schrodinger.application.matsci.coarsegrain module¶

Utilities for working with coarse grain structures

class schrodinger.application.matsci.coarsegrain.ParticleInfo(key, name, rgb, radius, mass)¶

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.

key¶: Alias for field number 0

mass¶: Alias for field number 4

name¶: Alias for field number 1

radius¶: Alias for field number 3

rgb¶: Alias for field number 2

exception schrodinger.application.matsci.coarsegrain.MixedAACGStructuresError¶

Bases: ValueError

Exception when input has a mix of CG and AA structures.

__init__(*args, **kwargs)¶

args¶

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

schrodinger.application.matsci.coarsegrain.get_base64_str_from_structure(st)¶

Return a base64 string from the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: str
Returns: the base64 string

schrodinger.application.matsci.coarsegrain.get_structure_from_base64_str(base64_str)¶

Return a structure from the given base64 string.

Parameters: astr (str) – the base64 string
Return type: schrodinger.structure.Structure
Returns: the structure

schrodinger.application.matsci.coarsegrain.is_martini_charge_type(atype)¶

Return True if the given Martini type is a charge type.

Parameters: atype (str) – the Martini type
Return type: bool
Returns: True if a Martini charge type

schrodinger.application.matsci.coarsegrain.is_martini_ring_type(atype)¶

Return True if the given Martini type is a ring type.

Parameters: atype (str) – the Martini type
Return type: bool
Returns: True if a Martini ring type

schrodinger.application.matsci.coarsegrain.get_martini_ring_type_from_type(atype)¶

Return the Martini ring type from the type.

Parameters: atype (str) – the Martini type
Return type: str
Returns: the Martini ring type

schrodinger.application.matsci.coarsegrain.is_martini_antifreeze_type(atype)¶

Return True if the given Martini type is an antifreeze type.

Parameters: atype (str) – the Martini type
Return type: bool
Returns: True if a Martini antifreeze type

schrodinger.application.matsci.coarsegrain.get_martini_antifreeze_type_from_type(atype)¶

Return the Martini antifreeze type from the type.

Parameters: atype (str) – the Martini type
Return type: str
Returns: the Martini antifreeze type

schrodinger.application.matsci.coarsegrain.is_martini_tiny_type(atype)¶

Return True if the given Martini type is a tiny type.

Parameters: atype (str) – the Martini type
Return type: bool
Returns: True if a Martini tiny type

schrodinger.application.matsci.coarsegrain.get_martini_tiny_type_from_type(atype)¶

Return the Martini tiny type from the type.

Parameters: atype (str) – the Martini type
Return type: str
Returns: the Martini tiny type

schrodinger.application.matsci.coarsegrain.get_martini_type_from_super_type(atype)¶

Return the Martini type from the super type, i.e. ring or antifreeze type.

Parameters: atype (str) – the Martini super type
Return type: str
Returns: the Martini type

schrodinger.application.matsci.coarsegrain.get_bead_count(struct, excluded_atom_ids=None)¶

Gets a dictionary containing the counts of the different “beads” in the coarse-grained structure.

Parameters

struct (schrodinger.structure.Structure) – the structure to get formula from
excluded_atom_ids (None or a list of atom ids) – exclude these atoms when computing the formula

Return type

dict

Returns

A dictionary whose keys are the “bead”/atom names and whose values are the number of beads/atoms

schrodinger.application.matsci.coarsegrain.get_atom_name_formula(struct, excluded_atom_ids=None)¶

Return a ‘molecular formula’ based on atom names (e.g., (BENZ)(W)20)

Parameters

struct (schrodinger.structure.Structure) – the structure to get formula from
excluded_atom_ids (None or a list of atom ids) – exclude these atoms when computing the formula

Return type

str

Returns

‘molecular formula’ based on atom names

class schrodinger.application.matsci.coarsegrain.InternalInfo(names, indices, data)¶

Bases: tuple

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

__len__()¶: Return len(self).

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

data¶: Alias for field number 2

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

Return first index of value.

Raises ValueError if the value is not present.

indices¶: Alias for field number 1

names¶: Alias for field number 0

schrodinger.application.matsci.coarsegrain.split_shadow_bond_tag(name)¶

Split the shadow bond tag from the given name.

Parameters: name (str) – the particle name
Return type: str, str
Returns: the given name less the shadow bond tag, the shadow bond tag (empty string if not present)

schrodinger.application.matsci.coarsegrain.get_martini_subtypes(type_tuple, martini_subtypes)¶

Return a list of Martini subtypes from the given type tuple.

Parameters

type_tuple (tuple) – a type tuple, for example bond type tuple, containing particle names
martini_subtypes (dict) – keys are site type tuples and values are Martini subtypes

Return type

list

Returns

contains Martini subtypes

schrodinger.application.matsci.coarsegrain.get_martini_eq_length(pair_type, martini_subtypes)¶

Return the Martini equilibrium length parameter.

Parameters

pair_type (tuple) – the bond pair type
martini_subtypes (dict) – keys are site type tuples and values are Martini subtypes

Return type

float

Returns

the equilibrium length parameter in Angstrom

schrodinger.application.matsci.coarsegrain.get_martini_bond_force_constant(pair_type, martini_subtypes)¶

Return the Martini bond force constant parameter.

Parameters

pair_type (tuple) – the bond pair type
martini_subtypes (dict) – keys are site type tuples and values are Martini subtypes

Return type

float

Returns

the bond force constant parameter in (kcal/mol)/Ang.^2

schrodinger.application.matsci.coarsegrain.get_martini_epsilon(pair_type, martini_subtypes)¶

Return the Martini epsilon parameter.

Parameters

pair_type (tuple) – the nonbond pair type
martini_subtypes (dict) – keys are site type tuples and values are Martini subtypes

Return type

float

Returns

the epsilon parameter in kcal/mol

schrodinger.application.matsci.coarsegrain.get_martini_sigma(pair_type, martini_subtypes)¶

Return the Martini sigma parameter.

Parameters

pair_type (tuple) – the nonbond pair type
martini_subtypes (dict) – keys are site type tuples and values are Martini subtypes

Return type

float

Returns

the sigma parameter in Ang.

schrodinger.application.matsci.coarsegrain.get_combined_exclusion_str(bad_str, exclude_rings=False)¶

Return a combined exclusion string.

Parameters

bad_str (str) – a bond, angle, or dihedral string, i.e. one of EXCLUDE_BONDS, EXCLUDE_BONDS_ANGLES, or EXCLUDE_BONDS_ANGLES_DIHEDRALS
exclude_rings (bool) – whether pairs in rings and fused-ring systems are also excluded

Return type

str

Returns

the combined exclusion string

schrodinger.application.matsci.coarsegrain.parse_combined_exclusion_str(combined_str)¶

Parse a combined exclusion string.

Parameters: combined_str (str) – a combined exclusion string obtained from get_combined_exclusion_str
Return type: str, bool
Returns: a bond, angle, or dihedral string, i.e. one of EXCLUDE_BONDS, EXCLUDE_BONDS_ANGLES, or EXCLUDE_BONDS_ANGLES_DIHEDRALS, and whether pairs in rings and fused-ring systems are also excluded

schrodinger.application.matsci.coarsegrain.get_type_dict_from_st(st, type_dict=None)¶

Return a sorted type dict for the given structure.

Parameters

st (schrodinger.structure.Structure) – the structure from which to obtain the type dict
type_dict (OrderedDict or None) – specify a type dict to include in the returned type dict (note that this type dict takes precedence over the type dict data for the given structure) or None if there isn’t one

Return type

OrderedDict

Returns

the sorted type dict, keys are particle names, values are ParticleInfo

schrodinger.application.matsci.coarsegrain.system_has_charged_particles(model)¶

Check if any particle in the given system has a charge based on the sites FFIO block

Parameters: model (schrodinger.application.desmond.cms.Cms or schrodinger.application.desmond.ffiostructure.FFIOStructure) – The system to check the FFIO site block for charges
Return type: bool
Returns: True if an FFIO sites block exists in the given system and contains at least one charged particle. False if there is either no such block or the block contains only neutral particles

schrodinger.application.matsci.coarsegrain.get_cg_cutoff_data(model)¶

Return the coarse grain cutoff data.

Parameters: model (schrodinger.application.desmond.cms.Cms) – The model structure
Raises: ValueError – if model is incorrect
Return type: dict
Returns: the coarse grain cutoff data, each key in the dictionary is a format specifier from the MSJ_*_COARSE_GRAIN_HEADER string and the value is the value for that format specifier

schrodinger.application.matsci.coarsegrain.compute_max_internal_distance(struct)¶

Compute the largest distance between any pair of atoms that are a) bonded, b) 1-3 in an angle or c) 1-4 in a dihedral

Parameters: struct (schrodinger.structure.Structure) – The structure to compute the distance over
Return type: float
Returns: The largest distance between any pair of atoms involved in a bond, angle or torsion

schrodinger.application.matsci.coarsegrain.get_coarse_grain_msj_header(struct)¶

Get the appropriate MSJ header text for this coarse grain structure

Parameters: struct (schrodinger.application.desmond.cms.Cms) – The structure to get the header for
Return type: str
Returns: The header text appropriate for this structure. An empty string is returned if the structure is not coarse-grained. The LJ header is used for coarse-grained systems with unrecognized non-bond potential type.

schrodinger.application.matsci.coarsegrain.get_coarse_grain_msj_family_header(struct)¶

Get any additional header text that needs to be inserted into the task stage of the msj file if this structure is coarse grain. This header can then be inserted when creating the .msj file by using the extra_task_text keyword to the desconfig.create_msj call. i.e. header = coarsegrain.get_coarse_grain_msj_family_header(system) desconfig.create_msj(stages, extra_task_text=header)

Parameters: struct (schrodinger.application.desmond.cms.Cms) – The structure to get the header for
Return type: str
Returns: The header text, if any, required for the current input. If no additional header text is required, an empty string is returned.

schrodinger.application.matsci.coarsegrain.validate_no_cg(struct=None, structs=None, rows=None)¶

Fail a validation check if any of the structures is a coarse grain structure

One and only one of struct, structs or rows should be given

Parameters

struct (schrodinger.structure.Structure) – The structure, if only a single structure is to be tested
structs (list) – A list of structures to test
rows (iterator of schrodinger.project.ProjectRow) – Project Table rows to check

Return type

(False, msg) or True

Returns

False and error message if the structure is coarse grain, True if everything is OK. Return value is acceptable for an AF2 valiator.

schrodinger.application.matsci.coarsegrain.set_as_coarse_grain(struct)¶

Mark struct as a coarse grain structure

Parameters: struct (schrodinger.structure.Structure) – The structure to mark
Raises: LicenseError – If the license is not valid for using coarse grained structures

schrodinger.application.matsci.coarsegrain.set_nonbond_potential_type(struct, nbtype)¶

Mark the structure with the non-bond pontential type

Parameters

struct (schrodinger.structure.Structure) – The structure to mark
nbtype (str) – Should be a module constant in the NONBOND_POTENTIALS list

Raises

ValueError – if nbtype is not in NONBOND_POTENTIALS
TypeError – if struct is not a coarse grain system

schrodinger.application.matsci.coarsegrain.set_angle_potential_type(struct, atype)¶

Mark the structure with the angle pontential type

Parameters

struct (schrodinger.structure.Structure) – The structure to mark
atype (str) – Should be a module constant in the ANGLES_KEYS list

Raises

ValueError – if atype is not in ANGLES_KEYS
TypeError – if struct is not a coarse grain system

schrodinger.application.matsci.coarsegrain.get_nonbond_potential_type(struct)¶

Return the type of non-bond potential for this structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: str or None
Returns: The value of the NB_TYPE_KEY property on the structure, or None if the structure is not a coarse grain structure or does not have this property set

schrodinger.application.matsci.coarsegrain.get_angle_potential_type(struct)¶

Return the type of angle potential for this structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: str or None
Returns: The value of the ANGLE_TYPE_KEY property on the structure, or None if the structure is not a coarse grain structure or does not have this property set

schrodinger.application.matsci.coarsegrain.is_lennard_jones(struct)¶

Check if this is a Lennard-Jones coarse grain structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: bool
Returns: True if this is a coarse grain Lennard-Jones structure, False if not

schrodinger.application.matsci.coarsegrain.is_repulsive_harmonic(struct)¶

Check if this is a repulsive harmonic coarse grain structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: bool
Returns: True if this is a coarse grain repulsive harmoic structure, False if not

schrodinger.application.matsci.coarsegrain.is_shifted_lennard_jones(struct)¶

Check if this is a shifted Lennard-Jones coarse grain structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: bool
Returns: True if this is a coarse grain shifted Lennard-Jones structure, False if not

schrodinger.application.matsci.coarsegrain.is_harmonic_angle(struct)¶

Check if this is a harmonic angle coarse grain structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: bool
Returns: True if this is a coarse grain harmonic angle structure, False if not

schrodinger.application.matsci.coarsegrain.is_trigonometric_angle(struct)¶

Check if this is a trigonometric angle coarse grain structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: bool
Returns: True if this is a coarse grain trigonometric angle structure, False if not

schrodinger.application.matsci.coarsegrain.is_martini_useries(model)¶

Check if the model is a Martini model with Useries

Parameters: model (cms.Cms) – The cms model to check
Return type: bool
Returns: True if this is a coarse grain model uses Martini model with Useries, False if not

schrodinger.application.matsci.coarsegrain.set_atom_coarse_grain_properties(struct, atom, name, rgb=(100, 100, 100), atom_type=400, formal_charge=0.0, partial_charge=0.0, radius=3.0, mass=12.0)¶

Set the properties required for a coarse grain particle atom

Parameters

structure (schrodinger.structure.Structure) – The structure containing the atom
atom (schrodinger.structure._StructureAtom) – The atom to set properties on
name (str) – The name of the coarse grain particle.
rgb (tuple) – The 0-255 tuple of red, green and blue that defines the atom color
atom_type (int) – The mmod atom type
formal_charge (int) – The formal charge
partial_charge (float) – The partial charge
radius (float) – The particle radius, in Angstrom
mass (float) – The particle mass

Raises

LicenseError – If the license is not valid for using coarse grained structures

schrodinger.application.matsci.coarsegrain.get_cg_molecule_hash(mol)¶

Return a hash for the given CG molecule.

Parameters: mol (schrodinger.structure._Molecule) – the molecule
Return type: str
Returns: the hash

schrodinger.application.matsci.coarsegrain.create_cg_molecule_name(mol)¶

Create a name for the passed molecule by getting the count of each type of bead in it The format is “A:4, B:5, …” where A and B are bead names and 4 and 5 are the counts of each in the molecule

Parameters: mol (structure._Molecule) – The molecule to get the name for
Return type: str
Returns: The molecule name

schrodinger.application.matsci.coarsegrain.collect_unique_structures(st, hash_getter=None)¶

Using the given structure and hasher collect unique instances of molecule structures as the keys of a dictionary with their values being lists of tuples of atom indices for all molecule instances.

Parameters

st (schrodinger.structure.Structure) – the structure containing the molecules
hash_getter (function) – the function used to obtain a unique hash for a given molecule, takes schrodinger.structure._Molecule, should return None if a hash can not be created

Return type

dict

Returns

keys are schrodinger.structure.Structure, values are lists of atom index tuples

schrodinger.application.matsci.coarsegrain.get_internal_info(atoms, data_getter=None, uniqueify=False)¶

Return information about the given internal.

Parameters

atoms (list) – contains schrodinger.structure._StructureAtom that define the internal
data_getter (function or None) – if given used to obtain data for the given internal, takes a list of schrodinger.struture._StructureAtom and returns a data tuple
uniqueify (bool) – if True then relevant internal coordinates will be uniqueified by type

Return type

InternalInfo

Returns

the internal info

schrodinger.application.matsci.coarsegrain.internals_iterator(sts_idxs_dict, idx_getter, data_getter=None, uniqueify=False)¶

Iterator that yields InternalInfo for each internal in the system defined by the given dictionary of unique molecular structures and atom indices of all molecule instances. Internal indices and data are obtained with the given getters.

Parameters

sts_idxs_dict (dict) – keys are schrodinger.structure.Structure, values are lists of atom index tuples, together they define the system
idx_getter (function) – gets indices of internals, takes a schrodinger.structure.Structure as kwarg ‘struct’ and yields index tuples
data_getter (function or None) – gets data of internals, takes a list of schrodinger.struture._StructureAtom and returns a data tuple
uniqueify (bool) – if True then relevant internal coordinates will be uniqueified by type

Return type

InternalInfo

Returns

each iteration yields an InternalInfo

schrodinger.application.matsci.coarsegrain.order_internal_by_name(atoms)¶

Order the atoms of the given internal coordinate by name.

Parameters: atoms (list) – contains structure._StructureAtom of the internal coordinate to be ordered
Return type: list
Returns: atoms sorted by name

schrodinger.application.matsci.coarsegrain.get_names(atoms, uniqueify=False)¶

Return the atom names for the given list of atoms.

Parameters

atoms (list) – contains structure._StructureAtom
uniqueify (bool) – if True then relevant internal coordinates will be uniqueified by type

Return type

tuple

Returns

contains atom names

schrodinger.application.matsci.coarsegrain.site_iterator(struct=None)¶

Create a site iterator from the given structure.

Parameters: struct (schrodinger.structure.Structure) – the structure
Return type: tuple
Returns: each iteration yields a tuple containing a single index

schrodinger.application.matsci.coarsegrain.fused_ring_nonbond_iterator(struct=None)¶

Create a fused ring nonbond iterator from the given structure.

Parameters: struct (schrodinger.structure.Structure) – the structure
Return type: tuple
Returns: each iteration yields a nonbond index pair tuple

class schrodinger.application.matsci.coarsegrain.Internals(astructure, uniqueify=False)¶

Bases: object

Manage the internal coordinates of a structure.

__init__(astructure, uniqueify=False)¶

Create an instance.

Parameters

astructure (structure.Structure) – the structure for which the internal coordinates are needed
uniqueify (bool) – if True then relevant internal coordinates will be uniqueified by type

avgInternals(internals)¶

Average the values of the internals in the given dictionary of internals.

Parameters: internals (dict) – keys are tuples of names of the constitutive atoms, values is a list of pair tuples containing (1) a tuple of atom indices and (2) a tuple of internal values
Return type: dict
Returns: keys are tuples of names of the constitutive atoms, values are pair tuples containing (1) tuple of tuples containing atom indices for all of the internals with the given key and (2) a tuple of average internal values

recursivelySort(internals)¶

Return the given dictionary of internal coordinates recursively sorted by the names of the constitutive atoms.

Parameters: internals (dict) – keys are tuples of names of the constitutive atoms, values are pair tuples containing (1) tuple of tuples containing atom indices for all of the internals with the given key and (2) a tuple of average internal values
Return type: OrderedDict
Returns: internals recursively sorted

setInternals(internals, info, internals_excluded=None)¶

Set internals.

Parameters

internals (dict) – keys are tuples of names of the constitutive atoms, values is a list of pair tuples containing (1) a tuple of atom indices and (2) a tuple of internal values
info (InternalInfo) – information for this internal
internals_excluded (dict or None) – contains internals that should be excluded from being set. keys are tuples of names of the constitutive atoms, values is a list of pair tuples containing (1) a tuple of atom indices and (2) a tuple of internal values or None if there isn’t one

Return type

bool

Returns

True if the internal was set, or False if it was not set due to already appearing in the internals_excluded dict

averageAndSort(internals)¶

Average and sort the given internals.

Parameters: internals (dict) – keys are tuples of names of the constitutive atoms, values is a list of pair tuples containing (1) a tuple of atom indices and (2) a tuple of internal values
Return type: dict
Returns: sorted keys where keys are tuples of names of the constitutive atoms, values are pair tuples containing (1) tuple of tuples containing atom indices for all of the internals with the given key and (2) a tuple of average internal values

setSites()¶: Set the sites dictionary.

setBonds()¶: Set the bonds dictionary.

setAngles()¶: Set angles dictionary.

setDihedrals()¶: Set dihedrals dictionary.

setImpropers()¶: Set impropers dictionary.

getNewAngles(new_bonds)¶

Return the new angles.

Parameters: new_bonds (list) – contains schrodinger.structure._StructureAtom pair tuples for new bonds
Return type: list
Returns: contains schrodinger.structure._StructureAtom triples tuples for new angles

getNewDihedrals(new_bonds)¶

Return the new dihedrals.

Parameters: new_bonds (list) – contains schrodinger.structure._StructureAtom pair tuples for new bonds
Return type: list
Returns: contains schrodinger.structure._StructureAtom quadruples tuples for new dihedrals

getNewImpropers(new_bonds)¶

Return the new impropers.

Parameters: new_bonds (list) – contains schrodinger.structure._StructureAtom pair tuples for new bonds
Return type: set
Returns: contains schrodinger.structure._StructureAtom quadruples tuples for new impropers

removeInternalsWithNewBonds()¶: Remove internals with new bonds.

findNewBonds(name_1, name_2, bonds_deep, exclude_what='Bonds')¶

Return the new bond pairs.

Parameters

name_1 (str) – the name of the first particle
name_2 (str) – the name of the second particle
bonds_deep (int) – the number of bonds separating the particles
exclude_what (str) – What nonbonds to exclude when regenerating the lists of included and excluded nonbonds after adding these bonds - should be one of the EXCLUDE_* constants, potentially combined for rings with get_combined_exclusion_str

Return type

list

Returns

contains schrodinger.structure._StructureAtom pair tuples for new bonds

updateFusedRingIdxsForNewBonds(new_bonds_tuples)¶

Update the fused ring idxs when a new set of bonds has been defined.

Parameters: new_bonds_tuples (list) – contains schrodinger.structure._StructureAtom pair tuples for new bonds

updateInternalsForNewBonds(new_bonds_tuples, exclude_what='Bonds')¶

Update the internals when a new set of bonds has been defined

Parameters

new_bonds_tuples (list) – contains schrodinger.structure._StructureAtom pair tuples for new bonds
exclude_what (str) – What nonbonds to exclude when regenerating the lists of included and excluded nonbonds after adding these bonds - should be one of the EXCLUDE_* constants, potentially combined for rings with get_combined_exclusion_str

setNonBonds(exclude_newbonds=True)¶

Set nonbonds dictionary.

Parameters: exclude_newbonds (bool) – If True, exclude new bonds added by the user. If False, only exclude pairs that are actually bonded.

setBasic(exclude_what='Bonds')¶

Set basic dictionaries.

Parameters: exclude_what (str) – What nonbonds to exclude - should be one of the EXCLUDE_* constants, potentially combined for rings with get_combined_exclusion_str

setFusedRingNonBonds(sts_idxs_dict=None)¶

Set fused ring nonbonds dictionary.

Parameters: sts_idxs_dict (dict) – keys are schrodinger.structure.Structure, values are lists of atom index tuples, together they define the system

handleRingExclusions()¶: Handle ring exclusions.

setIncludedExcludedNonBonds(exclude_what='Bonds')¶

Define which non-bond interactions are included and excluded

Parameters: exclude_what (str) – What to exclude - should be one of the EXCLUDE_* constants, potentially combined for rings with get_combined_exclusion_str

setAngleNonBonds()¶: Set angle nonbonds dictionary.

setNonAngleNonBonds()¶: Set the nonangle nonbonds dictionary.

setDihedralNonBonds()¶: Set dihedral nonbonds dictionary.

setNonAngleNonDihedralNonBonds()¶: Set the nonangle nondihedral nonbonds dictionary.

setBondNonBonds()¶: Set the bond nonbonds dictionary.

setAllPairs()¶: Set the all pairs dictionary.

mergeNonbonds(nonbonds, new_nonbonds)¶

Return a copy of the first nonbonds dict merged with the second.

Parameters

nonbonds (dict) – keys are tuples of names of the constitutive atoms, values is a list of pair tuples containing (1) a tuple of atom indices and (2) a tuple of internal values or None if there isn’t one
new_nonbonds (dict) – keys are tuples of names of the constitutive atoms, values is a list of pair tuples containing (1) a tuple of atom indices and (2) a tuple of internal values or None if there isn’t one

Return type

dict

Returns

merged nonbonds

class schrodinger.application.matsci.coarsegrain.FusedRing(rings)¶

Bases: object

Manage a fused ring.

__init__(rings)¶

Create an instance.

Parameters: rings (list) – contains schrodinger.structure._Ring

getAtomIndices()¶

Return a list of atom indices.

Return type: list
Returns: atom indices

static getFusedRings(st)¶

Return a list of fused ring objects for the given structure.

Parameters: st (structure.Structure) – the structure
Return type: list
Returns: contains FusedRing

schrodinger.application.matsci.coarsegrain.setCGBondLengths(st)¶

Set the bond lengths of the given CG structure according to the particle radii.

Parameters: st (structure.Structure) – the CG structure
Return type: structure.Structure
Returns: the CG structure with the new bond lengths

schrodinger.application.matsci.coarsegrain.fix_linear_angles(struct, internals=None, angles=None)¶

Return a copy of the given structure with linear angles fixed.

Parameters

struct (structure.Structure) – the structure whose angles will be fixed
internals (Internals or None) – the internals of the structure, if None it will be defined
angles (list or None) – contains tuples of atom names of the angles to be fixed, if None then all will be fixed

Return type

structure.Structure

Returns

the structure with angles fixed

schrodinger.application.matsci.coarsegrain.is_coarse_grain_input(input_file=None, input_sts=None)¶

Return True if the given structures are exclusively coarse-grained, False if exclusively atomistic, and raise a ValueError otherwise.

Parameters

input_file (str) – the input file
input_sts (list) – contains structure.Structure

Raises

ValueError – no input or a both coarse-grained and atomistic

Return type

bool

Returns

True if exclusively coarse-grained, False if exclusively atomistic

schrodinger.application.matsci.coarsegrain.get_unique_bonds(st)¶

Return a list of unique bonds for the given coarse grain structure.

Parameters: st (schrodinger.structure.Structure) – the coarse grain structure
Return type: list[schrodinger.structure._StructureBond]
Returns: unique bonds

schrodinger.application.matsci.coarsegrain.get_mass(st)¶

Return the mass of the given coarse grain structure.

Parameters: st (schrodinger.structure.Structure) – the coarse grain structure
Return type: float
Returns: the mass in g/mol