File formats/Formats/HIN - Revision history

AngelHerraez: HIN format details

2010-06-05T15:59:06Z

HIN format details

AngelHerraez: moved File Formats/Formats/HIN to File formats/Formats/HIN: consistency in upper/lowercase with other subpages

2010-06-02T23:22:20Z

moved File Formats/Formats/HIN to File formats/Formats/HIN: consistency in upper/lowercase with other subpages

AngelHerraez: more content - Features (un)supported by Jmol

2010-06-02T23:09:00Z

more content - Features (un)supported by Jmol

AngelHerraez: /* Sources */

2010-06-02T22:44:05Z

‎Sources

AngelHerraez: more content

2010-06-02T20:10:56Z

AngelHerraez: more content

2010-06-02T19:43:47Z

AngelHerraez: new page for details on HIN format

2010-06-02T19:29:21Z

new page for details on HIN format

New page

= The HIN file format =
This is a native format of Hyperchem, a software sold by
[http://www.hyper.com/ 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'')

== 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 <code>res</code> line is optional):
mol <number> <name>
res <number> <name> <PDB#> <previous-res#> <next-res#>

* A <code>'''mol'''</code> record starts the description of each molecule. It must be matched by an <code>'''endmol'''</code> record.
** <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).

* A <code>'''res'''</code> record starts the description of each residue in a molecule. It must be matched by an <code>'''endres'''</code> record.
** <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>'''PDB#'''</code>, <code>'''previous-res#'''</code> and <code>'''next-res#'''</code> preserve information originated in a [[File_formats/Coordinates#PDB|pdb]] file.

Each atom block contains a line and several optional lines:
atom <number> <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>

* <code>'''number'''</code> is the number of the atom in the molecule, starting with 1. Atom numbers must 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>'''element'''</code> is the chemical symbol (up to 3 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):
** 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.
* <code>'''charge'''</code> is the formal charge.
* <code>'''x y z'''</code> are the coordinates.
* <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#'''</code> is the number identifying the bonded atom;
** <code>'''nbor-bond'''</code> is the bond type:
*** s = single
*** d = double
*** t = triple
*** a = aromatic

Molecule closing lines (the <code>endres</code> line is present only when there was a <code>res</code> line before):
endres <res#>
endmol <mol#>

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

@@ Line 1: / Line 1: @@
 = The HIN file format =
-This is a native format of Hyperchem, a software sold by
+This is a native format of '''Hyperchem''', a software sold by
 [http://www.hyper.com/ 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.
+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'')
@@ Line 16: / Line 14: @@
 == Information ==
-st line (excluding comments) (''ignored by Jmol''):
+''These lines are ignored by Jmol, may they be present or not''.
   forcefield  <force-field-name>
-Optional lines (''ignored by Jmol''):
+  sys   <...>
-  sys
+  seed  <...>
-  seed
+  view  <...>
-  view
+  box   <...>
 == Molecular data ==
-Each molecule block contains molecule opening lines, several atom blocks and molecule closing lines.
+A file may contain one or more molecule blocks (delimited by <code>'''mol'''...'''endmol'''</code>) ''and Jmol will read them all into separate frames''.
-Molecule opening lines (the <code>res</code> line is optional):
+Molecule and residue opening lines (the <code>res</code> line is optional):
   mol <number> <name>
   res <number> <name> <PDB#> <previous-res#> <next-res#>
-* 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.
-** <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 file, starting with 1.
 ** <code>'''name'''</code> is a name or description for the molecule (up to 64 characters and enclosed in double quotes). ''Not supported by Jmol.''
@@ Line 48: / Line 49: @@
 * <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). Therefore a combination of atom number and molecule number uniquely identifies an atom in a file.
 ** <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). ''Supported by Jmol.''
@@ Line 61: / Line 62: @@
 ** <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>'''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# nbor-bond'''</code> describes 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.''
 *** <code>'''nbor#'''</code> is the number identifying the bonded atom;
 *** <code>'''nbor-bond'''</code> is the bond type:
@@ Line 69: / Line 70: @@
 **** a = aromatic
-* <code>'''vel'''</code> defines atomic velocities (Ãngstroms/picosecond), generated by a molecular dynamics calculation. ''Not supported by Jmol.''
+* <code>'''vel'''</code> defines atomic velocities (in Ã per 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. ''Not supported by Jmol.''
+* <code>'''mass'''</code> specifies a non-default mass for the atom (i.e. an isotope), 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. ''Not supported by Jmol.''
-Molecule closing lines (the <code>endres</code> line is present only when there was a <code>res</code> line before):
+Residue and molecule closing lines (the <code>endres</code> line is present only when there was a <code>res</code> line before):
   endres <res#>
   endmol <mol#>

@@ Line 33: / Line 33: @@
 * 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>'''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.''
 ** <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>'''PDB#'''</code>, <code>'''previous-res#'''</code> and <code>'''next-res#'''</code> preserve information originated in a [[File_formats/Coordinates#PDB|pdb]] file.
@@ Line 49: / Line 49: @@
 * <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>'''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>'''flags'''</code> is a series of one-letter flags (without spaces between them):
@@ Line 58: / Line 58: @@
 *** s = a selected atom;
 *** â = 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>'''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-bond'''</code> is the bond type:
@@ Line 69: / Line 69: @@
 **** a = aromatic
-* <code>'''vel'''</code> defines atomic velocities (Ãngstroms/picosecond), generated by a molecular dynamics calculation.
+* <code>'''vel'''</code> defines atomic velocities (Ãngstroms/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>'''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):
   endres <res#>
   endmol <mol#>
 = Sources =
 * ''Appendix D: HIN Files'' in the Reference Manual available as part of the installed HyperChem package.

← Older revision		Revision as of 22:44, 2 June 2010
Line 83:		Line 83:

	= Sources =		= Sources =
−	* ''Appendix D: HIN Files'' in the Reference Manual available ~~from Hypercube's web site~~.	+	* ''Appendix D: HIN Files'' in the Reference Manual available as part of the installed HyperChem package.

← Older revision	Revision as of 23:22, 2 June 2010
(No difference)