C++ Api To Mutate Pdb Residues

Question

[lucas.simon994]

Is there an open source library available to mutate pdb files with C++?

[Pierre Lindenbaum]

what is mutate ? changing a AA ? inserting ? deleting ? What is your aim? why do you need C++ ?

Answer 1

[Alex Reynolds]

There's an API here that reads in PDB records, but if it doesn't meet your needs, you might read the PDB file format documentation and use any number of parsing functions, such as scanf() found in the C standard library, to put textual PDB records into a data structure of your design, e.g. a vector of PDB records, of which there are several types (as described in the PDB file format documentation).

Either way, once you have your PDB data parsed into memory, you might write a mutate() function that iterates through and operates on instances of the desired PDB record type in your dataset, to change them per your specification. Or insert() and delete() functions that add or remove an instance of a particular record type, etc.

You might then code a write() function that writes the PDB records out to standard output or a text file, if the API I linked to doesn't offer that option. (EDIT: It looks like the API does allow writing records to output via C++ ostream. Take a look at the pdb++.h header file for a list of functions and a description of the PDB class.)

Answer 2

[Vladimir Chupakhin]

OpenEye OEChemTK - commercial, but open to the academic