schrodinger.application.matsci.kmc module¶

Utilities for working with VOTCA

class schrodinger.application.matsci.kmc.ColumnData(type, default)¶

Bases: tuple

default¶: Alias for field number 1

type¶: Alias for field number 0

class schrodinger.application.matsci.kmc.MoleculeData(index, name, mtype, posx, posy, posz)¶

Bases: tuple

index¶: Alias for field number 0

mtype¶: Alias for field number 2

name¶: Alias for field number 1

posx¶: Alias for field number 3

posy¶: Alias for field number 4

posz¶: Alias for field number 5

schrodinger.application.matsci.kmc.is_votca_prop(prop)¶

Check if a property is a votca property

Parameters: prop (str) – The property to check
Return type: str or None
Returns: If the property is a votca property, the type of property is returned as a module-level constant. If the property is not recognized as a VOTCA property, None is returned.

schrodinger.application.matsci.kmc.parse_mobility_or_velocity_prop(prop)¶

Parse a property name and return the information from it if it is a VOTCA mobility or velocity property

Parameters: prop (str) – The property to check
Return type: (int, str, str) or None
Returns: The integer is the field index, the first string is the charge (HOLE or ELECTRON) and the second string is the axis name. None is returned if the property is not a mobility or velocity property.

schrodinger.application.matsci.kmc.parse_field_prop(prop)¶

Parse a property name and return the information from it if it is a VOTCA field property

Parameters: prop (str) – The property to check
Return type: (int, str) or None
Returns: The integer is the field index, the string is the axis name. None is returned if the property is not a field property.

schrodinger.application.matsci.kmc.parse_database_prop(prop)¶

Parse a property name and return the information from it if it is a VOTCA database property

Parameters: prop (str) – The property to check
Return type: (int, list) or None
Returns: The integer is the field index, the list contains the charges (HOLE and/or ELECTRON). None is returned if the property is not a database property

class schrodinger.application.matsci.kmc.AxisData¶

Bases: object

Holds data that differs on the X, Y and Z axes

__init__()¶: Create an AxisData object

setComponent(axis, value)¶

Set the data for one axis

Parameters: axis (str or int) – Either the capital name of an axis (X, Y, Z) or the numerical index of that axis

class schrodinger.application.matsci.kmc.SQLCursor(path)¶

Bases: object

Context manager for reading or modifying an SQL database. Ensures that changes are committed and the cursor/connection are closed when finished.:

cmd = "black SQL magic"
with SQLCursor(path_to_sql_file) as cursor:
    cursor.execute(cmd)

__init__(path)¶

class schrodinger.application.matsci.kmc.Table(filename)¶

Bases: object

Base table class for internal and VOTCA SQL tables

TABLE_NAME = ''¶

COLUMNS = {}¶

CREATION_COMMAND = 'CREATE TABLE {name} ({columns});'¶

ADDROW_COMMAND = 'INSERT INTO {name} ({cols}) VALUES ({ph})'¶

NULL_ALLOWED = False¶

SQL_ID = '_id'¶

SQID = 'id'¶

NAME = 'name'¶

TYPE = 'type'¶

MOL = 'mol'¶

POSX = 'posX'¶

POSY = 'posY'¶

POSZ = 'posZ'¶

FRAME = 'frame'¶

TOP = 'top'¶

SEG = 'seg'¶

__init__(filename)¶

Create a Table instance

Parameters: filename (str) – The path to the SQL file

setCursor(cursor)¶

Set the SQL cursor this table should use

Parameters: cursor (sqlite3.Cursor) – The cursor to use for database read/writes

create()¶

Create this table in the database

Raises: SQLCreationError – If the cursor is not defined

getMoleculeInfo(molecule, centroid=True)¶

Get common database information for a molecule object

Parameters

molecule (schrodinger.structure._StructureMolecule) – The molecule object to get information for
centroid (bool) – Include information about the molecule’s centroid. If False, all centroid information will be 0.

Return type

MoleculeData

Returns

A MoleculeData object containing the information

static getSegmentType(molecule)¶

Get the segment type for this molecule

Segment names will be type_X, where X is the molecule number

Parameters: molecule (structure._Molecule) – The molecule object
Return type: str
Returns: The segment type for this molecule

static getAllSegmentTypes(struct)¶

Get all the segment types for this structure

Parameters: struct (structure.Structure) – The structure object
Return type: set
Returns: Each item of the set is the name of a segment type

class schrodinger.application.matsci.kmc.FramesTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The frames table

TABLE_NAME = 'frames'¶

TIME = 'time'¶

STEP = 'step'¶

BOX11 = 'box11'¶

BOX12 = 'box12'¶

BOX13 = 'box13'¶

BOX21 = 'box21'¶

BOX22 = 'box22'¶

BOX23 = 'box23'¶

BOX31 = 'box31'¶

BOX32 = 'box32'¶

BOX33 = 'box33'¶

CANRIGID = 'canRigid'¶

COLUMNS = {'box11': ColumnData(type='REAL', default=None), 'box12': ColumnData(type='REAL', default=None), 'box13': ColumnData(type='REAL', default=None), 'box21': ColumnData(type='REAL', default=None), 'box22': ColumnData(type='REAL', default=None), 'box23': ColumnData(type='REAL', default=None), 'box31': ColumnData(type='REAL', default=None), 'box32': ColumnData(type='REAL', default=None), 'box33': ColumnData(type='REAL', default=None), 'canRigid': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=0), 'step': ColumnData(type='INT', default=0), 'time': ColumnData(type='REAL', default=0)}¶

addRow(struct)¶

Add a frame row to the table

The main frame information is the PBC box

Parameters: struct (schrodinger.structure.Structure) – The structure with the PBC information

class schrodinger.application.matsci.kmc.MoleculesTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The molecules table

TABLE_NAME = 'molecules'¶

COLUMNS = {'frame': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'top': ColumnData(type='INT', default=0), 'type': ColumnData(type='TEXT', default=None)}¶

addRow(molecule)¶

Add a row

Parameters: molecule (schrodinger.structure._StructureMolecule) – The molecule object to add a row for

class schrodinger.application.matsci.kmc.SitesMixin¶

Bases: object

Mixin for votca and matsci site tables

HAS_E = 'has_e'¶

HAS_H = 'has_h'¶

OCCPE = 'occPe'¶

OCCPH = 'occPh'¶

COMMON_COLUMNS = {'UcCnNe': ColumnData(type='REAL', default=0), 'UcCnNh': ColumnData(type='REAL', default=0), 'UcNcCe': ColumnData(type='REAL', default=0), 'UcNcCh': ColumnData(type='REAL', default=0), 'UnCnNe': ColumnData(type='REAL', default=0), 'UnCnNh': ColumnData(type='REAL', default=0), 'has_e': ColumnData(type='INT', default=0), 'has_h': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'mol': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'occPe': ColumnData(type='REAL', default=-1), 'occPh': ColumnData(type='REAL', default=-1), 'posX': ColumnData(type='REAL', default=None), 'posY': ColumnData(type='REAL', default=None), 'posZ': ColumnData(type='REAL', default=None), 'type': ColumnData(type='TEXT', default=None)}¶

class schrodinger.application.matsci.kmc.SegmentsTable(filename)¶

Bases: schrodinger.application.matsci.kmc.SitesMixin, schrodinger.application.matsci.kmc.Table

The segments table

TABLE_NAME = 'segments'¶

EANION = 'eAnion'¶

ENEUTRAL = 'eNeutral'¶

ECATION = 'eCation'¶

COLUMNS = {'UcCnNe': ColumnData(type='REAL', default=0), 'UcCnNh': ColumnData(type='REAL', default=0), 'UcNcCe': ColumnData(type='REAL', default=0), 'UcNcCh': ColumnData(type='REAL', default=0), 'UnCnNe': ColumnData(type='REAL', default=0), 'UnCnNh': ColumnData(type='REAL', default=0), 'eAnion': ColumnData(type='REAL', default=0), 'eCation': ColumnData(type='REAL', default=0), 'eNeutral': ColumnData(type='REAL', default=0), 'frame': ColumnData(type='INT', default=0), 'has_e': ColumnData(type='INT', default=0), 'has_h': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'mol': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'occPe': ColumnData(type='REAL', default=-1), 'occPh': ColumnData(type='REAL', default=-1), 'posX': ColumnData(type='REAL', default=None), 'posY': ColumnData(type='REAL', default=None), 'posZ': ColumnData(type='REAL', default=None), 'top': ColumnData(type='INT', default=0), 'type': ColumnData(type='TEXT', default=None)}¶

addRow(molecule, stypes)¶

Add a row

Parameters

molecule (schrodinger.structure._StructureMolecule) – The molecule object to add a row for
stypes (dict) – Keys are segment names (atom pdbres names), values are the index of that segment

class schrodinger.application.matsci.kmc.SegmentTypesTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The segmentTypes table

TABLE_NAME = 'segmentTypes'¶

BASIS = 'basis'¶

ORBFILE = 'orbfile'¶

TORBNRS = 'torbnrs'¶

COORDFILE = 'coordfile'¶

CANRIGID = 'canRigid'¶

COLUMNS = {'basis': ColumnData(type='TEXT', default='noname'), 'canRigid': ColumnData(type='INT', default=0), 'coordfile': ColumnData(type='TEXT', default='nofile'), 'frame': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'orbfile': ColumnData(type='TEXT', default='nofile'), 'top': ColumnData(type='INT', default=0), 'torbnrs': ColumnData(type='TEXT', default='NOT_USED')}¶

addRow(stype, index)¶

Add a row

Parameters

stype (str) – The segment type name (should be an atom.pdbres name)
index (int) – The segment type index

class schrodinger.application.matsci.kmc.FragmentsTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The fragments table

TABLE_NAME = 'fragments'¶

SYMMETRY = 'symmetry'¶

LEG1 = 'leg1'¶

LEG2 = 'leg2'¶

LEG3 = 'leg3'¶

COLUMNS = {'frame': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'leg1': ColumnData(type='INT', default=1), 'leg2': ColumnData(type='INT', default=2), 'leg3': ColumnData(type='INT', default=3), 'mol': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'posX': ColumnData(type='REAL', default=None), 'posY': ColumnData(type='REAL', default=None), 'posZ': ColumnData(type='REAL', default=None), 'seg': ColumnData(type='INT', default=None), 'symmetry': ColumnData(type='INT', default=-1), 'top': ColumnData(type='INT', default=0), 'type': ColumnData(type='TEXT', default=None)}¶

addRow(molecule)¶

Add a row

Parameters: molecule (schrodinger.structure._StructureMolecule) – The molecule object to add a row for

class schrodinger.application.matsci.kmc.AtomsTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The atoms table

TABLE_NAME = 'atoms'¶

FRAG = 'frag'¶

RESNR = 'resnr'¶

RESNAME = 'resname'¶

WEIGHT = 'weight'¶

ELEMENT = 'element'¶

QMID = 'qmid'¶

QMPOSX = 'qmPosX'¶

QMPOSY = 'qmPosY'¶

QMPOSZ = 'qmPosZ'¶

COLUMNS = {'element': ColumnData(type='TEXT', default=None), 'frag': ColumnData(type='INT', default=None), 'frame': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'mol': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'posX': ColumnData(type='REAL', default=None), 'posY': ColumnData(type='REAL', default=None), 'posZ': ColumnData(type='REAL', default=None), 'qmPosX': ColumnData(type='REAL', default=0.0), 'qmPosY': ColumnData(type='REAL', default=0.0), 'qmPosZ': ColumnData(type='REAL', default=0.0), 'qmid': ColumnData(type='INT', default=0), 'resname': ColumnData(type='TEXT', default=None), 'resnr': ColumnData(type='INT', default=1), 'seg': ColumnData(type='INT', default=None), 'top': ColumnData(type='INT', default=0), 'type': ColumnData(type='INT', default=None), 'weight': ColumnData(type='REAL', default=None)}¶

addRow(atom)¶

Add a row

Parameters: atom (structure.Structure._StructureAtom) – The atom to add a row for

class schrodinger.application.matsci.kmc.PairsMixin¶

Bases: object

Mixin for Matsci and VOTCA pair tables

DRX = 'drx'¶

DRY = 'dry'¶

DRZ = 'drz'¶

COM_DRX = 'com_drx'¶

COM_DRY = 'com_dry'¶

COM_DRZ = 'com_drz'¶

PERIODIC_Z = 'periodic_z'¶

RATE12E = 'rate12e'¶

RATE21E = 'rate21e'¶

RATE12H = 'rate12h'¶

RATE21H = 'rate21h'¶

addRow(index, dimer, struct)¶

Add a row to the table

Parameters

index (int) – The index of this pair
dimer (schrodinger.application.matsci.clusterstruct.Dimer) – The Dimer object for this row

classmethod setRowValues(mols, val_dict, cursor)¶

Set the values of columns in the row for the given pair of molecules

Parameters

mols (iterable) – The two mol numbers involved in this pair
val_dict (dict) – Dict mapping column names to their values
cursor (sqlite3.Cursor) – The cursor to use

Raises

RuntimeError – If value has spaces

class schrodinger.application.matsci.kmc.PairsTable(filename)¶

Bases: schrodinger.application.matsci.kmc.PairsMixin, schrodinger.application.matsci.kmc.Table

The votca pairs table

TABLE_NAME = 'pairs'¶

SEG1 = 'seg1'¶

SEG2 = 'seg2'¶

SITE1 = 'seg1'¶

SITE2 = 'seg2'¶

LOE = 'lOe'¶

LOH = 'lOh'¶

HAS_E = 'has_e'¶

HAS_H = 'has_h'¶

JEFF2E = 'Jeff2e'¶

JEFF2H = 'Jeff2h'¶

COLUMNS = {'Jeff2e': ColumnData(type='REAL', default=0), 'Jeff2h': ColumnData(type='REAL', default=0), 'com_drx': ColumnData(type='REAL', default=None), 'com_dry': ColumnData(type='REAL', default=None), 'com_drz': ColumnData(type='REAL', default=None), 'drx': ColumnData(type='REAL', default=None), 'dry': ColumnData(type='REAL', default=None), 'drz': ColumnData(type='REAL', default=None), 'frame': ColumnData(type='INT', default=0), 'has_e': ColumnData(type='INT', default=0), 'has_h': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'lOe': ColumnData(type='REAL', default=0), 'lOh': ColumnData(type='REAL', default=0), 'rate12e': ColumnData(type='REAL', default=0), 'rate12h': ColumnData(type='REAL', default=0), 'rate21e': ColumnData(type='REAL', default=0), 'rate21h': ColumnData(type='REAL', default=0), 'seg1': ColumnData(type='INT', default=None), 'seg2': ColumnData(type='INT', default=None), 'top': ColumnData(type='INT', default=0), 'type': ColumnData(type='INT', default=0)}¶

COUPLING_COLUMNS = {'electron': ['Jeff2e'], 'hole': ['Jeff2h']}¶

class schrodinger.application.matsci.kmc.SuperExchangeTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The superExchange table

Note: unused

TABLE_NAME = 'superExchange'¶

COLUMNS = {'frame': ColumnData(type='INT', default=0), 'top': ColumnData(type='INT', default=0), 'type': ColumnData(type='TEXT', default=None)}¶

class schrodinger.application.matsci.kmc.SchrodingerTable(filename)¶

Bases: schrodinger.application.matsci.kmc.Table

The schrodinger table. This contains Schrodinger-specific information and is not used by VOTCA

TABLE_NAME = 'schrodinger'¶

NULL_ALLOWED = True¶

MOLFORM = 'mol_formula'¶

VOLUME = 'pbc_volume_Ang3'¶

JOBID = 'jobid'¶

STRUCTURE_PATH = 'structure_path'¶

STRUCTURE_FILE = 'structure_file'¶

CONCENTRATIONS_FILE = 'concentrations_file'¶

PAIR_DISTANCE = 'pair_distance_Ang'¶

PAIR_TYPE = 'pair_type'¶

VERSION = 'version'¶

JUMPFILE = 'jumpfile'¶

JUMPSUMMARY = 'jumpsummary'¶

RUNTIME = 'runtime'¶

SEED = 'seed'¶

FIELDX = 'fieldX'¶

FIELDY = 'fieldY'¶

FIELDZ = 'fieldZ'¶

AVECTOR = 'a_vector'¶

BVECTOR = 'b_vector'¶

CVECTOR = 'c_vector'¶

TEMPERATURE = 'temperature'¶

RATEFILE = 'ratefile'¶

CARRIERTYPE = 'carriertype'¶

SITE_KEYWORDS = 'site_keywords'¶

FIX_SITE_KEYWORDS = 'site_fix_keywords'¶

MATSCI_ENGINE = 'matsci_engine'¶

AVERAGE_JEFF = 'average_jeff'¶

COLUMNS = {'a_vector': ColumnData(type='TEXT', default=None), 'average_jeff': ColumnData(type='INT', default=1), 'b_vector': ColumnData(type='TEXT', default=None), 'c_vector': ColumnData(type='TEXT', default=None), 'carriertype': ColumnData(type='TEXT', default=None), 'concentrations_file': ColumnData(type='TEXT', default=None), 'fieldX': ColumnData(type='REAL', default=None), 'fieldY': ColumnData(type='REAL', default=None), 'fieldZ': ColumnData(type='REAL', default=None), 'jobid': ColumnData(type='TEXT', default=None), 'jumpsummary': ColumnData(type='TEXT', default=None), 'matsci_engine': ColumnData(type='INT', default=0), 'mol_formula': ColumnData(type='TEXT', default=None), 'pair_distance_Ang': ColumnData(type='REAL', default=0.0), 'pair_type': ColumnData(type='REAL', default=None), 'pbc_volume_Ang3': ColumnData(type='REAL', default=0.0), 'ratefile': ColumnData(type='TEXT', default=None), 'runtime': ColumnData(type='REAL', default=None), 'seed': ColumnData(type='INT', default=None), 'site_fix_keywords': ColumnData(type='TEXT', default=None), 'site_keywords': ColumnData(type='TEXT', default=None), 'structure_file': ColumnData(type='TEXT', default=None), 'structure_path': ColumnData(type='TEXT', default=None), 'temperature': ColumnData(type='REAL', default=None), 'version': ColumnData(type='REAL', default=0.92)}¶

addRow(struct)¶

Add a row

Parameters: struct (schrodinger.structure.Structure) – The structure for the database

class schrodinger.application.matsci.kmc.BaseDatabaseManager(struct, filename)¶

Bases: object

Manage initialization and filling of SQL database tables

SITES_TABLE = None¶

PAIRS_TABLE = None¶

class Cursor(manager)¶

Bases: schrodinger.application.matsci.kmc.SQLCursor

Context manager for obtaining a cursor object for use by the tables. Note that when adding many rows it saves a huge amount of time to create the cursor once and then close it when finished rather than create/close a cursor for each row.

__init__(manager)¶

__init__(struct, filename)¶

Create a BaseDatabaseManager instance

Parameters

struct (schrodinger.structure.Structure) – The structure to find dimers in
filename (str) – The name of the SQL file to create

fillSchrodinger()¶: Fill the schrodinger table

fillPairs(dist, pair_type='heavy')¶

Find all dimers in the given structure based on the normal Schrodinger dimer finding algorithm. Add all found dimers to the given SQL file.

Parameters

dist (float) – The distance threshold for defining dimers
pair_type (str) – Either SQL_HEAVY (heavy atom distances only) or SQL_ALL (all atoms are considered when determining pair distance)

Return type

int

Returns

The number of dimers found

initializeDatabase()¶: Should be overwritten by child classes to create the tables

class schrodinger.application.matsci.kmc.VotcaDatabaseManager(struct, filename)¶

Bases: schrodinger.application.matsci.kmc.BaseDatabaseManager

Database manager for votca engine

TABLE_CLASSES = (<class 'schrodinger.application.matsci.kmc.FramesTable'>, <class 'schrodinger.application.matsci.kmc.PairsTable'>, <class 'schrodinger.application.matsci.kmc.MoleculesTable'>, <class 'schrodinger.application.matsci.kmc.SegmentsTable'>, <class 'schrodinger.application.matsci.kmc.FragmentsTable'>, <class 'schrodinger.application.matsci.kmc.AtomsTable'>, <class 'schrodinger.application.matsci.kmc.SegmentTypesTable'>, <class 'schrodinger.application.matsci.kmc.SchrodingerTable'>, <class 'schrodinger.application.matsci.kmc.SuperExchangeTable'>)¶

SITES_TABLE¶: alias of schrodinger.application.matsci.kmc.SegmentsTable

PAIRS_TABLE¶: alias of schrodinger.application.matsci.kmc.PairsTable

initializeDatabase()¶: Create all the tables and fill all but the pairs table with initial data

fillAtoms()¶: Fill the atoms table

fillFragments()¶: Fill the fragments table

fillFrames()¶: Fill the frames table

fillMolecules()¶: Fill the molecules table

fillSegmentTypes()¶: Fill the segmentTypes table

fillSegments()¶

Fill the segments table

Raises: RuntimeError – If fillSegmentTypes has not been called yet

schrodinger.application.matsci.kmc.sql_command(cursor, cmd)¶

Perform the given command without closing the cursor or saving the results to the database

Parameters

cursor (sqlite3.Cursor) – The cursor used
cmd (str) – The SQL command to perform

Return type

bool

Returns

True if the command executed, False if the command raised a no such table error

Raises

sqlite3.OperationalError – in unknown circumstances

schrodinger.application.matsci.kmc.table_rows(db_path, table, orderby=None)¶

Generator for all the rows in a specific table of the database

Parameters

db_path (str or pathlib.Path) – The path to the database
table (str) – The name of the table to get the rows for

Return type

sqlite3.Row

Returns

Yields each row in the table

schrodinger.application.matsci.kmc.delete_all_rows(db_path, table)¶

Delete all the rows in this table

Parameters

db_path (str or pathlib.Path) – The path to the database
table (str) – The name of the table to get the rows for

schrodinger.application.matsci.kmc.is_no_table_error(exc)¶

Detect if this exception is due to the requested table not existing

Parameters: exc (Exception) – The Exception to check
Return type: bool
Returns: Whether this exception is for a missing table

schrodinger.application.matsci.kmc.add_schrodinger_column(db_path, name)¶

Add a column to the schrodinger table. This may be needed if the SQL file was created with an older version that didn’t include this column

Parameters

db_path (str or pathlib.Path) – The path to the SQL file
name (str) – The name of the column, must be a key in SchrodingerTable.COLUMNS

Raises

DuplicateColumnError – If the column already exists
KeyError – If name is not a SchrodingerTable column name

exception schrodinger.application.matsci.kmc.DuplicateColumnError¶

Bases: sqlite3.OperationalError

Specific to trying to ADD COLUMN when one already exists

schrodinger.application.matsci.kmc.add_column(cursor, table_name, col_name, extra_sql=None)¶

Add a column to a given database using the given cursor.

Parameters

cursor (sqlite3.Cursor) – The cursor to use for database read/writes
table_name (str) – The name of the table to add a column to
col_name (str) – The name of the new column
extra_sql (str or None) – Optional additional text to add to the sql command, for example, “REAL DEFAULT ‘0.0’”

Raises

DuplicateColumnError – If the column already exists in the table

schrodinger.application.matsci.kmc.get_dimer_com_sep(dimer, struct)¶

Get the centroid separation vector for a dimer taking into account periodic boundaries.

Parameters

dimer (schrodinger.application.matsci.clusterstruct.Dimer) – The Dimer object for this row
struct (schrodinger.structure.Structure) – The structure associated with this dimer

Return type

tuple(float, float, float)

Returns

the x, y, and z components of the centroid separation between the dimer molecules, taking into account PBC.

schrodinger.application.matsci.kmc.pairs_table_has_com(db_path)¶

Check if the pairs table has COM distance columns or not. This is useful for validating both GUI and driver and as a check before calling add_com_to_pairs_table.

Parameters: db_path (str) – The path to the SQL file
Return type: bool
Returns: True if the pairs table in the db already has COM_DX,Y,Z cols, otherwise False

schrodinger.application.matsci.kmc.matsci_pairs_table_has_periodic_z(db_path)¶

Check if the pairs table has PERIODIC_Z column or not. This is useful for validating / detecting outdated database.

Parameters: db_path (str) – The path to the SQL file
Return type: bool
Returns: True if the pairs table in the db has PERIODIC_Z col, otherwise False

schrodinger.application.matsci.kmc.missing_periodic_z_msg(db_path)¶

Get the error message to send to the user about missing PERIODIC_Z column.

Parameters: db_path – The path to the SQL file
Return type: str
Returns: The message to send to the user about missing PERIODIC_Z column.

schrodinger.application.matsci.kmc.add_com_to_pairs_table(db_path, struct=None)¶

Add center of mass (COM) distance to pairs table.

This function can work in one of two ways: provide a struct if one is available, or if a struct is not available, set struct=None and the necessary data will be gathered if available from the existing database tables.

Parameters

db_path (str) – The path to the SQL file
struct (Structure) – the structure with associated PBC and molecule information. If None, the PBC and molecule information will be obtained from the database, if it is available.

schrodinger.application.matsci.kmc.set_schrodinger_db_value(db_path, name, value)¶

Set the value of the given column in the Schrodinger table.

Parameters

db_path (str or pathlib.Path) – The path to the SQL file
name (str) – The name of the column, must be a key in SchrodingerTable.COLUMNS
value – The value to put into the database. The type of the parameter should be consistent with the expected type for that column.

schrodinger.application.matsci.kmc.store_schrodinger_job_props(db_path, mae_name, struct)¶

Store Schrodinger information about the current job in the database

Parameters

db_path (str or pathlib.Path) – The path to the SQL file
mae_name (str) – The name of the Maestro file that will hold the structure
struct (schrodinger.structure.Structure) – The structure to add corresponding job info props to

schrodinger.application.matsci.kmc.get_schrodinger_db_value(db_path, name)¶

Get the value for the given column from the Schrodinger table in the database

Parameters

db_path (str or pathlib.Path) – The path to the SQL file
name (str) – The name of the column to get the data from

Return type

variable or None

Returns

The value for the given column in the Schrodinger table, or None if no such table exists or no such column exists

schrodinger.application.matsci.kmc.get_db_structure_path(db_path, existence_check=True)¶

Get the path to the structure that created this database

Parameters

db_path (str or pathlib.Path) – The path to the SQL file
existence_check (bool) – If True, return None if the path in the database does not point to an existing file. If False, return the path regardless of whether the file exists.

Return type

pathlib.Path or None

Returns

The Path to the structure file, or None if no path is found in the database or existence_check=True and the file does not exist

schrodinger.application.matsci.kmc.add_pairs_to_database(struct, path, dist, pair_type='heavy')¶

Find all dimers in the given structure based on the normal Schrodinger dimer finding algorithm. Add all found dimers to the given VOTCA SQL file.

Parameters

struct (schrodinger.structure.Structure) – The structure with the pairs
path (str) – The path to the SQL database
dist (float) – The distance threshold for defining dimers
pair_type (str) – Either SQL_HEAVY (heavy atom distances only) or SQL_ALL (all atoms are considered when determining pair distance)

Return type

int

Returns

The number of dimers found

schrodinger.application.matsci.kmc.get_pairs_from_database(db_path)¶

Get the pairs from the database

Parameters: db_path (str or pathlib.Path) – The path to the SQL file
Return type: list
Returns: Each item of the list is a schrodinger.application.matsci.clusterstruct.Dimer object. The list is empty if the pairs table has not been populated. Note that the Dimer objects will not have set the home_atom or neighbor_atom properties of the neighbor_info property.

schrodinger.application.matsci.kmc.has_pair_data(db_path)¶

Check if the database has pair data

Parameters: db_path (str or pathlib.Path) – The path to the database
Return type: bool or str
Returns: If no data, False. If data, the distance type used to find pairs - either SQL_HEAVY or SQL_ALL

schrodinger.application.matsci.kmc.get_pair_info(db_path)¶

Get the parameters used to determine the existing pairs in the database

Parameters: db_path (str or pathlib.Path) – The path to the database
Return type: (str, float) or None
Returns: The type of distance used to find pairs (SQL_HEAVY or SQL_ALL) and the distance cutoff for pairs. None is returned if no pair data exists.

schrodinger.application.matsci.kmc.is_matsci_engine_db(db_path)¶

Get whether the database is made for the internal engine. Returns False if the corresponding column doesn’t exist in the database (older versions)

Parameters: db_path (str) – The path to database file
Return bool: Whether the database is for internal engine

schrodinger.application.matsci.kmc.get_database_manager_class(db_path=None, is_matsci=None)¶

Get the database manager class using either the database path or the explicit is_matsci bool

Parameters

db_path (str) – The path to an existing database file
is_matsci (bool) – Whether the database will be for matsci engine

Return BaseDatabaseManager

either MatSciDatabaseManager or VotcaDatabaseManager

schrodinger.application.matsci.kmc.get_sites_table(db_path)¶

Get the sites table class for the sql file

Parameters: db_path (str) – The path to sql file
Return type: SegmentsTable or MatSciSitesTable
Returns: The sites table class

schrodinger.application.matsci.kmc.get_pairs_table(db_path)¶

Get the pairs table class for the sql file

Parameters: db_path (str) – The path to sql file
Return type: PairsTable or MatSciPairsTable
Returns: The pairs table class

schrodinger.application.matsci.kmc.find_missing_coupling_data(path, charge)¶

Find any pair coupings that are 0

Parameters

path (str) – The path to the database file
charge (str) – Either HOLE or ELECTRON

Return type

list

Returns

Each item is a tuple with the molecule numbers of the two molecules involved in the missing coupling term.

schrodinger.application.matsci.kmc.find_missing_site_energies(path, charge)¶

Find any segment that has any site energy property equal to 0

Parameters

path (str) – The path to the database file
charge (str) – Either HOLE or ELECTRON

Return type

list

Returns

Each item is the integer SQID (which translates to molecule number) of any segment with missing site energy information

schrodinger.application.matsci.kmc.copy_rates_csv_to_db(db_path, e12_csv=None, e21_csv=None, h12_csv=None, h21_csv=None)¶

Copy rates from formatted rates csv file from ML workflow to sql database

Parameters

db_path (str) – the path to the database sql file
e12_csv (Optional[str]) – the path to the electron 12 rate csv file
e21_csv (Optional[str]) – the path to the electron 21 rate csv file
h12_csv (Optional[str]) – the path to the hole 12 rate csv file
h21_csv (Optional[str]) – the path to the hole 21 rate csv file

schrodinger.application.matsci.kmc.get_h_pair_rates_from_database(db_path)¶

Get the hole hopping rates from the database

Parameters: db_path (str or pathlib.Path) – The path to the SQL file
Return type: dict (key: tuple(int,int). val: float)
Returns: Dictionary where the key is the directed pair of site indices (source site, destination site) the val is the hole hopping rate in that direction

schrodinger.application.matsci.kmc.get_e_pair_rates_from_database(db_path)¶

Get the electron hopping rates from the database. Note: site indexes here are 1-indexed, taken directly from the database.

Parameters: db_path (str or pathlib.Path) – The path to the SQL file
Return type: dict (key: tuple(int,int). val: float)
Returns: Dictionary where the key is the directed pair of site indices (source site, destination site), the val is the electron hopping rate in that direction

schrodinger.application.matsci.kmc.get_pair_rates_from_database(db_path, particle_type='h')¶

Get the hopping rates from the database. Note: site indexes here are 1-indexed, taken directly from the database.

Parameters

db_path (str or pathlib.Path) – The path to the SQL file
particle_type (str) – H_ENDING for hole, or E_ENDING for electron

Return type

dict (key: tuple(int,int). val: float)

Returns

Dictionary where the key is the directed pair of site indices (source site, destination site), the val is the hopping rate in that direction

schrodinger.application.matsci.kmc.copy_sql_data(source, destination, table, columns)¶

Copy the column from table in the source database to the destination database

Parameters

source (str or pathlib.path) – the path to the source database
destination (str or pathlib.path) – the path to the destination database
table (str) – The name of the table to copy from
columns (list) – A list of column names to copy

Raises

IndexError – If the two databases do not have the same number of rows
DuplicateColumnError – If new_cals=True is used but the cols already exist in the destination table

schrodinger.application.matsci.kmc.set_column_constant(db_path, table, column, constant)¶

Set all rows of a given column to the value constant.

Caution: this loses all current data in that column.

Parameters

db_path (str) – The path to the SQL file
table (str) – The name of the table to copy from
column (str) – The name of the column
constant (float or str) – The value to set

exception schrodinger.application.matsci.kmc.SQLCreationError¶

Bases: Exception

Raised if an issue occurs when creating the database

schrodinger.application.matsci.kmc.generate_votca_database(struct, backend=None, matsci_engine=False)¶

Create a VOTCA SQL database and include data on species and pairs

Note that VOTCA requires the segments in a system be ordered such that all segments of the same type appear together in order. This function returns the reordered structure used to create the database. (segments=molecules)

Parameters

struct (schrodinger.structure.Structure) – The structure to create a database for
backend (scschrodigner.job.jobcontrol._Backend) – The backend if one exists
matsci_engine (bool) – Whether the database will be for the internal engine

Return type

str

Returns

The name of the sql file that was created

Raises

SQLCreationError – If the sql file can’t be created

class schrodinger.application.matsci.kmc.MatSciSitesTable(filename)¶

Bases: schrodinger.application.matsci.kmc.SitesMixin, schrodinger.application.matsci.kmc.Table

Sites table for the internal engine

TABLE_NAME = 'sites'¶

OCCP_SING = 'occP_singlet'¶

OCCP_TRIP = 'occP_triplet'¶

INJECTS_E = 'injects_e'¶

INJECTS_H = 'injects_h'¶

E_INJECTIONS = 'e_injections'¶

H_INJECTIONS = 'h_injections'¶

E_ANNIHILIATIONS = 'e_annihilations'¶

H_ANNIHILIATIONS = 'h_annihilations'¶

RAD_DECAYS = 'radiative_decays'¶

NONRAD_DECAYS = 'nonradiative_decays'¶

CURRENT_MAGNITUDE_E = 'current_magnitude_e'¶

CURRENT_X_E = 'current_x_e'¶

CURRENT_Y_E = 'current_y_e'¶

CURRENT_Z_E = 'current_z_e'¶

CURRENT_MAGNITUDE_H = 'current_magnitude_h'¶

CURRENT_X_H = 'current_x_h'¶

CURRENT_Y_H = 'current_y_h'¶

CURRENT_Z_H = 'current_z_h'¶

COLUMNS = {'UcCnNe': ColumnData(type='REAL', default=0), 'UcCnNh': ColumnData(type='REAL', default=0), 'UcNcCe': ColumnData(type='REAL', default=0), 'UcNcCh': ColumnData(type='REAL', default=0), 'UnCnNe': ColumnData(type='REAL', default=0), 'UnCnNh': ColumnData(type='REAL', default=0), 'current_magnitude_e': ColumnData(type='REAL', default=0), 'current_magnitude_h': ColumnData(type='REAL', default=0), 'current_x_e': ColumnData(type='REAL', default=0), 'current_x_h': ColumnData(type='REAL', default=0), 'current_y_e': ColumnData(type='REAL', default=0), 'current_y_h': ColumnData(type='REAL', default=0), 'current_z_e': ColumnData(type='REAL', default=0), 'current_z_h': ColumnData(type='REAL', default=0), 'e_annihilations': ColumnData(type='INT', default=0), 'e_injections': ColumnData(type='INT', default=0), 'h_annihilations': ColumnData(type='INT', default=0), 'h_injections': ColumnData(type='INT', default=0), 'has_e': ColumnData(type='INT', default=0), 'has_h': ColumnData(type='INT', default=0), 'id': ColumnData(type='INT', default=None), 'injects_e': ColumnData(type='INT', default=0), 'injects_h': ColumnData(type='INT', default=0), 'mol': ColumnData(type='INT', default=None), 'name': ColumnData(type='TEXT', default=None), 'nonradiative_decays': ColumnData(type='INT', default=0), 'occP_singlet': ColumnData(type='REAL', default=-1), 'occP_triplet': ColumnData(type='REAL', default=-1), 'occPe': ColumnData(type='REAL', default=-1), 'occPh': ColumnData(type='REAL', default=-1), 'posX': ColumnData(type='REAL', default=None), 'posY': ColumnData(type='REAL', default=None), 'posZ': ColumnData(type='REAL', default=None), 'radiative_decays': ColumnData(type='INT', default=0), 'type': ColumnData(type='TEXT', default=None)}¶

addRow(molecule)¶

Add a row

Parameters: molecule (schrodinger.structure._StructureMolecule) – The molecule object to add a row for

class schrodinger.application.matsci.kmc.MatSciPairsTable(filename)¶

Bases: schrodinger.application.matsci.kmc.PairsMixin, schrodinger.application.matsci.kmc.Table

Pairs table for the internal engine

TABLE_NAME = 'pairs'¶

SITE1 = 'site1'¶

SITE2 = 'site2'¶

JEFF2_12E = 'Jeff2_12e'¶

JEFF2_21E = 'Jeff2_21e'¶

JEFF2_12H = 'Jeff2_12h'¶

JEFF2_21H = 'Jeff2_21h'¶

LAMBDA_12E = 'Lambda_12e'¶

LAMBDA_21E = 'Lambda_21e'¶

LAMBDA_12H = 'Lambda_12h'¶

LAMBDA_21H = 'Lambda_21h'¶

DELTAE_12E = 'DeltaE_12e'¶

DELTAE_21E = 'DeltaE_21e'¶

DELTAE_12H = 'DeltaE_12h'¶

DELTAE_21H = 'DeltaE_21h'¶

JUMPS_12E = 'Jumps_12e'¶

JUMPS_21E = 'Jumps_21e'¶

JUMPS_12H = 'Jumps_12h'¶

JUMPS_21H = 'Jumps_21h'¶

COUPLING_COLUMNS = {'electron': ['Jeff2_12e', 'Jeff2_21e'], 'hole': ['Jeff2_12h', 'Jeff2_21h']}¶

LAMBDA_COLUMNS = {'electron': ['Lambda_12e', 'Lambda_21e'], 'hole': ['Lambda_12h', 'Lambda_21h']}¶

DELTAE_COLUMNS = {'electron': ['DeltaE_12e', 'DeltaE_21e'], 'hole': ['DeltaE_12h', 'DeltaE_21h']}¶

JUMP_COLUMNS = {'electron': ['Jumps_12e', 'Jumps_21e'], 'hole': ['Jumps_12h', 'Jumps_21h']}¶

RATE_COLUMNS = {'electron': ['rate12e', 'rate21e'], 'hole': ['rate12h', 'rate21h']}¶

COLUMNS = {'DeltaE_12e': ColumnData(type='REAL', default=0), 'DeltaE_12h': ColumnData(type='REAL', default=0), 'DeltaE_21e': ColumnData(type='REAL', default=0), 'DeltaE_21h': ColumnData(type='REAL', default=0), 'Jeff2_12e': ColumnData(type='REAL', default=0), 'Jeff2_12h': ColumnData(type='REAL', default=0), 'Jeff2_21e': ColumnData(type='REAL', default=0), 'Jeff2_21h': ColumnData(type='REAL', default=0), 'Jumps_12e': ColumnData(type='INT', default=0), 'Jumps_12h': ColumnData(type='INT', default=0), 'Jumps_21e': ColumnData(type='INT', default=0), 'Jumps_21h': ColumnData(type='INT', default=0), 'Lambda_12e': ColumnData(type='REAL', default=0), 'Lambda_12h': ColumnData(type='REAL', default=0), 'Lambda_21e': ColumnData(type='REAL', default=0), 'Lambda_21h': ColumnData(type='REAL', default=0), 'com_drx': ColumnData(type='REAL', default=None), 'com_dry': ColumnData(type='REAL', default=None), 'com_drz': ColumnData(type='REAL', default=None), 'drx': ColumnData(type='REAL', default=None), 'dry': ColumnData(type='REAL', default=None), 'drz': ColumnData(type='REAL', default=None), 'id': ColumnData(type='INT', default=None), 'periodic_z': ColumnData(type='INT', default=None), 'rate12e': ColumnData(type='REAL', default=0), 'rate12h': ColumnData(type='REAL', default=0), 'rate21e': ColumnData(type='REAL', default=0), 'rate21h': ColumnData(type='REAL', default=0), 'site1': ColumnData(type='INT', default=None), 'site2': ColumnData(type='INT', default=None)}¶

class schrodinger.application.matsci.kmc.MatSciDatabaseManager(struct, filename)¶

Bases: schrodinger.application.matsci.kmc.BaseDatabaseManager

Database manager for the internal database

TABLE_CLASSES = (<class 'schrodinger.application.matsci.kmc.MatSciSitesTable'>, <class 'schrodinger.application.matsci.kmc.MatSciPairsTable'>, <class 'schrodinger.application.matsci.kmc.SchrodingerTable'>)¶

SITES_TABLE¶: alias of schrodinger.application.matsci.kmc.MatSciSitesTable

PAIRS_TABLE¶: alias of schrodinger.application.matsci.kmc.MatSciPairsTable

initializeDatabase()¶: Create all the tables and fill all but the pairs table with initial data

fillSites()¶: Fill the sites table

schrodinger.application.matsci.kmc.add_charge_flag(parser)¶

Add the charge flag to the parser

Parameters: parser (parserutils.DriverParser or argparse._ArgumentGroup) – The parser or argument group to add the flag to

schrodinger.application.matsci.kmc.add_kmc_flags(parser)¶

Add KMC flags to the parser

Parameters: parser (parserutils.DriverParser or argparse._ArgumentGroup) – The parser or argument group to add the flag to

schrodinger.application.matsci.kmc.type_field(value)¶

Type the field command line parameter

Parameters: value (str) – The command line field parameter
Return type: list of tuple
Returns: Each item of the list is (X, Y, Z) field strengths in MV/m for one field. Field strengths are floats.
Raises: argparse.ArgumentTypeError – If the argument cannot be converted to a length 3 list of floats

schrodinger.application.matsci.kmc.get_sql_output_name(jobname)¶

Get the name of the SQL file that will be created

Parameters: jobname (str) – The name of the job
Return type: str
Returns: The name the output sql file will have

schrodinger.application.matsci.kmc.get_db_table_length(db_path, table)¶

Get the number of rows in the given table

Parameters

db_path (str) – The path to the database
table (str) – The name of the table

Return int

The number of rows

schrodinger.application.matsci.kmc.form_set_val_string(val_dict)¶

Create the string to set multiple values in a sql row

Parameters: val_dict (dict) – Dict mapping column names to their values
Return str: The string to put in sql comand

schrodinger.application.matsci.kmc.get_num_missing_data(sql_file, charge)¶

Get the number of missing sites and coupling data

Parameters

sql_file (str) – The path to the sql file
charge (str) – The charge to check for

Return type

tuple of int

Returns

The number of missing sites and couplings