molsystem package¶

Submodules¶

molsystem.atoms module¶

A dictionary-like object for holding atoms

For efficiency the atom-data is stored as arrays – numpy if possible, python lists otherwise, along with metadata to define the attributes (“columns”).

In some ways this a bit like pandas; however, we also need more control than a simple pandas dataframe provides….

molsystem.atoms.grouped(iterable, n)[source]¶: s -> (s0,s1,s2,…sn-1), (sn,sn+1,sn+2,…s2n-1), (s2n,…s3n-1), …

molsystem.bonds module¶

A dictionary-like object for holding bonds

Based on tables in an SQLite database.

molsystem.cell module¶

class molsystem.cell.Cell(a, b, c, alpha, beta, gamma)[source]¶

Bases: object

A class to handle cell parameters and their transformations.

property a¶: The length of the first cell vector.

property alpha¶: The angle between b and c.

property b¶: The length of the second cell vector.

property beta¶: The angle between a and c.

property c¶: The length of the third cell vector.

equal(other, tol=1e-06)[source]¶

Check if we are equal to another iterable to within a tolerance.

Parameters

other (iterable) – The other object to check against
tol (float = 1.0e-06) – The tolerance for comparing floating point numbers.

Returns

equals – Boolean indicating whether the two are equal.

Return type

bool

property gamma¶: The angle between a and b.

property parameters¶: The cell parameters as a list.

to_cartesians(uvw, as_array=False)[source]¶

Convert fraction coordinates to Cartesians

see https://en.wikipedia.org/wiki/Fractional_coordinates for a description.

Parameters: uvw ([N][3*float] or ndarray) – The fractional coordinates.
Returns: xyz – The Cartesian coordinates.
Return type: [N][float*3] or ndarray

to_cartesians_transform(as_array=False)[source]¶

Matrix to convert fractional coordinates to Cartesian.

see https://en.wikipedia.org/wiki/Fractional_coordinates for a description.

Parameters: as_array (bool = False) – Whether to return a numpy array or Python lists
Returns: transform – The transformation matrix
Return type: [N][float*3] or ndarray

to_fractionals(xyz, as_array=False)[source]¶

Convert Cartesian coordinates to fractional.

see https://en.wikipedia.org/wiki/Fractional_coordinates for a description.

Parameters: xyz ([N][3*float] or ndarray) – The Cartesian coordinates.
Returns: uvw – The ractional coordinates.
Return type: [N][float*3] or ndarray

to_fractionals_transform(as_array=False)[source]¶

Matrix to convert Cartesian coordinates to fractional.

see https://en.wikipedia.org/wiki/Fractional_coordinates for a description.

Parameters: as_array (bool = False) – Whether to return a numpy array or Python lists
Returns: transform – The transformation matrix
Return type: [N][float*3] or ndarray

property volume¶: The volume of the cell.

molsystem.cell.cos(value)[source]¶

molsystem.cell.sin(value)[source]¶

molsystem.cell_parameters module¶

molsystem.cif module¶

Functions for handling CIF files

class molsystem.cif.CIFMixin[source]¶

Bases: object

A mixin for handling CIF files.

from_cif_text(text, configuration=None)[source]¶

Create the system from a CIF file..

Parameters

text (str) – The text from the CIF file
configuration (int = None) – The configuration to use, defaults to the current configuration.

Returns

Return type

None

to_cif_text(configuration=None)[source]¶

Create the text of a CIF file from the confguration.

Parameters: configuration (int = None) – The configuration to use, defaults to the current configuration.
Returns: text – The text of the file.
Return type: str

to_mmcif_text(configuration=None)[source]¶

Create the text of a mmCIF file from the confguration.

Parameters: configuration (int = None) – The configuration to use, defaults to the current configuration.
Returns: text – The text of the file.
Return type: str

molsystem.column module¶

molsystem.elemental_data module¶

Tabulated data about the elements.

molsystem.frozencolumn module¶

molsystem.molfile module¶

Functions for handling MDL molfiles

class molsystem.molfile.MolFileMixin[source]¶

Bases: object

A mixin for handling MDL Molfiles.

from_molfile_text(data, configuration=None)[source]¶

Create the system from an MDL Molfile, version 3

Parameters

data (str) – The complete text of the Molfile.
configuration (int = None) – The configuration to use, defaults to the current configuration.

to_molfile_text(configuration=None, title=None, comment='Exported from SEAMM')[source]¶

Create the text of the Molfile from the system.

Parameters

configuration (int = None) – The configuration to use, defaults to the current configuration.
title (str = None) – The title for the structure, by default the system name.
comment (str = 'Exported from SEAMM') – Comment line

Returns

text – The text of the file.

Return type

str

molsystem.pdb module¶

Functions for handling PDB files

To Do¶

Need to understand more fully the PDB/mmcif format and the how to carry the information about residues, chains, hetero groups, waters, etc. At the moment this is ignoring much of the information, and putting residue, chain, etc information directly on atoms.

I think we should use templates and subsets, but am not (yet) sure.

Presumably this metadata is most useful for setting up complicated simulations.

File Format¶

For complete documentation, see http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

Order of records:

RECORD TYPE             EXISTENCE           CONDITIONS IF  OPTIONAL
--------------------------------------------------------------------------------------
HEADER                  Mandatory
OBSLTE                  Optional            Mandatory in  entries that have been
                                            replaced by a newer entry.
TITLE                   Mandatory
SPLIT                   Optional            Mandatory when  large macromolecular
                                            complexes  are split into multiple PDB
                                            entries.
CAVEAT                  Optional            Mandatory when there are outstanding  errors
                                            such  as chirality.
COMPND                  Mandatory
SOURCE                  Mandatory
KEYWDS                  Mandatory
EXPDTA                  Mandatory
NUMMDL                  Optional            Mandatory for  NMR ensemble entries.
MDLTYP                  Optional            Mandatory for  NMR minimized average
                                            Structures or when the entire  polymer
                                            chain contains C alpha or P atoms only.
AUTHOR                  Mandatory
REVDAT                  Mandatory
SPRSDE                  Optional            Mandatory for a replacement entry.
JRNL                    Optional            Mandatory for a publication describes
                                            the experiment.
REMARK 0                Optional            Mandatory for a re-refined structure
REMARK 1                Optional
REMARK 2                Mandatory
REMARK 3                Mandatory
REMARK N                Optional            Mandatory under certain conditions.
DBREF                   Optional            Mandatory for all polymers.
DBREF1/DBREF2           Optional            Mandatory when certain sequence  database
                                            accession  and/or sequence numbering
                                            does  not fit preceding DBREF format.
SEQADV                  Optional            Mandatory if sequence  conflict exists.
SEQRES                  Mandatory           Mandatory if ATOM records exist.
MODRES                  Optional            Mandatory if modified group exists  in the
                                            coordinates.
HET                     Optional            Mandatory if a non-standard group other
                                            than water appears in the coordinates.
HETNAM                  Optional            Mandatory if a non-standard group other
                                            than  water appears in the coordinates.
HETSYN                  Optional
FORMUL                  Optional            Mandatory if a non-standard group or
                                            water appears in the coordinates.
HELIX                   Optional
SHEET                   Optional
SSBOND                  Optional            Mandatory if a  disulfide bond is present.
LINK                    Optional            Mandatory if  non-standard residues appear
                                            in a  polymer
CISPEP                  Optional
SITE                    Optional
CRYST1                  Mandatory
ORIGX1 ORIGX2 ORIGX3    Mandatory
SCALE1 SCALE2 SCALE3    Mandatory
MTRIX1 MTRIX2 MTRIX3    Optional            Mandatory if  the complete asymmetric unit
                                            must  be generated from the given coordinates
                                            using non-crystallographic symmetry.
MODEL                   Optional            Mandatory if more than one model
                                            is  present in the entry.
ATOM                    Optional            Mandatory if standard residues exist.
ANISOU                  Optional
TER                     Optional            Mandatory if ATOM records exist.
HETATM                  Optional            Mandatory if non-standard group exists.
ENDMDL                  Optional            Mandatory if MODEL appears.
CONECT                  Optional            Mandatory if non-standard group appears
                                            and  if LINK or SSBOND records exist.
MASTER                  Mandatory
END                     Mandatory

Description of HETATM records:

COLUMNS       DATA  TYPE     FIELD         DEFINITION
-----------------------------------------------------------------------
- 6        Record name    "HETATM"
- 11       Integer        serial        Atom serial number.
- 16       Atom           name          Atom name.
          Character      altLoc        Alternate location indicator.
- 20       Residue name   resName       Residue name.
          Character      chainID       Chain identifier.
- 26       Integer        resSeq        Residue sequence number.
          AChar          iCode         Code for insertion of residues.
- 38       Real(8.3)      x             Orthogonal coordinates for X.
- 46       Real(8.3)      y             Orthogonal coordinates for Y.
- 54       Real(8.3)      z             Orthogonal coordinates for Z.
- 60       Real(6.2)      occupancy     Occupancy.
- 66       Real(6.2)      tempFactor    Temperature factor.
- 78       LString(2)     element       Element symbol; right-justified.
- 80       LString(2)     charge        Charge on the atom.

Description of CONECT records:

COLUMNS       DATA  TYPE      FIELD        DEFINITION
-------------------------------------------------------------------------
-  6        Record name    "CONECT"
- 11        Integer        serial       Atom  serial number
- 16        Integer        serial       Serial number of bonded atom
- 21        Integer        serial       Serial  number of bonded atom
- 26        Integer        serial       Serial number of bonded atom
- 31        Integer        serial       Serial number of bonded atom

class molsystem.pdb.PDBMixin[source]¶

Bases: object

A mixin for handling PDB files.

from_pdb_text(data, configuration=None)[source]¶

Create the system from a PDF file.

Parameters

data (str) – The complete text of the Molfile.
configuration (int = None) – The configuration to use, defaults to the current configuration.

to_pdb_text(configuration=None, title=None, comment='Exported from SEAMM')[source]¶

Create the text of the PDB file from the system.

Parameters

configuration (int = None) – The configuration to use, defaults to the current configuration.
title (str = None) – The title for the structure, by default the system name.
comment (str = 'Exported from SEAMM') – Comment line

Returns

text – The text of the file.

Return type

str

molsystem.system module¶

A dictionary-like object for holding a system

molsystem.systems module¶

A dictionary-like object for holding systems

class molsystem.systems.Systems[source]¶

Bases: collections.abc.MutableMapping

copy_system(other, name=None, filename=None, temporary=False, force=False)[source]¶: Create a copy of a system, optionally with a given name and filename.

create_system(name, filename=None, temporary=False, force=False)[source]¶: Create a system with a given name, and optionally a filename.

list()[source]¶: Return a list of the systems.

open_system(filename, name=None, temporary=False)[source]¶: Open an existing system with a given name.

overwrite(system, other)[source]¶: Overwrite a system with the contents of another.

molsystem.table module¶

molsystem.table.grouped(iterable, n)[source]¶: s -> (s0,s1,s2,…sn-1), (sn,sn+1,sn+2,…s2n-1), (s2n,…s3n-1), …

molsystem.template module¶

A dictionary-like object for holding templates

molsystem.templateatoms module¶

A dictionary-like object for holding atoms for the templates

molsystem.templateatoms.grouped(iterable, n)[source]¶: s -> (s0,s1,s2,…sn-1), (sn,sn+1,sn+2,…s2n-1), (s2n,…s3n-1), …

molsystem.templatebonds module¶

molsystem.topology module¶

Topological methods for the system

class molsystem.topology.TopologyMixin[source]¶

Bases: object

A mixin for handling topology.

bonded_neighbors(configuration=None, as_indices=False, first_index=0)[source]¶

The atoms bonded to each atom in the system.

Parameters

configuration (int = None) – The configuration to use, defaults to the current configuration.
as_indices (bool = False) – Whether to return 0-based indices (True) or atom ids (False)
first_index (int = 0) – The smallest index, e.g. 0 or 1

Returns

neighbors – list of atom ids for each atom id

Return type

{int: [int]} or [[int]] for indices

create_molecule_subsets(configuration=None)[source]¶

Create a subset for each molecule in a configuration.

By default they all reference an empty template ‘all’ of type ‘molecule’.

Parameters: configuration (int = None) – The configuration to use, defaults to the current configuration.
Returns: The ids of the subsets, one per molecule.
Return type: [int]

create_molecule_templates(configuration=None, create_subsets=True)[source]¶

Create a template for each unique molecule in a configuration.

By default also create subsets linking each template to the atoms of the molecules in the system.

Parameters

configuration (int = None) – The configuration to use, defaults to the current configuration.
create_subsets (bool = True) – If true, create subsets linking the templates to the molecules.

Returns

The ids of the templates, or if create_subsets is True a two-element list containing the list of templates and list of subsets.

Return type

[int] or [[int], [int]]

find_molecules(configuration=None, as_indices=False)[source]¶

Find the separate molecules in a system.

Parameters

configuration (int = None) – The configuration to use, defaults to the current configuration.
as_indices (bool = False) – Whether to return 0-based indices (True) or atom ids (False)

Returns

molecules – A list of lists of atom ids or indices for the molecules

Return type

[[int]*n_molecules]

Module contents¶

molsystem A general implementation for molecular and periodic systems.