Difference between revisions of "File formats/Formats/HIN"

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* A <code>'''mol'''</code> record starts the description of each molecule. It must be matched by an <code>'''endmol'''</code> record. A file may contain one or more <code>'''mol'''...'''endmol'''</code> blocks, ''and Jmol will read them all into separate frames''.
 
* A <code>'''mol'''</code> record starts the description of each molecule. It must be matched by an <code>'''endmol'''</code> record. A file may contain one or more <code>'''mol'''...'''endmol'''</code> blocks, ''and Jmol will read them all into separate frames''.
 
** <code>'''number'''</code> is the number of the molecule in the molecular system, starting with 1.
 
** <code>'''number'''</code> is the number of the molecule in the molecular system, starting with 1.
−
** <code>'''name'''</code> is a name or description for the molecule (up to 64 characters and enclosed in double quotes).
+
** <code>'''name'''</code> is a name or description for the molecule (up to 64 characters and enclosed in double quotes). ''Not supported by Jmol.''
  
 
* A <code>'''res'''</code> record starts the description of each residue in a molecule. It must be matched by an <code>'''endres'''</code> record. Each <code>'''mol'''...'''endmol'''</code> block may contain none, one or several <code>'''res'''...'''endres'''</code> blocks. ''Jmol does not currently support the residue information.''
 
* A <code>'''res'''</code> record starts the description of each residue in a molecule. It must be matched by an <code>'''endres'''</code> record. Each <code>'''mol'''...'''endmol'''</code> block may contain none, one or several <code>'''res'''...'''endres'''</code> blocks. ''Jmol does not currently support the residue information.''
 
** <code>'''number'''</code> is the number of the residue in the molecule, starting with 1.
 
** <code>'''number'''</code> is the number of the residue in the molecule, starting with 1.
−
** <code>'''name'''</code> is the name of the residue (up to 4 characters and must be defined in a TPL file).
+
** <code>'''name'''</code> is the name of the residue (up to 4 characters and must be defined in a TPL file).  
 
** <code>'''PDB#'''</code>, <code>'''previous-res#'''</code> and <code>'''next-res#'''</code> preserve information originated in a [[File_formats/Coordinates#PDB|pdb]] file.
 
** <code>'''PDB#'''</code>, <code>'''previous-res#'''</code> and <code>'''next-res#'''</code> preserve information originated in a [[File_formats/Coordinates#PDB|pdb]] file.
  
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* <code>'''atom'''</code>
 
* <code>'''atom'''</code>
 
** <code>'''at#'''</code> 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.  
 
** <code>'''at#'''</code> 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.  
−
** <code>'''name'''</code> is the name of the atom (up to 4 characters, without spaces or quotes).
+
** <code>'''name'''</code> is the name of the atom (up to 4 characters, without spaces or quotes). ''Not supported by Jmol.''
−
** <code>'''element'''</code> is the chemical symbol (up to 3 characters).
+
** <code>'''element'''</code> is the chemical symbol (up to 3 characters). ''Supported by Jmol.''
 
** <code>'''type'''</code> is the atom type assigned by a force field (up to 4 characters).
 
** <code>'''type'''</code> is the atom type assigned by a force field (up to 4 characters).
 
** <code>'''flags'''</code> is a series of one-letter flags (without spaces between them):
 
** <code>'''flags'''</code> is a series of one-letter flags (without spaces between them):
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*** s = a selected atom;
 
*** s = a selected atom;
 
*** – = no flag.
 
*** – = no flag.
−
** <code>'''charge'''</code> is the formal charge.
+
** <code>'''charge'''</code> is the formal charge. ''Jmol reads this as partial charge.''
−
** <code>'''x y z'''</code> are the coordinates.
+
** <code>'''x y z'''</code> are the coordinates. ''Supported by Jmol.''
 
** <code>'''cn'''</code> is the coordination number, or number of atoms covalently bonded to this atom (an integer, from 0 to 12).
 
** <code>'''cn'''</code> is the coordination number, or number of atoms covalently bonded to this atom (an integer, from 0 to 12).
−
** <code>'''nbor# nbor-bond'''</code> describes the bonded atoms and the type of bond for each (from 1 to 12 pairs of values, to describe all bonded atoms).
+
** <code>'''nbor# nbor-bond'''</code> describes the bonded atoms and the type of bond for each (from 1 to 12 pairs of values, to describe all bonded atoms). ''Supported by Jmol.''
 
*** <code>'''nbor#'''</code> is the number identifying the bonded atom;  
 
*** <code>'''nbor#'''</code> is the number identifying the bonded atom;  
 
*** <code>'''nbor-bond'''</code> is the bond type:  
 
*** <code>'''nbor-bond'''</code> is the bond type:  
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**** a = aromatic
 
**** a = aromatic
  
−
* <code>'''vel'''</code> defines atomic velocities (Ångstroms/picosecond), generated by a molecular dynamics calculation.
+
* <code>'''vel'''</code> defines atomic velocities (Ångstroms/picosecond), generated by a molecular dynamics calculation. ''Not supported by Jmol.''
  
−
* <code>'''mass'''</code> specifies a non-default mass for the atom, in atomic mass units.  
+
* <code>'''mass'''</code> specifies a non-default mass for the atom, in atomic mass units. ''Not supported by Jmol.''
  
 
* <code>'''basisset'''</code> is used for ''ab initio'' calculations (''not applicable to Jmol'').
 
* <code>'''basisset'''</code> is used for ''ab initio'' calculations (''not applicable to Jmol'').
  
−
* <code>'''formalcharge'''</code> is another way of defining a formal charge for the atom.
+
* <code>'''formalcharge'''</code> is another way of defining a formal charge for the atom. ''Not supported by Jmol.''
  
 
Molecule closing lines (the <code>endres</code> line is present only when there was a <code>res</code> line before):
 
Molecule closing lines (the <code>endres</code> line is present only when there was a <code>res</code> line before):
 
  endres <res#>
 
  endres <res#>
 
  endmol <mol#>
 
  endmol <mol#>
−
 
  
 
= Sources =
 
= Sources =
 
* ''Appendix D: HIN Files'' in the Reference Manual available as part of the installed HyperChem package.
 
* ''Appendix D: HIN Files'' in the Reference Manual available as part of the installed HyperChem package.

Revision as of 23:09, 2 June 2010

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). Not supported by Jmol.
  • 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). Not supported by Jmol.
    • element is the chemical symbol (up to 3 characters). Supported by Jmol.
    • 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. Jmol reads this as partial charge.
    • x y z are the coordinates. Supported by Jmol.
    • 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). Supported by Jmol.
      • 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. Not supported by Jmol.
  • mass specifies a non-default mass for the atom, in atomic mass units. Not supported by Jmol.
  • basisset is used for ab initio calculations (not applicable to Jmol).
  • formalcharge is another way of defining a formal charge for the atom. Not supported by Jmol.

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 as part of the installed HyperChem package.

Contributors

AngelHerraez

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