ProSHADE  0.7.5.1 (JAN 2021)
Protein Shape Detection
ProSHADE_internal_misc Namespace Reference

This namespace contains all the miscellaneous functions used throughout the code but unrelated to it. More...

Functions

void addToStringVector (std::vector< std::string > *vecToAddTo, std::string elementToAdd)
 Adds the element to the vector. More...
 
void addToSingleVector (std::vector< proshade_single > *vecToAddTo, proshade_single elementToAdd)
 Adds the element to the vector. More...
 
void addToDoubleVector (std::vector< proshade_double > *vecToAddTo, proshade_double elementToAdd)
 Adds the element to the vector. More...
 
void addToUnsignVector (std::vector< proshade_unsign > *vecToAddTo, proshade_unsign elementToAdd)
 Adds the element to the vector. More...
 
void addToSignedVector (std::vector< proshade_signed > *vecToAddTo, proshade_signed elementToAdd)
 Adds the element to the vector. More...
 
void addToDblPtrVector (std::vector< proshade_double * > *vecToAddTo, proshade_double *elementToAdd)
 Adds the element to the vector. More...
 
void addToSigPtrVector (std::vector< proshade_signed * > *vecToAddTo, proshade_signed *elementToAdd)
 Adds the element to the vector. More...
 
void addToUnsignVectorVector (std::vector< std::vector< proshade_unsign > > *vecToAddTo, std::vector< proshade_unsign > elementToAdd)
 Adds the element to the vector of vectors. More...
 
void addToDoubleVectorVector (std::vector< std::vector< proshade_double > > *vecToAddTo, std::vector< proshade_double > elementToAdd)
 Adds the element to the vector of vectors. More...
 
bool sortSymHlp (const proshade_double *a, const proshade_double *b)
 This function compares two arrays of two based on the fifth number, sorting lowest first. More...
 
bool sortSymHlpInv (const proshade_double *a, const proshade_double *b)
 This function compares two arrays of two based on the fifth number, sorting highest first. More...
 
bool sortDSymHlpInv (const proshade_double *a, const proshade_double *b)
 This function compares two arrays of the ProSHADE dihedral symmetry list based on combination of axes folds and heightst. More...
 
bool sortSymInvFoldHlp (const proshade_double *a, const proshade_double *b)
 This function compares two arrays of two based on the first number, sorting highest first. More...
 
void deepCopyAxisToDblPtrVector (std::vector< proshade_double * > *dblPtrVec, proshade_double *axis)
 Does a deep copy of a double array to a vector of double arrays. More...
 
void deepCopyBoundsSigPtrVector (std::vector< proshade_signed * > *sigPtrVec, proshade_signed *xFrom, proshade_signed *xTo, proshade_signed *yFrom, proshade_signed *yTo, proshade_signed *zFrom, proshade_signed *zTo)
 Does a deep copy of a signed int array to a vector of signed int arrays. More...
 
template<class chVar >
void checkMemoryAllocation (chVar checkVar, std::string fileP, unsigned int lineP, std::string funcP, std::string infoP="This error may occurs when ProSHADE requests memory to be\n : allocated to it and this operation fails. This could\n : happen when not enough memory is available, either due to\n : other processes using a lot of memory, or when the machine\n : does not have sufficient memory available. Re-run to see\n : if this problem persists.")
 Checks if memory was allocated properly. More...
 

Detailed Description

This namespace contains all the miscellaneous functions used throughout the code but unrelated to it.

The ProSHADE_internal_misc namespace contains all the functions which are useful, but not really related to shape description or data processing.

Function Documentation

◆ addToDblPtrVector()

void ProSHADE_internal_misc::addToDblPtrVector ( std::vector< proshade_double * > *  vecToAddTo,
proshade_double *  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of complex<double> and a single complex<double> element and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of complex<double>'s which should be elongated.
[in]elementToAddcomplex<double> to be added to the back of the vector.

Definition at line 143 of file ProSHADE_misc.cpp.

144 {
145  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
146 #if __cplusplus >= 201103L
147  vecToAddTo->emplace_back ( elementToAdd );
148 #else
149  vecToAddTo->push_back ( elementToAdd );
150 #endif
151 
152  //================================================ Done
153  return ;
154 
155 }

◆ addToDoubleVector()

void ProSHADE_internal_misc::addToDoubleVector ( std::vector< proshade_double > *  vecToAddTo,
proshade_double  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of proshade_double and a single proshade_double element and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of proshade_double's which should be elongated.
[in]elementToAddproshade_double to be added to the back of the vector.

Definition at line 77 of file ProSHADE_misc.cpp.

78 {
79  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
80 #if __cplusplus >= 201103L
81  vecToAddTo->emplace_back ( elementToAdd );
82 #else
83  vecToAddTo->push_back ( elementToAdd );
84 #endif
85 
86  //================================================ Done
87  return ;
88 
89 }

◆ addToDoubleVectorVector()

void ProSHADE_internal_misc::addToDoubleVectorVector ( std::vector< std::vector< proshade_double > > *  vecToAddTo,
std::vector< proshade_double >  elementToAdd 
)

Adds the element to the vector of vectors.

This function takes a pointer to a vector of vectors of doubles and a single vector of doubles and adds this element to the end of the vector of vectors. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of vectors of doubles which should be elongated.
[in]elementToAddvector of doubles to be added to the back of the vector.

Definition at line 210 of file ProSHADE_misc.cpp.

211 {
212  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
213 #if __cplusplus >= 201103L
214  vecToAddTo->emplace_back ( elementToAdd );
215 #else
216  vecToAddTo->push_back ( elementToAdd );
217 #endif
218 
219  //================================================ Done
220  return ;
221 
222 }

◆ addToSignedVector()

void ProSHADE_internal_misc::addToSignedVector ( std::vector< proshade_signed > *  vecToAddTo,
proshade_signed  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of proshade_signed and a single proshade_signed element and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of proshade_signed's which should be elongated.
[in]elementToAddproshade_signed to be added to the back of the vector.

Definition at line 121 of file ProSHADE_misc.cpp.

122 {
123  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
124 #if __cplusplus >= 201103L
125  vecToAddTo->emplace_back ( elementToAdd );
126 #else
127  vecToAddTo->push_back ( elementToAdd );
128 #endif
129 
130  //================================================ Done
131  return ;
132 
133 }

◆ addToSigPtrVector()

void ProSHADE_internal_misc::addToSigPtrVector ( std::vector< proshade_signed * > *  vecToAddTo,
proshade_signed *  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of proshade_signed pointers and a single proshade_signed pointer and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of complex<double>'s which should be elongated.
[in]elementToAddcomplex<double> to be added to the back of the vector.

Definition at line 166 of file ProSHADE_misc.cpp.

167 {
168  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
169 #if __cplusplus >= 201103L
170  vecToAddTo->emplace_back ( elementToAdd );
171 #else
172  vecToAddTo->push_back ( elementToAdd );
173 #endif
174 
175  //================================================ Done
176  return ;
177 
178 }

◆ addToSingleVector()

void ProSHADE_internal_misc::addToSingleVector ( std::vector< proshade_single > *  vecToAddTo,
proshade_single  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of proshade_single and a single proshade_single element and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of proshade_single's which should be elongated.
[in]elementToAddproshade_single to be added to the back of the vector.

Definition at line 55 of file ProSHADE_misc.cpp.

56 {
57  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
58 #if __cplusplus >= 201103L
59  vecToAddTo->emplace_back ( elementToAdd );
60 #else
61  vecToAddTo->push_back ( elementToAdd );
62 #endif
63 
64  //================================================ Done
65  return ;
66 
67 }

◆ addToStringVector()

void ProSHADE_internal_misc::addToStringVector ( std::vector< std::string > *  vecToAddTo,
std::string  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of strings and a single string element and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of strings which should be elongated.
[in]elementToAddString to be added to the back of the vector.

Definition at line 33 of file ProSHADE_misc.cpp.

34 {
35  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
36 #if __cplusplus >= 201103L
37  vecToAddTo->emplace_back ( elementToAdd );
38 #else
39  vecToAddTo->push_back ( elementToAdd );
40 #endif
41 
42  //================================================ Done
43  return ;
44 
45 }

◆ addToUnsignVector()

void ProSHADE_internal_misc::addToUnsignVector ( std::vector< proshade_unsign > *  vecToAddTo,
proshade_unsign  elementToAdd 
)

Adds the element to the vector.

This function takes a pointer to a vector of proshade_unsign and a single proshade_unsign element and adds this element to the end of the vector. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of proshade_unsign's which should be elongated.
[in]elementToAddproshade_unsign to be added to the back of the vector.

Definition at line 99 of file ProSHADE_misc.cpp.

100 {
101  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
102 #if __cplusplus >= 201103L
103  vecToAddTo->emplace_back ( elementToAdd );
104 #else
105  vecToAddTo->push_back ( elementToAdd );
106 #endif
107 
108  //================================================ Done
109  return ;
110 
111 }

◆ addToUnsignVectorVector()

void ProSHADE_internal_misc::addToUnsignVectorVector ( std::vector< std::vector< proshade_unsign > > *  vecToAddTo,
std::vector< proshade_unsign >  elementToAdd 
)

Adds the element to the vector of vectors.

This function takes a pointer to a vector of vectors of unsigns and a single vector of unsigns adds this element to the end of the vector of vectors. The reason for this function is to make vector elongation C++ standard independent (push_back vs. emplace_back)

Parameters
[in]vecToAddToPointer to vector of vectors of unsigns which should be elongated.
[in]elementToAddvector of unsigns to be added to the back of the vector.

Definition at line 188 of file ProSHADE_misc.cpp.

189 {
190  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
191 #if __cplusplus >= 201103L
192  vecToAddTo->emplace_back ( elementToAdd );
193 #else
194  vecToAddTo->push_back ( elementToAdd );
195 #endif
196 
197  //================================================ Done
198  return ;
199 
200 }

◆ checkMemoryAllocation()

template<class chVar >
void ProSHADE_internal_misc::checkMemoryAllocation ( chVar  checkVar,
std::string  fileP,
unsigned int  lineP,
std::string  funcP,
std::string  infoP = "This error may occurs when ProSHADE requests memory to be\n                    : allocated to it and this operation fails. This could\n                    : happen when not enough memory is available, either due to\n                    : other processes using a lot of memory, or when the machine\n                    : does not have sufficient memory available. Re-run to see\n                    : if this problem persists." 
)
inline

Checks if memory was allocated properly.

This function checks if the memory allocation has suceeded for a given pointer, printing error message if not.

Parameters
[in]checkVarPointer to be checked.

Definition at line 65 of file ProSHADE_misc.hpp.

65  : allocated to it and this operation fails. This could\n : happen when not enough memory is available, either due to\n : other processes using a lot of memory, or when the machine\n : does not have sufficient memory available. Re-run to see\n : if this problem persists." )
66  {
67  //============================================ Check against NULL
68  if ( checkVar == NULL )
69  {
70  throw ProSHADE_exception ( "Failed to allocate memory.", "E000007", fileP, lineP, funcP, infoP );
71  }
72 
73  //============================================ Done
74  return ;
75 
76  }

◆ deepCopyAxisToDblPtrVector()

void ProSHADE_internal_misc::deepCopyAxisToDblPtrVector ( std::vector< proshade_double * > *  dblPtrVec,
proshade_double *  axis 
)

Does a deep copy of a double array to a vector of double arrays.

This function deep copies a single symmetry axis ( proshade_double[6] ) into a vector of such arrays.

Parameters
[in]dblPtrVecPointer to vector of proshade_double arrays to which the second argument is to be deep copied.
[in]axisThe proshade_double array to be copied to the first argument.

Definition at line 287 of file ProSHADE_misc.cpp.

288 {
289  //================================================ Allocate new memory
290  proshade_double* symAx = new proshade_double[6];
291 
292  //================================================ Check memory allocation
293  ProSHADE_internal_misc::checkMemoryAllocation ( symAx, __FILE__, __LINE__, __func__ );
294 
295  //================================================ Copy the 6 values
296  symAx[0] = axis[0];
297  symAx[1] = axis[1];
298  symAx[2] = axis[2];
299  symAx[3] = axis[3];
300  symAx[4] = axis[4];
301  symAx[5] = axis[5];
302 
303  //================================================ Save
304  ProSHADE_internal_misc::addToDblPtrVector ( dblPtrVec, symAx );
305 
306  //================================================ Done
307  return ;
308 
309 }

◆ deepCopyBoundsSigPtrVector()

void ProSHADE_internal_misc::deepCopyBoundsSigPtrVector ( std::vector< proshade_signed * > *  sigPtrVec,
proshade_signed *  xFrom,
proshade_signed *  xTo,
proshade_signed *  yFrom,
proshade_signed *  yTo,
proshade_signed *  zFrom,
proshade_signed *  zTo 
)

Does a deep copy of a signed int array to a vector of signed int arrays.

This function deep copies a single bounds array ( proshade_signed[6] ) into a vector of such arrays.

Parameters
[in]sigPtrVecPointer to vector of proshade_signed arrays to which the second argument is to be deep copied.
[in]xFromPointer to the index value from which the x dimension start.
[in]xToPointer to the index value to which the x dimensions runs.
[in]yFromPointer to the index value from which the y dimension start.
[in]yToPointer to the index value to which the y dimensions runs.
[in]zFromPointer to the index value from which the z dimension start.
[in]zToPointer to the index value to which the z dimensions runs.

Definition at line 323 of file ProSHADE_misc.cpp.

324 {
325  //================================================ Allocate new memory
326  proshade_signed* bounds = NULL;
327  bounds = new proshade_signed[6];
328 
329  //================================================ Check memory allocation
330  ProSHADE_internal_misc::checkMemoryAllocation ( bounds, __FILE__, __LINE__, __func__ );
331 
332  //================================================ Copy the 6 values
333  bounds[0] = *xFrom;
334  bounds[1] = *xTo;
335  bounds[2] = *yFrom;
336  bounds[3] = *yTo;
337  bounds[4] = *zFrom;
338  bounds[5] = *zTo;
339 
340  //================================================ Save
341  ProSHADE_internal_misc::addToSigPtrVector ( sigPtrVec, bounds );
342 
343  //================================================ Done
344  return ;
345 
346 }

◆ sortDSymHlpInv()

bool ProSHADE_internal_misc::sortDSymHlpInv ( const proshade_double *  a,
const proshade_double *  b 
)

This function compares two arrays of the ProSHADE dihedral symmetry list based on combination of axes folds and heightst.

Parameters
[in]aThe first array to compare.
[in]bThe second array to compare.
[out]XBoolean whether the first is smaller than the second.

Definition at line 256 of file ProSHADE_misc.cpp.

257 {
258  //================================================ Get weighted averages
259  proshade_double aScore = ( ( a[0] * a[5] ) + ( a[6] * a[11] ) ) / ( a[0] + a[6] );
260  proshade_double bScore = ( ( b[0] * b[5] ) + ( b[6] * b[11] ) ) / ( b[0] + b[6] );
261 
262  //================================================ Compare
263  return ( aScore > bScore );
264 
265 }

◆ sortSymHlp()

bool ProSHADE_internal_misc::sortSymHlp ( const proshade_double *  a,
const proshade_double *  b 
)

This function compares two arrays of two based on the fifth number, sorting lowest first.

Parameters
[in]aThe first array to compare.
[in]bThe second array to compare.
[out]XBoolean whether the first is smaller than the second.

Definition at line 230 of file ProSHADE_misc.cpp.

231 {
232  //================================================ Compare
233  return ( a[5] < b[5] );
234 
235 }

◆ sortSymHlpInv()

bool ProSHADE_internal_misc::sortSymHlpInv ( const proshade_double *  a,
const proshade_double *  b 
)

This function compares two arrays of two based on the fifth number, sorting highest first.

Parameters
[in]aThe first array to compare.
[in]bThe second array to compare.
[out]XBoolean whether the first is smaller than the second.

Definition at line 243 of file ProSHADE_misc.cpp.

244 {
245  //======================================== Compare
246  return ( a[5] > b[5] );
247 
248 }

◆ sortSymInvFoldHlp()

bool ProSHADE_internal_misc::sortSymInvFoldHlp ( const proshade_double *  a,
const proshade_double *  b 
)

This function compares two arrays of two based on the first number, sorting highest first.

Parameters
[in]aThe first array to compare.
[in]bThe second array to compare.
[out]XBoolean whether the first is smaller than the second.

Definition at line 273 of file ProSHADE_misc.cpp.

274 {
275  //================================================ Compare
276  return ( a[0] > b[0] );
277 
278 }
ProSHADE_internal_misc::addToDblPtrVector
void addToDblPtrVector(std::vector< proshade_double * > *vecToAddTo, proshade_double *elementToAdd)
Adds the element to the vector.
Definition: ProSHADE_misc.cpp:143
ProSHADE_internal_misc::addToSigPtrVector
void addToSigPtrVector(std::vector< proshade_signed * > *vecToAddTo, proshade_signed *elementToAdd)
Adds the element to the vector.
Definition: ProSHADE_misc.cpp:166
ProSHADE_internal_misc::checkMemoryAllocation
void checkMemoryAllocation(chVar checkVar, std::string fileP, unsigned int lineP, std::string funcP, std::string infoP="This error may occurs when ProSHADE requests memory to be\n : allocated to it and this operation fails. This could\n : happen when not enough memory is available, either due to\n : other processes using a lot of memory, or when the machine\n : does not have sufficient memory available. Re-run to see\n : if this problem persists.")
Checks if memory was allocated properly.
Definition: ProSHADE_misc.hpp:65