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. This format specifies both atoms and bonds, as well as other atomic properties.
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.
Comment lines begin with a semicolon (;).
These lines are ignored by Jmol, may they be present or not. According to the HIN specification, the first line is compulsory, the others are optional (but other software may produce HIN-formatted files that lack the first line).
forcefield <force-field-name> sys <...> seed <...> view <...> box <...>
A file may contain one or more molecule blocks (delimited by
mol...endmol) and Jmol will read them all into separate frames.
Each molecule block contains molecule opening lines, several atom blocks and molecule closing lines. In biopolymers, the atom blocks may be grouped into residue blocks
res...endres), but Jmol does not currently support the residue information and will just read all atoms as part of the molecule.
Molecule and residue opening lines (the
res line is optional):
mol <number> <name> res <number> <name> <PDB#> <previous-res#> <next-res#>
molrecord starts the description of each molecule. It must be matched by an
numberis the number of the molecule in the file, starting with 1.
nameis a name or description for the molecule (up to 64 characters and enclosed in double quotes). Not supported by Jmol.
resrecord starts the description of each residue in a molecule. It must be matched by an
mol...endmolblock may contain none, one or several
res...endresblocks. Jmol does not currently support the residue information.
numberis the number of the residue in the molecule, starting with 1.
nameis the name of the residue (up to 4 characters and must be defined in a TPL file).
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>
at#is the number identifying the atom in the molecule (must start with 1 and be continuous through a molecule). Therefore a combination of atom number and molecule number uniquely identifies an atom in a file.
nameis the name of the atom (up to 4 characters, without spaces or quotes). Not supported by Jmol.
elementis the chemical symbol (up to 3 characters). Supported by Jmol.
typeis the atom type assigned by a force field (up to 4 characters).
flagsis 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;
- â = no flag.
chargeis the formal charge. Jmol reads this as partial charge.
x y zare the coordinates. Supported by Jmol.
cnis the coordination number, or number of atoms covalently bonded to this atom (an integer, from 0 to 12).
nbor# nbor-bonddescribes the bonded atoms and the type of bond for each (from 1 to 12 pairs of values, to describe all atoms bonded to the current one). Supported by Jmol.
nbor#is the number identifying the bonded atom;
nbor-bondis the bond type:
- s = single
- d = double
- t = triple
- a = aromatic
veldefines atomic velocities (in Ã per picosecond), generated by a molecular dynamics calculation. Not supported by Jmol.
massspecifies a non-default mass for the atom (i.e. an isotope), in atomic mass units. Not supported by Jmol.
basissetis used for ab initio calculations. Not applicable to Jmol.
formalchargeis another way of defining a formal charge for the atom. Not supported by Jmol.
Residue and molecule closing lines (the
endres line is present only when there was a
res line before):
endres <res#> endmol <mol#>
- Appendix D: HIN Files in the Reference Manual available as part of the installed HyperChem package.