number of residues in a specific chain

[Anonymous]

Dear all

sorry for the dumb question, but how can I get the number of residues on a specific chain of a complex?

thanks in advance

felipet

[Anonymous]

Hey Felipet,

There seems to be a few ways to do this. If you have loaded a pose as my_pose – First, you could use len(my_pose.chain_sequence( chain_id ). You could also use the chain_end and chain_begin functions from the conformation object:

start = my_pose.conformation().chain_begin( chain_id )
end = my_pose.conformation().chain_end( chain_id )

and then end – start +1 to get the length.

There are a number of chain utilities for converting to and from chain_id/char/string in core/pose/util. They should be imported with the ‘from rosetta import *’ command. Here are a few (the core::Size corresponds to the chain id ):

bool
has_chain(std::string const & chain, core::pose::Pose const & pose);

bool
has_chain(char const & chain, core::pose::Pose const & pose);

bool
has_chain(core::Size chain_id, core::pose::Pose const & pose);

std::set
get_jump_ids_from_chain_ids(std::set const chain_ids, core::pose::Pose const & pose);

core::Size
get_jump_id_from_chain_id(core::Size const & chain_id, core::pose::Pose const & pose);

//std::set get_chain_ids(core::pose::Pose const & pose);

core::Size
get_chain_id_from_chain(std::string const & chain, core::pose::Pose const & pose);

core::Size
get_chain_id_from_chain(char const & chain, core::pose::Pose const & pose);

utility::vector1
get_chain_ids_from_chain(std::string const & chain, core::pose::Pose const & pose);

utility::vector1
get_chain_ids_from_chain(char const & chain, core::pose::Pose const & pose);

utility::vector1
get_chain_ids_from_chains(utility::vector1 const & chains, core::pose::Pose const & pose);

char
get_chain_from_chain_id(core::Size const & chain_id, core::pose::Pose const & pose);

core::conformation::ResidueCOPs
get_chain_residues(core::pose::Pose const & pose, core::Size chain_id);

Hope this helps!

-Jared

[Author]

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