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