molSimplify 1.7.6__tar.gz → 2.0.0__tar.gz

{molsimplify-1.7.6 → molsimplify-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: molSimplify
-Version: 1.7.6
+Version: 2.0.0
 License:                     GNU GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
         
@@ -691,6 +691,9 @@ Requires-Dist: keras
 Requires-Dist: tensorflow
 Requires-Dist: pyyaml
 Requires-Dist: importlib-resources
+Requires-Dist: matplotlib
+Requires-Dist: pydentate
+Requires-Dist: setuptools
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-resource-path; extra == "dev"
@@ -700,6 +703,7 @@ Requires-Dist: beautifulsoup4; extra == "docs"
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: readthedocs-sphinx-ext; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Dynamic: license-file
 
 ![](./molSimplify/icons/logo_enhanced.png)
 [![Pytest](https://github.com/hjkgrp/molSimplify/actions/workflows/pytest.yaml/badge.svg)](https://github.com/hjkgrp/molSimplify/actions/workflows/pytest.yaml)
@@ -712,7 +716,7 @@ molSimplify is an open source toolkit for the automated, first-principles screen
 
 ### via pip, from PyPI
 
-Starting with version `1.7.4` molSimplify is available on [PyPI](https://pypi.org) enabled by the [openbabel-wheel](https://pypi.org/project/openbabel-wheel/) project.
+Starting with version `1.7.4`, molSimplify is available on [PyPI](https://pypi.org) enabled by the [openbabel-wheel](https://pypi.org/project/openbabel-wheel/) project. It is recommended to make a new conda environment with Python 3.8, activate it, and then run the following command:
 
 ```bash
 pip install molSimplify
@@ -728,11 +732,21 @@ To obtain the latest development version or if you plan to modify the code we re
    git clone https://github.com/hjkgrp/molSimplify.git
    cd molSimplify
    ```
-2. Locally install the molSimplify package using pip.
+2. Create a new conda environment and specify the desired Python version (we currently recommend 3.8). You can change the environment name `molsimp` according to your preference.
+
+   ```bash
+   conda create --name molsimp python=3.8
+   ```
+   Then activate the environment.
+   ```bash
+   conda activate molsimp
+   ```
+3. Locally install the molSimplify package using pip.
    ```bash
    pip install -e .[dev]
    ```
-3. To test your installation, you can run the command below at the root directory of molSimplify. You are good to go if all the tests are passed! Note, some test will be skipped because none of the optional dependencies are installed this way.
+   On Mac, the command to use is instead `pip install -e '.[dev]'` or `pip install -e .\[dev\]`.
+4. To test your installation, you can run the command below at the root directory of molSimplify. You are good to go if all the tests are passed! Note, some test will be skipped because none of the optional dependencies are installed this way.
    ```bash
    pytest
    ```
@@ -740,7 +754,7 @@ To obtain the latest development version or if you plan to modify the code we re
 ### via conda, from GitHub
 
 The easiest way of installing molSimplify including optional dependencies such as [xtb](https://github.com/grimme-lab/xtb) is via the [Conda](https://conda.io/docs/) package management system.
-1. Prerequisite: have [Anaconda or miniconda](https://www.anaconda.com/distribution/) installed on your system. **For M1 Macs, please use [Miniforge](https://github.com/conda-forge/miniforge) for Mac OSX arm64.** (We do not recommend simultaneously installing Anaconda and Miniforge - only install Miniforge.)
+1. Prerequisite: have [Anaconda](https://docs.anaconda.com/anaconda/) or [miniconda](https://docs.anaconda.com/miniconda/) installed on your system. We recommend use of the [libmamba solver](https://conda.github.io/conda-libmamba-solver/user-guide/). **For M1 Macs, please use [Miniforge](https://github.com/conda-forge/miniforge) for Mac OSX arm64.** (We do not recommend simultaneously installing Anaconda and Miniforge - only install Miniforge.)
 
 2. Clone molSimplify source from github and change into the directory.
 
@@ -791,13 +805,13 @@ molSimplify is research software. If you use it for work that results in a publi
 ```
 @Article {molSimplify,
 author = {Ioannidis, Efthymios I. and Gani, Terry Z. H. and Kulik, Heather J.},
-title = {molSimplify: A toolkit for automating discovery in inorganic chemistry},
+title = {molSimplify: A Toolkit for Automating Discovery in Inorganic Chemistry},
 journal = {Journal of Computational Chemistry},
 volume = {37},
 number = {22},
-pages = {2106--2117},
+pages = {2106-2117},
 issn = {1096-987X},
-url = {http://dx.doi.org/10.1002/jcc.24437},
+url = {http://doi.org/10.1002/jcc.24437},
 doi = {10.1002/jcc.24437},
 year = {2016},
 }
@@ -814,8 +828,20 @@ url = {https://doi.org/10.1021/acs.iecr.8b04015},
 doi = {10.1021/acs.iecr.8b04015},
 year = {2018},
 }
+
+@Article{molSimplify2.0,
+author = {Terrones, Gianmarco G. and St. Michel, Roland G. and Toney, Jacob W. and Ball, Akash K. and Wang, Yiran and Garrison, Aaron G. and Nandy, Aditya and Meyer, Ralf and Edholm, Freya and Oh, Changhwan and Pujet, Sebastian G. and Chu, Daniel B. K. and Muhammetgulyyev, Davut and Kulik, Heather J.},
+title = {molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry},
+volume = {66},
+number = {5},
+pages = {2753-2767},
+url = {https://doi.org/10.1021/acs.jcim.5c02733},
+doi = {10.1021/acs.jcim.5c02733},
+year = {2026},
+}
 ```
 
-If you use any machine learning (ML) models in molSimplify that results in a publication, please cite the corresponding reference in [this ML model reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md).
+If you use any machine learning (ML) models in molSimplify, please cite the corresponding reference in [this ML model reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md).
+For additional reference information, please see [here](https://molsimplify.readthedocs.io/en/latest/Citation.html).
 
 **Note that we have disabled developers' supports for Python 2.7 and will only release conda builds on Python 3.**

{molsimplify-1.7.6 → molsimplify-2.0.0}/README.md

@@ -9,7 +9,7 @@ molSimplify is an open source toolkit for the automated, first-principles screen
 
 ### via pip, from PyPI
 
-Starting with version `1.7.4` molSimplify is available on [PyPI](https://pypi.org) enabled by the [openbabel-wheel](https://pypi.org/project/openbabel-wheel/) project.
+Starting with version `1.7.4`, molSimplify is available on [PyPI](https://pypi.org) enabled by the [openbabel-wheel](https://pypi.org/project/openbabel-wheel/) project. It is recommended to make a new conda environment with Python 3.8, activate it, and then run the following command:
 
 ```bash
 pip install molSimplify
@@ -25,11 +25,21 @@ To obtain the latest development version or if you plan to modify the code we re
    git clone https://github.com/hjkgrp/molSimplify.git
    cd molSimplify
    ```
-2. Locally install the molSimplify package using pip.
+2. Create a new conda environment and specify the desired Python version (we currently recommend 3.8). You can change the environment name `molsimp` according to your preference.
+
+   ```bash
+   conda create --name molsimp python=3.8
+   ```
+   Then activate the environment.
+   ```bash
+   conda activate molsimp
+   ```
+3. Locally install the molSimplify package using pip.
    ```bash
    pip install -e .[dev]
    ```
-3. To test your installation, you can run the command below at the root directory of molSimplify. You are good to go if all the tests are passed! Note, some test will be skipped because none of the optional dependencies are installed this way.
+   On Mac, the command to use is instead `pip install -e '.[dev]'` or `pip install -e .\[dev\]`.
+4. To test your installation, you can run the command below at the root directory of molSimplify. You are good to go if all the tests are passed! Note, some test will be skipped because none of the optional dependencies are installed this way.
    ```bash
    pytest
    ```
@@ -37,7 +47,7 @@ To obtain the latest development version or if you plan to modify the code we re
 ### via conda, from GitHub
 
 The easiest way of installing molSimplify including optional dependencies such as [xtb](https://github.com/grimme-lab/xtb) is via the [Conda](https://conda.io/docs/) package management system.
-1. Prerequisite: have [Anaconda or miniconda](https://www.anaconda.com/distribution/) installed on your system. **For M1 Macs, please use [Miniforge](https://github.com/conda-forge/miniforge) for Mac OSX arm64.** (We do not recommend simultaneously installing Anaconda and Miniforge - only install Miniforge.)
+1. Prerequisite: have [Anaconda](https://docs.anaconda.com/anaconda/) or [miniconda](https://docs.anaconda.com/miniconda/) installed on your system. We recommend use of the [libmamba solver](https://conda.github.io/conda-libmamba-solver/user-guide/). **For M1 Macs, please use [Miniforge](https://github.com/conda-forge/miniforge) for Mac OSX arm64.** (We do not recommend simultaneously installing Anaconda and Miniforge - only install Miniforge.)
 
 2. Clone molSimplify source from github and change into the directory.
 
@@ -88,13 +98,13 @@ molSimplify is research software. If you use it for work that results in a publi
 ```
 @Article {molSimplify,
 author = {Ioannidis, Efthymios I. and Gani, Terry Z. H. and Kulik, Heather J.},
-title = {molSimplify: A toolkit for automating discovery in inorganic chemistry},
+title = {molSimplify: A Toolkit for Automating Discovery in Inorganic Chemistry},
 journal = {Journal of Computational Chemistry},
 volume = {37},
 number = {22},
-pages = {2106--2117},
+pages = {2106-2117},
 issn = {1096-987X},
-url = {http://dx.doi.org/10.1002/jcc.24437},
+url = {http://doi.org/10.1002/jcc.24437},
 doi = {10.1002/jcc.24437},
 year = {2016},
 }
@@ -111,8 +121,20 @@ url = {https://doi.org/10.1021/acs.iecr.8b04015},
 doi = {10.1021/acs.iecr.8b04015},
 year = {2018},
 }
+
+@Article{molSimplify2.0,
+author = {Terrones, Gianmarco G. and St. Michel, Roland G. and Toney, Jacob W. and Ball, Akash K. and Wang, Yiran and Garrison, Aaron G. and Nandy, Aditya and Meyer, Ralf and Edholm, Freya and Oh, Changhwan and Pujet, Sebastian G. and Chu, Daniel B. K. and Muhammetgulyyev, Davut and Kulik, Heather J.},
+title = {molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry},
+volume = {66},
+number = {5},
+pages = {2753-2767},
+url = {https://doi.org/10.1021/acs.jcim.5c02733},
+doi = {10.1021/acs.jcim.5c02733},
+year = {2026},
+}
 ```
 
-If you use any machine learning (ML) models in molSimplify that results in a publication, please cite the corresponding reference in [this ML model reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md).
+If you use any machine learning (ML) models in molSimplify, please cite the corresponding reference in [this ML model reference page](https://github.com/hjkgrp/molSimplify/blob/master/MLmodel-reference.md).
+For additional reference information, please see [here](https://molsimplify.readthedocs.io/en/latest/Citation.html).
 
 **Note that we have disabled developers' supports for Python 2.7 and will only release conda builds on Python 3.**

{molsimplify-1.7.6 → molsimplify-2.0.0}/molSimplify/Classes/atom3D.py

@@ -5,25 +5,28 @@
 #
 #  Department of Chemical Engineering, MIT
 
-from math import sqrt
+import numpy as np
 from typing import List, Optional
 from molSimplify.Classes.globalvars import globalvars
 
 
 class atom3D:
-    """ atom3D class. Base class in molSimplify for representing an element.
-
-        Parameters
-        ----------
-            Sym : str, optional
-                Symbol for atom3D instantiation. Element symbol. Default is 'C'.
-            xyz : list, optional
-                List of coordinates for new atom. Default is [0.0, 0.0, 0.0].
-            name : str, optional
-                Unique identifier for atom 3D instantiation. Default is False.
-            partialcharge : int, optional
-                Charge assigned to atom when added to mol. Default is None.
     """
+    atom3D class. Base class in molSimplify for representing an element.
+
+    Parameters
+    ----------
+        Sym : str, optional
+            Symbol for atom3D instantiation. Element symbol. Default is 'C'.
+        xyz : list, optional
+            List of coordinates for new atom. Default is [0.0, 0.0, 0.0].
+            Units of angstroms.
+        name : str, optional
+            Unique identifier for atom 3D instantiation. Default is False.
+        partialcharge : int, optional
+            Charge assigned to atom when added to mol. Default is None.
+    """
+
     def __init__(self,
                  Sym: str = 'C',
                  xyz: Optional[List[float]] = None,
@@ -40,8 +43,8 @@ class atom3D:
         self.partialcharge = partialcharge
         globs = globalvars()
         amass = globs.amass()
-        if Sym not in amass:  # assign default values if not in dictionary
-            print(("We didn't find the atomic mass of %s in the dictionary. Assigning default value of 12!\n" % (Sym)))
+        if Sym not in amass:  # Assign default values if not in dictionary.
+            print(f"We didn't find the atomic mass of {Sym} in the dictionary. Assigning default value of 12!\n")
             # Atomic mass
             self.mass = 12.0  # default atomic mass
             # Atomic number
@@ -65,7 +68,13 @@ class atom3D:
         # Coordinates
         if xyz is None:
             xyz = [0.0, 0.0, 0.0]
-        self.__xyz = xyz
+        elif not isinstance(xyz, (list, np.ndarray)) or len(xyz) != 3:
+            raise ValueError('xyz should be a list of length 3.')
+        try:
+            np.array(xyz, dtype=np.float64)
+        except ValueError:
+            raise ValueError('List xyz should consist of numbers.')
+        self.__xyz = list(xyz)
 
         # Temperature factor (only useful for proteins)
         self.Tfactor = Tfactor
@@ -100,109 +109,128 @@ class atom3D:
     #         return False
 
     def coords(self):
-        """ Get coordinates of a given atom.
+        """
+        Get coordinates of a given atom.
 
         Returns
         -------
             coords : list
                 List of coordinates in X, Y, Z format.
+                Units of angstroms.
         """
-        x, y, z = self.__xyz
-        return [x, y, z]
 
-    def distance(self, atom2) -> float:
-        """ Get distance from one atom3D class to another.
+        coords = self.__xyz.copy()
+        return coords
+
+    def distance(self, atom2):
+        """
+        Get distance from one atom3D class to another.
 
         Parameters
         ----------
             atom2 : atom3D
                 atom3D class of the atom to measure distance from.
 
-
         Returns
         -------
             dist : float
                 Distance in angstroms.
         """
+
         xyz = self.coords()
         point = atom2.coords()
-        dx = xyz[0]-point[0]
-        dy = xyz[1]-point[1]
-        dz = xyz[2]-point[2]
-        return sqrt(dx*dx+dy*dy+dz*dz)
+        dist = np.linalg.norm(np.array(xyz)-np.array(point))
+        return dist
 
     def distancev(self, atom2):
-        """ Get distance vector from one atom3D class to another.
+        """
+        Get distance vector from one atom3D class to another.
 
         Parameters
         ----------
             atom2 : atom3D
                 atom3D class of the atom to measure distance from.
 
-
         Returns
         -------
             dist_list : list
-                List of distances in vector form: [dx, dy, dz] with units of Angstroms.
+                List of distances in vector form: [dx, dy, dz] with units of angstroms.
         """
+
         xyz = self.coords()
         point = atom2.coords()
-        dx = xyz[0]-point[0]
-        dy = xyz[1]-point[1]
-        dz = xyz[2]-point[2]
-        return [dx, dy, dz]
+        dist_list = list(np.array(xyz)-np.array(point))
+        return dist_list
 
-    def ismetal(self, transition_metals_only=True) -> bool:
-        """ Identify whether an atom is a metal.
+    def ismetal(self, transition_metals_only=True, include_X=False) -> bool:
+        """
+        Identify whether an atom is a metal.
 
         Parameters
         ----------
             transition_metals_only : bool, optional
-                Identify only transition metals. Default is true.
+                Identify only transition metals.
+                Default is True.
+            include_X : bool, optional
+                Whether "X" atoms are considered metals.
+                Default is False.
 
         Returns
         -------
             metal : bool
                 Bool for whether or not an atom is a metal.
         """
-        return self.sym in globalvars().metalslist(transition_metals_only=transition_metals_only)
+
+        return self.sym in globalvars().metalslist(transition_metals_only=transition_metals_only,
+            include_X=include_X)
 
     def setcoords(self, xyz):
-        """ Set coordinates of an atom3D class to a new location.
+        """
+        Set coordinates of an atom3D class to a new location.
 
         Parameters
         ----------
             xyz : list
                 List of coordinates, has length 3: [X, Y, Z]
+                Units of angstroms.
         """
-        self.__xyz[0] = xyz[0]
-        self.__xyz[1] = xyz[1]
-        self.__xyz[2] = xyz[2]
+
+        if not isinstance(xyz, (list, np.ndarray)) or len(xyz) != 3:
+            raise ValueError('xyz should be a list of length 3.')
+        try:
+            np.array(xyz, dtype=np.float64)
+        except ValueError:
+            raise ValueError('List xyz should consist of numbers.')
+
+        self.__xyz = list(xyz)
 
     def symbol(self) -> str:
-        """ Return symbol of atom3D.
+        """
+        Return symbol of atom3D.
 
         Returns
         -------
             symbol : str
                 Element symbol for atom3D class.
         """
+
         return self.sym
 
     def mutate(self, newType='C'):
-        """ Mutate an element to another element in the atom3D.
+        """
+        Mutate an element to another element in the atom3D.
 
         Parameters
         ----------
             newType : str, optional
                 Element name for new element. Default is 'C'.
-
         """
+
         globs = globalvars()
         amass = globs.amass()
         if newType not in list(amass.keys()):
-            print(('Error, unknown atom atom type transformation to ' + str(newType)))
-            print('no changes made')
+            print(f'Error, unknown atom type transformation to {newType}.')
+            print('No changes made.')
         else:
             self.mass = amass[newType][0]
             self.atno = amass[newType][1]
@@ -211,25 +239,26 @@ class atom3D:
             self.sym = newType
 
     def translate(self, dxyz):
-        """ Move the atom3D by a displacement vector.
+        """
+        Move the atom3D by a displacement vector.
 
         Parameters
         ----------
             dxyz : list
                 Displacement vector of length 3: [dx, dy, dz].
-
+                Units of angstroms.
         """
-        x, y, z = self.__xyz
-        self.__xyz[0] = x + dxyz[0]
-        self.__xyz[1] = y + dxyz[1]
-        self.__xyz[2] = z + dxyz[2]
+
+        self.__xyz = list(np.array(self.__xyz)+np.array(dxyz))
 
     def setEDIA(self, score):
-        """ Sets the EDIA score of an individual atom3D.
+        """
+        Sets the EDIA score of an individual atom3D.
 
         Parameters
         ----------
             score : float
                 Desired EDIA score of atom
         """
+
         self.EDIA = score

{molsimplify-1.7.6 → molsimplify-2.0.0}/molSimplify/Classes/dft_obs.py

@@ -5,13 +5,16 @@
 #
 #  Dpt of Chemical Engineering, MIT
 
-from molSimplify.Informatics.lacRACAssemble import (
-    generate_all_ligand_autocorrelations,
-    generate_all_ligand_deltametrics,
+from molSimplify.Informatics.autocorrelation import(
     generate_full_complex_autocorrelations,
     generate_metal_autocorrelations,
     generate_metal_deltametrics,
-    generate_all_ligand_misc)
+    )
+from molSimplify.Informatics.lacRACAssemble import (
+    generate_all_ligand_autocorrelations_lac,
+    generate_all_ligand_deltametrics_lac,
+    generate_all_ligand_misc,
+    )
 from molSimplify.Classes.mol3D import mol3D
 
 # DFT observations used to postprocess DFT results by measuring ligand properties
@@ -54,47 +57,43 @@ class dft_observation:
                 results_dictionary['colnames'], results_dictionary['result_ax'], 'misc', 'ax')
             self.append_descriptors(
                 results_dictionary['colnames'], results_dictionary['result_eq'], 'misc', 'eq')
-        print(('after adding misc descriptors... ' +
-               str(len(self.descriptor_names))))
+        print(f'after adding misc descriptors... {len(self.descriptor_names)}')
         if self.coord == 6:  # oct only
-            results_dictionary = generate_all_ligand_autocorrelations(
+            results_dictionary = generate_all_ligand_autocorrelations_lac(
                 self.mol, depth=3, loud=loud, flag_name=flag_name)
             self.append_descriptors(
                 results_dictionary['colnames'], results_dictionary['result_ax_full'], 'f', 'ax')
             self.append_descriptors(
                 results_dictionary['colnames'], results_dictionary['result_eq_full'], 'f', 'eq')
-            print(('after adding full ax/eq descriptors... ' +
-                   str(len(self.descriptor_names))))
+            print(f'after adding full ax/eq descriptors... {len(self.descriptor_names)}')
             if not simple and not lig_only:
                 self.append_descriptors(
                     results_dictionary['colnames'], results_dictionary['result_ax_con'], 'lc', 'ax')
                 self.append_descriptors(
                     results_dictionary['colnames'], results_dictionary['result_eq_con'], 'lc', 'eq')
-                results_dictionary = generate_all_ligand_deltametrics(
+                results_dictionary = generate_all_ligand_deltametrics_lac(
                     self.mol, depth=3, loud=True, flag_name=flag_name)
                 self.append_descriptors(
                     results_dictionary['colnames'], results_dictionary['result_ax_con'], 'D_lc', 'ax')
                 self.append_descriptors(
                     results_dictionary['colnames'], results_dictionary['result_eq_con'], 'D_lc', 'eq')
 
-                print(('after adding lc ax/eq descriptors... ' +
-                       str(len(self.descriptor_names))))
+                print(f'after adding lc ax/eq descriptors... {len(self.descriptor_names)}')
         if not lig_only:
             if not simple:
                 results_dictionary = generate_metal_autocorrelations(
-                    self.mol, depth=3, loud=loud)
+                    self.mol, depth=3)
                 self.append_descriptors(
                     results_dictionary['colnames'], results_dictionary['results'], 'mc', 'all')
                 results_dictionary = generate_metal_deltametrics(
-                    self.mol, depth=3, loud=loud)
+                    self.mol, depth=3)
                 self.append_descriptors(
                     results_dictionary['colnames'], results_dictionary['results'], 'D_mc', 'all')
             results_dictionary = generate_full_complex_autocorrelations(
-                self.mol, depth=3, loud=loud)
+                self.mol, depth=3)
             self.append_descriptors(
                 results_dictionary['colnames'], results_dictionary['results'], 'f', 'all')
-        print(('after adding full complex descriptors... ' +
-               str(len(self.descriptor_names))))
+        print(f'after adding full complex descriptors... {len(self.descriptor_names)}')
 
     def append_descriptors(self, list_of_names, list_of_props, prefix, suffix):
         for names in list_of_names: