Avogadro::Core::CoordinateBlockGenerator#

class CoordinateBlockGenerator#

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

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

Unnamed Group

enum DistanceUnit#

Distance unit used in the output.

Values:

enumerator Angstrom#

enumerator Bohr#

inline void setDistanceUnit(DistanceUnit unit)#: Distance unit used in the output.

inline DistanceUnit distanceUnit() const#: Distance unit used in the output.

Public Types

enum class Mode#

The kind of block produced.

Values:

enumerator Cartesian#: One line of Cartesian or lattice coordinates per atom.

enumerator 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.

enumerator 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.

Public Functions

CoordinateBlockGenerator() = default#: Construct the default CoordinateBlockGenerator with an empty specification and Angstrom distance units.

inline void setMolecule(const Molecule *mol)#

inline const Molecule *molecule() const#

inline 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

inline std::string specification() const#

inline void setMode(Mode mode)#

inline Mode mode() const#

std::string generateCoordinateBlock()#: Generate and return the coordinate block.

inline 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.

inline 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.