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Cleaning up and adding IUPAC name, InChI, and InChIKey as names for c…
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…onfigurations.
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@paulsaxe
paulsaxe committed Oct 30, 2023
1 parent ef6c7c6 commit d699f98
Showing 1 changed file with 160 additions and 25 deletions.
185 changes: 160 additions & 25 deletions seamm/standard_parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,9 @@
"keep current name",
"use SMILES string",
"use Canonical SMILES string",
"use IUPAC name",
"use InChI",
"use InChIKey",
),
"format_string": "s",
"description": "System name:",
Expand All @@ -70,6 +73,9 @@
"keep current name",
"use SMILES string",
"use Canonical SMILES string",
"use IUPAC name",
"use InChI",
"use InChIKey",
),
"format_string": "s",
"description": "Configuration name:",
Expand All @@ -78,7 +84,7 @@
}


def structure_handling_description(P):
def structure_handling_description(P, **kwargs):
"""Return a standard description for how the structure will be handled.
Parameters
Expand Down Expand Up @@ -106,28 +112,43 @@ def structure_handling_description(P):
raise ValueError(f"Do not understand how to handle the structure: '{handling}'")

sysname = P["system name"]
if sysname == "use SMILES string":
text += " The name of the system will be the SMILES string given."
if sysname == "keep current name":
text += " The name of the system will not be changed."
elif sysname == "use SMILES string":
text += " The name of the system will be its SMILES."
elif sysname == "use Canonical SMILES string":
text += " The name of the system will be the canonical SMILES of the structure."
text += " The name of the system will be its canonical SMILES."
elif sysname == "use IUPAC name":
text += " The name of the system will be its IUPAC name."
elif sysname == "use InChI":
text += " The name of the system will be its InChI."
elif sysname == "use InChIKey":
text += " The name of the system will be its InChIKey."
else:
text += f" The name of the system will be {sysname}."
tmp = safe_format(sysname, **kwargs)
text += f" The name of the system will be '{tmp}'."

confname = P["configuration name"]
if confname == "use SMILES string":
text += " The name of the configuration will be the SMILES string given."
if confname == "keep current name":
text += " The name of the configuration will not be changed."
elif confname == "use SMILES string":
text += " The name of the configuration will be its SMILES."
elif confname == "use Canonical SMILES string":
text += (
" The name of the configuration will be the canonical SMILES of the "
"structure."
)
text += " The name of the configuration will be its canonical SMILES."
elif confname == "use IUPAC name":
text += " The name of the configuration will be its IUPAC name."
elif confname == "use InChI":
text += " The name of the configuration will be its InChI."
elif confname == "use InChIKey":
text += " The name of the configuration will be its InChIKey."
else:
text += f" The name of the configuration will be {confname}."
tmp = safe_format(confname, **kwargs)
text += f" The name of the configuration will be '{tmp}'."

return text


def multiple_structure_handling_description(P):
def multiple_structure_handling_description(P, **kwargs):
"""Return a standard description for how the new structures will be handled.
Parameters
Expand All @@ -148,9 +169,9 @@ def multiple_structure_handling_description(P):
if handling == "Overwrite the current configuration":
text += "overwrite the current configuration."
elif handling == "Create a new configuration":
text += "created as a new configuration of the current system."
text += "be added as a new configuration of the current system."
elif handling == "Create a new system and configuration":
text += "created in a new system and configuration."
text += "be added as a new system and configuration."
else:
raise ValueError(f"Do not understand how to handle the structure: '{handling}'")

Expand All @@ -164,22 +185,136 @@ def multiple_structure_handling_description(P):
raise ValueError(f"Do not understand how to handle the structure: '{handling}'")

sysname = P["system name"]
if sysname == "use SMILES string":
text += " The name of the system will be the SMILES string given."
if sysname == "keep current name":
text += " The name of the system will not be changed."
elif sysname == "use SMILES string":
text += " The name of the system will be its SMILES."
elif sysname == "use Canonical SMILES string":
text += " The name of the system will be the canonical SMILES of the structure."
text += " The name of the system will be its canonical SMILES."
elif sysname == "use IUPAC name":
text += " The name of the system will be its IUPAC name."
elif sysname == "use InChI":
text += " The name of the system will be its InChI."
elif sysname == "use InChIKey":
text += " The name of the system will be its InChIKey."
else:
text += f" The name of the system will be {sysname}."
tmp = safe_format(sysname, **kwargs)
text += f" The name of the system will be '{tmp}'."

confname = P["configuration name"]
if confname == "use SMILES string":
text += " The name of the configuration will be the SMILES string given."
if confname == "keep current name":
text += " The name of the configuration will not be changed."
elif confname == "use SMILES string":
text += " The name of the configuration will be its SMILES."
elif confname == "use Canonical SMILES string":
text += (
" The name of the configuration will be the canonical SMILES of the "
"structure."
text += " The name of the configuration will be its canonical SMILES."
elif confname == "use IUPAC name":
text += " The name of the configuration will be its IUPAC name."
elif confname == "use InChI":
text += " The name of the configuration will be its InChI."
elif confname == "use InChIKey":
text += " The name of the configuration will be its InChIKey."
else:
tmp = safe_format(confname, **kwargs)
text += f" The name of the configuration will be '{tmp}'."

return text


def set_names(system, configuration, P, _first=True, **kwargs):
"""Set the names of the system and configuration.
Parameters
----------
system : _System
The system being named
configuration : _Configuration
The configuration being named
P : dict(str, any)
The dictionary of parameter values, which must contain the standard structure
handling parameters.
_first : bool
Whether this is the first or a subseqnet structure.
kwargs : {str: str}
keyword arguments providing values that may be substituted in the names.
Returns
-------
str
The text for printing.
"""
sysname = P["system name"]
if sysname == "keep current name":
pass
elif sysname == "use SMILES string":
system.name = configuration.smiles
elif sysname == "use Canonical SMILES string":
system.name = configuration.canonical_smiles
elif sysname == "use IUPAC name":
system.name = configuration.PC_iupac_name(fallback=configuration.formula[0])
elif sysname == "use InChI":
system.name = configuration.inchi
elif sysname == "use InChIKey":
system.name = configuration.inchikey
else:
system.name = safe_format(sysname, **kwargs)

confname = P["configuration name"]
if confname == "keep current name":
pass
elif confname == "use SMILES string":
configuration.name = configuration.smiles
elif confname == "use Canonical SMILES string":
configuration.name = configuration.canonical_smiles
elif confname == "use IUPAC name":
configuration.name = configuration.PC_iupac_name(
fallback=configuration.formula[0]
)
elif confname == "use InChI":
configuration.name = configuration.inchi
elif confname == "use InChIKey":
configuration.name = configuration.inchikey
else:
configuration.name = safe_format(confname, **kwargs)

if _first:
text = "The first structure "

handling = P["structure handling"]
if handling == "Overwrite the current configuration":
text += "overwrote the current configuration, and was"
elif handling == "Create a new configuration":
text += "was added as a new configuration of the current system"
elif handling == "Create a new system and configuration":
text += "was added as a new system and configuration "
else:
raise ValueError(
f"Do not understand how to handle the structure: '{handling}'"
)
else:
text += f" The name of the configuration will be {confname}."
handling = P["subsequent structure handling"]
text = "This subsequent structure was "
if handling == "Create a new configuration":
text += "created as a new configuration of the current system"
elif handling == "Create a new system and configuration":
text += "created in a new system and configuration"
else:
raise ValueError(
f"Do not understand how to handle the structure: '{handling}'"
)

text += f" named '{system.name}' / '{configuration.name}'."
return text


def safe_format(s, *args, **kwargs):
while True:
try:
return s.format(*args, **kwargs)
except KeyError as e:
e = e.args[0]
kwargs[e] = "{%s}" % e

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