schrodinger.application.jaguar.autots_input module¶

Functions and classes for defining the input to a AutoTS workflow.

schrodinger.application.jaguar.autots_input.read_mae_files(fhlist: List[str], clean_st: bool, fileonly: bool = False, reset_bonding: bool = True) → Union[List[schrodinger.structure._structure.Structure], List[str]]¶

Process a list of mae files and return extant file paths or associated Structure instances if requested.

Parameters

fhlist – list of filehandles
clean_st – if True, cleanup structure file by removing dummy atoms, etc.
fileonly – if True, return only file paths, else Structures.
reset_bonding – if True and clean_st is True, redefine bonding using mmjag.

Returns

Structures or file paths.

class schrodinger.application.jaguar.autots_input.AutoTSInput(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jaguar_keywords: Optional[dict] = None, jobname: Optional[str] = None, add_autots_jaguar_defaults: bool = False)¶

Bases: schrodinger.application.jaguar.workflow_input.WorkflowInput

A class to completely specify a AutoTS calculation.

Example usage:

input = AutoTSInput()
# Set user-defined values
input.setValue('integerKW', 3)
input.setValue('floatKW', '7.0')
input.setValue('stringKW', 'foo')

# Print all keyword/value pairs.
for keyword in input:
    print "keyword '%s' has value %s" % (keyword, input[keyword])

# Handling the case of trying to set an unsupported keyword
try:
    input['mykeyword'] = 'value'
except WorkflowKeywordException as e:
    print e.allowed_keywords

input_file_keys = ['reactant', 'product', 'reactant_complex', 'product_complex', 'template_database_file', 'full_path_file', 'full_path_separated', 'conf_search_file', 'spectators', 'graft_structures']¶

workflow_name = 'AutoTS'¶

__init__(inputfile: Optional[str] = None, keywords: Optional[dict] = None, jaguar_keywords: Optional[dict] = None, jobname: Optional[str] = None, add_autots_jaguar_defaults: bool = False)¶

Create a AutoTSInput instance. If a keyword is specified in both ‘inputfile’ and ‘keywords’, then the values in ‘keywords’ will be set preferrentially. This also applies to ‘jaguar_keywords’.

Parameters

inputfile – Path to a AutoTS input file
keywords – AutoTS keyword/value pairs
jaguar_keywords – Jaguar &gen section keyword/value pairs
jobname – Name of job, if it is not None it will be set to the basename of the input file name.
add_autots_jaguar_defaults – if True add some custom Jaguar defaults

property reaction_smarts: str¶: Reaction smarts identifying input reaction

static generate_keywords() → dict¶: Initialize dictionary of all possible AutoTS keywords

setJaguarValues(keywords: dict)¶

Set multiple Jaguar &gen section keywords.

Parameters: keywords – Jaguar &gen section keyword/value pairs

updateJaguarUserKeywords(keywords: dict)¶

Update the Jaguar &gen section keywords of the user-defined settings only if previous settings exist.

Parameters: keywords (dict of string/anytype pairs) – Jaguar &gen section keyword/value pairs

getReactants(fileonly: bool = False, clean_st: bool = False, reset_bonding: bool = True) → Union[List[schrodinger.structure._structure.Structure], List[str]]¶

Return list of reactants. If no file(s) found, return empty list.

Parameters

fileonly – if True, return only file paths, else Structures.
clean_st – if True redefine bonding using mmlewis.
reset_bonding – if True and clean_st is True, redefine bonding using mmjag.

Returns

reactant Structures or file paths.

getProducts(fileonly: bool = False, clean_st: bool = False, reset_bonding: bool = True) → Union[List[schrodinger.structure._structure.Structure], List[str]]¶

Return list of products. If no file(s) found, return empty list.

Parameters

fileonly – if True, return only file paths, else Structures.
clean_st – if True redefine bonding using mmlewis.
reset_bonding – if True and clean_st is True, redefine bonding using mmjag.

Returns

product Structures or file paths.

getReactantComplex(clean_st: bool = False, reset_bonding: bool = True) → Optional[schrodinger.structure._structure.Structure]¶

Return Reactant Complex. If no file found, return NoneType.

Parameters

clean_st – if True redefine bonding using mmlewis.
reset_bonding – if True and clean_st is True, redefine bonding using mmjag.

Returns

Reactant Complex Structures or file path.

getProductComplex(clean_st: bool = False, reset_bonding: bool = True) → Optional[schrodinger.structure._structure.Structure]¶

Return Product Complex. If no file found, return NoneType.

Parameters

clean_st – if True redefine bonding using mmlewis.
reset_bonding – if True and clean_st is True, redefine bonding using mmjag.

Returns

Product Complex Structures or file path.

getSpectators(clean_st: bool = False) → Optional[List[schrodinger.structure._structure.Structure]]¶

Return spectator. If no file found, return NoneType.

Parameters: clean_st – if True redefine bonding using mmlewis.
Returns: Reactant Complex Structures or file path.

validate()¶

Perform a self-consistency check of all currently set keywords.

:raise WorkflowKeywordConflictError if conflicting values found :raise WorkflowConservationError if matter not conserved

validate_jaguar_keywords(strs)¶: Perform a check to ensure that Jaguar keywords are not set that AutoTS cannot handle.

setConstants()¶: Set any constants defined by keywords

read(inputfile: str)¶

Read an existing AutoTS input file. Any keywords specified in the input file will override existing values in this AutoTSInput instance.

Jaguar &gen section keywords are defined like:

&JaguarKeywords
  key=val
  key=val
  ...
&

Constraints can be defined with:

&Constraints
    st_title atom_index1 atom_index2... value
&

Parameters: inputfile – Path to a AutoTS input file

set_default_template_file()¶: If the default template file is not set and the keyword use_default_templates is True and that file exists, set the template file to the default one.

schrodinger.application.jaguar.autots_input.users_default_template_filename() → str¶: Returns the name of the users template file that should be found in .schrodinger/autots_templates. The file may or may not exist.