Hi list,
I am wondering what properties are attached to the various levels of a hierarchy and how to retrieve it. As an example, I would like to know how to get the one-character-code that is attached to a chain.
I have the feeling, this is not strictly feasible, though it is possible to get it as the last character in the particle name of the chain :
import IMP import IMP.atom
m=IMP.Model() struct_file_name = "/Users/schwarz/DATA/myPDB/1K8K.pdb" struct1k8k=IMP.atom.read_pdb(struct_file_name,m) c0=struct1k8k.get_child(0) print c0.get_name()
Will result in 'Chain A' being output. Looking at the other properties stored in my c0 chain, I see that everything seems to be integer, including a "chain" attribute that I try to access through
chainKey = c0.get_int_attributes()[2] c0.get_value(chainKey)
which results in the integer 65 being output...
My questions now : 1. Is there a way to get directly the one letter code of a chain ? 2. If not, is there a guaranty that the letter used in the particle name will always reflect the chain ID, or is there a fixed mapping between the value of the chainKey attribute and the chain one letter code ? 3. Is there a nicer way to get a keyType for instance from its string ? In my example, I retrieved chainKey as the third element of the integer keys list returned by get_int_attributes(), this is not very satisfying, and I thought of resorting to a function such as :
def getChainKey( chain ): for k in chain.get_int_attributes() : if k.get_string() == 'chain' : return k return None
Still, I wonder if there is an IMP mechanism I am not aware of, that I should prefer instead.
--Ben.S
The chain_id is the ascii value for the letter stored in the PDB file. I think the main reason for directly returning an int instead of the char is that 26 is kind of a small limit.
On Mar 22, 2011, at 8:07 AM, Benjamin SCHWARZ wrote:
> Hi list, > > I am wondering what properties are attached to the various levels of a hierarchy and how to retrieve it. > As an example, I would like to know how to get the one-character-code that is attached to a chain. > > I have the feeling, this is not strictly feasible, though it is possible to get it as the last character in the particle name of the chain : > > import IMP > import IMP.atom > > m=IMP.Model() > struct_file_name = "/Users/schwarz/DATA/myPDB/1K8K.pdb" > struct1k8k=IMP.atom.read_pdb(struct_file_name,m) > c0=struct1k8k.get_child(0) > print c0.get_name() > > Will result in 'Chain A' being output. Looking at the other properties stored in my c0 chain, I see that everything seems to be integer, including a "chain" attribute that I try to access through > > chainKey = c0.get_int_attributes()[2] > c0.get_value(chainKey) > > which results in the integer 65 being output... > > My questions now : > 1. Is there a way to get directly the one letter code of a chain ? > 2. If not, is there a guaranty that the letter used in the particle name will always reflect the chain ID, or is there a fixed mapping between the value of the chainKey attribute and the chain one letter code ? > 3. Is there a nicer way to get a keyType for instance from its string ? In my example, I retrieved chainKey as the third element of the integer keys list returned by get_int_attributes(), this is not very satisfying, and I thought of resorting to a function such as : > > def getChainKey( chain ): > for k in chain.get_int_attributes() : > if k.get_string() == 'chain' : > return k > return None > > Still, I wonder if there is an IMP mechanism I am not aware of, that I should prefer instead. > > --Ben.S > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
> The chain_id is the ascii value for the letter stored in the PDB file. I think the main reason for directly returning an int instead of the char is that 26 is kind of a small limit.
Oups, thanks Daniel, I missed that method in the documentation :
c0.get_as_chain().get_id()
does the trick.
I still have a question concerning the nice way for retrieving attribute Keys
>> 3. Is there a nicer way to get a keyType for instance from its string ? In my example, I retrieved chainKey as the third element of the integer keys list returned by get_int_attributes(), this is not very satisfying, and I thought of resorting to a function such as : >> >> def getChainKey( chain ): >> for k in chain.get_int_attributes() : >> if k.get_string() == 'chain' : >> return k >> return None >> >> Still, I wonder if there is an IMP mechanism I am not aware of, that I should prefer instead.
--Ben.S
For getting attribute keys, most decorators have methods to retrieve the keys they use eg Chain::get_id_key(). Some decorators may be missing those, please report ones you encounter which do.
On Mar 22, 2011, at 8:37 AM, Benjamin SCHWARZ wrote:
>> The chain_id is the ascii value for the letter stored in the PDB file. I think the main reason for directly returning an int instead of the char is that 26 is kind of a small limit. > > Oups, thanks Daniel, I missed that method in the documentation : > > c0.get_as_chain().get_id() > > does the trick. > > I still have a question concerning the nice way for retrieving attribute Keys > >>> 3. Is there a nicer way to get a keyType for instance from its string ? In my example, I retrieved chainKey as the third element of the integer keys list returned by get_int_attributes(), this is not very satisfying, and I thought of resorting to a function such as : >>> >>> def getChainKey( chain ): >>> for k in chain.get_int_attributes() : >>> if k.get_string() == 'chain' : >>> return k >>> return None >>> >>> Still, I wonder if there is an IMP mechanism I am not aware of, that I should prefer instead. > > --Ben.S > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
> For getting attribute keys, most decorators have methods to retrieve the keys they use eg Chain::get_id_key(). Great ! many thanks.
> Some decorators may be missing those, please report ones you encounter which do. ack
>>> The chain_id is the ascii value for the letter stored in the PDB file. I think the main reason for directly returning an int instead of the char is that 26 is kind of a small limit. >> >> Oups, thanks Daniel, I missed that method in the documentation : >> >> c0.get_as_chain().get_id() >> >> does the trick. >> >> I still have a question concerning the nice way for retrieving attribute Keys >> >>>> 3. Is there a nicer way to get a keyType for instance from its string ? In my example, I retrieved chainKey as the third element of the integer keys list returned by get_int_attributes(), this is not very satisfying, and I thought of resorting to a function such as : >>>> >>>> def getChainKey( chain ): >>>> for k in chain.get_int_attributes() : >>>> if k.get_string() == 'chain' : >>>> return k >>>> return None >>>> >>>> Still, I wonder if there is an IMP mechanism I am not aware of, that I should prefer instead. >> >> --Ben.S
On 3/22/11 8:07 AM, Benjamin SCHWARZ wrote: > I am wondering what properties are attached to the various levels of a > hierarchy and how to retrieve it. > As an example, I would like to know how to get the one-character-code > that is attached to a chain.
Check the documentation: http://salilab.org/imp/nightly/doc/html/classIMP_1_1atom_1_1Chain.html
There should never be a need to mess with keys and attributes in the way you're proposing - the decorators should always provide suitable methods.
> I have the feeling, this is not strictly feasible, though it is possible > to get it as the last character in the particle name of the chain :
The particle name is a tag for the benefit of you, the human. There is no guarantee that it ends in the chain ID, since you can set it to anything you want.
Ben
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Ben Webb -
Benjamin SCHWARZ -
Daniel Russel