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.

set_rotation(rotation_axis, theta)[source]

Set the rotation.

Parameters:
  • rotation_axisnumpy.array(3) in nanometers
  • theta – angle of rotation in degrees

Rotation happens after translation.

set_translation(translation_vector)[source]

Set the translation vector.

Parameters:translation_vectornumpy.array(3) in nanometers

Translation happens after rotation.

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.