CoordinateBlockGenerator Class Reference

The CoordinateBlockGenerator class creates an aligned, formatted block of atomic coordinates. More...

#include <coordinateblockgenerator.h>

Public Types
enum class	Mode {   Cartesian ,   ZMatrix ,   ZMatrixPadded }

Public Member Functions
	CoordinateBlockGenerator ()=default
void	setMolecule (const Molecule *mol)
const Molecule *	molecule () const
void	setSpecification (const std::string &spec)
std::string	specification () const
void	setMode (Mode mode)
Mode	mode () const
std::string	generateCoordinateBlock ()
bool	atomsReordered () const
Array< Index >	linearRows () const
enum	DistanceUnit {   Angstrom = 0 ,   Bohr }
void	setDistanceUnit (DistanceUnit unit)
DistanceUnit	distanceUnit () const

Detailed Description

<avogadro/core/coordinateblockgenerator.h>

See the setSpecification() documentation for details on specifying the block format.

Member Enumeration Documentation

DistanceUnit

enum DistanceUnit

Distance unit used in the output.

Mode

enum class Mode

strong

The kind of block produced.

Enumerator
Cartesian	One line of Cartesian or lattice coordinates per atom.
ZMatrix	A z-matrix, with the missing fields of the opening rows left out entirely along with the space that would have preceded them. This is the form Gaussian, NWChem, Q-Chem, Psi4, Molpro and CFOUR read.
ZMatrixPadded	A z-matrix whose opening rows are padded out with zeros, so that every row carries every field. This is the form ORCA's int, MOPAC and SIESTA read.

Constructor & Destructor Documentation

CoordinateBlockGenerator()

CoordinateBlockGenerator ( )

default

Construct the default CoordinateBlockGenerator with an empty specification and Angstrom distance units.

Member Function Documentation

setSpecification()

void setSpecification

(

const std::string &

spec

)

 The specification of the block format.
 The characters in the specification string indicate the information needed
 about each atom in the coordinate block.
 - @c #: Atom index (one-based index)
 - @c Z: Atomic number (e.g. "6" for carbon)
 - @c L: Atomic label (e.g., "C1" for first carbon)")
 - @c G: GAMESS-styled Atomic number (e.g. "6.0" for carbon)
 - @c S: Element symbol (e.g. "C" for carbon)
 - @c N: Element name (e.g. "Carbon")
 - @c x: X cartesian coordinate
 - @c y: Y cartesian coordinate
 - @c z: Z cartesian coordinate
 - @c a: 'a' lattice coordinate (unit cell required)
 - @c b: 'b' lattice coordinate (unit cell required)
 - @c c: 'c' lattice coordinate (unit cell required)
 - @c 0: A literal "0". Useful for optimization flags.
 - @c 1: A literal "1". Useful for optimization flags.
 - @c _: A space character. Useful for alignment.
 - @c ,: A literal comma, with no space added on either side of it.
   Useful for comma-delimited formats such as Molpro.

 In the z-matrix modes (see setMode()) a row describes one atom in terms
 of three earlier ones, and six further characters are recognized:
 - @c I: Index of the distance reference atom's row
 - @c J: Index of the angle reference atom's row
 - @c K: Index of the dihedral reference atom's row
 - @c R: Distance to the @c I atom
 - @c A: Angle at the @c I atom to the @c J atom, in degrees
 - @c T: Dihedral about the @c I - @c J axis to the @c K atom, in degrees

 All of these are one-based, and they number z-matrix @em rows rather
 than molecule atoms. The two agree unless the z-matrix had to be
 reordered, which atomsReordered() reports. @c # likewise gives the row
 number in these modes, so that it lines up with @c I, @c J and @c K.

 For example, the specification string

__SZxyz110

will be replaced by a molecule-specific block of text similar to the following:

C  6    1.126214  0.765886  0.000000 1 1 0
C  6    0.819345 -0.564955  0.000000 1 1 0
C  6   -0.598383 -0.795127  0.000000 1 1 0
C  6   -1.310706  0.370165  0.000000 1 1 0
S  16  -0.285330  1.757144  0.000000 1 1 0
H  1    2.130424  1.185837  0.000000 1 1 0
H  1    1.548377 -1.375303  0.000000 1 1 0
H  1   -1.033768 -1.794407  0.000000 1 1 0
H  1   -2.396173  0.450760  0.000000 1 1 0

setDistanceUnit()

void setDistanceUnit

(

DistanceUnit

unit

)

Distance unit used in the output.

distanceUnit()

DistanceUnit distanceUnit

(

)

const

Distance unit used in the output.

generateCoordinateBlock()

std::string generateCoordinateBlock

(

)

Generate and return the coordinate block.

atomsReordered()

bool atomsReordered

(

)

const

Whether the last z-matrix generated put the atoms in an order other than the molecule's own, so that the row numbers in the block do not match the atom numbering the user sees.

A z-matrix has to describe each atom against atoms already placed, which a molecule's atom order does not always allow. Always false after a Cartesian block, whose atoms are always in molecule order.

linearRows()

Array< Index > linearRows

(

)

const

The rows of the last z-matrix generated whose angle or dihedral is measured against three atoms too close to a straight line for the value to be meaningful.

The geometry is still described correctly, but such a coordinate cannot be read or edited sensibly, and a program rebuilding Cartesians from it may not reproduce the molecule exactly. Row numbers are zero-based, as indices into the block's lines; add one to match the # field.

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The documentation for this class was generated from the following file:

• coordinateblockgenerator.h