schrodinger.application.matsci.cg_mapping module¶

Utilities for mapping CG structures to AA

schrodinger.application.matsci.cg_mapping.get_chiral_hash(x)¶

schrodinger.application.matsci.cg_mapping.get_chiral_pair(x)¶

class schrodinger.application.matsci.cg_mapping.ATOM_DEFINITION(prop_name, idx, name, numberstr)¶

Bases: tuple

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

__len__()¶: Return len(self).

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

idx¶: Alias for field number 1

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

Return first index of value.

Raises ValueError if the value is not present.

name¶: Alias for field number 2

numberstr¶: Alias for field number 3

prop_name¶: Alias for field number 0

schrodinger.application.matsci.cg_mapping.get_cg_particle_indices(atom)¶

Return a list of CG particle indices for the given atom.

Parameters: atom (schrodinger.structure._StructureAtom) – the atom
Return type: list
Returns: CG particle indices

exception schrodinger.application.matsci.cg_mapping.NonContiguousBondingError(msg='Particles containing atoms that are not contiguously bonded are currently not supported.', *args, **kwargs)¶

Bases: Exception

Exception to handle non contiguous bonding in CG

__init__(msg='Particles containing atoms that are not contiguously bonded are currently not supported.', *args, **kwargs)¶: Exception with default error message

args¶

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

schrodinger.application.matsci.cg_mapping.extract_and_contract(struct, idxs=None, pbc=None, fast=False)¶

From the given indices and structure extract a structure and contract it according to the PBC.

Parameters

struct (structure.Structure) – the structure from which to extract
idxs (set or None) – a set of integer atom indices defining the structure to be extracted or None in which case all indices will be used
pbc (schrodinger.infra.structure.PBC) – A pre-computed PBC for the structure
fast (bool) – True if the computation should be done on a throw-away structure that will not be used for more than a center of mass calculation, False if the extracted structure must preserve properties such as atom formal charge and structure properties.

Return type

structure.Structure

Returns

the extracted and contracted structure

schrodinger.application.matsci.cg_mapping.get_center_of_mass_weight(atom)¶

Return the weight of the atom used for the center of mass calculation.

Parameters: atom (schrodinger.structure._StructureAtom) – the atom
Return type: float
Returns: the weight of the atom in amu

schrodinger.application.matsci.cg_mapping.center_of_mass(struct, idxs=None, pbc=None)¶

Return the center of mass of the given indices in the given structure accounting for if the structure has a PBC.

Parameters

struct (structure.Structure) – the structure containing the atoms for which the center of mass is needed
idxs (set or None) – a set of integer atom indices for which the center of mass is needed or None in which case all atoms will be used
pbc (schrodinger.infra.structure.PBC) – A pre-computed PBC for the structure

Return type

numpy.array

Returns

the center of mass

class schrodinger.application.matsci.cg_mapping.Particle¶

Bases: object

Create a coarse grain particle.

__init__()¶: Create an instance.

setXYZ(xyz=None, astructure=None, pbc=None)¶

Set the position of the given particle.

Parameters

xyz (numpy.array or None) – the position of the particle or None if there isn’t one
astructure (structure.Structure or None) – the structure from which the parent structure will be extracted and for which the center of mass is needed or None if there isn’t one
pbc (schrodinger.infra.structure.PBC) – A pre-computed PBC for the structure

setVDWRadius(vdw_radius=None)¶

Set the VDW radius in Ang.

Parameters: vdw_radius (float or None) – the VDW radius of the given particle in Ang. or None if there isn’t one

setAtomicWeight(atomic_weight=None)¶

Set the atomic weight in g/mol.

Parameters: atomic_weight (float or None) – the atomic weight of the given particle in g/mol or None if there isn’t one

setFormalCharge(formal_charge=None)¶

Set the formal charge.

Parameters: formal_charge (int) – the formal charge of the given particle or None if there isn’t one

setPartialCharge(partial_charge=None)¶

Set the partial charge.

Parameters: partial_charge (float) – the partial charge of the given particle or None if there isn’t one

setParentStructure(astructure)¶

Set the parent structure.

Parameters: astructure (structure.Structure) – the structure from which the parent structure will be extracted

setParentStructureStr()¶: Set the parent structure string.

setParentIndices(parent_indices)¶

Set the parent indices.

Parameters: parent_indices (list) – the parent indices, i.e. indices of the parent atomic structure for this particle

setParentCutBonds(astructure)¶

Set the parent cut bonds.

Parameters: astructure (structure.Structure) – the structure from which the parent structure was extracted and thus for which the bonding information is needed

setFormula(formula=None)¶

Set the formula of the given particle.

Parameters: formula (str or None) – the formula for the given particle or None if there isn’t one

setName(name)¶

Set the name of the given particle.

Parameters: name (str) – name of the particle

setRGBColor(rgb_color)¶

Set the RGB color of the given particle.

Parameters: rgb_color (tuple) – a triple of integers in [0, 255] that give an RGB color for the given particle

setAtomType(atom_type)¶

Set the atom type of the given particle.

Parameters: atom_type (int) – atom type of the given particle

setKey(key)¶

Set the key of the given particle, this is the key that indicates the parent structure string.

Parameters: key (str) – key of the given particle

defineAtom(astructure, index)¶

Define the given atom.

Parameters

astructure (structure.Structure) – the structure containing the atom to define
index (int) – index of the atom to define

static getParentIndices(cg_structure, cg_idx)¶

Return the parent indices for the given coarse grain particle index in the given coarse grain structure.

Parameters

cg_structure (structure.Structure) – the coarse grain structure
cg_idx (int) – the coarse grain particle index

Return type

tuple

Returns

the parent indices for the given coarse grain particle index

static getParentCutBonds(cg_structure, cg_idx, reverse=False)¶

Return the parent cut bonds for the given coarse grain particle index in the given coarse grain structure.

Parameters

cg_structure (structure.Structure) – the coarse grain structure
cg_idx (int) – the coarse grain particle index
reverse (bool) – by default the first atom index of a pair from the returned tuple of pairs is for the particle with the given index and the second atom index of the pair is for the outside particle, if reverse is True it reverses this ordering

Return type

tuple

Returns

the parent cut bonds for the given coarse grain particle index

static getParentBonds(cg_structure, cg_idx_i, cg_idx_j)¶

Return the parent bonds between the given coarse grain particles indices in the given coarse grain structure.

Parameters

cg_structure (structure.Structure) – the coarse grain structure
cg_idx_i (int) – the first coarse grain particle index
cg_idx_j (int) – the second coarse grain particle index

Return type

tuple

Returns

the parent bonds between the given coarse grain particle indices

class schrodinger.application.matsci.cg_mapping.CoarseGrainBond(name_1, idx_1, name_2, idx_2)¶

Bases: object

Manage a coarse grain bond.

FORMAT_START = '('¶

FORMAT_END = ')'¶

DUMMY_ELEMENT = 'DU'¶

__init__(name_1, idx_1, name_2, idx_2)¶

Create an instance.

Parameters

name_1 (str) – the name of particle 1
idx_1 (int) – the index particle 1
name_2 (str) – the name of particle 2
idx_2 (int) – the index particle 2

setParentData(cg_structure)¶

Set the parent data.

Parameters: cg_structure (structure.Structure) – the CG model

getAllParentIndices()¶

Return a tuple containing all parent indices.

Return type: tuple
Returns: contains all parent indices

setSmiles(st)¶

Set a unique SMILES for the parent indices.

Parameters: st (structure.Structure) – the parent model

setDefaultParticleLabels(st)¶

Set the default particle labels for the two coarse grain particles.

Parameters: st (structure.Structure) – the parent model

setChiralHash(st)¶

Set the chiral hash.

Parameters: st (structure.Structure) – the parent model

setParentBondsHash(st)¶

Set the parent bonds hash.

Parameters: st (structure.Structure) – the parent model

static formatParticleLabel(label)¶

Format the particle label.

Parameters: label (str) – the label to format
Return type: str
Returns: the formated label

class schrodinger.application.matsci.cg_mapping.CGMapperMixin¶

Bases: object

A common mixin class for mapping all-atoms molecules to coarse-grain

getAtomPolymerNames(atom, name)¶

Get the polymer names for this atom.

Parameters

atom (structure._StructureAtom) – the atom for which the names are needed
name (str) – polymer monomer name

Return type

list

Returns

polymer names

getAtomResidueNames(atom, name)¶

Get the residue names for this atom.

Parameters

atom (structure._StructureAtom) – the atom for which the names are needed
name (str) – residue name

Return type

list

Returns

residue names

getAtomDefinitions(atom, existing_definitions)¶

Get the definitions for this atom.

Parameters

atom (structure._StructureAtom) – the atom for which definition data is needed
existing_definitions (list) – Each item of the list is a (name, number) tuple from DEFINITION_KEYS that should be searched on the atom.

Return type

list

Returns

list of ATOM_DEFINITION for the passed atom

trimDefinitionDict(definition_dict)¶

Trim the given definition dictionary to get rid of redundant definitions.

Parameters: definition_dict (OrderedDict) – keys are particle type strings, values are tuples of tuples of integers of particle occurrences

static getUniqueDefNames(atom_definitions)¶

Gets the dictionary of names where the a single atom definition name is being used by multiple properties

Parameters: atom_definitions (list(AtomDefinition)) – List of all atom definitions
Returns: The dictionaries have keys as the definition names and the values of first dict is the property used by the definition and second dictionary values are list of properties ignored by the definition
Return type: dict, dict

getDefinitionDict(warn_logger=None)¶

Get definition dict.

Parameters: warn_logger (function) – If passed the warnings generated during generation of definitions will be passed to this function as a string
Return type: OrderedDict
Returns: keys are particle type strings, values are tuples of tuples of integers of particle occurrences

areContiguous(indices)¶

Return True if for the given indices the atoms are contiguously bonded, False otherwise.

Parameters: indices (tuple) – the indices to check

getParticles(particles, aname, acolor, aatom_type, akey)¶

Return list of particle objects.

Parameters

particles (list) – contains particle indices as lists of atom indices
aname (str) – name for the particles
acolor (tuple) – a triple of integers in [0, 255] that give an RGB color for the particles
aatom_type (int) – atom type for the particles
akey (str) – a structure property key indicating the parent structure string

Return type

list

Returns

contains Particle instances

inheritProperties(cg_structure)¶

Inherit properties for the CG model from the parent structure.

Parameters: cg_structure (structure.Structure) – the CG model

markParticleAtoms(particle_index, atom_indices)¶

Mark the atoms in the structure by particle index.

Parameters

particle_index (int) – the particle index
atom_indices (list) – contains the atom indices for this particle

buildCGFromParticles(all_particles, allow_unassigned=False)¶

Build coarse grain structure from the particle

Parameters

all_particles (list) – list of lists of Particles, where each list corresponds to each mapping group
allow_unassigned (bool) – If False particles not mapped will be ignored, if True they will be ignored leading to no CG bond creation.

Return type

structure.Structure

Returns

the new CG model

getAssignedAndUnassigned(all_particles)¶

Get currently mapped (assigned) and upmapped (unassigned) atoms in the all-atom structure.

Parameters: all_particles (list) – list of lists of Particles, where each list corresponds to each mapping group
Return type: tuple(set, set)
Returns: tuple where first element is indexes of all-atom atoms that have been assigned mapping scheme and second are the atoms that have not been assigned any mapping scheme

categorizeBonds()¶

Return a dictionary of categorized bonds.

Return type: OrderedDict
Returns: sorted keys where keys are pair tuples of coarse grain particle names, values are OrderedDicts where keys are (SMILES, chiral_hash) tuples and values are lists of CoarseGrainBond

class schrodinger.application.matsci.cg_mapping.CGMapper(struct)¶

Bases: schrodinger.application.matsci.cg_mapping.CGMapperMixin

Class create a mapped coarse grain model from an all-atom structure.

TYPE_MAX = 400¶

__init__(struct)¶

Initiate CGMapper class.

Parameters: struct (structure.Structure) – All-atom structure to be mapped to CG

getMappedParticles()¶

Create Particles for the assigned mapping scheme.

Return type: list(Particles)
Returns: list of lists of Particles, where each list corresponds to each mapping group

validateAllAssigned(all_particles)¶

Check if all the atoms in the structure have been assigned mapping scheme.

Parameters: all_particles (list) – list of lists of Particles, where each list corresponds to each mapping group
Raise: ValueError if all particle have not been assigned names

markCGBonds()¶: CG bonds that are mapped to same named atoms but resulted from different all-atom bonding environment will be marked as unique. Thus, resulting in individual parameters for each.

areContiguous(indices)¶

Return True if for the given indices the atoms are contiguously bonded, False otherwise.

Parameters: indices (tuple) – the indices to check

buildCGFromParticles(all_particles, allow_unassigned=False)¶

Build coarse grain structure from the particle

Parameters

all_particles (list) – list of lists of Particles, where each list corresponds to each mapping group
allow_unassigned (bool) – If False particles not mapped will be ignored, if True they will be ignored leading to no CG bond creation.

Return type

structure.Structure

Returns

the new CG model

categorizeBonds()¶

Return a dictionary of categorized bonds.

Return type: OrderedDict
Returns: sorted keys where keys are pair tuples of coarse grain particle names, values are OrderedDicts where keys are (SMILES, chiral_hash) tuples and values are lists of CoarseGrainBond

getAssignedAndUnassigned(all_particles)¶

Get currently mapped (assigned) and upmapped (unassigned) atoms in the all-atom structure.

Parameters: all_particles (list) – list of lists of Particles, where each list corresponds to each mapping group
Return type: tuple(set, set)
Returns: tuple where first element is indexes of all-atom atoms that have been assigned mapping scheme and second are the atoms that have not been assigned any mapping scheme

getAtomDefinitions(atom, existing_definitions)¶

Get the definitions for this atom.

Parameters

atom (structure._StructureAtom) – the atom for which definition data is needed
existing_definitions (list) – Each item of the list is a (name, number) tuple from DEFINITION_KEYS that should be searched on the atom.

Return type

list

Returns

list of ATOM_DEFINITION for the passed atom

getAtomPolymerNames(atom, name)¶

Get the polymer names for this atom.

Parameters

atom (structure._StructureAtom) – the atom for which the names are needed
name (str) – polymer monomer name

Return type

list

Returns

polymer names

getAtomResidueNames(atom, name)¶

Get the residue names for this atom.

Parameters

atom (structure._StructureAtom) – the atom for which the names are needed
name (str) – residue name

Return type

list

Returns

residue names

getDefinitionDict(warn_logger=None)¶

Get definition dict.

Parameters: warn_logger (function) – If passed the warnings generated during generation of definitions will be passed to this function as a string
Return type: OrderedDict
Returns: keys are particle type strings, values are tuples of tuples of integers of particle occurrences

getParticles(particles, aname, acolor, aatom_type, akey)¶

Return list of particle objects.

Parameters

particles (list) – contains particle indices as lists of atom indices
aname (str) – name for the particles
acolor (tuple) – a triple of integers in [0, 255] that give an RGB color for the particles
aatom_type (int) – atom type for the particles
akey (str) – a structure property key indicating the parent structure string

Return type

list

Returns

contains Particle instances

static getUniqueDefNames(atom_definitions)¶

Gets the dictionary of names where the a single atom definition name is being used by multiple properties

Parameters: atom_definitions (list(AtomDefinition)) – List of all atom definitions
Returns: The dictionaries have keys as the definition names and the values of first dict is the property used by the definition and second dictionary values are list of properties ignored by the definition
Return type: dict, dict

inheritProperties(cg_structure)¶

Inherit properties for the CG model from the parent structure.

Parameters: cg_structure (structure.Structure) – the CG model

mapCGStructure(cg_names, allow_unassigned, unique_bonds)¶

Map the passed cg_names to a coarse grain structure and build it from the all-atom structure.

Parameters

list – list of cg_names to be mapped
allow_unassigned (bool) – if True, not all atoms are required to be mapped to the CG model. In case of False a check would be done and ValueError will be raised if all atoms were not assigned mapping
unique_bonds (bool) – if True CG bonds that are mapped to same named atoms but resulted from different all-atom bonding environment will be marked as unique. If False the bonds will be considered indistinguishable

markParticleAtoms(particle_index, atom_indices)¶

Mark the atoms in the structure by particle index.

Parameters

particle_index (int) – the particle index
atom_indices (list) – contains the atom indices for this particle

trimDefinitionDict(definition_dict)¶

Trim the given definition dictionary to get rid of redundant definitions.

Parameters: definition_dict (OrderedDict) – keys are particle type strings, values are tuples of tuples of integers of particle occurrences