Reaction path diagrams (graphs).
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#include <ReactionPath.h >
Reaction path diagrams (graphs).
Definition at line 159 of file ReactionPath.h .
virtual ~ReactionPathDiagram ()
Destructor.
double maxFlow ()
The largest one-way flow value in any path.
double netFlow (size_t k1, size_t k2)
The net flow from node k1
to node k2
.
double flow (size_t k1, size_t k2)
The one-way flow from node k1
to node k2
.
bool hasNode (size_t k)
True if a node for species k exists.
void writeData (std::ostream &s)
void exportToDot (std::ostream &s)
Export the reaction path diagram.
void add (ReactionPathDiagram &d)
SpeciesNode * node (size_t k)
Path * path (size_t k1, size_t k2)
Path * path (size_t n)
size_t nPaths ()
size_t nNodes ()
void addNode (size_t k, const string &nm, double x=0.0)
void displayOnly (size_t k=npos )
void linkNodes (size_t k1, size_t k2, size_t rxn, double value, string legend="")
void include (const string &aaname)
void exclude (const string &aaname)
void include (vector< string > &names)
void exclude (vector< string > &names)
vector< string > & included ()
vector< string > & excluded ()
vector< size_t > species ()
vector< int > reactions ()
void findMajorPaths (double threshold, size_t lda, double *a)
void setFont (const string &font)
◆ ~ReactionPathDiagram()
Destructor.
Deletes all nodes and paths in the diagram.
Definition at line 81 of file ReactionPath.cpp .
◆ maxFlow()
The largest one-way flow value in any path.
Definition at line 170 of file ReactionPath.h .
◆ netFlow()
double netFlow
(
size_t
k1 ,
size_t
k2
)
inline
◆ flow()
double flow
(
size_t
k1 ,
size_t
k2
)
inline
The one-way flow from node k1
to node k2
.
Definition at line 180 of file ReactionPath.h .
◆ hasNode()
◆ writeData()
void writeData
(
std::ostream &
s )
◆ exportToDot()
void exportToDot
(
std::ostream &
s )
Export the reaction path diagram.
This method writes to stream s
the commands for the 'dot' program in the GraphViz
package from AT&T. (GraphViz may be downloaded from www.graphviz.org.)
To generate a postscript reaction path diagram from the output of this method saved in file paths.dot, for example, give the command:
dot -Tps paths.dot > paths.ps
double dot(InputIter x_begin, InputIter x_end, InputIter2 y_begin)
Function that calculates a templated inner product.
To generate a GIF image, replace -Tps with -Tgif
Definition at line 171 of file ReactionPath.cpp .
◆ add()
◆ node()
◆ path() [1/2]
Path * path
(
size_t
k1 ,
size_t
k2
)
inline
◆ path() [2/2]
◆ nPaths()
◆ nNodes()
◆ addNode()
void addNode
(
size_t
k ,
const string &
nm ,
double
x = 0.0
)
◆ displayOnly()
void displayOnly
(
size_t
k = npos
)
inline
◆ linkNodes()
void linkNodes
(
size_t
k1 ,
size_t
k2 ,
size_t
rxn ,
double
value ,
string
legend = ""
)
◆ include() [1/2]
void include
(
const string &
aaname )
inline
◆ exclude() [1/2]
void exclude
(
const string &
aaname )
inline
◆ include() [2/2]
void include
(
vector< string > &
names )
inline
◆ exclude() [2/2]
void exclude
(
vector< string > &
names )
inline
◆ included()
vector< string > & included
(
)
inline
◆ excluded()
vector< string > & excluded
(
)
inline
◆ species()
vector< size_t > species
(
)
◆ reactions()
vector< int > reactions
(
)
◆ findMajorPaths()
void findMajorPaths
(
double
threshold ,
size_t
lda ,
double *
a
)
◆ setFont()
void setFont
(
const string &
font )
inline
◆ title
◆ bold_color
string bold_color = "blue"
◆ normal_color
string normal_color = "steelblue"
◆ dashed_color
string dashed_color = "gray"
◆ element
◆ m_font
string m_font = "Helvetica"
◆ threshold
◆ bold_min
◆ dashed_max
◆ label_min
◆ x_size
◆ y_size
◆ name
string name = "reaction_paths"
◆ dot_options
string dot_options = "center=1;"
◆ flow_type
flow_t flow_type = NetFlow
◆ scale
◆ arrow_width
double arrow_width = -5.0
◆ show_details
bool show_details = false
◆ arrow_hue
double arrow_hue = 0.6666
◆ m_flxmax
◆ m_paths
map<size_t, map<size_t, Path *> > m_paths
protected
◆ m_nodes
◆ m_pathlist
◆ m_include
◆ m_exclude
◆ m_speciesNumber
vector<size_t> m_speciesNumber
protected
◆ m_rxns
Indices of reactions that are included in the diagram.
Definition at line 292 of file ReactionPath.h .
◆ m_local
The documentation for this class was generated from the following files: