File formats/Formats/HIN

The HIN file format

This is a native format of Hyperchem, a software sold by Hypercube Inc..

HIN files are text files that contain several records, each on a separate line. Each line, except for a comment, begins with a keyword.

A special feature of HIN files is that records can be added or potentially missing without affecting the operation of HyperChem.

The HIN file in addition to storing molecular information may also store information associated with annotations (text, line, ellipse, and rectangle). (This is not supported by Jmol)

Note: Several records that are not relevant to Jmol are omitted from this description.

Comments

Comment lines begin with a semicolon (;).

Information

1st line (excluding comments) (ignored by Jmol):

forcefield  <force-field-name>

Optional lines (ignored by Jmol):

sys 
seed
view
box 

Molecular data

Each molecule block contains molecule opening lines, several atom blocks and molecule closing lines.

Molecule opening lines (the res line is optional):

mol <number> <name>
res <number> <name> <PDB#> <previous-res#> <next-res#>

• A mol record starts the description of each molecule. It must be matched by an endmol record. A file may contain one or more mol...endmol blocks, and Jmol will read them all into separate frames.
  • number is the number of the molecule in the molecular system, starting with 1.
  • name is a name or description for the molecule (up to 64 characters and enclosed in double quotes).

• A res record starts the description of each residue in a molecule. It must be matched by an endres record. Each mol...endmol block may contain none, one or several res...endres blocks. Jmol does not currently support the residue information.
  • number is the number of the residue in the molecule, starting with 1.
  • name is the name of the residue (up to 4 characters and must be defined in a TPL file).
  • PDB#, previous-res# and next-res# preserve information originated in a pdb file.

Each atom block contains a line and several optional lines:

atom <at#> <name> <element> <type> <flags> <charge> <x> <y> <z> <cn> <nbor# nbor-bond>
vel  <at#>  <x>  <y>  <z>
mass  <at#> <mass>
basisset  <at#> <basis set>
formalcharge  <at#> <formal charge>

• atom
  • at# is the number identifying the atom in the molecule (must start with 1 and be continuous through a molecule). A combination of atom number and molecule number uniquely identifies an atom in a molecular system.
  • name is the name of the atom (up to 4 characters, without spaces or quotes).
  • element is the chemical symbol (up to 3 characters).
  • type is the atom type assigned by a force field (up to 4 characters).
  • flags is a series of one-letter flags (without spaces between them):
    • h = a heteroatom, as defined in PDB files;
    • i = atom is part of an improper torsion;
    • x = a united atom;
    • s = a selected atom;
    • – = no flag.
  • charge is the formal charge.
  • x y z are the coordinates.
  • cn is the coordination number, or number of atoms covalently bonded to this atom (an integer, from 0 to 12).
  • nbor# nbor-bond describes the bonded atoms and the type of bond for each (from 1 to 12 pairs of values, to describe all bonded atoms).
    • nbor# is the number identifying the bonded atom;
    • nbor-bond is the bond type:
      • s = single
      • d = double
      • t = triple
      • a = aromatic

• vel defines atomic velocities (Ångstroms/picosecond), generated by a molecular dynamics calculation.

• mass specifies a non-default mass for the atom, in atomic mass units.

• basisset is used for ab initio calculations (not applicable to Jmol).

• formalcharge is another way of defining a formal charge for the atom.

Molecule closing lines (the endres line is present only when there was a res line before):

endres <res#>
endmol <mol#>

Sources

• Appendix D: HIN Files in the Reference Manual available from Hypercube's web site.

Contributors

AngelHerraez