"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/CifFile.cpp" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

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.

CifFile.cpp  (pymol-open-source-2.2.0)	:	CifFile.cpp  (pymol-open-source-2.3.0)
skipping to change at line 91		skipping to change at line 91
static void tolowerinplace(char *p) {		static void tolowerinplace(char *p) {
for (; *p; p++) {		for (; *p; p++) {
if (*p <= 'Z' && *p >= 'A')		if (*p <= 'Z' && *p >= 'A')
*p -= 'Z' - 'z';		*p -= 'Z' - 'z';
}		}
}		}
// CIF stuff		// CIF stuff
static const char * EMPTY_STRING = "";		static const char * EMPTY_STRING = "";
static cif_array EMPTY_ARRAY(NULL);		static cif_array EMPTY_ARRAY(nullptr);
/*		/*
* Class to store CIF loops. Only for parsing, do not use in any higher level		* Class to store CIF loops. Only for parsing, do not use in any higher level
* reading functions.		* reading functions.
*/		*/
class cif_loop {		class cif_loop {
public:		public:
int ncols;		int ncols;
int nrows;		int nrows;
const char **values;		const char **values;
// methods		// methods
const char * get_value_raw(int row, int col) const;		const char * get_value_raw(int row, int col) const;
};		};
// get table value, return NULL if indices out of bounds		// get table value, return NULL if indices out of bounds
const char * cif_loop::get_value_raw(int row, int col) const {		const char * cif_loop::get_value_raw(int row, int col) const {
if (row >= nrows)		if (row >= nrows)
return NULL;		return nullptr;
return values[row * ncols + col];		return values[row * ncols + col];
}		}
// get the number of elements in this array		// get the number of elements in this array
int cif_array::get_nrows() const {		int cif_array::get_nrows() const {
return (col < 0) ? 1 : pointer.loop->nrows;		return (col < 0) ? 1 : pointer.loop->nrows;
}		}
// get array value, return NULL if row-index out of bounds		// get array value, return NULL if row-index out of bounds
// or value in ['.', '?']		// or value in ['.', '?']
const char * cif_array::get_value(int row) const {		const char * cif_array::get_value(int row) const {
if (col < 0)		if (col < 0)
return (row > 0) ? NULL : pointer.value;		return (row > 0) ? nullptr : pointer.value;
return pointer.loop->get_value_raw(row, col);		return pointer.loop->get_value_raw(row, col);
}		}
// get array value, return an empty string if missing		// get array value, return an empty string if missing
const char * cif_array::as_s(int row) const {		const char * cif_array::as_s(int row) const {
const char * s = get_value(row);		const char * s = get_value(row);
return s ? s : EMPTY_STRING;		return s ? s : EMPTY_STRING;
}		}
// get array value as integer, return d (default 0) if missing		// get array value as integer, return d (default 0) if missing
skipping to change at line 174		skipping to change at line 174
/*		/*
* Get a pointer to array or NULL if not found		* Get a pointer to array or NULL if not found
*		*
* Can lookup up to 3 different aliases, the first one found is returned.		* Can lookup up to 3 different aliases, the first one found is returned.
* Also supports an alias shortcut for the trivial case where mmCIF uses		* Also supports an alias shortcut for the trivial case where mmCIF uses
* a colon and CIF uses an underscore: (key="_foo?bar") is identical to		* a colon and CIF uses an underscore: (key="_foo?bar") is identical to
* (key="_foo.bar", alias1="_foo_bar")		* (key="_foo.bar", alias1="_foo_bar")
*/		*/
const cif_array * cif_data::get_arr(const char * key, const char * alias1, const char * alias2) const {		const cif_array * cif_data::get_arr(const char * key, const char * alias1, const char * alias2) const {
const char * p;		const char * p;
const char * aliases[] = {alias1, alias2, NULL};		const char * aliases[] = {alias1, alias2, nullptr};
m_str_cifarray_t::const_iterator it;		m_str_cifarray_t::const_iterator it;
for (int j = 0; key; key = aliases[j++]) {		for (int j = 0; key; key = aliases[j++]) {
// support alias shortcut: '?' matches '.' and '_'		// support alias shortcut: '?' matches '.' and '_'
if ((p = strchr(key, '?'))) {		if ((p = strchr(key, '?'))) {
std::string tmp(key);		std::string tmp(key);
for (const char * d = "._"; *d; ++d) {		for (const char * d = "._"; *d; ++d) {
// replace '?' by '.' or '_'		// replace '?' by '.' or '_'
tmp[p - key] = *d;		tmp[p - key] = *d;
if ((it = dict.find(tmp.c_str())) != dict.end())		if ((it = dict.find(tmp.c_str())) != dict.end())
return &it->second;		return &it->second;
}		}
} else {		} else {
if ((it = dict.find(key)) != dict.end())		if ((it = dict.find(key)) != dict.end())
return &it->second;		return &it->second;
}		}
}		}
return NULL;		return nullptr;
}		}
// Get a pointer to array or to a default value if not found		// Get a pointer to array or to a default value if not found
const cif_array * cif_data::get_opt(const char * key, const char * alias1, const char * alias2) const {		const cif_array * cif_data::get_opt(const char * key, const char * alias1, const char * alias2) const {
const cif_array * arr = get_arr(key, alias1, alias2);		const cif_array * arr = get_arr(key, alias1, alias2);
if (arr == NULL)		if (arr == nullptr)
return &EMPTY_ARRAY;		return &EMPTY_ARRAY;
return arr;		return arr;
}		}
// constructor		// constructor
cif_file::cif_file(const char* filename, const char* contents_) {		cif_file::cif_file(const char* filename, const char* contents_) {
if (contents_) {		if (contents_) {
contents = mstrdup(contents_);		contents = mstrdup(contents_);
} else {		} else {
contents = FileGetContents(filename, NULL);		contents = FileGetContents(filename, nullptr);
if (!contents)		if (!contents)
std::cerr << "ERROR: Failed to load file '" << filename << "'" << std::end l;		std::cerr << "ERROR: Failed to load file '" << filename << "'" << std::end l;
}		}
if (contents)		if (contents)
parse();		parse();
}		}
// destructor		// destructor
cif_file::~cif_file() {		cif_file::~cif_file() {
for (m_str_cifdatap_t::iterator it = datablocks.begin(),		for (auto& datablock : datablocks)
it_end = datablocks.end(); it != it_end; ++it)		delete datablock.second;
delete it->second;
if (contents)		if (contents)
mfree(contents);		mfree(contents);
}		}
// destructor		// destructor
cif_data::~cif_data() {		cif_data::~cif_data() {
for (m_str_cifdatap_t::iterator it = saveframes.begin(),		for (auto& saveframe : saveframes)
it_end = saveframes.end(); it != it_end; ++it)		delete saveframe.second;
delete it->second;
		for (auto& loop : loops)
for (v_cifloopp_t::iterator it = loops.begin(),		delete loop;
it_end = loops.end(); it != it_end; ++it)
delete *it;
}		}
// parse CIF contents		// parse CIF contents
bool cif_file::parse() {		bool cif_file::parse() {
char *p = contents;		char *p = contents;
char quote;		char quote;
char prev = '\0';		char prev = '\0';
std::vector<bool> keypossible;		std::vector<bool> keypossible;
skipping to change at line 281		skipping to change at line 278
*p = 0;		*p = 0;
p += 2;		p += 2;
}		}
prev = ';';		prev = ';';
} else { // will null the whitespace		} else { // will null the whitespace
char * q = p++;		char * q = p++;
while (!iswhitespace0(*p)) ++p;		while (!iswhitespace0(*p)) ++p;
prev = *p;		prev = *p;
if (p - q == 1 && (*q == '?' || *q == '.')) {		if (p - q == 1 && (*q == '?' || *q == '.')) {
// store values '.' (inapplicable) and '?' (unknown) as null-pointers		// store values '.' (inapplicable) and '?' (unknown) as null-pointers
q = NULL;		q = nullptr;
keypossible.push_back(false);		keypossible.push_back(false);
} else {		} else {
if (*p)		if (*p)
*(p++) = 0;		*(p++) = 0;
keypossible.push_back(true);		keypossible.push_back(true);
}		}
tokens.push_back(q);		tokens.push_back(q);
}		}
}		}
cif_data *current_data = NULL, *current_frame = NULL, *global_block = NULL;		cif_data *current_data = nullptr, *current_frame = nullptr, *global_block = nu llptr;
// parse into dictionary		// parse into dictionary
for (unsigned int i = 0, n = tokens.size(); i < n; i++) {		for (unsigned int i = 0, n = tokens.size(); i < n; i++) {
if (!keypossible[i]) {		if (!keypossible[i]) {
std::cout << "ERROR" << std::endl;		std::cout << "ERROR" << std::endl;
break;		break;
} else if (tokens[i][0] == '_') {		} else if (tokens[i][0] == '_') {
if (i + 1 == n) {		if (i + 1 == n) {
std::cout << "ERROR truncated" << std::endl;		std::cout << "ERROR truncated" << std::endl;
break;		break;
skipping to change at line 314		skipping to change at line 311
if (current_frame) {		if (current_frame) {
tolowerinplace(tokens[i]);		tolowerinplace(tokens[i]);
current_frame->dict[tokens[i]].set_value(tokens[i + 1]);		current_frame->dict[tokens[i]].set_value(tokens[i + 1]);
}		}
i++;		i++;
} else if (strcasecmp("loop_", tokens[i]) == 0) {		} else if (strcasecmp("loop_", tokens[i]) == 0) {
int ncols = 0;		int ncols = 0;
int nrows = 0;		int nrows = 0;
cif_loop *loop = NULL;		cif_loop *loop = nullptr;
// loop data		// loop data
if (current_frame) {		if (current_frame) {
loop = new cif_loop;		loop = new cif_loop;
// add to loops list		// add to loops list
current_frame->loops.push_back(loop);		current_frame->loops.push_back(loop);
}		}
// columns		// columns
End of changes. 12 change blocks.
20 lines changed or deleted		17 lines changed or added

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