=============
MolSystem
=============
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Description
-----------
Molsystem provides a general class for handling molecular and periodic systems. This is
the heart of SEAMM.
* Free software: GNU Lesser General Public License v3+
* Documentation: https://molsystem.readthedocs.io.
Features
--------
* Supports molecular and periodic (crystalline) systems.
* Support for pointgroup and spacegroup symmetry.
* Implemented as a SQL database, currently using SQLite, which provides permanence and a
disk file.
* Handles multiple systems, and for each system any number of
configurations. Configurations are different structures, generally having different
coordinates. Examples are conformers or frames in an MD trajectory.
* Configurations can have differing bonds, supporting reactive forcefields such as
ReaxFF.
* Configurations can also have differing numbers of atoms, supporting e.g. grand
canonical Monte Carlo.
* Support for templates and subsets. Templates can be used for creating or finding
structures in systems and subsets hold substes of atoms. An atom can be in multiple
subsets. For proteins, subsets can be used for residues and chains; for polymers,
monomers; and for fluids the subsets can track individual molecules.
* Subsets and templates handle the correspondance between atoms so if, for instance, the
ordering of atoms in residues are different, that can be handled using the
correspondances.
* Direct connection to and support of RDKit and OpenBabel molecules, allowing direct
transfer back and forth between configurations and those libraries.
* Properties of systems and configurations are stored in fact tables of integers,
floats, strings, and JSON, using a star schema. One of the dimensions is metadata
describing the property. This data warehousing approach is almost identical to that
used in CIF files, with the metadata being the CIF dictionaries.
* Good support of CIF files, with the ability to store data other than the actual atoms
using the properties warehouse.
* Direct support for SMILES, SMARTS and substructure searching.
* Scales to millions of systems and configurations, and databases in excess of 100 GB.
Credits
---------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the `National Science Foundation`_ under
award OAC-1547580 and CHE-2136142.
.. _MolSSI: https://www.molssi.org
.. _`National Science Foundation`: https://www.nsf.gov
=======
History
=======
2024.12.14 -- Bugfix: more issues with property handling.
* The types of properties were not kept when using Open Babel or RDKit, so when
properties were reread from an SDF file the JSON properties were converted into
strings, causing various errors. This is fixed.
2024.12.11 -- Bugfix: Properties in SDF files
* Transferring properties to the Open Babel and RDKit molecules was incorrect after
recent changes to the handling of properties. This fixes the problem, and now SDF
files have the properties correctly.
2024.12.7 -- Significant internal enhancement to property handling.
* An internal change, allowing listing and getting properties with wildcards,
working with multiple values at once. This is a significant change, but should
not affect the user interface. Also consolidated the property handling code for
configurations vs systems.
2024.11.27.1 -- Added support for charge in chemical formulae
* Added support for charge in chemical formulae, e.g. [H2 O]+.
2024.11.27 -- Bugfix: error with charge and multiplicity
* The charge and multiplicity of the system were not correctly set when creating a
system from a SMILES string using RDKit. More generally, the charge and
multiplicity were not correctly set from an RDKit molecule unless explicitly given
in the properties.
2024.11.23 -- Bugfix: error if OpenEye not available
* Fixed an issue with the import of OpenEye that caused an error if OpenEye was not
available.
2024.11.21.1 -- Versions of openbabel, openeye, and rdkit
* Added functions to get the versions of openbabel, openeye, and rdkit that are
installed.
2024.11.21 -- Added access to OpenEye mols and SMILES
* Added the ability to create a system from an OpenEye molecule and vice versa.
This gives access to the OpenEye toolkit for generating conformers, etc.
* Added the ability to create a system from a SMILES string and create the SMILES
string from a system using OpenEye.
2024.11.12 -- Added units to properties in Openbabel molecules
* Any properties on the system and configuration are optionally added to the
Openbabel Molecule object for e.g. writing to an SDF file. This adds the units of
the properties explicitly
2024.10.1 -- Bugfix: Incorrect coordinates from PubChem
* Fixed bug where the coordinates from PubChem were accidentally the 2-D rather than
3-D coordinates.
2024.8.17 -- Bugfix: current configuration not updated properly
* Existing instances of systems did not correctly update when the default
configuration was changed. This is release fixes the problem.
2024.8.5 -- Bugfix: creating H2 from SMILES failed
* Fixed bug where creating molecules consisting of just hydrogen failed because
RDKit by default ignores all hydrogens when reorienting the molecule.
2024.6.21 -- Switching default for SMILES to RDKit rather than OpenBabel
* RDKit seems more robust, and also the atom typing uses RDkit, so compatibility is
important.
2024.5.8 -- Added more control over RDKit and OpenBabel creating systems
* Added control to from_RDKMol and from_OBMol to allow selectively updating
the atoms, coordinates, and bonds
2024.5.6 -- Rotated molecule from SMILES, InChI, or InChIKey to standard orientation
* Molecules created from line notation are created in an random orientation. This
enhancement rotates them to the standard orientation, which will look nice for
small, symmetric molecules.
2024.5.5 -- Bugfix: bonds in RDKit
* There was an indexing bug translating bonds back from RDKit to SEAMM. The famous
0/1 problem!
2024.4.6 -- Added gradients
* Added gradient on atoms as a separate table alongside atoms, so they take no space
unless actually used.
2024.3.13 -- Handle uppercase X, Y, Z in strings for symmetry operators
* the Crystallographic Open Database CIF files seems to use upper case X, Y, Z in
explicit symmetry operators. These need to be lowercased in the code.
2023.12.5 -- Bugfixes for symmetry
* Fixed issue #72, where symmetry was not correctly handled for trigonal and
hexagonal cells where atoms had coordinates of 1/3 or 2/3.
2023.11.19 -- Bugfixes in symmetry and CIF files
* Reading CIF files could fail if the symmetry operators were given
* The symmetry handling did not recognize hexagonal spacegroups without :H. Changed
so if the hexagonal group name has neither :H or :R, the hexagonal setting is
assumed.
* When finding the spacegroup from the symmetry operators, hard-coded to the P1 case
to avoid what seems like a bug in spglib.
* Enhanced to use the full International Tables HM name for spacegroups, translating
the input to that standard name.
2023.11.5 -- Bugfix and improved symmetry handling
* Fixed bug with symmetry operators containing blanks, e.g. 'x, y, z' rather than
'x,y,z'
* Added handling of symmetry when get properties of atoms
* Added method to lower symmetry to P1/C1
2023.10.30 -- Support for InChI improved, RMSD and PubChem added...
* Adds support for aligning structures and calculating RMSD
* Adds support for working directly with PubChem to get structures, IUPAC names,
etc.
* Improves support for InChI, working around issues in both OpenBabel and RDKit.
* Added substantial new functionality for spacegroups and primitive cell handling,
but still not complete.
2023.9.20 -- Better support for primitive cells and spacegroups
* Added getting the spacegroup from the symmetry operators
* Fixed updating the coordinates from the primitive cell
2023.9.5 -- Support for velocities of atoms.
2023.8.30 -- Support for spacegroup symmetry.
2023.8.27 -- Bugfix: writing SDF did not handle charge and multiplicity.
2023.7.30 -- Improved handling of properties
* Added ability to get lists of systems or configurations filtered by name
* Improved handling of properties on just a system, not configuration
* Added ability to filter properties retrieved
* Improved handling of properties when creating OpenBabel OB_MOL object
2023.7.26 -- Bugfix: error in QCSchema bonds; enhancement: RDKit
* Fixed bug in the bond indices in QCSchema
* Added ability to use RDKit for SMILES and InChI
2023.7.18.1 -- Added support for creating structures from InChIKeys
* Uses PubChem to translate the InChiKey to InChI.
2023.7.18 -- Added support for InChI and InChIKeys
2023.7.9 -- Added JSON properties
* Added properties stored as JSON, which allows, vectors, tensors, etc.
2023.4.6 -- Enhancements for CIF files
* Handle uncertainties in CIF files expressed as '(x)' at end of value.
2023.3.30 -- Enhancements to QCSchema support
* Improved naming of molecule in QCSchema
* Added creation of configurations from QCSchema objects.
2023.2.13 -- Fixed issue with valence in RDkit for cations like NH4+
2022.11.20 -- Added a method to copy a configuration.
Added a new method to the `system` class, `copy_configuration`, that creates a copy of
the configuration using the same atomset and bonset, but new coordinates and cell so
that any changes to coordinates and cell are not shared between the configurations. By
default it copies the current configuration.
2022.11.18 -- Fixed bug with handling for Open Babel
The total charge and multiplicity were not correctly set when creating an Open Babel
molecule.
2022.11.3 -- Add handling of strain and improved handling of properties
Added methods for straining the unit cell, and also straining a configuration,
correctly handling the coordinates for an affine transformation. In the future will
add e.g. affine transformation of the centers of molecules, which is useful for
molecular fluids.
Added the system for properties, in addition to the configuration. This allows system
properties that are not associated with a particular configuration, which is often
appropriate for experimental results. It also makes it much easier to search for
systems where any configuration has a particular property.
2022.10.26 -- Improved database write performance.
Switched to write-ahead mode and tweaked memory settings. This gives a large
performance improvement (10x or more) for large database (~1 GB).
Raw data
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"description": "=============\nMolSystem\n=============\n\n.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/dftbplus_step\n :target: https://github.com/molssi-seamm/molsystem/pulls\n :alt: GitHub pull requests\n\n.. image:: https://github.com/molssi-seamm/molsystem/workflows/CI/badge.svg\n :target: https://github.com/molssi-seamm/molsystem/actions\n :alt: Build Status\n\n.. image:: https://codecov.io/gh/molssi-seamm/molsystem/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/molssi-seamm/molsystem\n :alt: Code Coverage\n\n.. image:: https://github.com/molssi-seamm/molsystem/workflows/CodeQL/badge.svg\n :target: https://github.com/molssi-seamm/molsystem/security/code-scanning\n :alt: Code Quality\n\n\n.. image:: https://github.com/molssi-seamm/molsystem/workflows/Release/badge.svg\n :target: https://molssi-seamm.github.io/molsystem/index.html\n :alt: Documentation Status\n\n.. image:: https://img.shields.io/pypi/v/molsystem.svg\n :target: https://pypi.python.org/pypi/molsystem\n :alt: PyPi VERSION\n\nDescription\n-----------\nMolsystem provides a general class for handling molecular and periodic systems. This is\nthe heart of SEAMM.\n\n* Free software: GNU Lesser General Public License v3+\n* Documentation: https://molsystem.readthedocs.io.\n\n\nFeatures\n--------\n\n* Supports molecular and periodic (crystalline) systems.\n* Support for pointgroup and spacegroup symmetry.\n* Implemented as a SQL database, currently using SQLite, which provides permanence and a\n disk file.\n* Handles multiple systems, and for each system any number of\n configurations. Configurations are different structures, generally having different\n coordinates. Examples are conformers or frames in an MD trajectory.\n* Configurations can have differing bonds, supporting reactive forcefields such as\n ReaxFF.\n* Configurations can also have differing numbers of atoms, supporting e.g. grand\n canonical Monte Carlo.\n* Support for templates and subsets. Templates can be used for creating or finding\n structures in systems and subsets hold substes of atoms. An atom can be in multiple\n subsets. For proteins, subsets can be used for residues and chains; for polymers,\n monomers; and for fluids the subsets can track individual molecules.\n* Subsets and templates handle the correspondance between atoms so if, for instance, the\n ordering of atoms in residues are different, that can be handled using the\n correspondances.\n* Direct connection to and support of RDKit and OpenBabel molecules, allowing direct\n transfer back and forth between configurations and those libraries.\n* Properties of systems and configurations are stored in fact tables of integers,\n floats, strings, and JSON, using a star schema. One of the dimensions is metadata\n describing the property. This data warehousing approach is almost identical to that\n used in CIF files, with the metadata being the CIF dictionaries.\n* Good support of CIF files, with the ability to store data other than the actual atoms\n using the properties warehouse.\n* Direct support for SMILES, SMARTS and substructure searching.\n* Scales to millions of systems and configurations, and databases in excess of 100 GB.\n\nCredits\n---------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\nDeveloped by the Molecular Sciences Software Institute (MolSSI_),\nwhich receives funding from the `National Science Foundation`_ under\naward OAC-1547580 and CHE-2136142.\n\n.. _MolSSI: https://www.molssi.org\n.. _`National Science Foundation`: https://www.nsf.gov\n\n\n=======\nHistory\n=======\n2024.12.14 -- Bugfix: more issues with property handling.\n * The types of properties were not kept when using Open Babel or RDKit, so when\n properties were reread from an SDF file the JSON properties were converted into\n strings, causing various errors. This is fixed.\n \n2024.12.11 -- Bugfix: Properties in SDF files\n * Transferring properties to the Open Babel and RDKit molecules was incorrect after\n recent changes to the handling of properties. This fixes the problem, and now SDF\n files have the properties correctly.\n \n2024.12.7 -- Significant internal enhancement to property handling.\n * An internal change, allowing listing and getting properties with wildcards,\n working with multiple values at once. This is a significant change, but should\n not affect the user interface. Also consolidated the property handling code for\n configurations vs systems.\n \n2024.11.27.1 -- Added support for charge in chemical formulae\n * Added support for charge in chemical formulae, e.g. [H2 O]+.\n\n2024.11.27 -- Bugfix: error with charge and multiplicity\n * The charge and multiplicity of the system were not correctly set when creating a\n system from a SMILES string using RDKit. More generally, the charge and\n multiplicity were not correctly set from an RDKit molecule unless explicitly given\n in the properties.\n \n2024.11.23 -- Bugfix: error if OpenEye not available\n * Fixed an issue with the import of OpenEye that caused an error if OpenEye was not\n available.\n \n2024.11.21.1 -- Versions of openbabel, openeye, and rdkit\n * Added functions to get the versions of openbabel, openeye, and rdkit that are\n installed.\n \n2024.11.21 -- Added access to OpenEye mols and SMILES\n * Added the ability to create a system from an OpenEye molecule and vice versa.\n This gives access to the OpenEye toolkit for generating conformers, etc.\n * Added the ability to create a system from a SMILES string and create the SMILES\n string from a system using OpenEye.\n \n2024.11.12 -- Added units to properties in Openbabel molecules\n * Any properties on the system and configuration are optionally added to the\n Openbabel Molecule object for e.g. writing to an SDF file. This adds the units of\n the properties explicitly\n \n2024.10.1 -- Bugfix: Incorrect coordinates from PubChem\n * Fixed bug where the coordinates from PubChem were accidentally the 2-D rather than\n 3-D coordinates.\n\n2024.8.17 -- Bugfix: current configuration not updated properly\n * Existing instances of systems did not correctly update when the default\n configuration was changed. This is release fixes the problem.\n \n2024.8.5 -- Bugfix: creating H2 from SMILES failed\n * Fixed bug where creating molecules consisting of just hydrogen failed because\n RDKit by default ignores all hydrogens when reorienting the molecule.\n\n2024.6.21 -- Switching default for SMILES to RDKit rather than OpenBabel\n * RDKit seems more robust, and also the atom typing uses RDkit, so compatibility is\n important.\n \n2024.5.8 -- Added more control over RDKit and OpenBabel creating systems\n * Added control to from_RDKMol and from_OBMol to allow selectively updating\n the atoms, coordinates, and bonds\n \n2024.5.6 -- Rotated molecule from SMILES, InChI, or InChIKey to standard orientation\n * Molecules created from line notation are created in an random orientation. This\n enhancement rotates them to the standard orientation, which will look nice for\n small, symmetric molecules.\n \n2024.5.5 -- Bugfix: bonds in RDKit\n * There was an indexing bug translating bonds back from RDKit to SEAMM. The famous\n 0/1 problem!\n \n2024.4.6 -- Added gradients\n * Added gradient on atoms as a separate table alongside atoms, so they take no space\n unless actually used.\n \n2024.3.13 -- Handle uppercase X, Y, Z in strings for symmetry operators\n * the Crystallographic Open Database CIF files seems to use upper case X, Y, Z in\n explicit symmetry operators. These need to be lowercased in the code.\n\n2023.12.5 -- Bugfixes for symmetry\n * Fixed issue #72, where symmetry was not correctly handled for trigonal and\n hexagonal cells where atoms had coordinates of 1/3 or 2/3.\n\n2023.11.19 -- Bugfixes in symmetry and CIF files\n * Reading CIF files could fail if the symmetry operators were given\n * The symmetry handling did not recognize hexagonal spacegroups without :H. Changed\n so if the hexagonal group name has neither :H or :R, the hexagonal setting is\n assumed.\n * When finding the spacegroup from the symmetry operators, hard-coded to the P1 case\n to avoid what seems like a bug in spglib.\n * Enhanced to use the full International Tables HM name for spacegroups, translating\n the input to that standard name.\n \n2023.11.5 -- Bugfix and improved symmetry handling\n * Fixed bug with symmetry operators containing blanks, e.g. 'x, y, z' rather than\n 'x,y,z'\n * Added handling of symmetry when get properties of atoms\n * Added method to lower symmetry to P1/C1\n\n2023.10.30 -- Support for InChI improved, RMSD and PubChem added...\n * Adds support for aligning structures and calculating RMSD\n * Adds support for working directly with PubChem to get structures, IUPAC names,\n etc.\n * Improves support for InChI, working around issues in both OpenBabel and RDKit.\n * Added substantial new functionality for spacegroups and primitive cell handling,\n but still not complete.\n\n2023.9.20 -- Better support for primitive cells and spacegroups\n * Added getting the spacegroup from the symmetry operators\n * Fixed updating the coordinates from the primitive cell\n\n2023.9.5 -- Support for velocities of atoms.\n\n2023.8.30 -- Support for spacegroup symmetry.\n\n2023.8.27 -- Bugfix: writing SDF did not handle charge and multiplicity.\n\n2023.7.30 -- Improved handling of properties\n * Added ability to get lists of systems or configurations filtered by name\n * Improved handling of properties on just a system, not configuration\n * Added ability to filter properties retrieved\n * Improved handling of properties when creating OpenBabel OB_MOL object\n \n2023.7.26 -- Bugfix: error in QCSchema bonds; enhancement: RDKit\n * Fixed bug in the bond indices in QCSchema\n * Added ability to use RDKit for SMILES and InChI\n\n2023.7.18.1 -- Added support for creating structures from InChIKeys\n * Uses PubChem to translate the InChiKey to InChI.\n \n2023.7.18 -- Added support for InChI and InChIKeys\n\n2023.7.9 -- Added JSON properties\n * Added properties stored as JSON, which allows, vectors, tensors, etc.\n \n2023.4.6 -- Enhancements for CIF files\n * Handle uncertainties in CIF files expressed as '(x)' at end of value.\n\n2023.3.30 -- Enhancements to QCSchema support\n * Improved naming of molecule in QCSchema\n * Added creation of configurations from QCSchema objects.\n\n2023.2.13 -- Fixed issue with valence in RDkit for cations like NH4+\n\n2022.11.20 -- Added a method to copy a configuration.\n Added a new method to the `system` class, `copy_configuration`, that creates a copy of\n the configuration using the same atomset and bonset, but new coordinates and cell so\n that any changes to coordinates and cell are not shared between the configurations. By\n default it copies the current configuration.\n\n2022.11.18 -- Fixed bug with handling for Open Babel\n The total charge and multiplicity were not correctly set when creating an Open Babel\n molecule.\n\n2022.11.3 -- Add handling of strain and improved handling of properties\n Added methods for straining the unit cell, and also straining a configuration,\n correctly handling the coordinates for an affine transformation. In the future will\n add e.g. affine transformation of the centers of molecules, which is useful for\n molecular fluids.\n\n Added the system for properties, in addition to the configuration. This allows system\n properties that are not associated with a particular configuration, which is often\n appropriate for experimental results. It also makes it much easier to search for\n systems where any configuration has a particular property.\n\n2022.10.26 -- Improved database write performance.\n Switched to write-ahead mode and tweaked memory settings. 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