schrodinger.application.matsci.order_parameter_mod module¶

Utilities for order parameter analysis.

class schrodinger.application.matsci.order_parameter_mod.Result(total_op, per_mol_op)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

per_mol_op¶: Alias for field number 1

total_op¶: Alias for field number 0

class schrodinger.application.matsci.order_parameter_mod.PerMolOP(mol_numbers, mol_ops)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

mol_numbers¶: Alias for field number 0

mol_ops¶: Alias for field number 1

schrodinger.application.matsci.order_parameter_mod.log(msg, **kwargs)¶

Add a message to the log file

Parameters: msg (str) – The message to log

Additional keyword arguments are passed to the textlogger.log_msg function

schrodinger.application.matsci.order_parameter_mod.get_name_w_mol_n(name, mol_n)¶

Return the name with the molecule number.

Parameters

name (str) – the name
mol_n (int) – the molecule number

Return type

str

Returns

the name with the molecule number

schrodinger.application.matsci.order_parameter_mod.get_name_wo_mol_n(name)¶

Return the name without the molecule number.

Parameters: name (str) – the name
Return type: (str, int) or (str, None)
Returns: the name without the molecule number and the molecule number if there is one

class schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin¶

Bases: object

Manages reducing vectors.

reduce_vec(n, m)¶

Specify how to reduce the reference director vector, n, and all of the description vectors, m, into an order parameter.

Parameters

n (numpy.array) – the reference director vector (row vector of length 3)
m (numpy.array) – the description vectors (matrix of size N X 3), where N is the number of molecules

Return type

float

Returns

the order parameter

schrodinger.application.matsci.order_parameter_mod.get_trj_from_cms_file(cms_file)¶

Return the trajectory from the given .cms file.

Parameters: cms_file (str) – the .cms file (can be a path)
Return type: list
Returns: contains the trajectory as a list of schrodinger.application.desmond.packages.traj.Frame

exception schrodinger.application.matsci.order_parameter_mod.AslException¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.matsci.order_parameter_mod.SmartsException¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.order_parameter_mod.DipoleDirector(*args, **kwargs)¶

Bases: schrodinger.application.desmond.packages.analysis.DipoleDirector, schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin

Manage a dipole director.

__init__(msys_model, cms_model, asl)¶

disableDyncalc()¶: Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()¶

reduce_vec(n, m)¶

Specify how to reduce the reference director vector, n, and all of the description vectors, m, into an order parameter.

Parameters

n (numpy.array) – the reference director vector (row vector of length 3)
m (numpy.array) – the description vectors (matrix of size N X 3), where N is the number of molecules

Return type

float

Returns

the order parameter

class schrodinger.application.matsci.order_parameter_mod.MomentOfInertiaDirector(*args, **kwargs)¶

Bases: schrodinger.application.desmond.packages.analysis.MomentOfInertiaDirector, schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin

Manage a moment of inertia director.

__init__(msys_model, cms_model, asl)¶

disableDyncalc()¶: Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()¶

reduce_vec(n, m)¶

Specify how to reduce the reference director vector, n, and all of the description vectors, m, into an order parameter.

Parameters

n (numpy.array) – the reference director vector (row vector of length 3)
m (numpy.array) – the description vectors (matrix of size N X 3), where N is the number of molecules

Return type

float

Returns

the order parameter

class schrodinger.application.matsci.order_parameter_mod.UniqueSmartsDirector(*args, **kwargs)¶

Bases: schrodinger.application.desmond.packages.analysis.SmartsDirector, schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin

Manage a unique SMARTS director.

__init__(msys_model, cms_model, asl, smarts)¶

Create an instance.

Parameters

msys_model (Desmond msys .System) – the msys object (from msys.LoadMAE)
cms_model (schrodinger.application.desmond.cms.Cms) – the cms object
asl (str) – the ASL for the descriptor
smarts (str) – the SMARTS for the descriptor

reduce_vec(n, m)¶

Specify how to reduce the reference director vector, n, and all of the description vectors, m, into an order parameter.

Parameters

n (numpy.array) – the reference director vector (row vector of length 3)
m (numpy.array) – the description vectors (matrix of size N X 3), where N is the number of molecules

Return type

float

Returns

the order parameter

disableDyncalc()¶: Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()¶

class schrodinger.application.matsci.order_parameter_mod.SmartsDirector(*args, **kwargs)¶

Bases: schrodinger.application.desmond.packages.analysis.SmartsDirector, schrodinger.application.matsci.order_parameter_mod.ReduceVecMixin

Manage a SMARTS director.

__init__(msys_model, cms_model, asl, smarts)¶

disableDyncalc()¶: Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()¶

reduce_vec(n, m)¶

Calculate Legendre polynomial P2 using the inner product of n and m as the input.

Parameters: m (N’x3 numpy.array where N’ is the number of chemical bonds.) – Output of SmartsDirector for one frame

class schrodinger.application.matsci.order_parameter_mod.Descriptor(name, group=None, asl=None, atype=None, smarts=None)¶

Bases: object

Manage a descriptor.

DIPOLE = 'dipole'¶

MOMENT_OF_INERTIA = 'moment_of_inertia'¶

SMARTS_NONUNIQUE_BONDS = 'SMARTS_nonunique_bonds'¶

SMARTS_UNIQUE_PAIR = 'SMARTS_unique_pair'¶

SMARTS_UNIQUE_TRIPLE_NORMAL = 'SMARTS_unique_triple_normal'¶

TYPES_TO_CLASSES = {'SMARTS_nonunique_bonds': <class 'schrodinger.application.matsci.order_parameter_mod.SmartsDirector'>, 'SMARTS_unique_pair': <class 'schrodinger.application.matsci.order_parameter_mod.UniqueSmartsDirector'>, 'SMARTS_unique_triple_normal': <class 'schrodinger.application.matsci.order_parameter_mod.UniqueSmartsDirector'>, 'dipole': <class 'schrodinger.application.matsci.order_parameter_mod.DipoleDirector'>, 'moment_of_inertia': <class 'schrodinger.application.matsci.order_parameter_mod.MomentOfInertiaDirector'>}¶

GROUP_KWARG = 'group'¶

ASL_KWARG = 'asl'¶

ATYPE_KWARG = 'atype'¶

SMARTS_KWARG = 'smarts'¶

__init__(name, group=None, asl=None, atype=None, smarts=None)¶

Create an instance.

Parameters

name (str) – the name of the descriptor
group (str or None) – the group of the descriptor or None if there isn’t one
asl (str) – the ASL for the descriptor or None if there isn’t one
atype (str) – the type of descriptor or None if there isn’t one
smarts (str or None) – the SMARTS for the descriptor or None if there isn’t one

getDescriptor(msys_obj, cms_obj)¶

Get the descriptor.

Parameters

msys_obj (Desmond msys .System) – the msys object (from msys.LoadMAE)
cms_obj (schrodinger.application.desmond.cms.Cms) – the cms object

Return type

schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer

Returns

descriptor subclasses of the given type

getFileName(basename)¶

Return a file name for this descriptor using the given base name.

Parameters: basename (str) – base name to use in naming the file
Return type: str
Returns: the descriptor file name

getPerMolFileName(basename)¶

Return a per molecule file name for this descriptor using the given base name.

Parameters: basename (str) – base name to use in naming the file
Return type: str
Returns: the descriptor per molecule file name

schrodinger.application.matsci.order_parameter_mod.get_descriptors_from_file(descriptors_file, logger=None)¶

Return a list of descriptors from the given descriptors file.

Parameters

descriptors_file (str) – .json file containing specifications for descriptors, i.e. ways to determine vectors used in computing the order parameters with respect to the director, a specification includes information like name, group, ASL, type, and SMARTS (can be a path)
logger (logging.Logger or None) – output logger or None if there isn’t one

Return type

list

Returns

contains Descriptor

class schrodinger.application.matsci.order_parameter_mod.Director(*args, **kwargs)¶

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Manage a director.

__init__(vec)¶

Create an instance.

Parameters: vec (numpy.array) – the director vector

disableDyncalc()¶: Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()¶

class schrodinger.application.matsci.order_parameter_mod.OrderParameter(cms_file, director_abc_coeffs, descriptors_file, logger=None)¶

Bases: object

Manage order parameter analysis.

__init__(cms_file, director_abc_coeffs, descriptors_file, logger=None)¶

Create an instance.

Parameters

cms_file (str) – the .cms file for the simulation on which to run the order parameter analysis (can be a path)
director_abc_coeffs (tuple) – coefficients of the static reference director vector in the lattice vector basis, for example (0, 0, 1) for the c-lattice vector or z-axis of a cubic cell
descriptors_file (str) – .json file containing specifications for descriptors, i.e. ways to determine vectors used in computing the order parameters with respect to the director, a specification includes information like name, group, ASL, type, and SMARTS (can be a path) (see get_descriptors_from_file for more information)
logger (logging.Logger or None) – output logger or None if there isn’t one

static getDirector(cms_obj, director_abc_coeffs)¶

Return the unit director vector object for the given cms (in Angstrom).

Parameters

cms_obj (schrodinger.application.desmond.cms.Cms) – the cms object
director_abc_coeffs (tuple) – coefficients of the static reference director vector in the lattice vector basis, for example (0, 0, 1) for the c-lattice vector or z-axis of a cubic cell

Return type

Director

Returns

the unit director vector object

run()¶: Run the order parameter analysis.