schrodinger.application.matsci.vsepr module¶

Determines the closest VSEPR geometry based on the metal coordination sphere

This module is used in the OPLS+M force field workflow

exception schrodinger.application.matsci.vsepr.VSEPRError¶

Bases: Exception

Base class of errors raised when determining the VSEPR geomemtry fails

exception schrodinger.application.matsci.vsepr.NonBondedMetalError¶

Bases: VSEPRError

Raised when there are no bonds to the metal and adding bonds was not requested

exception schrodinger.application.matsci.vsepr.SingleMetalRequiredError¶

Bases: VSEPRError

Raised when there are too many metals in the structure

exception schrodinger.application.matsci.vsepr.NoTemplateAvailableError¶

Bases: VSEPRError

Raised when there are too many bonds to the metal in the structure

schrodinger.application.matsci.vsepr.determine_vsepr_geometry(struct, **kwargs)¶

Determine the VSEPR geometry of the given structure

The geometry determined is returned from this function. In addition, the geometry as well as the RMS deviation from the ideal geometry are added as structure properties to the given structure.

Parameters:: struct (Structure) – The structure to check

Additional keyword arguments are passed to the VSEPRFinder class

Return type:

str

Returns:

A string giving the VSEPR geometry

Raises:

SingleMetalRequiredError – If there is more than 1 metal atom in struct
NonBondedMetalError – If there are no bonds to the metal and adding bonds to the metal was not requested
NoTemplateAvailableError – If there are too many bonds to the metal and no VSEPR template exists.

schrodinger.application.matsci.vsepr.determine_vsepr_geometries_from_file(input_file, basename, create_fit_sts=False, **kwargs)¶

Determine the VSEPR geometries for all structures in an input file, writing the results to an output structure file.

Parameters:

input_file (str) – The name of the input structure file
basename (str) – The base name for the structure and fits output files
create_fit_sts (bool) – Create a file with structures in it that show how the metal coordination sphere fits ideal VSEPR templates.

Additional keyword arguments are passed to the VSEPRFinder class

Return type:: str, str, int
Returns:: The name of the output and fit structure files (in that order), and the number of failed structures

class schrodinger.application.matsci.vsepr.VSEPRFinder(make_bonds=False, bond_tol=2.7, bond_h=False, allow_neighbors=False, logger=None)¶

Bases: object

Class used to find the VSEPR geometry of a single-metal organometallic complex.

After creating the object, call the run method to determine the geometry

NONE = 'None'¶

LINEAR = 'Linear'¶

BENT = 'Bent'¶

TRIGONAL_PLANAR = 'Trigonal planar'¶

TRIGONAL_PYRAMIDAL = 'Trigonal pyramidal'¶

T_SHAPED = 'T-Shaped'¶

TETRAHEDRAL = 'Tetrahedral'¶

SQ_PLANAR = 'Square planar'¶

SEESAW = 'Seesaw'¶

TRIGONAL_BIPYRAMIDAL = 'Trigonal bipyramidal'¶

SQ_PYRAMIDAL = 'Square pyramidal'¶

OCTAHEDRAL = 'Octahedral'¶

PENTAGONAL_BIPYRAMIDAL = 'Pentagonal bipyramidal'¶

SQUARE_ANTIPRISMATIC = 'Square antiprismatic'¶

TRICAPPED_TRIGONAL_PRISMATIC = 'Tricapped trigonal prismatic'¶

__init__(make_bonds=False, bond_tol=2.7, bond_h=False, allow_neighbors=False, logger=None)¶

Create a VSEPRFinder instance

Parameters:

make_bonds (bool) – If True create bonds to all atoms within bonding distance to the metal atom using the bond_tol and bond_h parameters. If False, the bonding in the structure will be used as given.
bond_tol (float) – The distance at which atoms near the metal should be considered bonded when make_bonds is True.
bond_h (bool) – When make_bonds is True, allow H atoms to bond to the metal
allow_neighbors (bool) – If True, allow atoms that are bonded together to also both be bonded to the metal. If False, only the atom nearer to the metal will be bonded.
logger (callable) – A function that takes a single string argument, used for logging information

run(struct)¶

Determine the VSEPR geometry of the given structure

The geometry name and rms fit are added to the structure as properties.

Parameters:: struct (Structure) – The structure to determine the geometry of
Return type:: str
Returns:: The VSEPR geometry name

log(msg)¶

Log a message if a logger has been supplied

Parameters:: msg (str) – The message to log

classmethod setUpTemplates()¶: Set up the templates for the VSEPR geometries

locateMetalAndNeighbors(struct)¶

Find the index of the metal atom and verify its neighbors

Parameters:

struct (Structure) – The structure to check

Return type:

int

Returns:

The index of the metal atom

Raises:

SingleMetalRequiredError – If there is more than 1 metal atom in struct
NonBondedMetalError – If there are no bonds to the metal and adding bonds to the metal was not requested

addBondsToMetal(struct, metal_index)¶

Add bonds between the metal atom and nearby atoms

Parameters:

struct (structure.Structure) – The structure to modify in place
metal_index (int) – The index of the metal atom

removeNeighborMatches(struct, matches, metal_index)¶

If 2 atoms close to the metal are also bonded to each other, remove the atom that is further from the metal.

Parameters:

struct (Structure) – The structure containing the atoms
matches (list) – List of atom indexes close to the metal
metal_index (int) – The index of the metal atom

Return type:

list

Returns:

A list of remaining indexes after neighbors have been removed

prepStructureForVSEPR(struct, metal_index)¶

Modify the structure to have similar characteristics as the template

Parameters:

struct (structure.Structure) – The structure to modify in place
metal_index (int) – The index of the metal atom

checkAgainstTemplate(struct, template, metal_index)¶

Computes the RMS of the given structure against the given template

Parameters:

struct (Structure) – The structure to check
template (Structure) – The template to check against
metal_index (int) – The index of the metal atom in struct

Return type:

float

Returns:

The RMS deviation of atoms in struct relative to the template

makeFitSt(struct, template)¶

Create a structure that combines the given structure and template, and add it to the list of fit structures.

Parameters:

struct (Structure) – The structure to check
template (Structure) – The template to check against

getBestRMS(struct, template, flippable_atoms)¶

Get the best RMS deviation between struct and template. The structure “as is” is checked as one possibility. Then if flippable_atoms are supplied, those two atoms are flipped and the flipped structure is checked. The return value is for the structure that better matches the template.

Flipping allows for checking different isomers (fac/mer for octahedral, cis/trans for square planer, R/S for tetrahedral, etc.)

Parameters:

struct (Structure) – The structure to check
template (Structure) – The template to check against
flippable_atoms (list) – Two atom indexes that can be flipped

Return type:

(Structure, float)

Returns:

The structure that best matches the template and the RMS deviation of that structure from the template

adjustOrderToTemplate(struct, template, metal_index)¶

Adjust the atom order of the given structure to best match the atom order of the given template.

The metal atom will be moved to position 1.

For some geometries, all non-metal atom positions are equivalent - such as trigonal planar, tetrahedral, octahedral. But some geometries it is very important for atoms to be in certain positions - such as axial vs equitorial in trigonal bipyramidal or square pyrimidal. For these, we manually force certain atoms to be in certain positions based on the current geometry of struct.

Parameters:

struct (Structure) – The structure to reorder
template (Structure) – The template to reorder against
metal_index (int) – The index of the metal atom in struct

Return type:

Structure, list(int)

Returns:

A new structure with the atoms from struct reordered, and a list of 2 atom indexes that can be flipped to form an isomer of the returned structure.

adjustSeeSawOrder(struct)¶

Adjust the atom ordering so that the atoms are ordered similarly to the template.