle	input,
		FileConstHandle	output,
		bool	print_diff = `false`
	)

Return true of the two have the same structure.

std::string RMF::get_message ( const Exception & e )

Use this instead of the more standard what() to get the message as what() presents issues for memory management with dynamically generated messages.

std::string RMF::get_signature_string ( FileConstHandle file )

This string can be saved and compared against the string generated with future versions of the library to make sure that the old files parse reasonably well. The strings are diffable.

FileConstHandle RMF::open_rmf_buffer_read_only ( BufferConstHandle buffer )

Open an RMF from a buffer in read-only mode.

Exceptions

RMF::IOException couldn't open file, or unsupported file format

Examples:: benchmark/benchmark_rmf.cpp.

FileConstHandle RMF::open_rmf_file_read_only ( std::string path )

Open an RMF from a file system path in read-only mode.

Parameters

path	the system path to the rmf file

Exceptions

RMF::IOException couldn't open file, or unsupported file format

Examples:: benchmark/benchmark_rmf.cpp.

void RMF::set_log_level ( std::string level )

Set the log level from a string. Supported values are:

Trace
Info
Warn
Error
Off

Log4CXX is required for logging to be supported.

Examples:: benchmark/benchmark_rmf.cpp.

void RMF::show_frames	(	FileConstHandle	fh,
		std::ostream &	out = `std::cout`
	)

Show the frame hierarchy rather than the node hierarchy.

void RMF::show_hierarchy	(	NodeConstHandle	root,
		std::ostream &	out
	)

Print out just the node names and types.

void RMF::show_hierarchy_with_decorators	(	NodeConstHandle	root,
		bool	verbose = `false`,
		std::ostream &	out = `std::cout`
	)

Print out the list of decorators that can be used to decorate each node based on the current attributes in the loaded frame..

void RMF::show_hierarchy_with_values	(	NodeConstHandle	root,
		std::ostream &	out
	)

Print out all attributes for each node for the current frame.

void RMF::show_info	(	RMF::FileConstHandle	rh,
		std::ostream &	out = `std::cout`
	)

Show various statistics about the file such as attributes and how often they are used.

void RMF::test_throw_exception ( )

This function simply throws an exception. It is here for testing.

void RMF::validate ( FileConstHandle fh )

Exceptions

exception if it is not valid and log any errors encountered.

Checks invariants, such as all representation leaves having coordinates and radii.

Variable Documentation

const NodeType RMF::ALIAS

Store a reference to another node. This node should be an alias decorator node and have no other data, at least for now. Aliases should be thought of as simply referencing existing objects in the scene, not creating new objects.

const FrameID RMF::ALL_FRAMES = FrameID(-1, FrameID::SpecialTag())

static

A constant used to denote that the particular operation refers to all frames in the file.

Definition at line 20 of file constants.h.

const NodeType RMF::BOND

These are mostly for display purposes e.g. to show a wireframe view of the molecule.

const NodeType RMF::CUSTOM

Programs can use these keys to store any extra data they want to put into the file.

const NodeType RMF::FEATURE

For example, the particles involved in scoring functions and their score can be encoded as feature nodes.

const RepresentationType RMF::GAUSSIAN_PARTICLE

Represent the structure with at set of decorator::GaussianParticle nodes.

const NodeType RMF::ORGANIZATIONAL

This includes nodes that are just RMF::ReferenceFrame nodes.

const RepresentationType RMF::PARTICLE

Representation via decorator::Particle nodes, the default.

Namespaces

Classes

Typedefs

Functions

Variables

Node Types

Frame Types

Representation Types

Batch data access

Key types

Names

Showing the hierarchy

Copy functions

Detailed Description

Typedef Documentation

Function Documentation

Variable Documentation