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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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< |
#include "babelconfig.hpp" |
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> |
#include "config.h" |
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#include "matrix3x3.hpp" |
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#include "vector3.hpp" |
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#include "mol.hpp" |
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namespace OpenBabel |
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{ |
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|
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< |
/*! \class OBStopwatch |
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< |
\brief Stopwatch class used for timing length of execution |
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> |
/*! \class OBStopwatch |
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> |
\brief Stopwatch class used for timing length of execution |
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|
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< |
The OBStopwatch class makes timing the execution of blocks of |
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< |
code to microsecond accuracy very simple. The class effectively |
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< |
has two functions, Start() and Elapsed(). The usage of the |
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< |
OBStopwatch class is demonstrated by the following code: |
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< |
\code |
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< |
OBStopwatch sw; |
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sw.Start(); |
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< |
//insert code here |
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cout << "Elapsed time = " << sw.Elapsed() << endl; |
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< |
\endcode |
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< |
*/ |
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> |
The OBStopwatch class makes timing the execution of blocks of |
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> |
code to microsecond accuracy very simple. The class effectively |
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> |
has two functions, Start() and Elapsed(). The usage of the |
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> |
OBStopwatch class is demonstrated by the following code: |
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> |
\code |
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> |
OBStopwatch sw; |
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> |
sw.Start(); |
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> |
//insert code here |
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> |
cout << "Elapsed time = " << sw.Elapsed() << endl; |
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> |
\endcode |
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> |
*/ |
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|
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< |
//! Deprecated: use the OBMessageHandler class instead |
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< |
//! \deprecated Throw an error through the OpenBabel::OBMessageHandler class |
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< |
OBAPI void ThrowError(char *str) |
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< |
{ |
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< |
obErrorLog.ThrowError("", str, obInfo); |
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< |
} |
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> |
//! Deprecated: use the OBMessageHandler class instead |
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> |
//! \deprecated Throw an error through the OpenBabel::OBMessageHandler class |
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> |
OBAPI void ThrowError(char *str) |
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> |
{ |
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> |
obErrorLog.ThrowError("", str, obInfo); |
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> |
} |
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|
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< |
//! Deprecated: use the OBMessageHandler class instead |
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< |
//! \deprecated Throw an error through the OpenBabel::OBMessageHandler class |
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< |
OBAPI void ThrowError(std::string &str) |
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< |
{ |
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< |
obErrorLog.ThrowError("", str, obInfo); |
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< |
} |
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> |
//! Deprecated: use the OBMessageHandler class instead |
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> |
//! \deprecated Throw an error through the OpenBabel::OBMessageHandler class |
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> |
OBAPI void ThrowError(std::string &str) |
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> |
{ |
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> |
obErrorLog.ThrowError("", str, obInfo); |
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> |
} |
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|
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// Comparison function (for sorting ints) returns a < b |
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< |
OBAPI bool OBCompareInt(const int &a,const int &b) |
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< |
{ |
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> |
// Comparison function (for sorting ints) returns a < b |
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> |
OBAPI bool OBCompareInt(const int &a,const int &b) |
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> |
{ |
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return(a<b); |
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< |
} |
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> |
} |
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|
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< |
// Comparison function (for sorting unsigned ints) returns a < b |
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< |
OBAPI bool OBCompareUnsigned(const unsigned int &a,const unsigned int &b) |
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< |
{ |
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> |
// Comparison function (for sorting unsigned ints) returns a < b |
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> |
OBAPI bool OBCompareUnsigned(const unsigned int &a,const unsigned int &b) |
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> |
{ |
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return(a<b); |
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< |
} |
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> |
} |
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|
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< |
// Comparison for doubles: returns a < (b + epsilon) |
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OBAPI bool IsNear(const double &a, const double &b, const double epsilon) |
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< |
{ |
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> |
// Comparison for doubles: returns a < (b + epsilon) |
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> |
OBAPI bool IsNear(const double &a, const double &b, const double epsilon) |
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> |
{ |
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return (fabs(a - b) < epsilon); |
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< |
} |
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> |
} |
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|
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< |
// Comparison for doubles: returns a < (0.0 + epsilon) |
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OBAPI bool IsNearZero(const double &a, const double epsilon) |
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< |
{ |
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> |
// Comparison for doubles: returns a < (0.0 + epsilon) |
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> |
OBAPI bool IsNearZero(const double &a, const double epsilon) |
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{ |
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return (fabs(a) < epsilon); |
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< |
} |
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> |
} |
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|
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//! Utility function: replace the last extension in string &src with new extension char *ext. |
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< |
OBAPI string NewExtension(string &src,char *ext) |
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< |
{ |
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> |
//! Utility function: replace the last extension in string &src with new extension char *ext. |
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> |
OBAPI string NewExtension(string &src,char *ext) |
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{ |
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unsigned int pos = (unsigned int)src.find_last_of("."); |
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string dst; |
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|
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if (pos != string::npos) |
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dst = src.substr(0,pos+1); |
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dst = src.substr(0,pos+1); |
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else |
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{ |
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> |
{ |
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dst = src; |
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dst += "."; |
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< |
} |
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> |
} |
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|
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dst += ext; |
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return(dst); |
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< |
} |
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> |
} |
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|
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//! Return the geometric centroid to an array of coordinates in double* format |
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//! and center the coordinates to the origin. Operates on the first "size" |
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//! coordinates in the array. |
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OBAPI vector3 center_coords(double *c, unsigned int size) |
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{ |
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< |
if (size == 0) |
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{ |
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< |
vector3 v(0.0f, 0.0f, 0.0f); |
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< |
return(v); |
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< |
} |
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> |
//! Return the geometric centroid to an array of coordinates in double* format |
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> |
//! and center the coordinates to the origin. Operates on the first "size" |
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> |
//! coordinates in the array. |
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> |
OBAPI vector3 center_coords(double *c, unsigned int size) |
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> |
{ |
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> |
if (size == 0) |
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> |
{ |
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> |
vector3 v(0.0f, 0.0f, 0.0f); |
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> |
return(v); |
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> |
} |
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unsigned int i; |
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double x=0,y=0,z=0; |
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for (i = 0;i < size;i++) |
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< |
{ |
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> |
{ |
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x += c[i*3]; |
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y += c[i*3+1]; |
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z += c[i*3+2]; |
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< |
} |
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> |
} |
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x /= (double) size; |
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y /= (double) size; |
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z /= (double) size; |
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for (i = 0;i < size;i++) |
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< |
{ |
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> |
{ |
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c[i*3] -= x; |
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c[i*3+1] -= y; |
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c[i*3+2] -= z; |
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< |
} |
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> |
} |
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vector3 v(x,y,z); |
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return(v); |
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< |
} |
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> |
} |
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|
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< |
//! Rotates the coordinate set *c by the transformation matrix m[3][3] |
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< |
//! Operates on the first "size" coordinates in the array. |
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< |
OBAPI void rotate_coords(double *c,double m[3][3],unsigned int size) |
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< |
{ |
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> |
//! Rotates the coordinate set *c by the transformation matrix m[3][3] |
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> |
//! Operates on the first "size" coordinates in the array. |
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> |
OBAPI void rotate_coords(double *c,double m[3][3],unsigned int size) |
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> |
{ |
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double x,y,z; |
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for (unsigned int i = 0;i < size;i++) |
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< |
{ |
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> |
{ |
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x = c[i*3]*m[0][0] + c[i*3+1]*m[0][1] + c[i*3+2]*m[0][2]; |
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y = c[i*3]*m[1][0] + c[i*3+1]*m[1][1] + c[i*3+2]*m[1][2]; |
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z = c[i*3]*m[2][0] + c[i*3+1]*m[2][1] + c[i*3+2]*m[2][2]; |
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c[i*3] = x; |
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c[i*3+1] = y; |
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c[i*3+2] = z; |
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< |
} |
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< |
} |
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> |
} |
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> |
} |
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|
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< |
//! Calculate the RMS deviation between the first N coordinates of *r and *f |
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< |
OBAPI double calc_rms(double *r,double *f, unsigned int N) |
| 154 |
< |
{ |
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< |
if (N == 0) |
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< |
return 0.0f; // no RMS deviation between two empty sets |
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> |
//! Calculate the RMS deviation between the first N coordinates of *r and *f |
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> |
OBAPI double calc_rms(double *r,double *f, unsigned int N) |
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> |
{ |
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> |
if (N == 0) |
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> |
return 0.0f; // no RMS deviation between two empty sets |
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|
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|
double d2=0.0; |
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for (unsigned int i = 0;i < N;i++) |
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< |
{ |
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> |
{ |
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d2 += SQUARE(r[i*3] - f[i*3]) + |
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< |
SQUARE(r[i*3+1] - f[i*3+1]) + |
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< |
SQUARE(r[i*3+2] - f[i*3+2]); |
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< |
} |
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> |
SQUARE(r[i*3+1] - f[i*3+1]) + |
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> |
SQUARE(r[i*3+2] - f[i*3+2]); |
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> |
} |
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|
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d2 /= (double) N; |
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return(sqrt(d2)); |
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< |
} |
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> |
} |
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|
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< |
//! Rotate the coordinates of 'atoms' |
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< |
//! such that tor == ang - atoms in 'tor' should be ordered such |
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< |
//! that the 3rd atom is the pivot around which atoms rotate |
| 173 |
< |
OBAPI void SetRotorToAngle(double *c,vector<int> &tor,double ang,vector<int> &atoms) |
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< |
{ |
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> |
//! Rotate the coordinates of 'atoms' |
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> |
//! such that tor == ang - atoms in 'tor' should be ordered such |
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> |
//! that the 3rd atom is the pivot around which atoms rotate |
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> |
OBAPI void SetRotorToAngle(double *c,vector<int> &tor,double ang,vector<int> &atoms) |
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> |
{ |
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|
double v1x,v1y,v1z,v2x,v2y,v2z,v3x,v3y,v3z; |
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|
double c1x,c1y,c1z,c2x,c2y,c2z,c3x,c3y,c3z; |
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double c1mag,c2mag,radang,costheta,m[9]; |
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c1mag = SQUARE(c1x)+SQUARE(c1y)+SQUARE(c1z); |
| 204 |
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c2mag = SQUARE(c2x)+SQUARE(c2y)+SQUARE(c2z); |
| 205 |
|
if (c1mag*c2mag < 0.01) |
| 206 |
< |
costheta = 1.0; //avoid div by zero error |
| 206 |
> |
costheta = 1.0; //avoid div by zero error |
| 207 |
|
else |
| 208 |
< |
costheta = (c1x*c2x + c1y*c2y + c1z*c2z)/(sqrt(c1mag*c2mag)); |
| 208 |
> |
costheta = (c1x*c2x + c1y*c2y + c1z*c2z)/(sqrt(c1mag*c2mag)); |
| 209 |
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|
| 210 |
|
if (costheta < -0.999999) |
| 211 |
< |
costheta = -0.999999; |
| 211 |
> |
costheta = -0.999999; |
| 212 |
|
if (costheta > 0.999999) |
| 213 |
< |
costheta = 0.999999; |
| 213 |
> |
costheta = 0.999999; |
| 214 |
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|
| 215 |
|
if ((v2x*c3x + v2y*c3y + v2z*c3z) > 0.0) |
| 216 |
< |
radang = -acos(costheta); |
| 216 |
> |
radang = -acos(costheta); |
| 217 |
|
else |
| 218 |
< |
radang = acos(costheta); |
| 218 |
> |
radang = acos(costheta); |
| 219 |
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|
| 220 |
|
// |
| 221 |
|
// now we have the torsion angle (radang) - set up the rot matrix |
| 253 |
|
vector<int>::iterator i; |
| 254 |
|
int j; |
| 255 |
|
for (i = atoms.begin();i != atoms.end();i++) |
| 256 |
< |
{ |
| 256 |
> |
{ |
| 257 |
|
j = *i; |
| 258 |
|
c[j] -= tx; |
| 259 |
|
c[j+1] -= ty; |
| 267 |
|
c[j] += tx; |
| 268 |
|
c[j+1] += ty; |
| 269 |
|
c[j+2] += tz; |
| 270 |
< |
} |
| 271 |
< |
} |
| 270 |
> |
} |
| 271 |
> |
} |
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|
| 273 |
< |
//! Safely open the supplied filename and return an ifstream, throwing an error |
| 274 |
< |
//! to the default OBMessageHandler error log if it fails. |
| 275 |
< |
OBAPI bool SafeOpen(ifstream &fs,char *filename) |
| 276 |
< |
{ |
| 273 |
> |
//! Safely open the supplied filename and return an ifstream, throwing an error |
| 274 |
> |
//! to the default OBMessageHandler error log if it fails. |
| 275 |
> |
OBAPI bool SafeOpen(ifstream &fs,char *filename) |
| 276 |
> |
{ |
| 277 |
|
#ifdef WIN32 |
| 278 |
|
string s = filename; |
| 279 |
|
if (s.find(".bin") != string::npos) |
| 280 |
< |
fs.open(filename,ios::binary); |
| 280 |
> |
fs.open(filename,ios::binary); |
| 281 |
|
else |
| 282 |
|
#endif |
| 283 |
|
|
| 284 |
< |
fs.open(filename); |
| 284 |
> |
fs.open(filename); |
| 285 |
|
|
| 286 |
|
if (!fs) |
| 287 |
< |
{ |
| 287 |
> |
{ |
| 288 |
|
string error = "Unable to open file \'"; |
| 289 |
|
error += filename; |
| 290 |
|
error += "\' in read mode"; |
| 291 |
< |
obErrorLog.ThrowError(__FUNCTION__, error, obError); |
| 291 |
> |
obErrorLog.ThrowError(__func__, error, obError); |
| 292 |
|
return(false); |
| 293 |
< |
} |
| 293 |
> |
} |
| 294 |
|
|
| 295 |
|
return(true); |
| 296 |
< |
} |
| 296 |
> |
} |
| 297 |
|
|
| 298 |
|
|
| 299 |
< |
//! Safely open the supplied filename and return an ofstream, throwing an error |
| 300 |
< |
//! to the default OBMessageHandler error log if it fails. |
| 301 |
< |
OBAPI bool SafeOpen(ofstream &fs,char *filename) |
| 302 |
< |
{ |
| 299 |
> |
//! Safely open the supplied filename and return an ofstream, throwing an error |
| 300 |
> |
//! to the default OBMessageHandler error log if it fails. |
| 301 |
> |
OBAPI bool SafeOpen(ofstream &fs,char *filename) |
| 302 |
> |
{ |
| 303 |
|
#ifdef WIN32 |
| 304 |
|
string s = filename; |
| 305 |
|
if (s.find(".bin") != string::npos) |
| 306 |
< |
fs.open(filename,ios::binary); |
| 306 |
> |
fs.open(filename,ios::binary); |
| 307 |
|
else |
| 308 |
|
#endif |
| 309 |
|
|
| 310 |
< |
fs.open(filename); |
| 310 |
> |
fs.open(filename); |
| 311 |
|
|
| 312 |
|
if (!fs) |
| 313 |
< |
{ |
| 313 |
> |
{ |
| 314 |
|
string error = "Unable to open file \'"; |
| 315 |
|
error += filename; |
| 316 |
|
error += "\' in write mode"; |
| 317 |
< |
obErrorLog.ThrowError(__FUNCTION__, error, obError); |
| 317 |
> |
obErrorLog.ThrowError(__func__, error, obError); |
| 318 |
|
return(false); |
| 319 |
< |
} |
| 319 |
> |
} |
| 320 |
|
|
| 321 |
|
return(true); |
| 322 |
< |
} |
| 322 |
> |
} |
| 323 |
|
|
| 324 |
< |
//! Safely open the supplied filename and return an ifstream, throwing an error |
| 325 |
< |
//! to the default OBMessageHandler error log if it fails. |
| 326 |
< |
OBAPI bool SafeOpen(ifstream &fs,string &filename) |
| 327 |
< |
{ |
| 328 |
< |
return(SafeOpen(fs,(char*)filename.c_str())); |
| 329 |
< |
} |
| 330 |
< |
|
| 331 |
< |
//! Safely open the supplied filename and return an ofstream, throwing an error |
| 332 |
< |
//! to the default OBMessageHandler error log if it fails. |
| 333 |
< |
OBAPI bool SafeOpen(ofstream &fs,string &filename) |
| 334 |
< |
{ |
| 335 |
< |
return(SafeOpen(fs,(char*)filename.c_str())); |
| 336 |
< |
} |
| 324 |
> |
//! Safely open the supplied filename and return an ifstream, throwing an error |
| 325 |
> |
//! to the default OBMessageHandler error log if it fails. |
| 326 |
> |
OBAPI bool SafeOpen(ifstream &fs,string &filename) |
| 327 |
> |
{ |
| 328 |
> |
return(SafeOpen(fs,(char*)filename.c_str())); |
| 329 |
> |
} |
| 330 |
|
|
| 331 |
< |
//! Shift the supplied string to uppercase |
| 332 |
< |
OBAPI void ToUpper(std::string &s) |
| 333 |
< |
{ |
| 331 |
> |
//! Safely open the supplied filename and return an ofstream, throwing an error |
| 332 |
> |
//! to the default OBMessageHandler error log if it fails. |
| 333 |
> |
OBAPI bool SafeOpen(ofstream &fs,string &filename) |
| 334 |
> |
{ |
| 335 |
> |
return(SafeOpen(fs,(char*)filename.c_str())); |
| 336 |
> |
} |
| 337 |
> |
|
| 338 |
> |
//! Shift the supplied string to uppercase |
| 339 |
> |
OBAPI void ToUpper(std::string &s) |
| 340 |
> |
{ |
| 341 |
|
if (s.empty()) |
| 342 |
< |
return; |
| 342 |
> |
return; |
| 343 |
|
unsigned int i; |
| 344 |
|
for (i = 0;i < s.size();i++) |
| 345 |
< |
if (isalpha(s[i]) && !isdigit(s[i])) |
| 346 |
< |
s[i] = toupper(s[i]); |
| 347 |
< |
} |
| 345 |
> |
if (isalpha(s[i]) && !isdigit(s[i])) |
| 346 |
> |
s[i] = toupper(s[i]); |
| 347 |
> |
} |
| 348 |
|
|
| 349 |
< |
//! Shift the supplied char* to uppercase |
| 350 |
< |
OBAPI void ToUpper(char *cptr) |
| 351 |
< |
{ |
| 349 |
> |
//! Shift the supplied char* to uppercase |
| 350 |
> |
OBAPI void ToUpper(char *cptr) |
| 351 |
> |
{ |
| 352 |
|
char *c; |
| 353 |
|
for (c = cptr;*c != '\0';c++) |
| 354 |
< |
if (isalpha(*c) && !isdigit(*c)) |
| 355 |
< |
*c = toupper(*c); |
| 356 |
< |
} |
| 354 |
> |
if (isalpha(*c) && !isdigit(*c)) |
| 355 |
> |
*c = toupper(*c); |
| 356 |
> |
} |
| 357 |
|
|
| 358 |
< |
//! Shift the supplied string to lowercase |
| 359 |
< |
OBAPI void ToLower(std::string &s) |
| 360 |
< |
{ |
| 358 |
> |
//! Shift the supplied string to lowercase |
| 359 |
> |
OBAPI void ToLower(std::string &s) |
| 360 |
> |
{ |
| 361 |
|
if (s.empty()) |
| 362 |
< |
return; |
| 362 |
> |
return; |
| 363 |
|
unsigned int i; |
| 364 |
|
for (i = 0;i < s.size();i++) |
| 365 |
< |
if (isalpha(s[i]) && !isdigit(s[i])) |
| 366 |
< |
s[i] = tolower(s[i]); |
| 367 |
< |
} |
| 365 |
> |
if (isalpha(s[i]) && !isdigit(s[i])) |
| 366 |
> |
s[i] = tolower(s[i]); |
| 367 |
> |
} |
| 368 |
|
|
| 369 |
< |
//! Shift the supplied char* to lowercase |
| 370 |
< |
OBAPI void ToLower(char *cptr) |
| 371 |
< |
{ |
| 369 |
> |
//! Shift the supplied char* to lowercase |
| 370 |
> |
OBAPI void ToLower(char *cptr) |
| 371 |
> |
{ |
| 372 |
|
char *c; |
| 373 |
|
for (c = cptr;*c != '\0';c++) |
| 374 |
< |
if (isalpha(*c) && !isdigit(*c)) |
| 375 |
< |
*c = tolower(*c); |
| 376 |
< |
} |
| 374 |
> |
if (isalpha(*c) && !isdigit(*c)) |
| 375 |
> |
*c = tolower(*c); |
| 376 |
> |
} |
| 377 |
|
|
| 378 |
< |
//! "Clean" the supplied atom type, shifting the first character to uppercase, |
| 379 |
< |
//! the second character (if it's a letter) to lowercase, and terminating with a NULL |
| 380 |
< |
//! to strip off any trailing characters |
| 381 |
< |
OBAPI void CleanAtomType(char *id) |
| 382 |
< |
{ |
| 378 |
> |
//! "Clean" the supplied atom type, shifting the first character to uppercase, |
| 379 |
> |
//! the second character (if it's a letter) to lowercase, and terminating with a NULL |
| 380 |
> |
//! to strip off any trailing characters |
| 381 |
> |
OBAPI void CleanAtomType(char *id) |
| 382 |
> |
{ |
| 383 |
|
id[0] = toupper(id[0]); |
| 384 |
|
if (isalpha(id[1]) == 0) |
| 385 |
< |
id[1] = '\0'; |
| 385 |
> |
id[1] = '\0'; |
| 386 |
|
else |
| 387 |
|
{ |
| 388 |
< |
id[1] = tolower(id[1]); |
| 388 |
> |
id[1] = tolower(id[1]); |
| 389 |
|
id[2] = '\0'; |
| 390 |
|
} |
| 391 |
< |
} |
| 391 |
> |
} |
| 392 |
|
|
| 393 |
< |
//! Transform the supplied vector<OBInternalCoord*> into cartesian and update |
| 394 |
< |
//! the OBMol accordingly. |
| 395 |
< |
//! Implements <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml#zmatrixCoordinatesIntoCartesianCoordinates">blue-obelisk:zmatrixCoordinatesIntoCartesianCoordinates</a> |
| 396 |
< |
OBAPI void InternalToCartesian(std::vector<OBInternalCoord*> &vic,OBMol &mol) |
| 397 |
< |
{ |
| 393 |
> |
//! Transform the supplied vector<OBInternalCoord*> into cartesian and update |
| 394 |
> |
//! the OBMol accordingly. |
| 395 |
> |
//! Implements <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml#zmatrixCoordinatesIntoCartesianCoordinates">blue-obelisk:zmatrixCoordinatesIntoCartesianCoordinates</a> |
| 396 |
> |
OBAPI void InternalToCartesian(std::vector<OBInternalCoord*> &vic,OBMol &mol) |
| 397 |
> |
{ |
| 398 |
|
vector3 n,nn,v1,v2,v3,avec,bvec,cvec; |
| 399 |
|
double dst = 0.0, ang = 0.0, tor = 0.0; |
| 400 |
|
OBAtom *atom; |
| 402 |
|
int index; |
| 403 |
|
|
| 404 |
|
if (vic.empty()) |
| 405 |
< |
return; |
| 405 |
> |
return; |
| 406 |
|
|
| 407 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
| 407 |
> |
obErrorLog.ThrowError(__func__, |
| 408 |
|
"Ran OpenBabel::InternalToCartesian", obAuditMsg); |
| 409 |
|
|
| 410 |
|
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
| 411 |
< |
{ |
| 411 |
> |
{ |
| 412 |
|
index = atom->GetIdx(); |
| 413 |
|
|
| 414 |
< |
if (!vic[index]) // make sure we always have valid pointers |
| 415 |
< |
return; |
| 414 |
> |
// make sure we always have valid pointers |
| 415 |
> |
if (index >= vic.size() || !vic[index]) |
| 416 |
> |
return; |
| 417 |
|
|
| 418 |
|
if (vic[index]->_a) // make sure we have a valid ptr |
| 419 |
< |
{ |
| 419 |
> |
{ |
| 420 |
|
avec = vic[index]->_a->GetVector(); |
| 421 |
|
dst = vic[index]->_dst; |
| 422 |
< |
} |
| 422 |
> |
} |
| 423 |
|
else |
| 424 |
< |
{ |
| 424 |
> |
{ |
| 425 |
|
// atom 1 |
| 426 |
|
atom->SetVector(0.0, 0.0, 0.0); |
| 427 |
|
continue; |
| 428 |
< |
} |
| 428 |
> |
} |
| 429 |
|
|
| 430 |
|
if (vic[index]->_b) |
| 431 |
< |
{ |
| 431 |
> |
{ |
| 432 |
|
bvec = vic[index]->_b->GetVector(); |
| 433 |
|
ang = vic[index]->_ang * DEG_TO_RAD; |
| 434 |
< |
} |
| 434 |
> |
} |
| 435 |
|
else |
| 436 |
< |
{ |
| 436 |
> |
{ |
| 437 |
|
// atom 2 |
| 438 |
|
atom->SetVector(dst, 0.0, 0.0); |
| 439 |
|
continue; |
| 440 |
< |
} |
| 440 |
> |
} |
| 441 |
|
|
| 442 |
|
if (vic[index]->_c) |
| 443 |
< |
{ |
| 443 |
> |
{ |
| 444 |
|
cvec = vic[index]->_c->GetVector(); |
| 445 |
|
tor = vic[index]->_tor * DEG_TO_RAD; |
| 446 |
< |
} |
| 446 |
> |
} |
| 447 |
|
else |
| 448 |
< |
{ |
| 448 |
> |
{ |
| 449 |
|
// atom 3 |
| 450 |
|
cvec = VY; |
| 451 |
< |
tor = 90. * DEG_TO_RAD; |
| 452 |
< |
} |
| 451 |
> |
tor = 90.0 * DEG_TO_RAD; |
| 452 |
> |
} |
| 453 |
|
|
| 454 |
|
v1 = avec - bvec; |
| 455 |
|
v2 = avec - cvec; |
| 468 |
|
v2 = avec + v3 - v1; |
| 469 |
|
|
| 470 |
|
atom->SetVector(v2); |
| 471 |
< |
} |
| 471 |
> |
} |
| 472 |
|
|
| 473 |
|
// Delete dummy atoms |
| 474 |
|
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
| 475 |
< |
if (atom->GetAtomicNum() == 0) |
| 476 |
< |
mol.DeleteAtom(atom); |
| 477 |
< |
} |
| 475 |
> |
if (atom->GetAtomicNum() == 0) |
| 476 |
> |
mol.DeleteAtom(atom); |
| 477 |
> |
} |
| 478 |
|
|
| 479 |
< |
//! Use the supplied OBMol and its Cartesian coordinates to generate |
| 480 |
< |
//! a set of internal (z-matrix) coordinates as supplied in the |
| 481 |
< |
//! vector<OBInternalCoord*> argument. |
| 482 |
< |
//! Implements <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml#cartesianCoordinatesIntoZmatrixCoordinates">blue-obelisk:cartesianCoordinatesIntoZmatrixCoordinates</a>. |
| 483 |
< |
OBAPI void CartesianToInternal(std::vector<OBInternalCoord*> &vic,OBMol &mol) |
| 484 |
< |
{ |
| 479 |
> |
//! Use the supplied OBMol and its Cartesian coordinates to generate |
| 480 |
> |
//! a set of internal (z-matrix) coordinates as supplied in the |
| 481 |
> |
//! vector<OBInternalCoord*> argument. |
| 482 |
> |
//! Implements <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml#cartesianCoordinatesIntoZmatrixCoordinates">blue-obelisk:cartesianCoordinatesIntoZmatrixCoordinates</a>. |
| 483 |
> |
OBAPI void CartesianToInternal(std::vector<OBInternalCoord*> &vic,OBMol &mol) |
| 484 |
> |
{ |
| 485 |
|
double r,sum; |
| 486 |
|
OBAtom *atom,*nbr,*ref; |
| 487 |
|
vector<OBNodeBase*>::iterator i,j,m; |
| 488 |
|
|
| 489 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
| 489 |
> |
obErrorLog.ThrowError(__func__, |
| 490 |
|
"Ran OpenBabel::CartesianToInternal", obAuditMsg); |
| 491 |
|
|
| 492 |
|
//set reference atoms |
| 493 |
|
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
| 494 |
< |
{ |
| 494 |
> |
{ |
| 495 |
|
if (atom->GetIdx() == 1) |
| 496 |
< |
continue; |
| 496 |
> |
continue; |
| 497 |
|
else if (atom->GetIdx() == 2) |
| 498 |
< |
{ |
| 498 |
> |
{ |
| 499 |
|
vic[atom->GetIdx()]->_a = mol.GetAtom(1); |
| 500 |
|
continue; |
| 501 |
< |
} |
| 501 |
> |
} |
| 502 |
|
else if (atom->GetIdx() == 3) |
| 503 |
< |
{ |
| 503 |
> |
{ |
| 504 |
|
if( (atom->GetVector()-mol.GetAtom(2)->GetVector()).length_2() |
| 505 |
< |
<(atom->GetVector()-mol.GetAtom(1)->GetVector()).length_2()) |
| 506 |
< |
{ |
| 505 |
> |
<(atom->GetVector()-mol.GetAtom(1)->GetVector()).length_2()) |
| 506 |
> |
{ |
| 507 |
|
vic[atom->GetIdx()]->_a = mol.GetAtom(2); |
| 508 |
|
vic[atom->GetIdx()]->_b = mol.GetAtom(1); |
| 509 |
< |
} |
| 509 |
> |
} |
| 510 |
|
else |
| 511 |
< |
{ |
| 511 |
> |
{ |
| 512 |
|
vic[atom->GetIdx()]->_a = mol.GetAtom(1); |
| 513 |
|
vic[atom->GetIdx()]->_b = mol.GetAtom(2); |
| 514 |
< |
} |
| 514 |
> |
} |
| 515 |
|
continue; |
| 516 |
< |
} |
| 516 |
> |
} |
| 517 |
|
sum=1.0E10; |
| 518 |
|
ref = mol.GetAtom(1); |
| 519 |
|
for(nbr = mol.BeginAtom(j);nbr && (i != j);nbr = mol.NextAtom(j)) |
| 520 |
< |
{ |
| 520 |
> |
{ |
| 521 |
|
r = (atom->GetVector()-nbr->GetVector()).length_2(); |
| 522 |
|
if((r < sum) && (vic[nbr->GetIdx()]->_a != nbr) && |
| 523 |
< |
(vic[nbr->GetIdx()]->_b != nbr)) |
| 524 |
< |
{ |
| 523 |
> |
(vic[nbr->GetIdx()]->_b != nbr)) |
| 524 |
> |
{ |
| 525 |
|
sum = r; |
| 526 |
|
ref = nbr; |
| 527 |
< |
} |
| 528 |
< |
} |
| 527 |
> |
} |
| 528 |
> |
} |
| 529 |
|
|
| 530 |
|
vic[atom->GetIdx()]->_a = ref; |
| 531 |
|
if (ref->GetIdx() >= 3) |
| 532 |
< |
{ |
| 532 |
> |
{ |
| 533 |
|
vic[atom->GetIdx()]->_b = vic[ref->GetIdx()]->_a; |
| 534 |
|
vic[atom->GetIdx()]->_c = vic[ref->GetIdx()]->_b; |
| 535 |
< |
} |
| 535 |
> |
} |
| 536 |
|
else |
| 537 |
< |
{ |
| 537 |
> |
{ |
| 538 |
|
if(ref->GetIdx()== 1) |
| 539 |
< |
{ |
| 539 |
> |
{ |
| 540 |
|
vic[atom->GetIdx()]->_b = mol.GetAtom(2); |
| 541 |
|
vic[atom->GetIdx()]->_c = mol.GetAtom(3); |
| 542 |
< |
} |
| 542 |
> |
} |
| 543 |
|
else |
| 544 |
< |
{//ref->GetIdx()== 2 |
| 544 |
> |
{//ref->GetIdx()== 2 |
| 545 |
|
vic[atom->GetIdx()]->_b = mol.GetAtom(1); |
| 546 |
|
vic[atom->GetIdx()]->_c = mol.GetAtom(3); |
| 547 |
< |
} |
| 548 |
< |
} |
| 549 |
< |
} |
| 547 |
> |
} |
| 548 |
> |
} |
| 549 |
> |
} |
| 550 |
|
|
| 551 |
|
//fill in geometries |
| 552 |
|
unsigned int k; |
| 553 |
|
vector3 v1,v2; |
| 554 |
|
OBAtom *a,*b,*c; |
| 555 |
|
for (k = 2;k <= mol.NumAtoms();k++) |
| 556 |
< |
{ |
| 556 |
> |
{ |
| 557 |
|
atom = mol.GetAtom(k); |
| 558 |
|
a = vic[k]->_a; |
| 559 |
|
b = vic[k]->_b; |
| 560 |
|
c = vic[k]->_c; |
| 561 |
|
if (k == 2) |
| 562 |
< |
{ |
| 562 |
> |
{ |
| 563 |
|
vic[k]->_dst = (atom->GetVector() - a->GetVector()).length(); |
| 564 |
|
continue; |
| 565 |
< |
} |
| 565 |
> |
} |
| 566 |
|
|
| 567 |
|
v1 = atom->GetVector() - a->GetVector(); |
| 568 |
|
v2 = b->GetVector() - a->GetVector(); |
| 570 |
|
vic[k]->_ang = vectorAngle(v1,v2); |
| 571 |
|
|
| 572 |
|
if (k == 3) |
| 573 |
< |
continue; |
| 573 |
> |
continue; |
| 574 |
|
vic[k]->_tor = CalcTorsionAngle(atom->GetVector(), |
| 575 |
|
a->GetVector(), |
| 576 |
|
b->GetVector(), |
| 577 |
|
c->GetVector()); |
| 578 |
< |
} |
| 578 |
> |
} |
| 579 |
|
|
| 580 |
|
//check for linear geometries and try to correct if possible |
| 581 |
|
bool done; |
| 582 |
|
double ang; |
| 583 |
|
for (k = 2;k <= mol.NumAtoms();k++) |
| 584 |
< |
{ |
| 584 |
> |
{ |
| 585 |
|
ang = fabs(vic[k]->_ang); |
| 586 |
|
if (ang > 5.0 && ang < 175.0) |
| 587 |
< |
continue; |
| 587 |
> |
continue; |
| 588 |
|
atom = mol.GetAtom(k); |
| 589 |
|
done = false; |
| 590 |
|
for (a = mol.BeginAtom(i);a && a->GetIdx() < k && !done;a = mol.NextAtom(i)) |
| 591 |
< |
for (b=mol.BeginAtom(j);b && b->GetIdx()<a->GetIdx() && !done;b = mol.NextAtom(j)) |
| 591 |
> |
for (b=mol.BeginAtom(j);b && b->GetIdx()<a->GetIdx() && !done;b = mol.NextAtom(j)) |
| 592 |
|
{ |
| 593 |
< |
v1 = atom->GetVector() - a->GetVector(); |
| 594 |
< |
v2 = b->GetVector() - a->GetVector(); |
| 595 |
< |
ang = fabs(vectorAngle(v1,v2)); |
| 596 |
< |
if (ang < 5.0 || ang > 175.0) |
| 597 |
< |
continue; |
| 593 |
> |
v1 = atom->GetVector() - a->GetVector(); |
| 594 |
> |
v2 = b->GetVector() - a->GetVector(); |
| 595 |
> |
ang = fabs(vectorAngle(v1,v2)); |
| 596 |
> |
if (ang < 5.0 || ang > 175.0) |
| 597 |
> |
continue; |
| 598 |
|
|
| 599 |
< |
for (c = mol.BeginAtom(m);c && c->GetIdx() < atom->GetIdx();c = mol.NextAtom(m)) |
| 600 |
< |
if (c != atom && c != a && c != b) |
| 601 |
< |
break; |
| 602 |
< |
if (!c) |
| 603 |
< |
continue; |
| 599 |
> |
for (c = mol.BeginAtom(m);c && c->GetIdx() < atom->GetIdx();c = mol.NextAtom(m)) |
| 600 |
> |
if (c != atom && c != a && c != b) |
| 601 |
> |
break; |
| 602 |
> |
if (!c) |
| 603 |
> |
continue; |
| 604 |
|
|
| 605 |
< |
vic[k]->_a = a; |
| 606 |
< |
vic[k]->_b = b; |
| 607 |
< |
vic[k]->_c = c; |
| 608 |
< |
vic[k]->_dst = v1.length(); |
| 609 |
< |
vic[k]->_ang = vectorAngle(v1,v2); |
| 610 |
< |
vic[k]->_tor = CalcTorsionAngle(atom->GetVector(), |
| 611 |
< |
a->GetVector(), |
| 612 |
< |
b->GetVector(), |
| 613 |
< |
c->GetVector()); |
| 614 |
< |
done = true; |
| 605 |
> |
vic[k]->_a = a; |
| 606 |
> |
vic[k]->_b = b; |
| 607 |
> |
vic[k]->_c = c; |
| 608 |
> |
vic[k]->_dst = v1.length(); |
| 609 |
> |
vic[k]->_ang = vectorAngle(v1,v2); |
| 610 |
> |
vic[k]->_tor = CalcTorsionAngle(atom->GetVector(), |
| 611 |
> |
a->GetVector(), |
| 612 |
> |
b->GetVector(), |
| 613 |
> |
c->GetVector()); |
| 614 |
> |
done = true; |
| 615 |
|
} |
| 616 |
< |
} |
| 617 |
< |
} |
| 616 |
> |
} |
| 617 |
> |
} |
| 618 |
|
|
| 619 |
< |
OBAPI void qtrfit (double *r,double *f,int size, double u[3][3]) |
| 620 |
< |
{ |
| 619 |
> |
OBAPI void qtrfit (double *r,double *f,int size, double u[3][3]) |
| 620 |
> |
{ |
| 621 |
|
register int i; |
| 622 |
|
double xxyx, xxyy, xxyz; |
| 623 |
|
double xyyx, xyyy, xyyz; |
| 639 |
|
xzyz = 0.0; |
| 640 |
|
|
| 641 |
|
for (i = 0; i < size; i++) |
| 642 |
< |
{ |
| 642 |
> |
{ |
| 643 |
|
rx = r[i*3]; |
| 644 |
|
ry = r[i*3+1]; |
| 645 |
|
rz = r[i*3+2]; |
| 656 |
|
xzyx += fz * rx; |
| 657 |
|
xzyy += fz * ry; |
| 658 |
|
xzyz += fz * rz; |
| 659 |
< |
} |
| 659 |
> |
} |
| 660 |
|
|
| 661 |
|
c[4*0+0] = xxyx + xyyy + xzyz; |
| 662 |
|
|
| 696 |
|
u[0][2] = 2.0 * (q[3] * q[1] - q[0] * q[2]); |
| 697 |
|
u[1][2] = 2.0 * (q[3] * q[2] + q[0] * q[1]); |
| 698 |
|
u[2][2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3]; |
| 699 |
< |
} |
| 699 |
> |
} |
| 700 |
|
|
| 701 |
|
|
| 702 |
|
|
| 703 |
< |
static double Roots[4]; |
| 703 |
> |
static double Roots[4]; |
| 704 |
|
|
| 705 |
|
#define ApproxZero 1E-7 |
| 706 |
|
#define IsZero(x) ((double)fabs(x)<ApproxZero) |
| 713 |
|
|
| 714 |
|
#ifdef OLD_RMAT |
| 715 |
|
|
| 716 |
< |
/*FUNCTION */ |
| 717 |
< |
/* recieves: the co-efficients for a general |
| 718 |
< |
* equation of degree one. |
| 719 |
< |
* Ax + B = 0 !! |
| 720 |
< |
*/ |
| 721 |
< |
OBAPI static int SolveLinear(double A,double B) |
| 722 |
< |
{ |
| 716 |
> |
/*FUNCTION */ |
| 717 |
> |
/* recieves: the co-efficients for a general |
| 718 |
> |
* equation of degree one. |
| 719 |
> |
* Ax + B = 0 !! |
| 720 |
> |
*/ |
| 721 |
> |
OBAPI static int SolveLinear(double A,double B) |
| 722 |
> |
{ |
| 723 |
|
if( IsZero(A) ) |
| 724 |
< |
return( 0 ); |
| 724 |
> |
return( 0 ); |
| 725 |
|
Roots[0] = -B/A; |
| 726 |
|
return( 1 ); |
| 727 |
< |
} |
| 727 |
> |
} |
| 728 |
|
|
| 729 |
< |
/*FUNCTION */ |
| 730 |
< |
/* recieves: the co-efficients for a general |
| 731 |
< |
* linear equation of degree two. |
| 732 |
< |
* Ax^2 + Bx + C = 0 !! |
| 733 |
< |
*/ |
| 734 |
< |
OBAPI static int SolveQuadratic(double A,double B,double C) |
| 735 |
< |
{ |
| 729 |
> |
/*FUNCTION */ |
| 730 |
> |
/* recieves: the co-efficients for a general |
| 731 |
> |
* linear equation of degree two. |
| 732 |
> |
* Ax^2 + Bx + C = 0 !! |
| 733 |
> |
*/ |
| 734 |
> |
OBAPI static int SolveQuadratic(double A,double B,double C) |
| 735 |
> |
{ |
| 736 |
|
register double Descr, Temp, TwoA; |
| 737 |
|
|
| 738 |
|
if( IsZero(A) ) |
| 739 |
< |
return( SolveLinear(B,C) ); |
| 739 |
> |
return( SolveLinear(B,C) ); |
| 740 |
|
|
| 741 |
|
TwoA = A+A; |
| 742 |
|
Temp = TwoA*C; |
| 743 |
|
Descr = B*B - (Temp+Temp); |
| 744 |
|
if( Descr<0.0 ) |
| 745 |
< |
return( 0 ); |
| 745 |
> |
return( 0 ); |
| 746 |
|
|
| 747 |
|
if( Descr>0.0 ) |
| 748 |
< |
{ |
| 748 |
> |
{ |
| 749 |
|
Descr = sqrt(Descr); |
| 750 |
|
#ifdef ORIG |
| 751 |
|
|
| 753 |
|
Roots[1] = (-B+Descr)/TwoA; |
| 754 |
|
#else |
| 755 |
|
/* W. Press, B. Flannery, S. Teukolsky and W. Vetterling, |
| 756 |
< |
* "Quadratic and Cubic Equations", Numerical Recipes in C, |
| 757 |
< |
* Chapter 5, pp. 156-157, 1989. |
| 758 |
< |
*/ |
| 756 |
> |
* "Quadratic and Cubic Equations", Numerical Recipes in C, |
| 757 |
> |
* Chapter 5, pp. 156-157, 1989. |
| 758 |
> |
*/ |
| 759 |
|
Temp = (B<0.0)? -0.5*(B-Descr) : -0.5*(B+Descr); |
| 760 |
|
Roots[0] = Temp/A; |
| 761 |
|
Roots[1] = C/Temp; |
| 762 |
|
#endif |
| 763 |
|
|
| 764 |
|
return( 2 ); |
| 765 |
< |
} |
| 765 |
> |
} |
| 766 |
|
Roots[0] = -B/TwoA; |
| 767 |
|
return( 1 ); |
| 768 |
< |
} |
| 768 |
> |
} |
| 769 |
|
|
| 770 |
< |
/*FUNCTION */ |
| 771 |
< |
/* task: to return the cube root of the |
| 772 |
< |
* given value taking into account |
| 773 |
< |
* that it may be negative. |
| 774 |
< |
*/ |
| 775 |
< |
OBAPI static double CubeRoot(double X) |
| 776 |
< |
{ |
| 770 |
> |
/*FUNCTION */ |
| 771 |
> |
/* task: to return the cube root of the |
| 772 |
> |
* given value taking into account |
| 773 |
> |
* that it may be negative. |
| 774 |
> |
*/ |
| 775 |
> |
OBAPI static double CubeRoot(double X) |
| 776 |
> |
{ |
| 777 |
|
if( X>=0.0 ) |
| 778 |
< |
{ |
| 778 |
> |
{ |
| 779 |
|
return pow( X, OneThird ); |
| 780 |
< |
} |
| 780 |
> |
} |
| 781 |
|
else |
| 782 |
< |
return -pow( -X, OneThird ); |
| 783 |
< |
} |
| 782 |
> |
return -pow( -X, OneThird ); |
| 783 |
> |
} |
| 784 |
|
|
| 785 |
< |
OBAPI static int SolveCubic(double A,double B,double C,double D) |
| 786 |
< |
{ |
| 785 |
> |
OBAPI static int SolveCubic(double A,double B,double C,double D) |
| 786 |
> |
{ |
| 787 |
|
register double TwoA, ThreeA, BOver3A; |
| 788 |
|
register double Temp, POver3, QOver2; |
| 789 |
|
register double Desc, Rho, Psi; |
| 790 |
|
|
| 791 |
|
|
| 792 |
|
if( IsZero(A) ) |
| 793 |
< |
{ |
| 793 |
> |
{ |
| 794 |
|
return( SolveQuadratic(B,C,D) ); |
| 795 |
< |
} |
| 795 |
> |
} |
| 796 |
|
|
| 797 |
|
TwoA = A+A; |
| 798 |
|
ThreeA = TwoA+A; |
| 805 |
|
Desc = QOver2*QOver2 + Rho; |
| 806 |
|
|
| 807 |
|
if( Desc<=0.0 ) |
| 808 |
< |
{ |
| 808 |
> |
{ |
| 809 |
|
Rho = sqrt( -Rho ); |
| 810 |
|
Psi = OneThird*acos(-QOver2/Rho); |
| 811 |
|
Temp = CubeRoot( Rho ); |
| 815 |
|
Roots[1] = Temp*cos( Psi+TwoThirdsPI )-BOver3A; |
| 816 |
|
Roots[2] = Temp*cos( Psi+FourThirdsPI )-BOver3A; |
| 817 |
|
return( 3 ); |
| 818 |
< |
} |
| 818 |
> |
} |
| 819 |
|
|
| 820 |
|
if( Desc> 0.0 ) |
| 821 |
< |
{ |
| 821 |
> |
{ |
| 822 |
|
Temp = CubeRoot( -QOver2 ); |
| 823 |
|
Roots[0] = Temp+Temp-BOver3A; |
| 824 |
|
Roots[1] = -Temp-BOver3A; |
| 825 |
|
return( 2 ); |
| 826 |
< |
} |
| 826 |
> |
} |
| 827 |
|
|
| 828 |
|
Desc = sqrt( Desc ); |
| 829 |
|
Roots[0] = CubeRoot(Desc-QOver2)-CubeRoot(Desc+QOver2) - BOver3A; |
| 830 |
|
|
| 831 |
|
return( 1 ); |
| 832 |
< |
} |
| 832 |
> |
} |
| 833 |
|
#endif |
| 834 |
|
|
| 835 |
|
|
| 836 |
|
#define MAX_SWEEPS 50 |
| 837 |
|
|
| 838 |
< |
OBAPI void ob_make_rmat(double a[3][3],double rmat[9]) |
| 839 |
< |
{ |
| 838 |
> |
OBAPI void ob_make_rmat(double a[3][3],double rmat[9]) |
| 839 |
> |
{ |
| 840 |
|
double onorm, dnorm; |
| 841 |
|
double b, dma, q, t, c, s,d[3]; |
| 842 |
|
double atemp, vtemp, dtemp,v[3][3]; |
| 846 |
|
memset((char*)d,'\0',sizeof(double)*3); |
| 847 |
|
|
| 848 |
|
for (j = 0; j < 3; j++) |
| 849 |
< |
{ |
| 849 |
> |
{ |
| 850 |
|
for (i = 0; i < 3; i++) |
| 851 |
< |
v[i][j] = 0.0; |
| 851 |
> |
v[i][j] = 0.0; |
| 852 |
|
|
| 853 |
|
v[j][j] = 1.0; |
| 854 |
|
d[j] = a[j][j]; |
| 855 |
< |
} |
| 855 |
> |
} |
| 856 |
|
|
| 857 |
|
for (l = 1; l <= MAX_SWEEPS; l++) |
| 858 |
< |
{ |
| 858 |
> |
{ |
| 859 |
|
dnorm = 0.0; |
| 860 |
|
onorm = 0.0; |
| 861 |
|
for (j = 0; j < 3; j++) |
| 862 |
< |
{ |
| 862 |
> |
{ |
| 863 |
|
dnorm = dnorm + (double)fabs(d[j]); |
| 864 |
|
for (i = 0; i <= j - 1; i++) |
| 865 |
< |
{ |
| 865 |
> |
{ |
| 866 |
|
onorm = onorm + (double)fabs(a[i][j]); |
| 867 |
< |
} |
| 868 |
< |
} |
| 867 |
> |
} |
| 868 |
> |
} |
| 869 |
|
|
| 870 |
|
if((onorm/dnorm) <= 1.0e-12) |
| 871 |
< |
goto Exit_now; |
| 871 |
> |
goto Exit_now; |
| 872 |
|
for (j = 1; j < 3; j++) |
| 873 |
< |
{ |
| 873 |
> |
{ |
| 874 |
|
for (i = 0; i <= j - 1; i++) |
| 875 |
< |
{ |
| 875 |
> |
{ |
| 876 |
|
b = a[i][j]; |
| 877 |
|
if(fabs(b) > 0.0) |
| 878 |
< |
{ |
| 878 |
> |
{ |
| 879 |
|
dma = d[j] - d[i]; |
| 880 |
|
if((fabs(dma) + fabs(b)) <= fabs(dma)) |
| 881 |
< |
t = b / dma; |
| 881 |
> |
t = b / dma; |
| 882 |
|
else |
| 883 |
< |
{ |
| 883 |
> |
{ |
| 884 |
|
q = 0.5 * dma / b; |
| 885 |
|
t = 1.0/((double)fabs(q) + (double)sqrt(1.0+q*q)); |
| 886 |
|
if(q < 0.0) |
| 887 |
< |
t = -t; |
| 888 |
< |
} |
| 887 |
> |
t = -t; |
| 888 |
> |
} |
| 889 |
|
c = 1.0/(double)sqrt(t * t + 1.0); |
| 890 |
|
s = t * c; |
| 891 |
|
a[i][j] = 0.0; |
| 892 |
|
for (k = 0; k <= i-1; k++) |
| 893 |
< |
{ |
| 893 |
> |
{ |
| 894 |
|
atemp = c * a[k][i] - s * a[k][j]; |
| 895 |
|
a[k][j] = s * a[k][i] + c * a[k][j]; |
| 896 |
|
a[k][i] = atemp; |
| 897 |
< |
} |
| 897 |
> |
} |
| 898 |
|
for (k = i+1; k <= j-1; k++) |
| 899 |
< |
{ |
| 899 |
> |
{ |
| 900 |
|
atemp = c * a[i][k] - s * a[k][j]; |
| 901 |
|
a[k][j] = s * a[i][k] + c * a[k][j]; |
| 902 |
|
a[i][k] = atemp; |
| 903 |
< |
} |
| 903 |
> |
} |
| 904 |
|
for (k = j+1; k < 3; k++) |
| 905 |
< |
{ |
| 905 |
> |
{ |
| 906 |
|
atemp = c * a[i][k] - s * a[j][k]; |
| 907 |
|
a[j][k] = s * a[i][k] + c * a[j][k]; |
| 908 |
|
a[i][k] = atemp; |
| 909 |
< |
} |
| 909 |
> |
} |
| 910 |
|
for (k = 0; k < 3; k++) |
| 911 |
< |
{ |
| 911 |
> |
{ |
| 912 |
|
vtemp = c * v[k][i] - s * v[k][j]; |
| 913 |
|
v[k][j] = s * v[k][i] + c * v[k][j]; |
| 914 |
|
v[k][i] = vtemp; |
| 915 |
< |
} |
| 915 |
> |
} |
| 916 |
|
dtemp = c*c*d[i] + s*s*d[j] - 2.0*c*s*b; |
| 917 |
|
d[j] = s*s*d[i] + c*c*d[j] + 2.0*c*s*b; |
| 918 |
|
d[i] = dtemp; |
| 919 |
< |
} /* end if */ |
| 920 |
< |
} /* end for i */ |
| 921 |
< |
} /* end for j */ |
| 922 |
< |
} /* end for l */ |
| 919 |
> |
} /* end if */ |
| 920 |
> |
} /* end for i */ |
| 921 |
> |
} /* end for j */ |
| 922 |
> |
} /* end for l */ |
| 923 |
|
|
| 924 |
< |
Exit_now: |
| 924 |
> |
Exit_now: |
| 925 |
|
|
| 926 |
|
/* max_sweeps = l;*/ |
| 927 |
|
|
| 928 |
|
for (j = 0; j < 3-1; j++) |
| 929 |
< |
{ |
| 929 |
> |
{ |
| 930 |
|
k = j; |
| 931 |
|
dtemp = d[k]; |
| 932 |
|
for (i = j+1; i < 3; i++) |
| 933 |
< |
if(d[i] < dtemp) |
| 933 |
> |
if(d[i] < dtemp) |
| 934 |
|
{ |
| 935 |
< |
k = i; |
| 936 |
< |
dtemp = d[k]; |
| 935 |
> |
k = i; |
| 936 |
> |
dtemp = d[k]; |
| 937 |
|
} |
| 938 |
|
|
| 939 |
|
if(k > j) |
| 940 |
< |
{ |
| 940 |
> |
{ |
| 941 |
|
d[k] = d[j]; |
| 942 |
|
d[j] = dtemp; |
| 943 |
|
for (i = 0; i < 3 ; i++) |
| 944 |
< |
{ |
| 944 |
> |
{ |
| 945 |
|
dtemp = v[i][k]; |
| 946 |
|
v[i][k] = v[i][j]; |
| 947 |
|
v[i][j] = dtemp; |
| 948 |
< |
} |
| 949 |
< |
} |
| 950 |
< |
} |
| 948 |
> |
} |
| 949 |
> |
} |
| 950 |
> |
} |
| 951 |
|
|
| 952 |
|
r1[0] = v[0][0]; |
| 953 |
|
r1[1] = v[1][0]; |
| 989 |
|
rmat[6] = v3[0]; |
| 990 |
|
rmat[7] = v3[1]; |
| 991 |
|
rmat[8] = v3[2]; |
| 992 |
< |
} |
| 992 |
> |
} |
| 993 |
|
|
| 994 |
< |
static int get_roots_3_3(double mat[3][3], double roots[3]) |
| 995 |
< |
{ |
| 994 |
> |
static int get_roots_3_3(double mat[3][3], double roots[3]) |
| 995 |
> |
{ |
| 996 |
|
double rmat[9]; |
| 997 |
|
|
| 998 |
|
ob_make_rmat(mat,rmat); |
| 1012 |
|
roots[2]=(double)Roots[2]; |
| 1013 |
|
|
| 1014 |
|
return 1; |
| 1015 |
< |
} |
| 1015 |
> |
} |
| 1016 |
|
|
| 1017 |
< |
OBAPI double superimpose(double *r,double *f,int size) |
| 1018 |
< |
{ |
| 1017 |
> |
OBAPI double superimpose(double *r,double *f,int size) |
| 1018 |
> |
{ |
| 1019 |
|
int i,j; |
| 1020 |
|
double x,y,z,d2; |
| 1021 |
|
double mat[3][3],rmat[3][3],mat2[3][3],roots[3]; |
| 1022 |
|
|
| 1023 |
|
/* make inertial cross tensor */ |
| 1024 |
|
for(i=0;i<3;i++) |
| 1025 |
< |
for(j=0;j<3;j++) |
| 1026 |
< |
mat[i][j]=0.0; |
| 1025 |
> |
for(j=0;j<3;j++) |
| 1026 |
> |
mat[i][j]=0.0; |
| 1027 |
|
|
| 1028 |
|
for(i=0;i < size;i++) |
| 1029 |
< |
{ |
| 1029 |
> |
{ |
| 1030 |
|
mat[0][0]+=r[3*i] *f[3*i]; |
| 1031 |
|
mat[1][0]+=r[3*i+1]*f[3*i]; |
| 1032 |
|
mat[2][0]+=r[3*i+2]*f[3*i]; |
| 1036 |
|
mat[0][2]+=r[3*i] *f[3*i+2]; |
| 1037 |
|
mat[1][2]+=r[3*i+1]*f[3*i+2]; |
| 1038 |
|
mat[2][2]+=r[3*i+2]*f[3*i+2]; |
| 1039 |
< |
} |
| 1039 |
> |
} |
| 1040 |
|
|
| 1041 |
|
d2=mat[0][0]*(mat[1][1]*mat[2][2]-mat[1][2]*mat[2][1]) |
| 1042 |
< |
-mat[0][1]*(mat[1][0]*mat[2][2]-mat[1][2]*mat[2][0]) |
| 1043 |
< |
+mat[0][2]*(mat[1][0]*mat[2][1]-mat[1][1]*mat[2][0]); |
| 1042 |
> |
-mat[0][1]*(mat[1][0]*mat[2][2]-mat[1][2]*mat[2][0]) |
| 1043 |
> |
+mat[0][2]*(mat[1][0]*mat[2][1]-mat[1][1]*mat[2][0]); |
| 1044 |
|
|
| 1045 |
|
|
| 1046 |
|
/* square matrix= ((mat transpose) * mat) */ |
| 1047 |
|
for(i=0;i<3;i++) |
| 1048 |
< |
for(j=0;j<3;j++) |
| 1048 |
> |
for(j=0;j<3;j++) |
| 1049 |
|
{ |
| 1050 |
< |
x=mat[0][i]*mat[0][j]+mat[1][i]*mat[1][j]+mat[2][i]*mat[2][j]; |
| 1051 |
< |
mat2[i][j]=mat[i][j]; |
| 1052 |
< |
rmat[i][j]=x; |
| 1050 |
> |
x=mat[0][i]*mat[0][j]+mat[1][i]*mat[1][j]+mat[2][i]*mat[2][j]; |
| 1051 |
> |
mat2[i][j]=mat[i][j]; |
| 1052 |
> |
rmat[i][j]=x; |
| 1053 |
|
} |
| 1054 |
|
get_roots_3_3(rmat,roots); |
| 1055 |
|
|
| 1064 |
|
roots[2]=roots[2]<0.0001? 0.0: 1.0/(double)sqrt(roots[2]); |
| 1065 |
|
|
| 1066 |
|
if(d2<0.0) |
| 1067 |
< |
{ |
| 1067 |
> |
{ |
| 1068 |
|
if( (roots[0]>=roots[1]) && (roots[0]>=roots[2]) ) |
| 1069 |
< |
roots[0]*=-1.0; |
| 1069 |
> |
roots[0]*=-1.0; |
| 1070 |
|
if( (roots[1]>roots[0]) && (roots[1]>=roots[2]) ) |
| 1071 |
< |
roots[1]*=-1.0; |
| 1071 |
> |
roots[1]*=-1.0; |
| 1072 |
|
if( (roots[2]>roots[1]) && (roots[2]>roots[0]) ) |
| 1073 |
< |
roots[2]*=-1.0; |
| 1074 |
< |
} |
| 1073 |
> |
roots[2]*=-1.0; |
| 1074 |
> |
} |
| 1075 |
|
|
| 1076 |
|
for(i=0;i<3;i++) |
| 1077 |
< |
for(j=0;j<3;j++) |
| 1078 |
< |
mat[i][j]=roots[0]*rmat[i][0]*rmat[j][0]+ |
| 1079 |
< |
roots[1]*rmat[i][1]*rmat[j][1]+ |
| 1080 |
< |
roots[2]*rmat[i][2]*rmat[j][2]; |
| 1077 |
> |
for(j=0;j<3;j++) |
| 1078 |
> |
mat[i][j]=roots[0]*rmat[i][0]*rmat[j][0]+ |
| 1079 |
> |
roots[1]*rmat[i][1]*rmat[j][1]+ |
| 1080 |
> |
roots[2]*rmat[i][2]*rmat[j][2]; |
| 1081 |
|
|
| 1082 |
|
/* and multiply into original inertial cross matrix, mat2 */ |
| 1083 |
|
for(i=0;i<3;i++) |
| 1084 |
< |
for(j=0;j<3;j++) |
| 1085 |
< |
rmat[i][j]=mat[0][j]*mat2[i][0]+ |
| 1086 |
< |
mat[1][j]*mat2[i][1]+ |
| 1087 |
< |
mat[2][j]*mat2[i][2]; |
| 1084 |
> |
for(j=0;j<3;j++) |
| 1085 |
> |
rmat[i][j]=mat[0][j]*mat2[i][0]+ |
| 1086 |
> |
mat[1][j]*mat2[i][1]+ |
| 1087 |
> |
mat[2][j]*mat2[i][2]; |
| 1088 |
|
|
| 1089 |
|
/* rotate all coordinates */ |
| 1090 |
|
d2 = 0.0; |
| 1091 |
|
for(i=0;i<size;i++) |
| 1092 |
< |
{ |
| 1092 |
> |
{ |
| 1093 |
|
x=f[3*i]*rmat[0][0]+f[3*i+1]*rmat[0][1]+f[3*i+2]*rmat[0][2]; |
| 1094 |
|
y=f[3*i]*rmat[1][0]+f[3*i+1]*rmat[1][1]+f[3*i+2]*rmat[1][2]; |
| 1095 |
|
z=f[3*i]*rmat[2][0]+f[3*i+1]*rmat[2][1]+f[3*i+2]*rmat[2][2]; |
| 1101 |
|
y = r[i*3+1] - f[i*3+1]; |
| 1102 |
|
z = r[i*3+2] - f[i*3+2]; |
| 1103 |
|
d2 += x*x+y*y+z*z; |
| 1104 |
< |
} |
| 1104 |
> |
} |
| 1105 |
|
|
| 1106 |
|
d2 /= (double) size; |
| 1107 |
|
|
| 1108 |
|
return((double)sqrt(d2)); |
| 1109 |
< |
} |
| 1109 |
> |
} |
| 1110 |
|
|
| 1111 |
< |
OBAPI void get_rmat(double *rvec,double *r,double *f,int size) |
| 1112 |
< |
{ |
| 1111 |
> |
OBAPI void get_rmat(double *rvec,double *r,double *f,int size) |
| 1112 |
> |
{ |
| 1113 |
|
int i,j; |
| 1114 |
|
double x,d2; |
| 1115 |
|
double mat[3][3],rmat[3][3],mat2[3][3],roots[3]; |
| 1116 |
|
|
| 1117 |
|
/* make inertial cross tensor */ |
| 1118 |
|
for(i=0;i<3;i++) |
| 1119 |
< |
for(j=0;j<3;j++) |
| 1120 |
< |
mat[i][j]=0.0; |
| 1119 |
> |
for(j=0;j<3;j++) |
| 1120 |
> |
mat[i][j]=0.0; |
| 1121 |
|
|
| 1122 |
|
for(i=0;i < size;i++) |
| 1123 |
< |
{ |
| 1123 |
> |
{ |
| 1124 |
|
mat[0][0]+=r[3*i] *f[3*i]; |
| 1125 |
|
mat[1][0]+=r[3*i+1]*f[3*i]; |
| 1126 |
|
mat[2][0]+=r[3*i+2]*f[3*i]; |
| 1130 |
|
mat[0][2]+=r[3*i] *f[3*i+2]; |
| 1131 |
|
mat[1][2]+=r[3*i+1]*f[3*i+2]; |
| 1132 |
|
mat[2][2]+=r[3*i+2]*f[3*i+2]; |
| 1133 |
< |
} |
| 1133 |
> |
} |
| 1134 |
|
|
| 1135 |
|
d2=mat[0][0]*(mat[1][1]*mat[2][2]-mat[1][2]*mat[2][1]) |
| 1136 |
< |
-mat[0][1]*(mat[1][0]*mat[2][2]-mat[1][2]*mat[2][0]) |
| 1137 |
< |
+mat[0][2]*(mat[1][0]*mat[2][1]-mat[1][1]*mat[2][0]); |
| 1136 |
> |
-mat[0][1]*(mat[1][0]*mat[2][2]-mat[1][2]*mat[2][0]) |
| 1137 |
> |
+mat[0][2]*(mat[1][0]*mat[2][1]-mat[1][1]*mat[2][0]); |
| 1138 |
|
|
| 1139 |
|
/* square matrix= ((mat transpose) * mat) */ |
| 1140 |
|
for(i=0;i<3;i++) |
| 1141 |
< |
for(j=0;j<3;j++) |
| 1141 |
> |
for(j=0;j<3;j++) |
| 1142 |
|
{ |
| 1143 |
< |
x=mat[0][i]*mat[0][j]+mat[1][i]*mat[1][j]+mat[2][i]*mat[2][j]; |
| 1144 |
< |
mat2[i][j]=mat[i][j]; |
| 1145 |
< |
rmat[i][j]=x; |
| 1143 |
> |
x=mat[0][i]*mat[0][j]+mat[1][i]*mat[1][j]+mat[2][i]*mat[2][j]; |
| 1144 |
> |
mat2[i][j]=mat[i][j]; |
| 1145 |
> |
rmat[i][j]=x; |
| 1146 |
|
} |
| 1147 |
|
get_roots_3_3(rmat,roots); |
| 1148 |
|
|
| 1157 |
|
roots[2]=(roots[2]<0.0001) ? 0.0: 1.0/(double)sqrt(roots[2]); |
| 1158 |
|
|
| 1159 |
|
if(d2<0.0) |
| 1160 |
< |
{ |
| 1160 |
> |
{ |
| 1161 |
|
if( (roots[0]>=roots[1]) && (roots[0]>=roots[2]) ) |
| 1162 |
< |
roots[0]*=-1.0; |
| 1162 |
> |
roots[0]*=-1.0; |
| 1163 |
|
if( (roots[1]>roots[0]) && (roots[1]>=roots[2]) ) |
| 1164 |
< |
roots[1]*=-1.0; |
| 1164 |
> |
roots[1]*=-1.0; |
| 1165 |
|
if( (roots[2]>roots[1]) && (roots[2]>roots[0]) ) |
| 1166 |
< |
roots[2]*=-1.0; |
| 1167 |
< |
} |
| 1166 |
> |
roots[2]*=-1.0; |
| 1167 |
> |
} |
| 1168 |
|
|
| 1169 |
|
for(i=0;i<3;i++) |
| 1170 |
< |
for(j=0;j<3;j++) |
| 1171 |
< |
mat[i][j]=roots[0]*rmat[i][0]*rmat[j][0]+ |
| 1172 |
< |
roots[1]*rmat[i][1]*rmat[j][1]+ |
| 1173 |
< |
roots[2]*rmat[i][2]*rmat[j][2]; |
| 1170 |
> |
for(j=0;j<3;j++) |
| 1171 |
> |
mat[i][j]=roots[0]*rmat[i][0]*rmat[j][0]+ |
| 1172 |
> |
roots[1]*rmat[i][1]*rmat[j][1]+ |
| 1173 |
> |
roots[2]*rmat[i][2]*rmat[j][2]; |
| 1174 |
|
|
| 1175 |
|
/* and multiply into original inertial cross matrix, mat2 */ |
| 1176 |
|
for(i=0;i<3;i++) |
| 1177 |
< |
for(j=0;j<3;j++) |
| 1178 |
< |
rmat[i][j]=mat[0][j]*mat2[i][0]+ |
| 1179 |
< |
mat[1][j]*mat2[i][1]+ |
| 1180 |
< |
mat[2][j]*mat2[i][2]; |
| 1177 |
> |
for(j=0;j<3;j++) |
| 1178 |
> |
rmat[i][j]=mat[0][j]*mat2[i][0]+ |
| 1179 |
> |
mat[1][j]*mat2[i][1]+ |
| 1180 |
> |
mat[2][j]*mat2[i][2]; |
| 1181 |
|
|
| 1182 |
|
rvec[0] = rmat[0][0]; |
| 1183 |
|
rvec[1] = rmat[0][1]; |
| 1188 |
|
rvec[6] = rmat[2][0]; |
| 1189 |
|
rvec[7] = rmat[2][1]; |
| 1190 |
|
rvec[8] = rmat[2][2]; |
| 1191 |
< |
} |
| 1191 |
> |
} |
| 1192 |
|
|
| 1193 |
|
} // end namespace OpenBabel |
| 1194 |
|
|
