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Re: _chem_comp.formula???

Paula Fitzgerald (paula_fitzgerald@Merck.Com)
Thu, 5 Oct 95 16:03:45 EDT 

Herb Bernstein writes:

> There is a warning not to use the chemical_formula category for macro
> molecules, but there does not seem to be a chem_comp.formula to
> use for a het group.  Perhaps there should be a chem_comp_formula
> category linked to the items in the chemical_formula category, or,
> perhaps, the chemical and chemical formula categories should be
> used for macro-molecules.

I have added data items _chem_comp.formula and _chem_comp.formula_weight.
In doing so I borrowed from the definitions in the CHEMICAL_FORMULA category,
but I simplified this to only allow for C12 H14 N7 O4 type representations
(that is, I specifically have not allowed for sorting out the formula to
try and approximate the structure, which the core definitions do allow.

The new data items are:

- - - - -

save__chem_comp.formula
    _item_description.description
;              The formula for the chemical component.  Formulae are written
               according to the rules:

               1. Only recognised element symbols may be used.

               2. Each element symbol is followed by a 'count' number. A count
                  of '1' may be omitted.

               3. A space or parenthesis must separate each element symbol and
                  its count, but in general parentheses are not used.

               4. The order of elements with the formula should be: C, then H,
                  then the other elements in alphabetical order of their symbol.
                  This is the 'Hill' system used by Chemical Abstracts.
;
    _item.name                  '_chem_comp.formula'
    _item.category_id             chem_comp
    _item.mandatory_code          no
    _item_type.code               text
     loop_
    _item_examples.case          'C18 H19 N7 O8 S'
     save_

save__chem_comp.formula_weight
    _item_description.description
;              Formula mass in daltons of the chemical component.
;
    _item.name                  '_chem_comp.formula_weight'
    _item.category_id             chem_comp
    _item.mandatory_code          no
     loop_
    _item_range.maximum
    _item_range.minimum
                                  .    1.0
                                 1.0   1.0
    _item_type.code               float
     save_

- - - - -

One little detail - John's has recently modified the _item_range specifiers
to be more precise about greater than or equal to sorts of things.  But I'm
not very used to reading these things yet - I think what the above means is
that the formula weight must be greater than or equal to 1.0.

Paula

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