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Data Structures | |
struct | SmilesCompound |
Defines | |
#define | SMILESCOMPOUND_VERSION "1.4.0" |
#define | SMILESCOMPOUND_DATE "16-Mar-2004" |
#define | BOOLEAN_FALSE 0 |
Boolean variables are simulated with the defines BOOLEAN_FALSE and BOOLEAN_TRUE. | |
#define | BOOLEAN_TRUE 1 |
Boolean variables are simulated with the defines BOOLEAN_FALSE and BOOLEAN_TRUE. | |
#define | SmilesCompound_increaseCounter(scPtr) ( (scPtr->counter)++) |
The member counter of structure SmilesCompound is increased by one. | |
#define | SmilesCompound_decreaseCounter(scPtr) ( (scPtr->counter)--) |
The member counter of structure SmilesCompound is decreased by one. | |
Typedefs | |
typedef SmilesCompound * | SmilesCompound_Ptr |
A pointer to structure SmilesCompound is assigned the name SmilesCompound_Ptr . | |
Functions | |
SmilesCompound_Ptr | SmilesCompound_create (char *const name, char *const smiles, const int daylight_type,\FILE *errorLogFile) |
Creates a SmilesCompound structure. | |
void | SmilesCompound_destroy (void *scPtr) |
Destroys a SmilesCompound structure. | |
void | SmilesCompound_display (void *scPtr, FILE *outputStream) |
Displays a structure SmilesCompound. | |
SmilesCompound_Ptr | SmilesCompound_copy (const SmilesCompound_Ptr scPtr) |
Returns a deepcopy of the SmilesCompound scPtr . | |
int | SmilesCompound_identical (const void *scPtr1, const void *scPtr2) |
Checks if the two SmilesCompounds scPtr1 and scPtr2 have identical char* smiles . | |
void | SmilesCompound_setName (const SmilesCompound_Ptr scPtr, const char *const name) |
The name of structure SmilesCompound is set to name as the only name. | |
void | SmilesCompound_addName (const SmilesCompound_Ptr scPtr, const char *const name) |
name is added to the list of names of structure SmilesCompound. | |
StringArray_Ptr | SmilesCompound_getStringArrayOfNames (const SmilesCompound_Ptr scPtr) |
The member sAPtr (contains the name(s)) of structure SmilesCompound is returned. | |
int | SmilesCompound_removeFromArrayOfNames (const SmilesCompound_Ptr scPtr, const char *name) |
All names of scPtr that are identical to name are removed from the StringArray that contains the names. | |
int | SmilesCompound_setSmiles (const SmilesCompound_Ptr scPtr, char *smiles, const int daylight_type,\FILE *errorLogFile) |
The member smiles of structure SmilesCompound is set. | |
char * | SmilesCompound_getSmiles (const SmilesCompound_Ptr scPtr) |
The member smiles of structure SmilesCompound is returned. | |
void | SmilesCompound_setCounter (const SmilesCompound_Ptr scPtr, const int counter) |
The member counter of structure SmilesCompound is set. | |
int | SmilesCompound_getCounter (const SmilesCompound_Ptr scPtr) |
The member counter of structure SmilesCompound is returned. | |
void | SmilesCompound_setMoleculeHandle (const SmilesCompound_Ptr scPtr, const dt_Handle moleculeHandle) |
The member moleculeHandle of structure SmilesCompound is set. | |
dt_Handle | SmilesCompound_getMoleculeHandle (const SmilesCompound_Ptr scPtr) |
The member moleculeHandle of structure SmilesCompound is returned. |
This structure stores the data of one SMILES, SMIRKS or SMARTS.
The structure is created with SmilesCompound_create, destroyed with SmilesCompound_destroy and displayed with SmilesCompound_display. With SmilesCompound_setnameOfMember and SmilesCompound_getnameOfMember the values of the individual members of the structure SmilesCompound could be set or gotten. SmilesCompound_identical checks if the smiles
of two SmilesCompounds are identical (returns BOOLEAN_TRUE) or non-identical (returns BOOLEAN_FALSE). Non-Identity is only true if both smiles
are canonical.
If a SmilesCompound is created with a SMILES, member smiles
stores the canonical SMILES of that compound to allow for a idenditcal check (SmilesCompound_identical). Canonical SMIRKS are not supported by the Daylight Toolkit. Hence, the uniqueness check fails, if two reactions share the same semantics but differ lexicographically. The same holds for SMARTS.
The name of a SMILES, SMIRKS or SMARTS is stored in a StringArray. Thus, it is possible to store more than one name for a given SMILES, SMIRKS or SMARTS. Detailed information about accessibility of the name is provided by the documentation of the respective functions (SmilesCompound_setName, SmilesCompound_addName and SmilesCompound_getStringArrayOfNames).
smiles
or the name of a SMILES, SMIRKS or SMART is set (SmilesCompound_setName, SmilesCompound_addName and SmilesCompound_setSmiles) the provided string is copied via strncpy
. Hence, the string provided as an argument has to be freed by the caller of the function.smiles
- string containing the SMILES, SMIRKS or SMARTS of one compoundcounter
- counts the occurence of a specific SMILES (does not work for SMIRKS and SMARTS as they cannot be converted to a canonical representation)sAPtr
- pointer on structure StringArray that stores one or more names of the SMILES, SMIRKS or SMARTSmoleculeHandle
- dt_Handle on a Daylight object that correspoinds to smiles
fingerprintHandle
- dt_Handle on a Daylight fingerprint object that corresponds to smiles
02/12/2003 - Uli Fechner - 1.0.2 - added the member counter
and the functions SmilesCompound_getCounter, SmilesCompound_setCounter, SmilesCompound_increaseCounter and SmilesCompound_decreaseCounter; added the member moleculeHandle
and the functions SmilesCompound_getMoleculeHandle and SmilesCompound_setMoleculeHandle
03/12/2003 - Uli Fechner - 1.0.3 - added support for write out of errors revieved from dt_smilinerrors (SmilesCompound_create); added function SmilesCompound_identical @ version 04/12/2003 - Uli Fechner - 1.0.4 - SmilesCompound_create stores now the canonical SMILES to allow for identical check between two SmilesCompouns; small change in SmilesCompound_display
08/12/2003 - Uli Fechner - 1.0.5 - changes in SmilesCompound_create to allow for the checking of a successful creation
10/12/2003 - Uli Fechner - 1.1.0 - changed the storage of a compound name from char* to StringArray; modified function SmilesCompound_create, SmilesCompound_destroy, SmilesCompound_display, SmilesCompound_setName, SmilesCompound_addName and SmilesCompound_getName accordingly; change in SmilesCompound_identical: if two SmilesCompounds are identical the StringArray of the source SmilesCompound is concatenated to the StringArray of the target compound
17/12/2003 - Uli Fechner - 1.2.0 - changed the name of SmilesCompound_getName to SmilesCompound_getStringArrayOfNames; complete re-write of SmilesCompound_setSmiles (changed return type from void to int); added SmilesCompound_copy
19/12/2003 - Uli Fechner - 1.2.1 - added function SmilesCompound_removeFromArrayOfNames; major bugifx in SmilesCompound_identical
29/01/2004 - Tina Grabowski - 1.3.0 - major change: added support for SMARTS; corresponding changes in SmilesCompound_create and SmilesCompound_setSmiles
16/03/2004 - UF - 1.4.0 - added member fingerprint and the functions SmilesCompound_getFingerprint and SmilesCompound_setFingerprint; renamed member daylightHandle
to moleculeHandle
in the complete file; renamed functions SmilesCompound_get/setDaylightHandle to SmilesCompound_get/setMoleculeHandle accordingly \code
Definition in file smilesCompound.c.
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Boolean variables are simulated with the defines BOOLEAN_FALSE and BOOLEAN_TRUE.
Definition at line 94 of file smilesCompound.c. |
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Boolean variables are simulated with the defines BOOLEAN_FALSE and BOOLEAN_TRUE.
Definition at line 103 of file smilesCompound.c. |
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Definition at line 3 of file smilesCompound.c. Referenced by displayVersionInformation(). |
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The member
Definition at line 126 of file smilesCompound.c. |
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The member
Definition at line 115 of file smilesCompound.c. |
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Definition at line 2 of file smilesCompound.c. Referenced by displayVersionInformation(). |
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A pointer to structure SmilesCompound is assigned the name
Definition at line 84 of file smilesCompound.c. Referenced by main(), readDataFromStream(), SmilesCompound_copy(), SmilesCompound_create(), SmilesCompound_destroy(), SmilesCompound_display(), and SmilesCompound_identical(). |
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If
Definition at line 466 of file smilesCompound.c. References MemoryError, SmilesCompound::sAPtr, StringArray_addElement(), and StringArray_create(). |
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Returns a deepcopy of the SmilesCompound
Definition at line 369 of file smilesCompound.c. References SmilesCompound::counter, MemoryError, SmilesCompound::moleculeHandle, SmilesCompound::sAPtr, SmilesCompound::smiles, SmilesCompound_Ptr, and StringArray_copy(). |
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Creates a SmilesCompound structure.
The structure SmilesCompound is created. The memory of the structure itself and of its members is allocated automatically. The name and the SMILES, SMIRKS or SMARTS string have to be provided as arguments.
Definition at line 208 of file smilesCompound.c. References BOOLEAN_FALSE, SmilesCompound::counter, DAYLIGHT_SMARTS, DAYLIGHT_SMILES, DAYLIGHT_SMIRKS, MemoryError, SmilesCompound::moleculeHandle, SmilesCompound::sAPtr, SmilesCompound::smiles, SmilesCompound_Ptr, StringArray_addElement(), StringArray_create(), and StringArray_destroy(). Referenced by readDataFromStream(). |
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Destroys a SmilesCompound structure.
The structure SmilesCompound the pointer
Definition at line 309 of file smilesCompound.c. References AbortProgram, SmilesCompound::moleculeHandle, SmilesCompound::sAPtr, SmilesCompound::smiles, SmilesCompound_Ptr, and StringArray_destroy(). Referenced by readDataFromStream(), and SmilesCompound_setSmiles(). |
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Displays a structure SmilesCompound.
The structure SmilesCompound the pointer
Definition at line 347 of file smilesCompound.c. References SmilesCompound::sAPtr, SmilesCompound_getCounter(), SmilesCompound_getSmiles(), SmilesCompound_Ptr, StringArray_display(), and StringArray_getNumberOfElements(). Referenced by readDataFromStream(). |
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The member
Definition at line 652 of file smilesCompound.c. References SmilesCompound::counter. Referenced by main(), SmilesCompound_display(), SmilesCompound_identical(), and SmilesCompound_removeFromArrayOfNames(). |
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The member
Definition at line 676 of file smilesCompound.c. References SmilesCompound::moleculeHandle. Referenced by main(). |
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The member
Definition at line 628 of file smilesCompound.c. References SmilesCompound::smiles. Referenced by main(), and SmilesCompound_display(). |
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The member
Definition at line 494 of file smilesCompound.c. References SmilesCompound::sAPtr, and StringArray_Ptr. Referenced by main(), and SmilesCompound_removeFromArrayOfNames(). |
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Checks if the two SmilesCompounds
If the two SmilesCompounds
Definition at line 405 of file smilesCompound.c. References BOOLEAN_FALSE, BOOLEAN_TRUE, SmilesCompound_getCounter(), SmilesCompound_Ptr, SmilesCompound_setCounter(), and StringArray_concatenate(). Referenced by readDataFromStream(). |
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All names of
Definition at line 511 of file smilesCompound.c. References SmilesCompound_getCounter(), SmilesCompound_getStringArrayOfNames(), SmilesCompound_setCounter(), and StringArray_removeElement(). |
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The member
Definition at line 640 of file smilesCompound.c. References SmilesCompound::counter. Referenced by SmilesCompound_identical(), and SmilesCompound_removeFromArrayOfNames(). |
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The member
Definition at line 664 of file smilesCompound.c. References SmilesCompound::moleculeHandle. |
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The name of structure SmilesCompound is set to
The member
Definition at line 434 of file smilesCompound.c. References MemoryError, SmilesCompound::sAPtr, StringArray_addElement(), StringArray_create(), and StringArray_destroy(). |
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The member
If the function is called the previous
Definition at line 544 of file smilesCompound.c. References BOOLEAN_FALSE, BOOLEAN_TRUE, DAYLIGHT_SMARTS, DAYLIGHT_SMILES, DAYLIGHT_SMIRKS, MemoryError, SmilesCompound::moleculeHandle, SmilesCompound::sAPtr, SmilesCompound::smiles, SmilesCompound_destroy(), and StringArray_destroy(). |