Jan wrote:
>>Are you just talking about the AIB groups 22 & 23 ?
>>
>>Do you think that we should allow O1 as an acceptable atom
>>name for the carbonyl oxygen?
>>
> no, I suggest the combination of element type and connection pattern to
> determine an amino acid
The connection pattern is currently used to identify an AminoMonomer.
For a _group_ to be an AminoMonomer it must contain the following:
* atoms with the following names:
- N
- CA
- C
- O
* the atoms must also be connected correctly
- N + CA
- CA + C
- C + O
Note that I cannot check bond orders for these because .pdb files do not
contain bond order information.
> 0. Ala Arg Asp ...
I think that you are saying that the *group name* should be used to
determine whether or not something is an amino acid.
At this point I think that would be very difficult. There is too much code
that depends upon the presence of all the key atoms. In particular, all of
the secondary structure shapes are dependant upon the presence of CA-C=O
> 1. *.CA only: within(4.2, *.CA) != (*.N, *.O, *.OXT, *.C)
I do not understand what you are suggesting here.
The current support for AlphaMonomer (for alpha-carbon-only models) is as
follows:
* a _single_ atom in a group whose name is CA
> 2. default naming *.CA *.C *.N *.O
These names are currently required.
> 3. connection C?-[-N?-C?-C?=(-O?] -N?) only the CAlpha should branch
> within the same residue (and N ? case of Pro)
I do not understand what you are saying here.
>>If we make this change, do you think that it will cause
>>other problems?
>>
>>
> if we include the connection that made an amino acid we should get amino
> acids?
As described above, connectivity is currently used to determine if a group
is an AminoMonomer.
> But there are ~1000 HETERO components with N?-C?-C?-O? connection
> (without checking branching e.g. Guanosine derivate: OMG N7
> C5 C6 O6)
I do not understand what you are saying here.
Miguel
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