schrodinger.application.bioluminate.antibody.assembly module

class schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl(model: str, template: str)

Bases: object

model: str
template: str
__init__(model: str, template: str) None
class schrodinger.application.bioluminate.antibody.assembly.AtomPair(model: str, template: str)

Bases: object

model: str
template: str
__init__(model: str, template: str) None
class schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction(align_asl: schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair], region_to_replace: str, domain_structure: schrodinger.structure._structure.Structure)

Bases: object

align_asl: schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl
bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]
region_to_replace: str
domain_structure: schrodinger.structure._structure.Structure
classmethod fromDict(information_dictionary)
__init__(align_asl: schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair], region_to_replace: str, domain_structure: schrodinger.structure._structure.Structure) None
schrodinger.application.bioluminate.antibody.assembly.assemble_domains(template_structure: schrodinger.structure._structure.Structure, assembly_instructions: List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction]) schrodinger.structure._structure.Structure

Assemble the built model domains onto the template structure.

Parameters
  • template_structure – the structure to replace the domains of

  • assembly_instructions – a list of instructions specifying which domains to apply to which regions of the template

Returns

a copy of the template structure with any instruction-specified domains inserted to replace the corresponding template domains

schrodinger.application.bioluminate.antibody.assembly.align_structures(*, alignment_target: schrodinger.structure._structure.Structure, structure_to_align: schrodinger.structure._structure.Structure, alignment_asl: schrodinger.application.bioluminate.antibody.assembly.AlignmentAsl) schrodinger.structure._structure.Structure

align the domain structure to the specified region of the template

Parameters
  • alignment_target – template to align the domain of interest to

  • structure_to_align – domain of interest to align to the template

  • alignment_asl – alignment ASLs for template and model

Returns

a copy of structure_to_align with new aligned coordinates

schrodinger.application.bioluminate.antibody.assembly.replace_domain(*, structure_to_modify: schrodinger.structure._structure.Structure, replacement_domain: schrodinger.structure._structure.Structure, replaced_region_asl: str, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]) None

Remove the atoms in the replaced region and merge in the replacement domain

Parameters
  • structure_to_modify – structure to add the new domain to

  • replacement_domain – modeled structure to merge into the modified structure

  • replaced_region_asl – region on the modified structure to replace

  • bonds – list of AtomPair objects specifying the model and template atoms to use to bond the structures together

schrodinger.application.bioluminate.antibody.assembly.get_map_model_to_template(model_structure: schrodinger.structure._structure.Structure, template_structure: schrodinger.structure._structure.Structure, region_to_replace_asl: str) Dict[str, Dict[str, str]]

Get a mapping of the model structure to the template structure.

Parameters
  • model_structure – the structure that is being projected onto the template

  • template_structure – the structure that is being projected onto

  • region_to_replace_asl – the region of the template structure that is being replaced

schrodinger.application.bioluminate.antibody.assembly.get_region_to_replace(template_structure: schrodinger.structure._structure.Structure, region_to_replace_asl: str) schrodinger.structure._structure.Structure

Get the region of the template structure that is being replaced.

Parameters
  • template_structure – the structure that is being projected onto

  • region_to_replace_asl – the region of the template structure that is being replaced

schrodinger.application.bioluminate.antibody.assembly.map_chains(st: schrodinger.structure._structure.Structure) Dict[str, str]

Map the chains in the structure to their chain types.

Parameters

st – the structure to map the chains of

schrodinger.application.bioluminate.antibody.assembly.rename_chains_in_bonds(bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair], map_model_to_template: Dict[str, Dict[str, str]]) None

Rename the chains in the bonds.

Parameters
  • bonds – the bonds to rename the chains of

  • map_model_to_template – the mapping of the model structure to the template structure

schrodinger.application.bioluminate.antibody.assembly.rename_chain_in_asl(asl: str, map_old_to_new: Dict[str, str]) str

Rename the chain name in the ASL if chain name is specified.

Parameters
  • asl – the ASL to rename the chains of

  • map_old_to_new – the mapping of the old name to the new name

schrodinger.application.bioluminate.antibody.assembly.rename_chains_in_structure(map_model_to_template: Dict[str, Dict[str, str]], model_structure: schrodinger.structure._structure.Structure) None

Rename the chains in the structure.

Parameters
  • map_model_to_template – the mapping of the model structure to the template structure

  • model_structure – the structure that is being projected onto

schrodinger.application.bioluminate.antibody.assembly.remove_atoms_by_asl(st: schrodinger.structure._structure.Structure, asl: str) None
schrodinger.application.bioluminate.antibody.assembly.adjust_resnums(st: schrodinger.structure._structure.Structure, replacement_domain: schrodinger.structure._structure.Structure, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]) None

Adjust the resnums in the structure to ensure all res nums are unique.

Parameters
  • st – the structure to renumber the residues of

  • replacement_domain – the structure that is being projected onto the template

  • bonds – the bonds that will be formed

schrodinger.application.bioluminate.antibody.assembly.get_atom(st: schrodinger.structure._structure.Structure, asl: str) schrodinger.structure._structure.StructureAtom

Get an atom from the structure.

Parameters
  • st – the structure to get the atom from

  • asl – the ASL describing the atom

schrodinger.application.bioluminate.antibody.assembly.create_bonds(structure_to_modify: schrodinger.structure._structure.Structure, replacement_domain: schrodinger.structure._structure.Structure, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]) None

Create specified bonds within the modeled structure

Parameters
  • structure_to_modify – the template structure to form the bonds in

  • replacement_domain – the structure of the modelled domain which has been added to the structure_to_modify

  • bonds – AtomPair objects with ASLs relative to the original structures which are being combined

schrodinger.application.bioluminate.antibody.assembly.minimize_new_bonds(structure_to_minimize: schrodinger.structure._structure.Structure, assembly_instructions: List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction]) None

Minimize the structure after bonds are formed.

Parameters
  • structure_to_minimize – the structure to minimize

  • assembly_instructions – a list of instructions

schrodinger.application.bioluminate.antibody.assembly.check_bond_length(st: schrodinger.structure._structure.Structure, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]) None

Check if the bond length is greater than 6 angstroms and if it is, raise an error.

Parameters
  • st – the structure to check

  • bonds – the bonds to check

schrodinger.application.bioluminate.antibody.assembly.get_atoms_to_minimize(structure_to_minimize: schrodinger.structure._structure.Structure, bonds: List[schrodinger.application.bioluminate.antibody.assembly.AtomPair]) Iterator[schrodinger.structure._structure.StructureAtom]

Get the atoms to minimize. These atoms are the atoms contained within the bonds and their neighbors.

Parameters
  • structure_to_minimize – the structure to minimize

  • bonds – the bonds that were formed