"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "contrib/mmtf-c/mmtf_parser.cpp" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

mmtf_parser.cpp  (pymol-v1.8.6.0.tar.bz2)	:	mmtf_parser.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 307		skipping to change at line 307
free(thing->atomIdList);		free(thing->atomIdList);
free(thing->altLocList);		free(thing->altLocList);
free(thing->occupancyList);		free(thing->occupancyList);
free(thing->groupIdList);		free(thing->groupIdList);
free(thing->groupTypeList);		free(thing->groupTypeList);
free(thing->secStructList);		free(thing->secStructList);
free(thing->insCodeList);		free(thing->insCodeList);
free(thing->sequenceIndexList);		free(thing->sequenceIndexList);
free(thing->groupsPerChain);		free(thing->groupsPerChain);
free(thing->chainsPerModel);		free(thing->chainsPerModel);
		// PyMOL
		free(thing->pymolRepsList);
		free(thing->pymolColorList);
}		}
void MMTF_BioAssembly_destroy(MMTF_BioAssembly* bio_assembly) {		void MMTF_BioAssembly_destroy(MMTF_BioAssembly* bio_assembly) {
IF_NULL_PTRERROR_RETURN(bio_assembly, );		IF_NULL_PTRERROR_RETURN(bio_assembly, );
FREE_LIST(MMTF_Transform, bio_assembly->transformList);		FREE_LIST(MMTF_Transform, bio_assembly->transformList);
free(bio_assembly->name);		free(bio_assembly->name);
}		}
void MMTF_Transform_destroy(MMTF_Transform* transform) {		void MMTF_Transform_destroy(MMTF_Transform* transform) {
IF_NULL_PTRERROR_RETURN(transform, );		IF_NULL_PTRERROR_RETURN(transform, );
free(transform->chainIndexList);		free(transform->chainIndexList);
}		}
skipping to change at line 472		skipping to change at line 476
return output;		return output;
}		}
// Delta decode		// Delta decode
int32_t* MMTF_parser_delta_decode(const int32_t* input, uint32_t input_length, u int32_t* output_length) {		int32_t* MMTF_parser_delta_decode(const int32_t* input, uint32_t input_length, u int32_t* output_length) {
(*output_length) = input_length;		(*output_length) = input_length;
int32_t* output = MALLOC_ARRAY(int32_t, (*output_length)); // The output nee ds to be freed by the calling process		int32_t* output = MALLOC_ARRAY(int32_t, (*output_length)); // The output nee ds to be freed by the calling process
IF_NULL_ALLOCERROR_RETURN_NULL(output);		IF_NULL_ALLOCERROR_RETURN_NULL(output);
output[0] = input[0];		if (input_length > 0) {
		output[0] = input[0];
		}
uint32_t i;		uint32_t i;
for (i = 1; i < input_length; ++i) {		for (i = 1; i < input_length; ++i) {
output[i] = output[i - 1] + input[i];		output[i] = output[i - 1] + input[i];
}		}
return output;		return output;
}		}
// Recursive indexing decode		// Recursive indexing decode
int32_t* MMTF_parser_recursive_indexing_decode_from_16(const int16_t* input, uin t32_t input_length, uint32_t* output_length) {		int32_t* MMTF_parser_recursive_indexing_decode_from_16(const int16_t* input, uin t32_t input_length, uint32_t* output_length) {
skipping to change at line 496		skipping to change at line 503
if (input[i] != INT16_MAX && input[i] != INT16_MIN) {		if (input[i] != INT16_MAX && input[i] != INT16_MIN) {
++(*output_length);		++(*output_length);
}		}
}		}
int32_t* output = (int32_t*)MALLOC_ARRAY(int32_t, (*output_length)); // The output needs to be freed by the calling process		int32_t* output = (int32_t*)MALLOC_ARRAY(int32_t, (*output_length)); // The output needs to be freed by the calling process
IF_NULL_ALLOCERROR_RETURN_NULL(output);		IF_NULL_ALLOCERROR_RETURN_NULL(output);
size_t j = 0;		size_t j = 0;
output[j] = 0;
		if (input_length > 0) {
		output[0] = 0;
		}
for (i = 0; i < input_length; ++i) {		for (i = 0; i < input_length; ++i) {
output[j] += input[i];		output[j] += input[i];
if (input[i] != INT16_MAX && input[i] != INT16_MIN && j + 1 < *output_le ngth) {		if (input[i] != INT16_MAX && input[i] != INT16_MIN && j + 1 < *output_le ngth) {
++j;		++j;
output[j] = 0;		output[j] = 0;
}		}
}		}
skipping to change at line 756		skipping to change at line 766
default:		default:
fprintf(stderr, "Error in %s: the entry encoded in the MMTF is not a str ing.\n", __FUNCTION__);		fprintf(stderr, "Error in %s: the entry encoded in the MMTF is not a str ing.\n", __FUNCTION__);
return NULL;		return NULL;
}		}
char* result = NULL;		char* result = NULL;
MMTF_parser_put_string(object, &result);		MMTF_parser_put_string(object, &result);
return result;		return result;
}		}
		static
char MMTF_parser_fetch_char(const msgpack_object* object) {		char MMTF_parser_fetch_char(const msgpack_object* object) {
switch (object->type) {		switch (object->type) {
#ifdef MMTF_ACCEPT_MSGPACK_BIN_AS_STR		#ifdef MMTF_ACCEPT_MSGPACK_BIN_AS_STR
case MMTF_MSGPACK_TYPE(BIN):		case MMTF_MSGPACK_TYPE(BIN):
fprintf(stderr, "Warning in %s: type BIN, expected STR ('%.*s')\n", __FU NCTION__,		fprintf(stderr, "Warning in %s: type BIN, expected STR ('%.*s')\n", __FU NCTION__,
object->via.bin.size, object->via.bin.ptr);		object->via.bin.size, object->via.bin.ptr);
#endif		#endif
case MMTF_MSGPACK_TYPE(STR):		case MMTF_MSGPACK_TYPE(STR):
break;		break;
default:		default:
skipping to change at line 793		skipping to change at line 804
}		}
return result;		return result;
}		}
float MMTF_parser_fetch_float(const msgpack_object* object) {		float MMTF_parser_fetch_float(const msgpack_object* object) {
switch (object->type) {		switch (object->type) {
case /* FLOAT64 */ MMTF_MSGPACK_TYPE(FLOAT):		case /* FLOAT64 */ MMTF_MSGPACK_TYPE(FLOAT):
#if MSGPACK_VERSION_MAJOR >= 2		#if MSGPACK_VERSION_MAJOR >= 2
case /* FLOAT32 */ 0x0a: // msgpack-c >= 2.1		case /* FLOAT32 */ 0x0a: // msgpack-c >= 2.1
return (float)object->via.f64;
#endif		#endif
		return (float)object->via.f64;
default:		default:
fprintf(stderr, "Error in %s: the entry encoded in the MMTF is not a flo at.\n", __FUNCTION__);		fprintf(stderr, "Error in %s: the entry encoded in the MMTF is not a flo at.\n", __FUNCTION__);
return NAN;		return NAN;
}		}
}		}
/*		/*
* Fetch a compressed typed array		* Fetch a compressed typed array
*/		*/
static		static
skipping to change at line 958		skipping to change at line 969
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int8_array, secStructList);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int8_array, secStructList);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, bFactorList);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, bFactorList);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, xCoordList);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, xCoordList);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, yCoordList);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, yCoordList);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, zCoordList);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, zCoordList);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, occupancyList);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, float_array, occupancyList);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int32_array, chainsPerModel);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int32_array, chainsPerModel);
FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int32_array, groupsPerChain);		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int32_array, groupsPerChain);
FETCH_AND_ASSIGN_WITHCOUNT(thing, string_array, experimentalMethods);		FETCH_AND_ASSIGN_WITHCOUNT(thing, string_array, experimentalMethods);
FETCH_AND_ASSIGN_ARRAY(thing, float, unitCell);		FETCH_AND_ASSIGN_ARRAY(thing, float, unitCell);
		// PyMOL
		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int32_array, pymolRepsList);
		FETCH_AND_ASSIGN_DUMMYCOUNT(thing, int32_array, pymolColorList);
MAP_ITERATE_END();		MAP_ITERATE_END();
return true;		return true;
}		}
/*		/*
* Decode a MMTF_container from a string		* Decode a MMTF_container from a string
*/		*/
bool MMTF_unpack_from_string(const char* buffer, size_t msgsize, MMTF_container* thing) {		bool MMTF_unpack_from_string(const char* buffer, size_t msgsize, MMTF_container* thing) {
bool status;		bool status;
End of changes. 7 change blocks.
3 lines changed or deleted		19 lines changed or added

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