automol 2023.8.0__tar.gz

automol-2023.8.0/LICENSE

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automol-2023.8.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: automol
+Version: 2023.8.0
+Summary: 
+Author: Andreas Copan
+Author-email: avcopan@gmail.com
+Requires-Python: >=3.10,<3.13
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Dist: Mako (>=1.2.4,<2.0.0)
+Requires-Dist: PyYAML (>=6.0.1,<7.0.0)
+Requires-Dist: ipython (>=8.14.0,<9.0.0)
+Requires-Dist: ipywidgets (>=8.1.0,<9.0.0)
+Requires-Dist: more-itertools (>=10.1.0,<11.0.0)
+Requires-Dist: networkx (>=3.1,<4.0)
+Requires-Dist: numpy (>=1.25.2,<2.0.0)
+Requires-Dist: pandas (>=2.0.3,<3.0.0)
+Requires-Dist: py3Dmol (>=2.0.3,<3.0.0)
+Requires-Dist: pyparsing (>=3.1.1,<4.0.0)
+Requires-Dist: pytest (>=7.4.0,<8.0.0)
+Requires-Dist: qcelemental (>=0.26.0,<0.27.0)
+Requires-Dist: rdkit (>=2023.3.3,<2024.0.0)
+Requires-Dist: scipy (>=1.11.2,<2.0.0)
+Description-Content-Type: text/markdown
+
+# Library: AutoChem
+[//]: # (Badges)
+[![CircleCI](https://circleci.com/gh/Auto-Mech/automol/tree/dev.svg?style=shield)](https://circleci.com/gh/Auto-Mech/autoio/tree/dev)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/version.svg)](https://anaconda.org/auto-mech/autoio)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/platforms.svg)](https://anaconda.org/auto-mech/autoio)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/installer/conda.svg)](https://conda.anaconda.org/auto-mech/autoio)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/latest_release_date.svg)](https://conda.anaconda.org/auto-mech/autoio)
+
+Andreas V. Copan, Kevin B. Moore III, Sarah N. Elliott, and Stephen J. Klippenstein
+
+Autochem is a library of molecular toolkit packages, including automol, phydat, and transformations. 
+
+## Installation
+```python
+>>> conda install automol -c auto-mech
+```
+
+<hr size=20>
+
+## Package: phydat
+### Description
+physical constants and data 
+
+### Usage
+Our pytest tests serve as an example for building filesystems
+
+<hr>
+
+## Package: transformations
+### Description
+The Python package "transformations" is developed externally by Christoph Gohlke.
+A README is provided with this package. Further copyright information is provided in 
+_transformations.py
+
+### Usage
+
+<hr>
+
+## Package: automol
+### Description
+- graph
+- geom
+- zmat
+- inchi
+- smiles
+- reac
+- rotor
+External
+- openbabel
+- rdkit
+

automol-2023.8.0/README.md

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+# Library: AutoChem
+[//]: # (Badges)
+[![CircleCI](https://circleci.com/gh/Auto-Mech/automol/tree/dev.svg?style=shield)](https://circleci.com/gh/Auto-Mech/autoio/tree/dev)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/version.svg)](https://anaconda.org/auto-mech/autoio)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/platforms.svg)](https://anaconda.org/auto-mech/autoio)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/installer/conda.svg)](https://conda.anaconda.org/auto-mech/autoio)
+[![Anaconda-Server Badge](https://anaconda.org/auto-mech/automol/badges/latest_release_date.svg)](https://conda.anaconda.org/auto-mech/autoio)
+
+Andreas V. Copan, Kevin B. Moore III, Sarah N. Elliott, and Stephen J. Klippenstein
+
+Autochem is a library of molecular toolkit packages, including automol, phydat, and transformations. 
+
+## Installation
+```python
+>>> conda install automol -c auto-mech
+```
+
+<hr size=20>
+
+## Package: phydat
+### Description
+physical constants and data 
+
+### Usage
+Our pytest tests serve as an example for building filesystems
+
+<hr>
+
+## Package: transformations
+### Description
+The Python package "transformations" is developed externally by Christoph Gohlke.
+A README is provided with this package. Further copyright information is provided in 
+_transformations.py
+
+### Usage
+
+<hr>
+
+## Package: automol
+### Description
+- graph
+- geom
+- zmat
+- inchi
+- smiles
+- reac
+- rotor
+External
+- openbabel
+- rdkit

automol-2023.8.0/automol/__init__.py

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+""" molecular descriptor libraries
+
+automol module hierarchy
+========================
+
+Terminology note: The basic interconvertible molecular types, or "basic types",
+are graph, geom, inchi, smiles, and zmat. Types like formula, inchi_key, and
+vmat are not considered basic types because they cannot be converted
+*back* to the other basic types.
+
+Level 1: No dependencies; no interdependencies
+
+ - par
+ - util
+ - error
+ - mult
+ - formula
+ - inchi_key
+ - vmat
+ - prop
+ - embed
+
+Level 2: L1 dependencies; hierarchical interdependency (descending)
+
+*The base modules contain functions that do not require convertion to another
+basic type.*
+
+ - amchi.base
+ - smiles.base
+ - geom.base
+ - graph.base   [L2 dependencies: geom.base, amchi.base]
+ - zmat.base    [L2 dependencies: geom.base]
+
+Level 3: L1-2 dependencies; hierarchical interdependency (descending)
+
+ - extern       [contains RDKit interface needed for working with InChIs]
+ - inchi.base   [L3 dependencies: extern]
+ - chi.base     [L3 dependencies: extern, inchi.base]
+
+Level 4: L1-3 dependencies; hierarchical interdependency (descending)
+
+*The final modules in level 4 contain all contents from their base modules,
+along with additional functions requiring conversion to another basic type.*
+
+ - geom
+ - graph        [L4 dependencies: geom]
+ - amchi        [L4 dependencies: graph, geom]
+ - inchi        [L4 dependencies: amchi, graph, geom]
+ - chi          [L4 dependencies: amchi, inchi, graph, geom]
+ - smiles       [L4 dependencies: graph]
+ - zmat         [L4 dependencies: graph, geom]
+
+Level 5: L1-4 dependencies; hierarchical interdependency (descending)
+
+ - pot
+ - etrans
+ - combine
+ - reac
+ - rotor        [L5 dependencies: reac]
+ - symm         [L5 dependencies: reac, rotor]
+"""
+
+# L1
+from automol import par
+from automol import util
+from automol import error
+from automol import mult
+from automol import formula
+from automol import inchi_key
+from automol import vmat
+from automol import prop
+from automol import embed
+# L2
+# L3
+from automol import extern
+# L4
+from automol import graph
+from automol import geom
+from automol import amchi
+from automol import inchi
+from automol import smiles
+from automol import zmat
+# L5
+from automol import pot
+from automol import etrans
+from automol import combine
+from automol import reac
+from automol import rotor
+from automol import symm
+
+
+__all__ = [
+    # L1
+    'par',
+    'util',
+    'error',
+    'mult',
+    'formula',
+    'inchi_key',
+    'vmat',
+    'prop',
+    'embed',
+    # L2
+    # L3
+    'extern',
+    # L4
+    'graph',
+    'geom',
+    'amchi',
+    'inchi',
+    'smiles',
+    'smiles',
+    'zmat',
+    # L5
+    'pot',
+    'etrans',
+    'combine',
+    'reac',
+    'rotor',
+    'symm'
+]

automol-2023.8.0/automol/amchi/__init__.py

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+""" AMChI (AutoMech Chemical Identifier) strings
+
+Closely follows the InChI format, although canonicalizations may differ.
+Extends InChI to allow for resonance double-bond stereo.
+"""
+
+# L2
+# # constructor
+from automol.amchi.base._core import from_data
+# # recalculate/standardize
+from automol.amchi.base._core import standard_form
+# # getters
+from automol.amchi.base._core import prefix
+from automol.amchi.base._core import version
+from automol.amchi.base._core import formula_layer
+from automol.amchi.base._core import main_layers
+from automol.amchi.base._core import charge_layers
+from automol.amchi.base._core import stereo_layers
+from automol.amchi.base._core import isotope_layers
+from automol.amchi.base._core import ts_layers
+# # setters
+from automol.amchi.base._core import with_inchi_prefix
+from automol.amchi.base._core import reflect
+from automol.amchi.base._core import canonical_enantiomer
+from automol.amchi.base._core import reflect_reaction
+from automol.amchi.base._core import canonical_enantiomer_reaction
+# # conversions
+from automol.amchi.base._core import formula
+from automol.amchi.base._core import formula_string
+from automol.amchi.base._core import connectivity
+from automol.amchi.base._core import without_stereo
+from automol.amchi.base._core import racemic
+from automol.amchi.base._core import are_enantiomers
+from automol.amchi.base._core import are_diastereomers
+# # properties
+# # # formula layer
+from automol.amchi.base._core import symbols
+from automol.amchi.base._core import canonical_indices
+# # # main layers
+from automol.amchi.base._core import bonds
+from automol.amchi.base._core import hydrogen_valences
+# # # charge layers
+from automol.amchi.base._core import charge
+# # # stereo layers
+from automol.amchi.base._core import bond_stereo_parities
+from automol.amchi.base._core import atom_stereo_parities
+from automol.amchi.base._core import is_inverted_enantiomer
+from automol.amchi.base._core import is_canonical_enantiomer
+from automol.amchi.base._core import is_canonical_enantiomer_reaction
+from automol.amchi.base._core import is_canonical_reaction_direction
+from automol.amchi.base._core import is_enantiomer_list
+from automol.amchi.base._core import is_enantiomer_reaction
+# # # isotope layers
+from automol.amchi.base._core import bond_isotope_stereo_parities
+from automol.amchi.base._core import atom_isotope_stereo_parities
+from automol.amchi.base._core import is_inverted_isotope_enantiomer
+# # other properties
+from automol.amchi.base._core import has_multiple_components
+from automol.amchi.base._core import has_stereo
+from automol.amchi.base._core import has_mobile_hydrogens
+from automol.amchi.base._core import low_spin_multiplicity
+from automol.amchi.base._core import is_enantiomer
+# # comparisons
+from automol.amchi.base._core import same_connectivity
+from automol.amchi.base._core import equivalent
+# # split/join
+from automol.amchi.base._core import split
+from automol.amchi.base._core import join
+# # sort
+from automol.amchi.base._core import sorted_
+from automol.amchi.base._core import argsort
+# # helpers
+from automol.amchi.base._core import join_layers
+from automol.amchi.base._core import split_layers
+from automol.amchi.base._core import join_layer_strings
+from automol.amchi.base._core import _split_layer_string
+# L4
+# # conversions
+from automol.amchi._conv import amchi_key
+from automol.amchi._conv import smiles
+from automol.amchi._conv import graph
+from automol.amchi._conv import geometry
+from automol.amchi._conv import conformers
+from automol.amchi._conv import zmatrix
+from automol.amchi._conv import rdkit_molecule
+from automol.amchi._conv import rdkit_reaction
+from automol.amchi._conv import display
+from automol.amchi._conv import display_reaction
+# # derived properties
+from automol.amchi._conv import is_complete
+# # derived transformations
+from automol.amchi._conv import add_stereo
+from automol.amchi._conv import expand_stereo
+# drawing tools
+from automol.amchi._draw import draw
+from automol.amchi._draw import draw_grid
+# assessment tools
+from automol.amchi._assess import is_valid_multiplicity
+
+# allow this as an alias
+is_chiral = is_enantiomer
+
+
+__all__ = [
+    # L2
+    # # constructor
+    'from_data',
+    # # recalculate/standardize
+    'standard_form',
+    # # getters
+    'prefix',
+    'version',
+    'formula_layer',
+    'main_layers',
+    'charge_layers',
+    'stereo_layers',
+    'isotope_layers',
+    'ts_layers',
+    # # setters
+    'with_inchi_prefix',
+    'reflect',
+    'canonical_enantiomer',
+    'reflect_reaction',
+    'canonical_enantiomer_reaction',
+    # # conversions
+    'formula',
+    'formula_string',
+    'connectivity',
+    'without_stereo',
+    'racemic',
+    'are_enantiomers',
+    'are_diastereomers',
+    # # properties
+    # # # formula layer
+    'symbols',
+    'canonical_indices',
+    # # # main layers
+    'bonds',
+    'hydrogen_valences',
+    # # # charge layers
+    'charge',
+    # # # stereo layers
+    'bond_stereo_parities',
+    'atom_stereo_parities',
+    'is_inverted_enantiomer',
+    'is_canonical_enantiomer',
+    'is_canonical_enantiomer_reaction',
+    'is_canonical_reaction_direction',
+    'is_enantiomer_list',
+    'is_enantiomer_reaction',
+    # # # isotope layers
+    'bond_isotope_stereo_parities',
+    'atom_isotope_stereo_parities',
+    'is_inverted_isotope_enantiomer',
+    # # other properties
+    'has_multiple_components',
+    'is_enantiomer',
+    'is_chiral',
+    'has_stereo',
+    'has_mobile_hydrogens',
+    'low_spin_multiplicity',
+    # # comparisons
+    'same_connectivity',
+    'equivalent',
+    # # split/join
+    'split',
+    'join',
+    # # sort
+    'sorted_',
+    'argsort',
+    'join_layers',
+    'split_layers',
+    'join_layer_strings',
+    '_split_layer_string',
+    # L4
+    # # conversions
+    'amchi_key',
+    'smiles',
+    'graph',
+    'geometry',
+    'conformers',
+    'zmatrix',
+    'rdkit_molecule',
+    'rdkit_reaction',
+    'display',
+    'display_reaction',
+    # # derived properties
+    'is_complete',
+    # # derived transformations
+    'add_stereo',
+    'expand_stereo',
+    # drawing tools
+    'draw',
+    'draw_grid',
+    # assessment tools
+    'is_valid_multiplicity',
+]

automol-2023.8.0/automol/amchi/_assess.py

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+""" Checks that have to be done at the high-level of amchi directory
+    since they require other automol imports
+"""
+
+import numbers
+import automol.graph
+from automol.amchi._conv import graph
+
+
+def is_valid_multiplicity(chi, mul):
+    """ is this multiplicity compatible with this amchi string?
+
+    :param chi: ChI string
+    :type chi: str
+    :param mul: multiplicity
+    :type mul: int
+    :returns: validity of amchi multiplicity
+    :rtype: bool
+    """
+    assert isinstance(mul, numbers.Integral)
+    return mul in automol.graph.possible_spin_multiplicities(
+        graph(chi, stereo=False))