schrodinger.application.bioluminate.antibody.assembly_yaml module¶
- class schrodinger.application.bioluminate.antibody.assembly_yaml.AntibodyFormat(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
schrodinger.StrEnum
- BISPECIFIC = 'bispecific'¶
- MONOSPECIFIC = 'monospecific'¶
- FAB = 'fab'¶
- FV = 'fv'¶
- class schrodinger.application.bioluminate.antibody.assembly_yaml.ChainData(sequence: str, resids: List[str], seqtype: schrodinger.application.prime.packages.antibody.SeqType, residues: Any)¶
Bases:
object
- sequence: str¶
- seqtype: schrodinger.application.prime.packages.antibody.SeqType¶
- residues: Any¶
- __init__(sequence: str, resids: List[str], seqtype: schrodinger.application.prime.packages.antibody.SeqType, residues: Any) None ¶
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_driver_parser() argparse.ArgumentParser ¶
Return a parser that knows only the arguments that the driver job shouldn’t pass through to the subjobs.
- schrodinger.application.bioluminate.antibody.assembly_yaml.parse_args(argv: List[str]) argparse.Namespace ¶
Parse the command-line arguments.
- schrodinger.application.bioluminate.antibody.assembly_yaml.validate_format_arguments(yaml_contents: Dict[str, any]) None ¶
When the format argument is set, validate that the other arguments are set correctly. There must be at least one argument set for the format specified.
- Parameters
yaml_contents – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.has_data_for_format(args: Dict[str, Any], arg_keys: List[str]) bool ¶
Return a boolean indicating whether there are arguments for a specific format.
- Parameters
args – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.ensure_no_domains_reused(args: Dict[str, Any]) None ¶
Validate that the domains are not reused in the arguments.
- Parameters
args – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_job_spec_from_args(argv: List[str]) schrodinger.job.launchapi.JobSpecification ¶
Return the job specification necessary to run under job control.
- Parameters
argv – List of command-line arguments, including the script name.
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_log_filename(args: argparse.Namespace) str ¶
Get the file name for the log file.
- Parameters
args – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_default_log_filename(args: argparse.Namespace) str ¶
Get the default log file name.
- Parameters
args – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_all_domain_structure_files(yaml_files: List[str]) Iterator[str] ¶
Read in a list of yaml files and return a list of all domain structure files.
- Parameters
yaml_files – list of yaml files
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_domain_structure_files(yaml_dicts: Dict[str, Any]) Iterator[str] ¶
Read in a dictionary of dictionaries and yield the domain structure file names.
- Parameters
yaml_dicts – instruction dictionaries from the yaml files
- schrodinger.application.bioluminate.antibody.assembly_yaml.load_yaml_dictionaries(yaml_filenames: List[str]) Iterator[Dict[str, Any]] ¶
Read the yaml file and yield yaml dictionaries.
- Parameters
yaml_filenames – list of yaml files
- schrodinger.application.bioluminate.antibody.assembly_yaml.extract_input_st_filenames(input_args: Dict[str, Any]) Dict[str, Any] ¶
Extract the input structures.
- Parameters
input_args – command-line arguments in a dictionary format
- schrodinger.application.bioluminate.antibody.assembly_yaml.make_instructions(yaml_dicts: Dict[str, Any]) schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction ¶
Read a dictionary of dictionaries and create assembly.DomainAssemblyInstructions.
- Parameters
yaml_dicts – instruction dictionary from the yaml files
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_output_filename(input_filename: str) str ¶
Derives output file name from input file name.
- Parameters
input_filename – input file name
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_instructions_from_yaml(args: argparse.Namespace) List[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction] ¶
Read the yaml file and create a list of instructions.
- Parameters
args – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.read_structures(args: argparse.Namespace) Dict[str, Any] ¶
Transform the namespace into a dictionary where the input structures have been read in.
- Parameters
args – command-line arguments
- schrodinger.application.bioluminate.antibody.assembly_yaml.compile_instructions_for_format(format: str, input_domains: Dict[str, schrodinger.structure._structure.Structure], template_structure: schrodinger.structure._structure.Structure) Iterator[schrodinger.application.bioluminate.antibody.assembly.DomainAssemblyInstruction] ¶
Compile the assembly instructions from files supplied by the user.
- Parameters
input_dict – the dictionary describing the input
- schrodinger.application.bioluminate.antibody.assembly_yaml.compute_template_data(struct: schrodinger.structure._structure.Structure) Dict[str, Any] ¶
Get the sequence, resid list, and sequence type for each chain in the structure.
- Parameters
struct – structure to compute data for
- schrodinger.application.bioluminate.antibody.assembly_yaml.compute_data(antibody: schrodinger.structure._structure.Structure) Dict[str, Any] ¶
Get the sequence, resid list, and sequence type for each chain in the antibody.
- Parameters
antibody – structure to compute data for
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_chain_pairs(disulfide_bonds: List[Tuple[schrodinger.structure._structure.StructureAtom, schrodinger.structure._structure.StructureAtom]], template_data: Dict[str, Any]) List[Tuple[str, str]] ¶
Get the heavy and light chain pairs.
- Parameters
disulfide_bonds – the disulfide bonds
template_data – the template data
- schrodinger.application.bioluminate.antibody.assembly_yaml.compute_domain_data(input_structures: Dict[str, schrodinger.structure._structure.Structure]) Dict[str, Any] ¶
Compute the domain data.
- Parameters
input_structures – the input structures
- schrodinger.application.bioluminate.antibody.assembly_yaml.match_input_parts(input_dict: Dict[str, Any]) None ¶
Match the input parts.
- Parameters
input_dict – the domain data
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_matching_domain(template_data: Dict[str, Any], domain_key: str, template_domain_used: Dict[str, list]) Tuple[Dict[str, Any], int] ¶
Get the matching template domain.
- Parameters
template_data – the dictionary of the template data
domain_key – the domain key
template_domain_used – the dictionary of the template domains used
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_arm_index(domain_key: str, template_domain_used: Dict[str, bool]) int ¶
Get the arm index.
- Parameters
domain_key – the domain key
template_domain_used – the template domains that have been used
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_domain_key_pair(domain_key: str) str ¶
Get the domain key pair.
- Parameters
domain_key – the domain key
- schrodinger.application.bioluminate.antibody.assembly_yaml.single_ab_chain(domain_label: str) bool ¶
Check if the domain label implies two chains.
- Parameters
domain_label – the domain label
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_next_unused_arm_index(template_domain_used: Dict[str, int]) int ¶
Get the next unused arm index.
- Parameters
template_domain_used – the template domains that have been used
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_matching_arm(template_data: Dict[str, Any], arm_index: int) Dict[str, Any] ¶
Get the matching arm.
- Parameters
template_data – the dictionary of the template data
arm_index – the index of the arm
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_template_domain(matching_arm: Dict[str, Any], domain_name: str) Dict[str, Any] ¶
Get the template domain.
- Parameters
matching_arm_chains – the matching arm chains
domain_name – the domain name
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_align_asl(domain_key: str, struct_dict: Dict[str, Any]) str ¶
Get the alignment asl for the domain.
- Parameters
domain_key – the domain key
struct_dict – the structure dictionary
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_segment_indices(chain_dict: Dict[str, Any], domain_key: str) Tuple[int, int] ¶
Get the segment indices of the chain: either the segment describing the FV region or the segment describing the FAB region depending on the domain key provided for domain alignment.
- Parameters
chain_dict – the chain dictionary
domain_key – the domain key
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_start_range_end_lists(resids: List[str], align_start_index: int, align_end_index: int) Tuple[List[str], List[str], List[str]] ¶
Take the residues and based on the start and end of the alignment, determine if there are insertion codes and if the align asl is simply a range of numbers or needs to contain addtional strings.
- Parameters
resids – the list of resids
align_start_index – the index of the start of the alignment
align_end_index – the index of the end of the alignment
- Returns
the start, range, and end resid lists
The start and end lists are populated if there are insertion codes at the start and end. The range list is populated as the largest range of unambiguous resids.
Example: resids = [‘H:1’, ‘H:1A’, ‘H:2’, ‘H:3’, ‘H:3A’, ‘H:4’, ‘H:5’, ‘H:6’, ‘H:6A’] align_start_index = 1 align_end_index = 7 start_resids = [‘H:1A’] (if ‘H:1A’ was in the range it would include ‘H:1’) range_resids = [‘H:2’, ‘H:3’, ‘H:3A’, ‘H:4’, ‘H:5’] end_resids = [‘H:6’] (if ‘H:6’ was in the range it would include ‘H:6A’)
- schrodinger.application.bioluminate.antibody.assembly_yaml.form_resid_defaultdict(resids: List[str]) Dict[str, List[str]] ¶
Get a dictionary where the keys are each residue number and the values are the corresonding resid list (any resid with the same resnum).
- Parameters
resids – the list of resids
- schrodinger.application.bioluminate.antibody.assembly_yaml.form_inscode_asl(resids: List[str]) str ¶
Form the inscode asl.
- Parameters
resids – the list of resids to make an iscode asl for
- schrodinger.application.bioluminate.antibody.assembly_yaml.form_range_asl(resids: List[str]) str ¶
Get the starting and ending resid from a list and make an asl with the range between those two resids.
- Parameters
resids – the list of resids to make a range asl for
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_bond_asl(domain_key: str, domain_dict: Dict[str, Any], template_dict: Dict[str, Any]) List[Dict[str, str]] ¶
Get the domain bond asl for the domain.
- Parameters
domain_key – the domain key
domain_dict – the domain dictionary
template_dict – the template dictionary
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_matching_chains(domain_dict: Dict[str, Any], template_dict: Dict[str, Any]) Iterator[Tuple[str, str]] ¶
Get the map of domain to template.
- Parameters
domain_dict – the domain dictionary
template_dict – the template dictionary
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_heavy_light_chains(struct_dict: Dict[str, Any]) Tuple[str, str] ¶
Get the heavy and light chain, chain names where the structure dictionary contains only one heavy and one light chain. An error will be raised if there are more than one heavy or light chain.
- Parameters
struct_dict – the domain dictionary
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_domain_bond(domain_key: str, domain_chain: schrodinger.application.bioluminate.antibody.assembly_yaml.ChainData, template_chain: schrodinger.application.bioluminate.antibody.assembly_yaml.ChainData) Dict[str, str] ¶
Get the domain bond.
- Parameters
domain_chain – the domain chain
template_chain – the template chain
- schrodinger.application.bioluminate.antibody.assembly_yaml.get_bond_residue(residues: Iterator[Any], index: int) str ¶
Get the model atom.
- Parameters
residues – the residues
index – the index
- schrodinger.application.bioluminate.antibody.assembly_yaml.main(argv=None)¶