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AddChain

Reads a PDB file from disk and concatenates it to the existing pose.

<AddChain name="(&string)" file_name="(&string)" new_chain="(1&bool)" scorefxn="(score12 &string)" random_access="(0&bool)" swap_chain_number="(0 &Size)" spm_reference_name="(&string)" update_PDBInfo="(1 &bool)"/>
  • file_name: the name of the PDB file on disk.
  • new_chain: should the pose be concatenated as a new chain or just at the end of the existing pose?
  • scorefxn: used for scoring the pose at the end of the concatenation. Also calls to detect_disulfides are made in the code.
  • random_access: If true, you can write a list of file names in the file_name field. At parse time one of these file names will be picked at random and throughout the trajectory this file name will be used. This saves command line variants.
  • swap_chain_number: If specified, AddChain will delete the chain with number 'swap_chain_number' and add the new chain instead.
  • spm_reference_name: The name of a pose saved with SavePoseMover. Use this instead of file_name
  • swap_chain_number: There is some interaction between swap_chain_number and new_chain; probably you can use only one. Swap chain with specified chain number.
  • update_PDBInfo: When true (default) it will reset the PDBInfo of the merged pose, residue count starting from 1 on the first chain, chains starting from A. PDB numbering starting from 1 in each chain. When false, it will merge the info from the two PDBInfos from each Pose "by appending the second one to the first one. If both Poses have the same chain name, they will keep it (with the expected issues); be aware of that when setting this option to false. This option is always true when swap_chain_number is called.

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