ProSHADE  0.7.6.0 (JUL 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 addToUnsPtrVector (std::vector< proshade_unsign * > *vecToAddTo, proshade_unsign *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 sortSymFoldHlp (const proshade_double *a, const proshade_double *b)
 
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 233 of file ProSHADE_misc.cpp.

234 {
235  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
236 #if __cplusplus >= 201103L
237  vecToAddTo->emplace_back ( elementToAdd );
238 #else
239  vecToAddTo->push_back ( elementToAdd );
240 #endif
241 
242  //================================================ Done
243  return ;
244 
245 }

◆ 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 211 of file ProSHADE_misc.cpp.

212 {
213  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
214 #if __cplusplus >= 201103L
215  vecToAddTo->emplace_back ( elementToAdd );
216 #else
217  vecToAddTo->push_back ( elementToAdd );
218 #endif
219 
220  //================================================ Done
221  return ;
222 
223 }

◆ addToUnsPtrVector()

void ProSHADE_internal_misc::addToUnsPtrVector ( 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 pointers and a single proshade_unsign 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 proshade_unsign pointer's which should be elongated.
[in]elementToAddproshade_unsign pointer to be added to the back of the vector.

Definition at line 189 of file ProSHADE_misc.cpp.

190 {
191  //================================================ Based on the compiler C++11 support, use the correct vector addition function.
192 #if __cplusplus >= 201103L
193  vecToAddTo->emplace_back ( elementToAdd );
194 #else
195  vecToAddTo->push_back ( elementToAdd );
196 #endif
197 
198  //================================================ Done
199  return ;
200 
201 }

◆ 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 67 of file ProSHADE_misc.hpp.

67  : 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." )
68  {
69  //============================================ Check against NULL
70  if ( checkVar == nullptr )
71  {
72  throw ProSHADE_exception ( "Failed to allocate memory.", "E000007", fileP, lineP, funcP, infoP );
73  }
74 
75  //============================================ Done
76  return ;
77 
78  }

◆ 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[7] ) 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 310 of file ProSHADE_misc.cpp.

311 {
312  //================================================ Allocate new memory
313  proshade_double* symAx = new proshade_double[7];
314 
315  //================================================ Check memory allocation
316  ProSHADE_internal_misc::checkMemoryAllocation ( symAx, __FILE__, __LINE__, __func__ );
317 
318  //================================================ Copy the 6 values
319  symAx[0] = axis[0];
320  symAx[1] = axis[1];
321  symAx[2] = axis[2];
322  symAx[3] = axis[3];
323  symAx[4] = axis[4];
324  symAx[5] = axis[5];
325  symAx[6] = axis[6];
326 
327  //================================================ Save
328  ProSHADE_internal_misc::addToDblPtrVector ( dblPtrVec, symAx );
329 
330  //================================================ Done
331  return ;
332 
333 }

◆ 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 347 of file ProSHADE_misc.cpp.

348 {
349  //================================================ Allocate new memory
350  proshade_signed* bounds = nullptr;
351  bounds = new proshade_signed[6];
352 
353  //================================================ Check memory allocation
354  ProSHADE_internal_misc::checkMemoryAllocation ( bounds, __FILE__, __LINE__, __func__ );
355 
356  //================================================ Copy the 6 values
357  bounds[0] = *xFrom;
358  bounds[1] = *xTo;
359  bounds[2] = *yFrom;
360  bounds[3] = *yTo;
361  bounds[4] = *zFrom;
362  bounds[5] = *zTo;
363 
364  //================================================ Save
365  ProSHADE_internal_misc::addToSigPtrVector ( sigPtrVec, bounds );
366 
367  //================================================ Done
368  return ;
369 
370 }

◆ 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 279 of file ProSHADE_misc.cpp.

280 {
281  //================================================ Get weighted averages
282  proshade_double aScore = ( ( a[0] * a[5] ) + ( a[6] * a[11] ) ) / ( a[0] + a[6] );
283  proshade_double bScore = ( ( b[0] * b[5] ) + ( b[6] * b[11] ) ) / ( b[0] + b[6] );
284 
285  //================================================ Compare
286  return ( aScore > bScore );
287 
288 }

◆ 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 253 of file ProSHADE_misc.cpp.

254 {
255  //================================================ Compare
256  return ( a[5] < b[5] );
257 
258 }

◆ 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 266 of file ProSHADE_misc.cpp.

267 {
268  //======================================== Compare
269  return ( a[5] > b[5] );
270 
271 }

◆ 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 296 of file ProSHADE_misc.cpp.

297 {
298  //================================================ Compare
299  return ( a[0] > b[0] );
300 
301 }
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:67