The Gnome Chemistry Utils C++ classes. More...

Classes
class	Application
class	Atom
class	AtomPair
class	AtomMatchState
class	Bond
struct	ChainElt
class	Chain
class	Chem3dDoc
class	CmdContext
	error output channel. More...
class	Cycle
class	Cylinder
	This class represents and draws a cylinder. More...
class	DialogOwner
class	Dialog
class	Document
class	Element
	Chemical element. More...
class	parse_error
class	FormulaElt
class	FormulaAtom
class	FormulaBlock
class	FormulaResidue
	Residue. More...
class	Formula
class	GLDocument
class	GLView
class	Isotope
class	IsotopicPattern
struct	LoaderStruct
class	Loader
	class used to implement serialization engines. More...
class	Matrix
class	GLMatrix
class	Matrix2D
class	Molecule
class	Object
struct	SymbolResidue
class	Residue
class	SpaceGroup
	Handle crystallographic space group symmetry. More...
class	Sphere
class	Transform3d
	Handle 3D transformations, such as space group definitions. More...
class	UIManager
	base class for a user interface manager More...
class	Value
class	SimpleValue
class	DimensionalValue
class	StringValue
class	LocalizedStringValue
class	Vector
	3D vector. More...
class	Vector3f
class	Window

Typedefs
typedef unsigned	TypeId
typedef bool(*	BuildMenuCb )(Object target, UIManager uim, Object *object, double x, double y)
typedef unsigned	SignalId

Enumerations
enum	Display3DMode
enum	Action { ActionException, ActionDelete, ActionIgnore }
enum	FormulaParseMode
enum	MatrixType
enum	GcuTypeId
enum	RuleId
enum	ContentType { ContentTypeUnknown, ContentType3D, ContentType2D, ContentTypeCrystal, ContentTypeSpectrum, ContentTypeMisc, ContentTypeInvalid }

Functions
Vector	operator* (double f, Vector const &v)
Vector3f	operator* (float f, Vector3f const &v)
xmlNodePtr	FindNodeByNameAndId (xmlNodePtr node, const char name, const char id=NULL)
bool	ReadPosition (xmlNodePtr node, const char id, double x, double y, double z=NULL)
bool	WritePosition (xmlDocPtr xml, xmlNodePtr node, const char *id, double x, double y, double z=0.0)
bool	ReadColor (xmlNodePtr node, const char id, float red, float green, float blue, float *alpha=NULL)
bool	WriteColor (xmlDocPtr xml, xmlNodePtr node, const char *id, double red, double green, double blue, double alpha=1.0)
GOColor	ReadColor (xmlNodePtr node)
void	WriteColor (xmlNodePtr node, GOColor color)
bool	ReadRadius (xmlNodePtr node, GcuAtomicRadius &radius)
bool	WriteRadius (xmlDocPtr xml, xmlNodePtr node, const GcuAtomicRadius &radius)
char const *	GetStaticScale (char *buf)
void	WriteFloat (xmlNodePtr node, char const *name, double value)
bool	ReadFloat (xmlNodePtr node, char const *name, double &value, double default_value=0.)
void	WriteInt (xmlNodePtr node, char const *name, int value)
bool	ReadInt (xmlNodePtr node, char const *name, int &value, int default_value=0)
void	WriteDate (xmlNodePtr node, char const name, GDate const date)
bool	ReadDate (xmlNodePtr node, char const name, GDate date)

Detailed Description

The Gnome Chemistry Utils C++ classes.

The namespace used for all C++ classes provided by the Gnome Chemistry Utils base library.

Typedef Documentation

typedef bool(* gcu::BuildMenuCb)(Object *target, UIManager *uim, Object *object, double x, double y)

The type of callbacks for adding new items to the contextual menu of an object.

Parameters

target	the Object whose menu is being built.
uim	the UIManager to populate.
object	the Object on which occured the mouse click.
x	x coordinate of the mouse click.
y	y coordinate of the mouse click.

Definition at line 108 of file object.h.

typedef unsigned gcu::SignalId

The types of the signals used in Object::EmitSignal() and Object::OnSignal(). Each signal must type be retrieved from a call to Object::CreateNewSignalId().

Definition at line 151 of file object.h.

typedef unsigned gcu::TypeId

The type of an object instance. Either predefined types are defined in the enum above or dynamically defined types by calls to Object::AddType.

Definition at line 95 of file object.h.

Enumeration Type Documentation

enum gcu::Action

gcu/document.h Represents what should be done when an error occurs on an object.

Enumerator:

ActionException	Throw an exception
ActionDelete	Delete the object
ActionIgnore	Ignore the error

Definition at line 49 of file gcu/document.h.

enum gcu::ContentType

The list of supported data types.

Enumerator:

ContentTypeUnknown	Unknown content.
ContentType3D	3D molecular structure.
ContentType2D	2D molecular structure.
ContentTypeCrystal	Crystal structure.
ContentTypeSpectrum	Spectral data.
ContentTypeMisc	Miscalleneous contents. Might include anything.
ContentTypeInvalid	Invalid data.

Definition at line 35 of file gcu/structs.h.

enum gcu::Display3DMode

3D display mode. Possible values are:

BALL_AND_STICK: use ball and stick representation; atoms are represented by spheres with a radius equal to 20% of their van der Waals radius and bonds are displayed as cylinders Multiple bonds are displayed as multiple cylinders.
SPACEFILL: use space filling representation; atoms are represented by spheres with a radius equal their van der Waals radius; bonds are not displayed.
CYLINDERS: only bonds are represented as cylinders, atoms just end the cylinders.
WIREFRAME: bonds are represented as narrow lines, atoms just end the lines.

Definition at line 45 of file chem3ddoc.h.

enum gcu::FormulaParseMode

gcu/formula.h The way formula should be interpreted when they contain symbols that might represent both an atom or a group of atoms such as Ac and Pr. Possible values are:

GCU_FORMULA_PARSE_GUESS: try to determine the most probable interpretation of the symbol,
GCU_FORMULA_PARSE_ATOM: always interpret as atoms,
GCU_FORMULA_PARSE_RESIDUE: always interpret as groups,
GCU_FORMULA_PARSE_ASK: ask the user for each encountered instance,
GCU_FORMULA_PARSE_NO_CASE: this one is unrelated and can ba combined with any of the previous values, just make the parsing stricktly case sensitive.

Definition at line 52 of file formula.h.

enum gcu::GcuTypeId

This enumeration is used to determine the type of an Object instance. Possible values are:

NoType invalid type
AtomType an atom
FragmentType several atoms linked and represented by a text such as COOH (only in GChemPaint).
BondType a bond between two (or more) atoms.
MoleculeType a molecule.
ChainType a chain of atoms.
CycleType a cycle.
ReactantType a molecule involved in a reaction (only in GChemPaint).
ReactionArrowType a reaction arrow (only in GChemPaint).
ReactionOperatorType a + sign in a reaction (only in GChemPaint).
ReactionType a reaction.
MesomeryType a mesomery representation (only in GChemPaint).
MesomeryArrowType a double headed arrow used to represent mesomery (only in GChemPaint).
DocumentType a document, generally the top node in the objects tree.
TextType some text (only in GChemPaint).
OtherType if the type of an object is at least equal to OtherType, then it is a dynamically created type returned by the static Object::AddType method.

Some types are not used in the Gnome Chemistry Utils, but only in GChemPaint and might disappear from this list in future versions and replaced by dynamically created types.

Definition at line 71 of file object.h.

enum gcu::MatrixType

This enumeration is used to determine the type a Matrix. Possible values are:

euler: matrix used to find absolute positions from the position inside the solid using Euler's angles.
antieuler: the inverse of euler.
rotation: matrix representing the rotation to apply to the solid.

This enumeration is used in one of the constructors (Matrix(Psi, Theta, Phi, Type)) of class Matrix.

Definition at line 44 of file matrix.h.

enum gcu::RuleId

This enumeration is used to maintain a set of rules about the possible hierarchical of the document. They are used with two class names or ids. Possible values are:

RuleMayContain an instance of the first class may contain an instance of the second. This implies that an instance of the second class may be in an instance of the first (see RuleMayBeIn);
RuleMustContain an instance of the first class may contain an instance of the second class (implies RuleMayContain); if no instance of the first class is present, the object is not valid.
RuleMayBeIn an instance of the first class may be the child of an instance of the second class (see also RuleMayContain);
RuleMustBeIn an instance of the first class must be the child of an instance of the second class, otherwise it is not valid.

Definition at line 139 of file object.h.

Function Documentation

xmlNodePtr gcu::FindNodeByNameAndId	(	xmlNodePtr	node,
		const char *	name,
		const char *	id = `NULL`
	)

ReadPosition

Parameters

node,:	a pointer to the current parsed XML Node.
name,:	the name of the searched node.
id,:	the id property of the node or NULL if not significant. This parameter might be omitted in the last case.

Helper method used to search the xmlNode instance of name Name and with id property equal to id in the children of node. When id is NULL, the searched node does not have an id property. When id is not NULL, the searched node should be unique.

Returns: the matching node or NULL.

char const* gcu::GetStaticScale ( char * buf )

Parameters

buf,: a string to convert to a static instance.

This function is used to replace a dynamically allocated string by a static instance. It works managing a set of string instances. It is used for scale names (as for radii and electronegativity), hence its name.

Returns: a static version of buf or NULL if a new static string could not be created.

Vector gcu::operator*	(	double	f,
		Vector const &	v
	)

Parameters

f	a multiplication factor
v	the vector to multiply

Returns: the product of f and v.

Vector3f gcu::operator*	(	float	f,
		Vector3f const &	v
	)

Parameters

f	a multiplication factor
v	the vector to multiply

Returns: the product of f and v.

bool gcu::ReadColor	(	xmlNodePtr	node,
		const char *	id,
		float *	red,
		float *	green,
		float *	blue,
		float *	alpha = `NULL`
	)

Parameters

node,:	a pointer to the xmlNode representing an Object instance.
id,:	the value of the id property of the color. This is used for Object instances having at least two colors.
red,:	a pointer to the red component of the color.
green,:	a pointer to the green component of the color.
blue,:	a pointer to the blue component of the color.
alpha,:	a pointer to the alpha component of the color or NULL if tranparency is not managed.

This method can be used to load a color in an Object instance. It should be used in cunjunction with WriteColor() which executes the inverse operation. If id is NULL, a color with no id property will be search and parsed.

Returns: true on success and false on failure.

GOColor gcu::ReadColor ( xmlNodePtr node )

Parameters

node,: a pointer to the xmlNode from which the color must be retrieved. Builds a GOColor from the node properties.

Returns: the GOColor found or black (0xff).

bool gcu::ReadDate	(	xmlNodePtr	node,
		char const *	name,
		GDate *	date
	)

Parameters

node	a pointer to an XML node.
name	the property name.
date	where to store the result.

Retrieves date from the node property with name name. On failure, date will be cleared using g_date_clear().

Returns: true if the date could be retrieved. This method is locale independent. The date must be stored in the format MM/DD/YYYY.

bool gcu::ReadFloat	(	xmlNodePtr	node,
		char const *	name,
		double &	value,
		double	default_value = `0.`
	)

Parameters

node	a pointer to an XML node.
name	the property name.
value	where to store the result.
default_value	the default value for the property if the property can't be retrieved.

Retrieves value from the node property with name name. Sets the default value if somthing goes wrong. This method is locale independent.

Returns: true if the value could be retrieved.

bool gcu::ReadInt	(	xmlNodePtr	node,
		char const *	name,
		int &	value,
		int	default_value = `0`
	)

Parameters

node	a pointer to an XML node.
name	the property name.
value	where to store the result.
default_value	the default value for the property if the property can't be retrieved.

Retrieves value from the node property with name name. Sets the default value if somthing goes wrong.

Returns: true if the value could be retrieved.

bool gcu::ReadPosition	(	xmlNodePtr	node,
		const char *	id,
		double *	x,
		double *	y,
		double *	z = `NULL`
	)

Parameters

node,:	a pointer to the xmlNode representing an Object instance.
id,:	the value of the id property of the position. This is used for example for arrows because both the head and the tail of the arrow are positions.
x,:	a pointer to the x coordinate of the position.
y,:	a pointer to the y coordinate of the position.
z,:	a pointer to the z coordinate of the position or NULL for 2D objects.

This method can be used to load the coordinates of a point in an Object instance. It should be used in cunjunction with WritePosition() which executes the inverse operation. If id is NULL, a position with no id property will be search and parsed.

Returns: true on success and false on failure.

bool gcu::ReadRadius	(	xmlNodePtr	node,
		GcuAtomicRadius &	radius
	)

Parameters

node,:	a pointer to the xmlNode representing an Object instance.
radius,:	a GcuAtomicRadius structure.

This function parses the XML node representing a radius (written using WriteRadius()) and fills the fields in the GcuAtomicRadius structure with the data parsed.

Returns: true on success and false on failure.

bool gcu::WriteColor	(	xmlDocPtr	xml,
		xmlNodePtr	node,
		const char *	id,
		double	red,
		double	green,
		double	blue,
		double	alpha = `1.0`
	)

Parameters

xml,:	a pointer to the xmlDoc used to serialize the document.
node,:	a pointer to the xmlNode representing an Object instance.
id,:	the value of the id property of the color. This is used for Object instances having at least two colors. of the arrow are positions.
red,:	the red component of the color.
green,:	the green component of the color.
blue,:	the blue component of the color.
alpha,:	the alpha component of the color.

Save a color as an XML node added to the children of node. This color can then be parsed using ReadColor().

Returns: true on success and false on failure.

void gcu::WriteColor	(	xmlNodePtr	node,
		GOColor	color
	)

Parameters

node,:	a pointer to the xmlNode to which the color must be serialized.
color,:	a pointer to the xmlNode from which the color must be retrieved. Serializes color to node.

void gcu::WriteDate	(	xmlNodePtr	node,
		char const *	name,
		GDate const *	date
	)

Parameters

node	a pointer to an XML node.
name	the property name.
date	the date to serialize.

Adds date as a property with name name to node. This method is locale independent. The date will be stored in the format MM/DD/YYYY.

void gcu::WriteFloat	(	xmlNodePtr	node,
		char const *	name,
		double	value
	)

Parameters

node	a pointer to an XML node.
name	the property name.
value	the value for the property.

Adds value as a property with name name to node. This method is locale independent.

void gcu::WriteInt	(	xmlNodePtr	node,
		char const *	name,
		int	value
	)

Parameters

node	a pointer to an XML node.
name	the property name.
value	the value for the property.

Adds value as a property with name name to node.

bool gcu::WritePosition	(	xmlDocPtr	xml,
		xmlNodePtr	node,
		const char *	id,
		double	x,
		double	y,
		double	z = `0.0`
	)

WritePosition

Parameters

xml,:	a pointer to the xmlDoc used to serialize the document.
node,:	a pointer to the xmlNode representing an Object instance.
id,:	the value of the id property of the position. This is used for example for arrows because both the head and the tail of the arrow are positions.
x,:	the x coordinate of the position.
y,:	the y coordinate of the position.
z,:	the z coordinate of the position.

Save a position as an XML node added to the children of node. This position can then be parsed using ReadPosition().

Returns: true on success and false on failure.

bool gcu::WriteRadius	(	xmlDocPtr	xml,
		xmlNodePtr	node,
		const GcuAtomicRadius &	radius
	)

Parameters

xml,:	a pointer to the xmlDoc used to serialize the document.
node,:	a pointer to the xmlNode representing an Object instance.
radius,:	a GcuAtomicRadius structure.

Save a radius as an XML node added to the children of node. This radius can then be parsed using ReadRadius().

Returns: true on success and false on failure.

Classes

Typedefs

Enumerations

Functions

Detailed Description

Typedef Documentation

Enumeration Type Documentation

Function Documentation