meld.system.protein¶
- class meld.system.protein.ProteinBase[source]¶
Base class for other Protein classes.
Provides functionality for translation/rotation and adding H-bonds.
- add_disulfide(res_index_i, res_index_j)[source]¶
Add a disulfide bond.
Parameters: - res_index_i – one-based index of residue i
- res_index_j – one-based index of residue j
Note
indexing starts from one and the residue numbering from the PDB file is ignored. When loading from a PDB or creating a sequence, residue name must be CYX, not CYS.
- class meld.system.protein.ProteinMoleculeFromPdbFile(pdb_path)[source]¶
Create a new protein molecule from a pdb file. This class is dumb and relies on AmberTools for the heavy lifting.
Parameters: pdb_path – string path to the pdb file Note
no processing happens to this pdb file. It must be understandable by tleap and atoms/residues may need to be added/deleted/renamed. These manipulations should happen to the file before MELD is invoked.
- class meld.system.protein.ProteinMoleculeFromSequence(sequence)[source]¶
Class to create a protein from sequence. This class will create a protein molecule from sequence. This class is pretty dumb and relies on AmberTools to do all of the heavy lifting.
Parameters: sequence – sequence of the protein to create The sequence is specified in Amber/Leap format. There are special NRES and CRES variants for the N- and C-termini. Different protonation states are also available via different residue names. E.g. ASH for neutral ASP.