MTK++ Latest version: 0.2.0

Classes | Typedefs | Functions | Variables
MTKpp Namespace Reference

MTK++ namespace. More...

Classes

class  MTKException
class  gaAverage
 Performs chromosome averaging. More...
class  gaChromosome
 Container for gaGenes. More...
class  gaCrossOver
 Performs recombination of gaChromosomes. More...
class  gaGaussian
 Contains gaussian information used by gaSelection. More...
class  gaGene
 Class to handle genes. More...
class  gaIndividual
 Container for gaChromosomes. More...
class  gaMutate
 Performs mutation of gaChromosomes. More...
class  gaOperators
 This class performs the GA operations including crossover, mutation, averaging, etc. More...
class  gaOutput
 Class to handle the GA output. More...
class  gaPopulation
 Container for gaIndividuals. More...
class  gaRegion
 Container for gaPopulations. More...
class  gaSelection
 Selects gaIndividuals from gaPopulation based on fitness. More...
class  gaWorld
 Container for gaRegions. More...
struct  edge
 Container for edge info. More...
class  graph
 Container for graphs. More...
class  vertex
 Container for vertex info. More...
class  error
 Error object used in errorHandler. More...
class  errorHandler
 Error Handling within MTK++. More...
class  amber
 AMBER MM potentials. More...
class  amberAngle
 AMBER angle energy and gradient. More...
class  amberBond
 AMBER bond energy and gradient. More...
class  amberImproper
 AMBER improper energy and gradient. More...
class  amberNonBonded
 AMBER non-bonded energy and gradient. More...
class  amberTorsion
 AMBER torsion energy and gradient. More...
class  mmPotential
 Base class for MM potentials. More...
struct  Angle
 Container for Angle info. More...
class  atom
 Container for atom info. More...
struct  atomTypeTMP
class  atomTypes
class  atomTyper
struct  Bond
 Container for Bond info. More...
class  collection
 Container for molecules. More...
class  complex
 complex More...
struct  conformer
 Container for conformer info. More...
class  conformers
 This class creates and operators on conformers, however, the conformers are stored in molecule. More...
class  connections
 Class to assign bonds, angles, torsion and improper. More...
struct  element
 element information More...
class  elements
 Container for element information. More...
class  fingerPrint
 Generates very simple molecular fingerprints. More...
struct  funcGroup
 Container for functional group info. More...
class  functionalize
 Determines functional groups in molecules using predefined fragments. More...
class  hybridize
 Determines hybridizations of atoms in a molecule. More...
struct  hydrophobe
 Container for hydrophobic group info. More...
class  hydrophobize
 Determines the hydrophobic groups in a molecule. More...
struct  Improper
 Container for Improper info. More...
class  ligProtonate
 Class to add hydrogens to small molecules. More...
class  metalCenter
 Container for metal centers. More...
class  metalGroup
 Container for metal centers. More...
class  molecule
 Container for submolecules, bonds, angles, torsions, and impropers. More...
struct  atomType
struct  bondParam
struct  angleParam
struct  torsionParam
struct  improperParam
struct  hBondParam
struct  equivalentAtomsParam
struct  LJ612SE
class  parameters
struct  clique
 Container for clique info. More...
class  pharmacophore
 Determines the Maximum Common Pharmacophore (MCP) between two molecules. More...
class  proProtonate
 Class to add hydrogens to proteins. More...
class  protonate
 Class to add hydrogens. More...
struct  ring
 Container for ring info. More...
class  rings
 Determines rings in a molecule. More...
class  selection
 Allows for the selection of certain parts of the collection. More...
class  seqAlign
 Sequence Alignment. More...
struct  stdAtom
 Container for standard atom info. More...
struct  stdBond
 Container for standard bond info. More...
struct  stdImproper
 Container for standard improper info. More...
struct  stdLoop
 Container for standard loop info. More...
struct  stdAlias
 Container for standard alias info. More...
struct  stdRing
 Container for standard ring info. More...
struct  stdFeature
 Container for standard feature info. More...
struct  stdFuncGroup
 Container for standard functional group. More...
struct  stdConnTorsion
 Container for standard connection torsions. More...
struct  stdRotBond
 Container for standard rotatable bonds. More...
class  stdFrag
 Container for stdAtoms, stdBond, stdImpropers, stdLoops, stdAlias'. More...
class  stdGroup
class  stdLibrary
class  submolecule
 Container for atoms and bonds. More...
class  superimpose
 Functions to align molecules. More...
struct  Torsion
 Container for Torsion info. More...
class  watProtonate
 Class to add hydrogens to water molecules. More...
class  acParser
 Reads and writes AMBER antechamber format files. More...
class  amberParser
 Reads and writes amber prmtop/crd files. More...
class  atomTypeParser
 Parses atom type xml files using xercesc. More...
struct  AtomLine
 Temporary container for atom info. More...
class  baseParser
 base class to all parsers More...
class  dcParser
 Reads divcon output files and write divcon input files. More...
class  dMParser
 sheet/table parser More...
class  elementParser
 Reads element xml file. More...
class  frcmodParser
 Reads and writes AMBER frcmod format files. More...
class  gaParser
 Reads GA xml files. More...
class  gaussianParser
 Reads and writes gaussian format files. More...
class  mol2Parser
 Reads and writes MOL2 format files. More...
class  molParser
 Reads and writes MOL format files. More...
class  mtkppParser
 Reads and writes MTK++ State xml files. More...
class  pamParser
 Reads pam format files. More...
class  paramParser
 Reads parameter xml files. More...
class  parsingException
struct  pdbInfo
 Container for PDB info. More...
class  pdbParser
 Reads and writes PDB format files. More...
class  prepParser
 Reads and writes AMBER prep format files. More...
class  sdfParser
 Reads and writes SDF format files. More...
class  stdLibParser
class  xyzParser
 Reads and writes XYZ format files. More...
class  zmatParser
 Reads and writes z-matrix format files. More...
class  BaseStats
 Base class for statistical routines. More...
class  ols
 Ordinary Least Squares. More...
class  pca
 Principal Component Analysis. More...
class  pls
 Partial Least Squares. More...
class  sheet
class  table
 Extension of eigen::matrix to store labels. More...
class  DivConInterface
 A class to interface with DivCon. More...
class  idObject
class  idObjectList
class  object
 Base object to enforce a virtual destructor. More...
class  vector3d
 A 3-dimensional vector class. More...

Typedefs

typedef boost::shared_ptr< objectobject_ptr

Functions

void setSeed (int seed)
 Set Random Number Generation Seed.
double ranNumBetweenZeroAndOne ()
 Returns a random number (double) between 0 and 1.
double ranNumBetweenZeroAndX (int X)
 Returns a random number (double) between 0 and X.
void lbfgs_ (int *n, int *m, double *x, double *f, double *g, int *diagco, double *diag, int *iprint, double *eps, double *xtol, double *w, int *iflag)
void lb1_ (int *iprint, int *iter, int *nfun, double *gnorm, int *n, int *m, double *x, double *f, double *g, double *stp, int *finish)
void daxpy_ (int *n, double *da, double *dx, int *incx, double *dy, int *incy)
double ddot_ (int *n, double *dx, int *incx, double *dy, int *incy)
void mcsrch_ (int *n, double *x, double *f, double *g, double *s, double *stp, double *ftol, double *xtol, int *maxfev, int *info, int *nfev, double *wa)
void mcstep_ (double *stx, double *fx, double *dx, double *sty, double *fy, double *dy, double *stp, double *fp, double *dp, int *brackt, double *stpmin, double *stpmax, int *info)
std::string i2s (int i)
std::string d2s (double d)
int readInputFile (std::string inputFile, std::vector< std::vector< std::string > > &inputFileContents)
 Read generic input file.
int readListFile (std::string listFile, std::vector< std::string > &listFileContents)
 Read generic list file.
void splitString (std::string &s, const std::string s2, std::vector< std::string > &v, int i)
 Splits string.
std::string stripString (std::string const &str, char const *sepSet)
 Returns a string with leading/trailing characters of a set stripped.
std::string removeCharacter (const std::string &s, const char &c)
 Remove character from string.
std::string replaceCharacter (const std::string &s, const char &c, const char &n)
 Replace character in string.
std::string addCharacter (const std::string &s, char c, int i)
 Add character to the string.
bool FieldExists (std::string &s, int i, int j)
 A check to see if a file field exist or not.
std::string GetAlphaChar (std::string &s, int i)
 Get the first alpha character in the string.
std::string int2String (int i)
 Convert an int to a string.
std::string uLongKind2String (ULONG_KIND i)
 Convert an int to a string.
unsigned int string2UInt (std::string s)
 Convert a string to an unsigned integer.
int string2Int (std::string s)
 Convert a string to an integer.
std::string double2String (double d)
 Convert a double to a string.
std::string double2String (double d, int precision)
 Convert a double to a string.
double string2Double (std::string s)
 Convert a string to a double.
std::string toUpper (std::string s)
 Converts to upper case.
std::string toLower (std::string s)
 Converts to lower case.
std::string baseName (std::string name)
 Returns a base of the string, e.g "asdf" gets returned from "asdf.mol".
std::string extName (std::string e)
 Returns a file extension, e.g "mol" gets returned from "asdf.mol".
bool fileExists (const std::string &fileName)
 Returns a boolean if a file exists or not.
bool containsSubStr (const std::string &s, const std::string &ss)
 Returns a boolean if a string contains a certain sub-string.
std::string replaceSubStr (const std::string &s1, const std::string &s2, const std::string &s3)
 Replace part of string with another string.
void copyright (std::ostream &os)
int diagonalize (ublas::matrix< double, ublas::column_major > &eigenvectors, ublas::vector< double > &eigenvalues)
 Diagonalize a matrix.
int svd (ublas::matrix< double, ublas::column_major > &H, ublas::vector< double > &s, ublas::matrix< double, ublas::column_major > &U, ublas::matrix< double, ublas::column_major > &VT)
 Singular Value Decomposition (SVD)
void eigenValueSort (ublas::matrix< double, ublas::column_major > &eigenvectors, ublas::vector< double > &eigenvalues, int order)
 Sorts eigenvalues and applies this ordering on the eigenvector matrix.
void eigenValueSort (MatrixXd &eigenvectors, VectorXd &eigenvalues, int order)
 Sorts eigenvalues and applies this ordering on the eigenvector matrix.
int index2dTo1d (int i, int j)
int indexAB (int a, int b, unsigned int Nb)
int indexABC (int a, int b, int c, unsigned int Nb, unsigned int Nc)
ULONG_KIND indexABC_ULL (int a, int b, int c, unsigned int Nb, unsigned int Nc)
int indexABCD (int a, int b, int c, int d, unsigned int Nb, unsigned int Nc, unsigned int Nd)
ULONG_KIND indexABCD_ULL (int a, int b, int c, int d, unsigned int Nb, unsigned int Nc, unsigned int Nd)
int indexABCDb (int a, int b, int c, int d, unsigned int Nb, unsigned int Nc, unsigned int Nd)
void printHeader (std::ostream &os, std::string prog_name, std::vector< std::string > authors)
 Print MTK++ and Program Headers.
void setRandomNumberSeed (int seed)
 Set Random Number Generation Seed.
double randomDoubleBetweenZeroAndOne ()
 Returns a random number (double) between 0 and 1.
double randomDoubleBetweenZeroAndX (int X)
 Returns a random number (double) between 0 and X.
int randomIntegerBetweenZeroAndX (int X)
 Returns a random number (double) between 0 and X.

Variables

errorHandler errorLogger
 Error Logger.
static int c__1 = 1
parametersParameters = NULL
stdLibraryStdLibrary = NULL
const unsigned int MAXATOMS = 1000
 Maximum number of atoms.
const double BIGNUM = 1.e12
 Very Large Number.
const double APPROXZERO = 1.e-6
 Very Large Number.
const double PI = 3.14159265359
 PI.
const double PIt2 = PI * 2
 (PI)^2
const double INVPI = 1.0/PI
 (PI)^3/2
const double RAD2DEG = 180.0/PI
 Radian to Degree.
const double DEG2RAD = 1.0/RAD2DEG
 Degree to Radian.
const double ANG2BOHR = 0.529177249
 Angstrom to Bohr.
const double BOHR2ANG = 1.0/ANG2BOHR
 Bohr to Angstrom.
const double H2KCALMOL = 627.5095
 Hartree to kcal/mol.
const double E2KCAL = 18.2223
 electron to kcal
const double HB2TOKCALMOLA2 = H2KCALMOL*BOHR2ANG*BOHR2ANG
 Hartree/Bohr^2 to kcal/mol A^2.
const double BONDTOLERANCE = 0.4
 definition of a bond, covRadius1 + covRadius + tolerance Bond Types and Hybridization, J. Comp. Chem. 12, 891-898, 1991
const double SP2ANGLE = 115.0
 sp2 versus sp3 angle cutoff
const double SPANGLE = 160.0
 sp versus sp2 angle cutoff
const double AMBIGUOUSANGLE = 122.0
 Angle below which the type of an atom with 2 heavy bonded atom should be reconsidered.
const int MESSAGE = 0
 Generic message type.
const int MTK_ERROR = 1
 Error message tyoe.
const int WARNING = 2
 Warning message type.
const int mDEBUG = 3
 Debug message type.
const int INFO = 4
 Info message type.

Detailed Description

MTK++ namespace.


Typedef Documentation

typedef boost::shared_ptr< object > MTKpp::object_ptr

Function Documentation

void MTKpp::setSeed ( int  seed) [inline]

Set Random Number Generation Seed.

double MTKpp::ranNumBetweenZeroAndOne ( ) [inline]
double MTKpp::ranNumBetweenZeroAndX ( int  X) [inline]

Returns a random number (double) between 0 and X.

References ranNumBetweenZeroAndOne(), and X.

Referenced by MTKpp::gaSelection::__random(), MTKpp::gaGene::initialize(), MTKpp::gaPopulation::initialize(), and MTKpp::gaGene::mutate().

void MTKpp::lbfgs_ ( int *  n,
int *  m,
double *  x,
double *  f,
double *  g,
int *  diagco,
double *  diag,
int *  iprint,
double *  eps,
double *  xtol,
double *  w,
int *  iflag 
)

References c__1, daxpy_(), ddot_(), lb1_(), and mcsrch_().

Referenced by main().

void MTKpp::lb1_ ( int *  iprint,
int *  iter,
int *  nfun,
double *  gnorm,
int *  n,
int *  m,
double *  x,
double *  f,
double *  g,
double *  stp,
int *  finish 
)

Referenced by lbfgs_().

void MTKpp::daxpy_ ( int *  n,
double *  da,
double *  dx,
int *  incx,
double *  dy,
int *  incy 
)

Referenced by lbfgs_().

double MTKpp::ddot_ ( int *  n,
double *  dx,
int *  incx,
double *  dy,
int *  incy 
)

Referenced by lbfgs_().

void MTKpp::mcsrch_ ( int *  n,
double *  x,
double *  f,
double *  g,
double *  s,
double *  stp,
double *  ftol,
double *  xtol,
int *  maxfev,
int *  info,
int *  nfev,
double *  wa 
)

References mcstep_().

Referenced by lbfgs_().

void MTKpp::mcstep_ ( double *  stx,
double *  fx,
double *  dx,
double *  sty,
double *  fy,
double *  dy,
double *  stp,
double *  fp,
double *  dp,
int *  brackt,
double *  stpmin,
double *  stpmax,
int *  info 
)

Referenced by mcsrch_().

std::string MTKpp::i2s ( int  i) [inline]
std::string MTKpp::d2s ( double  d) [inline]
int MTKpp::readInputFile ( std::string  inputFile,
std::vector< std::vector< std::string > > &  inputFileContents 
) [inline]

Read generic input file.

Parameters:
inputFile
inputFileContentslist of options from file

example:

    # Read a PDB file
    readPdb file.pdb
    addHs /col/mol # Add Hydrogen atoms
    # Write out MOL file
    writeMol file.mol
Returns:
success

References errorLogger, INFO, MTK_ERROR, splitString(), stripString(), and MTKpp::errorHandler::throwError().

Referenced by main().

int MTKpp::readListFile ( std::string  listFile,
std::vector< std::string > &  listFileContents 
) [inline]

Read generic list file.

Parameters:
listFile
listFileContentslist file
Returns:
success

Referenced by main().

void MTKpp::splitString ( std::string &  s,
const std::string  s2,
std::vector< std::string > &  v,
int  i 
)
std::string MTKpp::stripString ( std::string const &  str,
char const *  sepSet 
)

Returns a string with leading/trailing characters of a set stripped.

Parameters:
strstring to work on
sepSetseparator
Returns:
string

Referenced by main(), MTKpp::frcmodParser::Read(), MTKpp::pdbParser::Read(), MTKpp::dcParser::Read(), MTKpp::prepParser::readFragment(), MTKpp::prepParser::readHeader(), and readInputFile().

std::string MTKpp::removeCharacter ( const std::string &  s,
const char &  c 
)

Remove character from string.

Parameters:
sstring to work on
ccharacter to remove
Returns:
new string

Referenced by MTKpp::baseParser::determineElement(), MTKpp::molParser::ReadAtomLine(), MTKpp::mol2Parser::ReadAtomLine(), and MTKpp::sdfParser::ReadAtomLine().

std::string MTKpp::replaceCharacter ( const std::string &  s,
const char &  c,
const char &  n 
)

Replace character in string.

Parameters:
sstring to work on
ccharacter to be replaced
nnew character
Returns:
new string

Referenced by main(), and MTKpp::gaussianParser::Read().

std::string MTKpp::addCharacter ( const std::string &  s,
char  c,
int  i 
)

Add character to the string.

Parameters:
sstring to work on
ccharacter to add
inumber of times to add
Returns:
new string
bool MTKpp::FieldExists ( std::string &  s,
int  i,
int  j 
)

A check to see if a file field exist or not.

Parameters:
sstring to check
istart point
jend point
Returns:
boolean yes/no

Referenced by MTKpp::molParser::ReadAtomLine(), and MTKpp::sdfParser::ReadAtomLine().

std::string MTKpp::GetAlphaChar ( std::string &  s,
int  i 
)

Get the first alpha character in the string.

Parameters:
sstring to check
istart point
Returns:
an alphabetic letter in a string at position number.

Referenced by MTKpp::baseParser::determineElement(), and MTKpp::mol2Parser::ReadAtomLine().

std::string MTKpp::int2String ( int  i)

Convert an int to a string.

Parameters:
iint to be converted
Returns:
string

Referenced by MTKpp::gaussianParser::getForceConstantZMAT(), main(), and MTKpp::pdbParser::Read().

std::string MTKpp::uLongKind2String ( ULONG_KIND  i)

Convert an int to a string.

Parameters:
iint to be converted
Returns:
string
unsigned int MTKpp::string2UInt ( std::string  s)

Convert a string to an unsigned integer.

Parameters:
sstring to be converted
Returns:
unsigned int

Referenced by MTKpp::sdfParser::Read().

int MTKpp::string2Int ( std::string  s)

Convert a string to an integer.

Parameters:
sstring to be converted
Returns:
int

Referenced by main(), and MTKpp::frcmodParser::Read().

std::string MTKpp::double2String ( double  d)

Convert a double to a string.

Parameters:
dDouble to be converted
Returns:
string

Referenced by MTKpp::gaussianParser::getForceConstantZMAT(), main(), and MTKpp::dcParser::Read().

std::string MTKpp::double2String ( double  d,
int  precision 
)

Convert a double to a string.

Parameters:
dDouble to be converted
precisionNumber precision
Returns:
string
double MTKpp::string2Double ( std::string  s)

Convert a string to a double.

Parameters:
sstring to be converted
Returns:
double

Referenced by main(), MTKpp::pamParser::Read(), MTKpp::frcmodParser::Read(), MTKpp::gaussianParser::Read(), MTKpp::pdbParser::Read(), and MTKpp::prepParser::readHeader().

std::string MTKpp::toUpper ( std::string  s)

Converts to upper case.

Parameters:
sstring to convert
Returns:
string

Referenced by main().

std::string MTKpp::toLower ( std::string  s)

Converts to lower case.

Parameters:
sstring to convert
Returns:
string

Referenced by MTKpp::pdbParser::Read().

std::string MTKpp::baseName ( std::string  name)

Returns a base of the string, e.g "asdf" gets returned from "asdf.mol".

Parameters:
namestring to check
Returns:
string

Referenced by main(), MTKpp::dcParser::Read(), and MTKpp::dcParser::Write().

std::string MTKpp::extName ( std::string  e)

Returns a file extension, e.g "mol" gets returned from "asdf.mol".

Parameters:
estring to check
Returns:
string

Referenced by main().

bool MTKpp::fileExists ( const std::string &  fileName)

Returns a boolean if a file exists or not.

Parameters:
fileNamefile name
Returns:
boolean

Referenced by main().

bool MTKpp::containsSubStr ( const std::string &  s,
const std::string &  ss 
)

Returns a boolean if a string contains a certain sub-string.

Parameters:
smain string
sssub-string
Returns:
boolean

Referenced by main(), MTKpp::gaussianParser::Read(), and MTKpp::prepParser::readFragment().

std::string MTKpp::replaceSubStr ( const std::string &  s1,
const std::string &  s2,
const std::string &  s3 
)

Replace part of string with another string.

Parameters:
s1main string
s2sub-string to be replaced
s3string that will be entered into the new string
Returns:
new string

Referenced by main().

void MTKpp::copyright ( std::ostream &  os)
int MTKpp::diagonalize ( ublas::matrix< double, ublas::column_major > &  eigenvectors,
ublas::vector< double > &  eigenvalues 
) [inline]

Diagonalize a matrix.

Diag(S): Diagonalizing S involves finding U such that: transpose(U) * S * U = D where D is the diagonal matrix containig the eigenvalues, and U is the eigenvector matrix.

Parameters:
eigenvectorsMatrix to be diagonalized, it is destroyed, returned containing the eigenvectors
eigenvaluesVector of resulting eigenvalues
Returns:
success

Referenced by main().

int MTKpp::svd ( ublas::matrix< double, ublas::column_major > &  H,
ublas::vector< double > &  s,
ublas::matrix< double, ublas::column_major > &  U,
ublas::matrix< double, ublas::column_major > &  VT 
) [inline]

Singular Value Decomposition (SVD)

From boost documentation gesvd --> simple driver gesdd --> divide and conquer driver

gesvd/gesdd computes the singular value decomposition (SVD) of M-by-N matrix A, optionally computing the left and/or right singular vectors. The SVD is written

A = U * S * V^T or A = U * S * V^H

where S is an M-by-N matrix which is zero except for its min(m,n) diagonal elements, U is an M-by-M orthogonal/unitary matrix, and V is an N-by-N orthogonal/unitary matrix. The diagonal elements of S are the singular values of A; they are real and non-negative, and are returned in descending order. The first min(m,n) columns of U and V are the left and right singular vectors of A. (Note that the routine returns V^T or V^H, not V.

A_nxp = U_nxn S_nxp V^T_pxp

Other links http://en.wikipedia.org/wiki/Singular_value_decomposition http://www.netlib.org/lapack/lug/node32.html

Returns:
success
void MTKpp::eigenValueSort ( ublas::matrix< double, ublas::column_major > &  eigenvectors,
ublas::vector< double > &  eigenvalues,
int  order 
) [inline]

Sorts eigenvalues and applies this ordering on the eigenvector matrix.

Parameters:
eigenvectorsEigenvector matrix
eigenvaluesEigenvalue matrix
orderAscending = 0, Desending = 1

Referenced by MTKpp::superimpose::fit(), MTKpp::gaussianParser::getForceConstant(), MTKpp::rings::getPlaneNormal(), MTKpp::superimpose::getRotationMatrix(), main(), and MTKpp::pca::run().

void MTKpp::eigenValueSort ( MatrixXd &  eigenvectors,
VectorXd &  eigenvalues,
int  order 
) [inline]

Sorts eigenvalues and applies this ordering on the eigenvector matrix.

Parameters:
eigenvectorsEigenvector matrix
eigenvaluesEigenvalue matrix
orderAscending = 0, Desending = 1
int MTKpp::index2dTo1d ( int  i,
int  j 
) [inline]
int MTKpp::indexAB ( int  a,
int  b,
unsigned int  Nb 
) [inline]
int MTKpp::indexABC ( int  a,
int  b,
int  c,
unsigned int  Nb,
unsigned int  Nc 
) [inline]
ULONG_KIND MTKpp::indexABC_ULL ( int  a,
int  b,
int  c,
unsigned int  Nb,
unsigned int  Nc 
) [inline]
int MTKpp::indexABCD ( int  a,
int  b,
int  c,
int  d,
unsigned int  Nb,
unsigned int  Nc,
unsigned int  Nd 
) [inline]
ULONG_KIND MTKpp::indexABCD_ULL ( int  a,
int  b,
int  c,
int  d,
unsigned int  Nb,
unsigned int  Nc,
unsigned int  Nd 
) [inline]
int MTKpp::indexABCDb ( int  a,
int  b,
int  c,
int  d,
unsigned int  Nb,
unsigned int  Nc,
unsigned int  Nd 
) [inline]
void MTKpp::printHeader ( std::ostream &  os,
std::string  prog_name,
std::vector< std::string >  authors 
)

Print MTK++ and Program Headers.

References copyright().

Referenced by main().

void MTKpp::setRandomNumberSeed ( int  seed) [inline]

Set Random Number Generation Seed.

Referenced by MTKpp::pls::setSEED().

double MTKpp::randomDoubleBetweenZeroAndOne ( ) [inline]

Returns a random number (double) between 0 and 1.

Referenced by randomDoubleBetweenZeroAndX().

double MTKpp::randomDoubleBetweenZeroAndX ( int  X) [inline]

Returns a random number (double) between 0 and X.

References randomDoubleBetweenZeroAndOne(), and X.

Referenced by randomIntegerBetweenZeroAndX().

int MTKpp::randomIntegerBetweenZeroAndX ( int  X) [inline]

Returns a random number (double) between 0 and X.

References randomDoubleBetweenZeroAndX().

Referenced by MTKpp::pls::runCV().


Variable Documentation

Error Logger.

error logger global variable

Referenced by MTKpp::submolecule::addAtom(), MTKpp::molecule::addBond(), MTKpp::molecule::addFunctionalGroup(), MTKpp::proProtonate::addHydrogens(), MTKpp::ligProtonate::addHydrogens(), MTKpp::molecule::addHydrogens(), MTKpp::molecule::addRing(), MTKpp::connections::assignAngles(), MTKpp::connections::assignBonds(), MTKpp::connections::assignDisulfideBonds(), MTKpp::connections::assignImpropers(), MTKpp::collection::assignMetalParameters(), MTKpp::collection::assignMetalPartners(), MTKpp::connections::assignStd(), MTKpp::connections::assignStdAngles(), MTKpp::connections::assignStdBonds(), MTKpp::connections::assignStdBondsAngles(), MTKpp::atomTyper::assignStdFunctionalGroups(), MTKpp::atomTyper::assignStdHydrophobicGroups(), MTKpp::atomTyper::assignStdRings(), MTKpp::connections::assignStdTorsions(), MTKpp::connections::assignTorsions(), MTKpp::atomTyper::atomTypeByLib(), MTKpp::connections::bondByLibrary(), MTKpp::connections::BondExists(), MTKpp::proProtonate::buildDummyAtoms(), MTKpp::proProtonate::buildMissingAtoms(), MTKpp::protonate::buildMissingHeavyAtoms(), MTKpp::mmPotential::calcEnergy(), MTKpp::molecule::delAtom(), MTKpp::molecule::delFunctionalGroup(), MTKpp::rings::determine(), MTKpp::collection::determineMetalEnvironments(), MTKpp::molecule::determineValences(), MTKpp::collection::findMetals(), MTKpp::fingerPrint::generate1DFP(), MTKpp::molecule::generateAdjMatrix(), MTKpp::stdFrag::generateCoordinates(), MTKpp::molecule::generateFeatureDistMatrix(), MTKpp::fingerPrint::generateFragmentFP(), MTKpp::molecule::generateHeavyAdjMatrix(), MTKpp::fingerPrint::generateSimpleFP(), MTKpp::pdbParser::get1LCode(), MTKpp::molecule::getAngleParams(), MTKpp::molecule::getAngles(), MTKpp::molecule::getAtomKinds(), MTKpp::molecule::getAtomSymbols(), MTKpp::molecule::getAtomTypes(), MTKpp::proProtonate::getBestTorsions(), MTKpp::molecule::getBond(), MTKpp::molecule::getBondParams(), MTKpp::molecule::getBonds(), MTKpp::molecule::getCoordinates(), MTKpp::gaussianParser::getForceConstantZMAT(), MTKpp::molecule::getHeavyAtomIndices(), MTKpp::molecule::getHeavyAtomSymbols(), MTKpp::molecule::getHeavyAtomTypes(), MTKpp::molecule::getImpropers(), MTKpp::stdLibrary::getL(), MTKpp::complex::getLigFlags(), MTKpp::collection::getLJParams(), MTKpp::molecule::getMMCharges(), MTKpp::molecule::getMMImpropers(), MTKpp::collection::getMMnonBondedPairs(), MTKpp::molecule::getMMnonBondedPairs(), MTKpp::molecule::getMMResidues(), MTKpp::molecule::getMMTorsions(), MTKpp::collection::getNumExcluded14Atoms(), MTKpp::collection::getNumExcludedAtoms(), MTKpp::molecule::getNumMMImpropers(), MTKpp::collection::getNumMMnonBondedPairs(), MTKpp::molecule::getNumMMTorsions(), MTKpp::collection::getParameters(), MTKpp::rings::getPlaneNormal(), MTKpp::complex::getRecFlags(), MTKpp::molecule::getRotatableBonds(), MTKpp::molecule::getTorsions(), MTKpp::collection::hasMetal(), MTKpp::protonate::initialize(), MTKpp::superimpose::initializeCorrespondences(), MTKpp::seqAlign::initMatchMatrix(), MTKpp::rings::kekulize(), MTKpp::molecule::kekulizeRings(), main(), MTKpp::prepParser::openFile(), MTKpp::protonate::optimizePolarHs(), MTKpp::proProtonate::optimizePolarHs(), MTKpp::paramParser::paramParser(), MTKpp::selection::parse(), MTKpp::pdbParser::pdbParser(), MTKpp::atomTyper::perceiveCysteines(), MTKpp::atomTyper::perceiveHistidines(), MTKpp::seqAlign::printPAM(), MTKpp::seqAlign::printResults(), MTKpp::pamParser::Read(), MTKpp::pdbParser::Read(), MTKpp::prepParser::Read(), MTKpp::prepParser::readFragment(), readInputFile(), MTKpp::hybridize::readParameters(), MTKpp::molecule::removeHydrogens(), MTKpp::watProtonate::run(), MTKpp::seqAlign::run(), MTKpp::pca::run(), MTKpp::connections::run(), MTKpp::functionalize::run(), MTKpp::protonate::runCol(), MTKpp::hybridize::runLabute(), MTKpp::hybridize::runLabute3(), MTKpp::protonate::runMol(), MTKpp::molecule::setInSolution(), MTKpp::seqAlign::setPAMSize(), MTKpp::seqAlign::setPAMValue(), MTKpp::seqAlign::setQuery(), MTKpp::seqAlign::setTemplate(), MTKpp::molecule::setTorsion(), MTKpp::watProtonate::setup(), MTKpp::complex::setup(), MTKpp::molecule::setupConformers(), MTKpp::stdLibParser::stdLibParser(), MTKpp::seqAlign::traceBack(), MTKpp::pdbParser::updateMolCoords(), MTKpp::prepParser::Write(), and MTKpp::molecule::~molecule().

int MTKpp::c__1 = 1 [static]

Referenced by lbfgs_().

const unsigned int MTKpp::MAXATOMS = 1000
const double MTKpp::BIGNUM = 1.e12
const double MTKpp::APPROXZERO = 1.e-6

Very Large Number.

const double MTKpp::PI = 3.14159265359
const double MTKpp::PIt2 = PI * 2

(PI)^2

Referenced by MTKpp::ligProtonate::getBestTorsions(), and main().

const double MTKpp::INVPI = 1.0/PI

(PI)^3/2

1.0/(PI)

Referenced by main().

const double MTKpp::RAD2DEG = 180.0/PI
const double MTKpp::DEG2RAD = 1.0/RAD2DEG
const double MTKpp::ANG2BOHR = 0.529177249
const double MTKpp::BOHR2ANG = 1.0/ANG2BOHR
const double MTKpp::H2KCALMOL = 627.5095
const double MTKpp::E2KCAL = 18.2223

Hartree/Bohr^2 to kcal/mol A^2.

         H      627.5095 kcal/mol           1 B               1 B
        --- . -------------------- .  -------------- .  ---------------- = 2240.87 kcal/mol A^2
        B^2         1 H                0.5291772 A      0.5291772 A
       

Referenced by MTKpp::gaussianParser::getForceConstant(), MTKpp::gaussianParser::getForceConstantZMAT(), main(), and MTKpp::gaussianParser::Read().

const double MTKpp::BONDTOLERANCE = 0.4

definition of a bond, covRadius1 + covRadius + tolerance Bond Types and Hybridization, J. Comp. Chem. 12, 891-898, 1991

Referenced by MTKpp::connections::BondExists(), and MTKpp::ligProtonate::getBestTorsions().

const double MTKpp::SP2ANGLE = 115.0

sp2 versus sp3 angle cutoff

Referenced by MTKpp::hybridize::runMeng().

const double MTKpp::SPANGLE = 160.0

sp versus sp2 angle cutoff

Referenced by MTKpp::hybridize::runMeng().

const double MTKpp::AMBIGUOUSANGLE = 122.0

Angle below which the type of an atom with 2 heavy bonded atom should be reconsidered.

Referenced by MTKpp::hybridize::runMeng().

const int MTKpp::MESSAGE = 0

Generic message type.

Referenced by main(), and MTKpp::paramParser::paramParser().

const int MTKpp::MTK_ERROR = 1

Error message tyoe.

Referenced by MTKpp::molecule::addFunctionalGroup(), MTKpp::connections::assignStdAngles(), MTKpp::atomTyper::assignStdFunctionalGroups(), MTKpp::atomTyper::assignStdHydrophobicGroups(), MTKpp::atomTyper::assignStdRings(), MTKpp::connections::assignStdTorsions(), MTKpp::connections::bondByLibrary(), MTKpp::protonate::buildMissingHeavyAtoms(), MTKpp::molecule::determineValences(), MTKpp::molecule::generateAdjMatrix(), MTKpp::molecule::generateFeatureDistMatrix(), MTKpp::molecule::generateHeavyAdjMatrix(), MTKpp::molecule::getAngleParams(), MTKpp::molecule::getAngles(), MTKpp::molecule::getAtomKinds(), MTKpp::molecule::getAtomSymbols(), MTKpp::molecule::getAtomTypes(), MTKpp::molecule::getBond(), MTKpp::molecule::getBondParams(), MTKpp::molecule::getBonds(), MTKpp::molecule::getCoordinates(), MTKpp::gaussianParser::getForceConstantZMAT(), MTKpp::molecule::getHeavyAtomIndices(), MTKpp::molecule::getHeavyAtomSymbols(), MTKpp::molecule::getHeavyAtomTypes(), MTKpp::molecule::getImpropers(), MTKpp::molecule::getMMCharges(), MTKpp::molecule::getMMImpropers(), MTKpp::molecule::getMMnonBondedPairs(), MTKpp::molecule::getMMResidues(), MTKpp::molecule::getMMTorsions(), MTKpp::molecule::getNumMMImpropers(), MTKpp::molecule::getNumMMTorsions(), MTKpp::molecule::getTorsions(), MTKpp::superimpose::initializeCorrespondences(), main(), readInputFile(), MTKpp::watProtonate::run(), MTKpp::pca::run(), MTKpp::connections::run(), MTKpp::protonate::runMol(), MTKpp::molecule::setInSolution(), MTKpp::molecule::setTorsion(), MTKpp::watProtonate::setup(), and MTKpp::stdLibParser::stdLibParser().

const int MTKpp::WARNING = 2
const int MTKpp::mDEBUG = 3

Debug message type.

const int MTKpp::INFO = 4

Info message type.

Referenced by MTKpp::molecule::addBond(), MTKpp::molecule::addFunctionalGroup(), MTKpp::proProtonate::addHydrogens(), MTKpp::molecule::addHydrogens(), MTKpp::molecule::addRing(), MTKpp::connections::assignAngles(), MTKpp::connections::assignBonds(), MTKpp::connections::assignDisulfideBonds(), MTKpp::connections::assignImpropers(), MTKpp::collection::assignMetalParameters(), MTKpp::collection::assignMetalPartners(), MTKpp::connections::assignStd(), MTKpp::connections::assignStdAngles(), MTKpp::connections::assignStdBonds(), MTKpp::connections::assignStdBondsAngles(), MTKpp::atomTyper::assignStdFunctionalGroups(), MTKpp::atomTyper::assignStdHydrophobicGroups(), MTKpp::atomTyper::assignStdRings(), MTKpp::connections::assignStdTorsions(), MTKpp::connections::assignTorsions(), MTKpp::atomTyper::atomTypeByLib(), MTKpp::connections::BondExists(), MTKpp::proProtonate::buildDummyAtoms(), MTKpp::proProtonate::buildMissingAtoms(), MTKpp::protonate::buildMissingHeavyAtoms(), MTKpp::molecule::delAtom(), MTKpp::molecule::delFunctionalGroup(), MTKpp::collection::determineMetalEnvironments(), MTKpp::molecule::determineValences(), MTKpp::collection::findMetals(), MTKpp::stdFrag::generateCoordinates(), MTKpp::molecule::generateFeatureDistMatrix(), MTKpp::proProtonate::getBestTorsions(), MTKpp::gaussianParser::getForceConstantZMAT(), MTKpp::molecule::getMMTorsions(), MTKpp::molecule::getRotatableBonds(), MTKpp::collection::hasMetal(), MTKpp::protonate::initialize(), MTKpp::molecule::kekulizeRings(), main(), MTKpp::protonate::optimizePolarHs(), MTKpp::proProtonate::optimizePolarHs(), MTKpp::atomTyper::perceiveCysteines(), MTKpp::atomTyper::perceiveHistidines(), MTKpp::prepParser::Read(), MTKpp::prepParser::readFragment(), readInputFile(), MTKpp::molecule::removeHydrogens(), MTKpp::watProtonate::run(), MTKpp::pca::run(), MTKpp::connections::run(), MTKpp::protonate::runCol(), MTKpp::protonate::runMol(), MTKpp::seqAlign::setQuery(), MTKpp::seqAlign::setTemplate(), MTKpp::watProtonate::setup(), MTKpp::molecule::setupConformers(), and MTKpp::molecule::~molecule().

Generated on Fri Dec 23 2011 09:28:55 for MTK++ by Doxygen 1.7.5.1