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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