I'm wondering if it is possible to incorporate a program like DSSP that also assigns polyproline type II helix? I've seen that there are some methods like DSSP-PPII, SEGNO, PROSS etc. and Perhaps there could be an option to be able to switch between programs like for example, DSSP or DSSP-PPII?
Yes it is, and the answer is straightforward.
idpconfgen requires a command to call an external application in order to predict secondary structure. That command has to be passed to the idpconfgen sscalc client. For example:
idpconfgen sscalc mkdssp ...
That will use mkdssp as an external program to calculate secondary structure. At the current state, idpconfgen can use any other program as long as it runs in the terminal, receives a PDB/mmCIF file as input, and outputs a parseable result. However, in order to accommodate new third party programs we need to implement the execution command and its parsing routines. idpconfgen is made modular, so this is easy.
this is the function that runs the mkdssp command. The developer needs to create a new function to accommodate the new program. If you follow the code, you'll see that this function executes mkdssp and captures its output. Additional options will also require a dictionary of choices at the level of the CLI.
In summary, to accommodate a new program, you need to develop a need function that controls the execution of that program via subprocess, captures the output, and parses the output returns a tuple of 3 elements:
The lines of the original PDB corresponding to that segment.
It is important to note here that I use DSSP to decide where the PDBs need to be split. We need to split PDBs at breaks in the backbone, which are many in the database to avoid artifacts in the torsion angles. That is why after sscalc pdbs have the suffix seg# where # is a integer.
A user have asked:
Yes it is, and the answer is straightforward.
idpconfgenrequires acommandto call an external application in order to predict secondary structure. That command has to be passed to theidpconfgen sscalcclient. For example:That will use
mkdsspas an external program to calculate secondary structure. At the current state,idpconfgencan use any other program as long as it runs in theterminal, receives aPDB/mmCIFfile as input, and outputs a parseable result. However, in order to accommodate new third party programs we need to implement the execution command and its parsing routines.idpconfgenis made modular, so this is easy.https://github.com/julie-forman-kay-lab/IDPConformerGenerator/blob/2da78306456f3a49477bdde801414359d6e98e28/src/idpconfgen/cli_sscalc.py#L161
this is the function that runs the
mkdsspcommand. The developer needs to create a new function to accommodate the new program. If you follow the code, you'll see that this function executesmkdsspand captures its output. Additional options will also require a dictionary of choices at the level of the CLI.https://github.com/julie-forman-kay-lab/IDPConformerGenerator/blob/2da78306456f3a49477bdde801414359d6e98e28/src/idpconfgen/libs/libparse.py#L110
mkdssp_w_splitcan be further abstracted if needed.Finally, this is the function that parses DSSP output:
https://github.com/julie-forman-kay-lab/IDPConformerGenerator/blob/2da78306456f3a49477bdde801414359d6e98e28/src/idpconfgen/libs/libparse.py#L140
In summary, to accommodate a new program, you need to develop a need function that controls the execution of that program via
subprocess, captures the output, and parses the output returns a tuple of 3 elements:It is important to note here that I use DSSP to decide where the PDBs need to be split. We need to split PDBs at breaks in the backbone, which are many in the database to avoid artifacts in the torsion angles. That is why after
sscalcpdbs have the suffixseg#where#is a integer.