meld.system.protein

Classes

ProteinBase()

Base class for other Protein classes.

ProteinMoleculeFromPdbFile(pdb_path)

Create a new protein molecule from a pdb file.

ProteinMoleculeFromSequence(sequence)

Class to create a protein from sequence.

class meld.system.protein.ProteinBase[source]

Base class for other Protein classes.

Provides functionality for translation/rotation and adding H-bonds.

add_bond(res_index_i, res_index_j, atom_name_i, atom_name_j, bond_type)[source]

Add a general bond.

Parameters
  • res_index_i – one-based index of residue i

  • res_index_j – one-based index of residue j

  • atom_name_i – string name of i

  • atom_name_j – string name of j

  • bond_type – string specifying the “S”, “D”,”T”… bond

Note

indexing starts from one and the residue numbering from the PDB file is ignored.

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.

add_frcmod_file(fname)[source]

Add a frcmod file. This will be needed when using residues that are not defined in the general amber force field

add_lib_file(fname)[source]

Add a lib file. This will be needed when using residues that are not defined in the general amber force field

add_prep_file(fname)[source]

Add a prep file. This will be needed when using residues that are not defined in the general amber force field

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.

add_bond(res_index_i, res_index_j, atom_name_i, atom_name_j, bond_type)

Add a general bond.

Parameters
  • res_index_i – one-based index of residue i

  • res_index_j – one-based index of residue j

  • atom_name_i – string name of i

  • atom_name_j – string name of j

  • bond_type – string specifying the “S”, “D”,”T”… bond

Note

indexing starts from one and the residue numbering from the PDB file is ignored.

add_disulfide(res_index_i, res_index_j)

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.

add_frcmod_file(fname)

Add a frcmod file. This will be needed when using residues that are not defined in the general amber force field

add_lib_file(fname)

Add a lib file. This will be needed when using residues that are not defined in the general amber force field

add_prep_file(fname)

Add a prep file. This will be needed when using residues that are not defined in the general amber force field

set_rotation(rotation_axis, theta)

Set the rotation.

Parameters
  • rotation_axisnumpy.array(3) in nanometers

  • theta – angle of rotation in degrees

Rotation happens after translation.

set_translation(translation_vector)

Set the translation vector.

Parameters

translation_vectornumpy.array(3) in nanometers

Translation happens after rotation.

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.

add_bond(res_index_i, res_index_j, atom_name_i, atom_name_j, bond_type)

Add a general bond.

Parameters
  • res_index_i – one-based index of residue i

  • res_index_j – one-based index of residue j

  • atom_name_i – string name of i

  • atom_name_j – string name of j

  • bond_type – string specifying the “S”, “D”,”T”… bond

Note

indexing starts from one and the residue numbering from the PDB file is ignored.

add_disulfide(res_index_i, res_index_j)

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.

add_frcmod_file(fname)

Add a frcmod file. This will be needed when using residues that are not defined in the general amber force field

add_lib_file(fname)

Add a lib file. This will be needed when using residues that are not defined in the general amber force field

add_prep_file(fname)

Add a prep file. This will be needed when using residues that are not defined in the general amber force field

set_rotation(rotation_axis, theta)

Set the rotation.

Parameters
  • rotation_axisnumpy.array(3) in nanometers

  • theta – angle of rotation in degrees

Rotation happens after translation.

set_translation(translation_vector)

Set the translation vector.

Parameters

translation_vectornumpy.array(3) in nanometers

Translation happens after rotation.