#include "includes.h"
Go to the source code of this file.
Defines | |
#define | RETROFLUX_VERSION "0.3.4" |
#define | RETROFLUX_DATE "06-Aug-2004" |
Functions | |
int | main (int argc, char *argv[]) |
Main function of the program. | |
int | filterMolecules (char *reactants, const List_Ptr filterSmilesPtr, FILE *errorLogFile) |
Takes a SMILES string with several molecules and checks if one of these molecules is contained in filterSmilesPtr . | |
void | enqueueMolecules (char *reactants, char *reactionName, const SmilesCompound_Ptr product,\const List_Ptr listPtr, FILE *errorLogFile) |
Takes a SMILES string with several molecules and adds each molecule to reactants . | |
void | parseClp (const int argc, char *argv[], CLP_Ptr clpPtr) |
Parses the command line parameters. | |
List_Ptr | readDataFromFile (const char *const filename, const int daylight_type, const int uniqueData,\FILE *errorLogFile) |
List_Ptr | readDataFromStream (FILE *inputStream, const char *const nameOfStream,\const int daylight_type, const int uniqueData, FILE *errorLogFile) |
Reads the data of a stream and stores it in a structure List. | |
DoubleArrayPtr | getFileProperties (FILE *inputStream, const char *const nameOfStream) |
Examines the properties of a file stream. | |
void | displayHelpText (const CLP_Ptr clpPtr) |
Displays the help text on standard error. | |
void | displayVersionInformation (void) |
Displays the version information text on standard error. | |
List_Ptr | readDataFromFile (const char *const filename, const int daylight_type,\const int uniqueData, FILE *errorLogFile) |
Reads the data of a file and stores it in a structure List. |
All other files are included here via the inclusion of the file includes.h.
17/12/2003 - Uli Fechner - 0.2 - changed function prototype of enqueueMolecules; major changes in enqueueMolecules; adjusted corresponding function call in retroflux
07/01/2004 - UF - 0.3 - introduced the filter SMILES file; added function filterMolecules, changes in retroflux, parseClp and displayHelpText
30/01/2004 - UF - 0.3.1 - small changes in enqueueMolecules, filterMolecules and readDataFromStream to reflect changes in the file smilesCompound.c
23/02/2004 - UF - 0.3.2 - added a reaction counter in the stderr output (retroflux)
16/03/2004 - UF - 0.3.3 - function SmilesCompound_getDaylightHandle was renamed to SmilesCompound_getMoleculeHandle; this change is now reflected in retroflux
06/08/2004 - UF - 0.3.4 - changes in readDataFromFile and readDataFromStream
Definition in file retroflux.c.
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Definition at line 63 of file retroflux.c. Referenced by displayHelpText(), displayVersionInformation(), and main(). |
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Definition at line 62 of file retroflux.c. Referenced by displayHelpText(), displayVersionInformation(), and main(). |
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Displays the help text on standard error.
Definition at line 735 of file retroflux.c. References CLP_Ptr, RETROFLUX_DATE, and RETROFLUX_VERSION. Referenced by parseClp(). |
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Displays the version information text on standard error.
Definition at line 779 of file retroflux.c. References CLP_DATE, CLP_VERSION, DOUBLEARRAY_DATE, DOUBLEARRAY_VERSION, DOUBLELINKEDLIST_DATE, DOUBLELINKEDLIST_VERSION, GENERALDEFINES_DATE, GENERALDEFINES_VERSION, GIVENCLP_DATE, GIVENCLP_VERSION, INCLUDES_DATE, INCLUDES_VERSION, RETROFLUX_DATE, RETROFLUX_VERSION, SMILESCOMPOUND_DATE, and SMILESCOMPOUND_VERSION. Referenced by parseClp(). |
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Takes a SMILES string with several molecules and adds each molecule to
This function takes a SMILES string with several molecules that are separated by a '.' (
Definition at line 345 of file retroflux.c. References BOOLEAN_FALSE, DAYLIGHT_SMILES, List_insertTail(), List_Ptr, MemoryError, SmilesCompound_copy(), SmilesCompound_destroy(), SmilesCompound_getStringArrayOfNames(), SmilesCompound_Ptr, SmilesCompound_setSmiles(), and StringArray_mapConcatenate(). Referenced by main(). |
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Takes a SMILES string with several molecules and checks if one of these molecules is contained in
This function takes a SMILES string with several molecules that are separated by a '.' (
Definition at line 286 of file retroflux.c. References BOOLEAN_FALSE, BOOLEAN_TRUE, DAYLIGHT_SMILES, List_isContained(), List_Ptr, MemoryError, SmilesCompound_create(), SmilesCompound_destroy(), and SmilesCompound_Ptr. Referenced by main(). |
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Examines the properties of a file stream. The number of columns, characters per column and the number of rows are counted and the result of this examination are stored in a structure DoubleArray. This DoubleArray contains three elements regarded to the properties of dataFile:
Definition at line 647 of file retroflux.c. References AbortProgram, DoubleArray_create(), DoubleArray_setValue(), DoubleArrayPtr, FileIntegrityError, and MemoryError. Referenced by readDataFromStream(). |
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Main function of the program. The main function just calls the other functions. It is reduced to contain only function calls whenever possible.
Definition at line 105 of file retroflux.c. References BOOLEAN_FALSE, BOOLEAN_TRUE, CLP_create(), CLP_destroy(), CLP_display(), CLP_getErrorLogFile(), CLP_getFilterFile(), CLP_getOutputFile(), CLP_getReactionFile(), CLP_Ptr, DAYLIGHT_SMILES, DAYLIGHT_SMIRKS, enqueueMolecules(), FileWriteError, filterMolecules(), List_destroy(), List_display(), List_getNext(), List_getNumberOfNodes(), List_hasNext(), List_Ptr, List_remove(), List_rewind(), List_setName(), parseClp(), readDataFromFile(), readDataFromStream(), RETROFLUX_DATE, RETROFLUX_VERSION, SmilesCompound_getCounter(), SmilesCompound_getMoleculeHandle(), SmilesCompound_getStringArrayOfNames(), SmilesCompound_Ptr, and StringArray_getElement(). |
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Parses the command line parameters. The command line parameters are parsed here. Additionally, it is checked whether the standard in is connected to a terminal. If this is the case, no input file is provided and the help text of the program is printed on standard error. It is also checked here if there are any incompatibilities of the options provided at the command line. If so, the program aborts with an appropriate error message.
Definition at line 407 of file retroflux.c. References AbortProgram, BOOLEAN_FALSE, BOOLEAN_TRUE, CLP_getOutputFile(), CLP_Ptr, CLP_setErrorLogFile(), CLP_setFilterFile(), CLP_setOutputFile(), CLP_setReactionFile(), displayHelpText(), displayVersionInformation(), Given_CLP_Ptr, GivenClp_create(), GivenClp_destroy(), GivenClp_getOption(), GivenClp_setOption(), MandatoryOption, and MemoryError. Referenced by main(). |
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Reads the data of a file and stores it in a structure List.
Definition at line 495 of file retroflux.c. References FileReadError, List_Ptr, and readDataFromStream(). Referenced by main(). |
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Reads the data of a stream and stores it in a structure List.
Definition at line 527 of file retroflux.c. References BOOLEAN_FALSE, DoubleArray_destroy(), DoubleArray_getValue(), DoubleArrayPtr, getFileProperties(), List_create(), List_insertTail(), List_Ptr, MemoryError, SmilesCompound_create(), SmilesCompound_destroy(), SmilesCompound_display(), SmilesCompound_identical(), SmilesCompound_Ptr, StringArray_addElement(), StringArray_create(), StringArray_destroy(), StringArray_display(), StringArray_getNumberOfElements(), and StringArray_Ptr. Referenced by main(), and readDataFromFile(). |