schrodinger.application.matsci.cg_mapping module

Utilities for mapping CG structures to AA

Copyright Schrodinger, LLC. All rights reserved.

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
Return type

list

Returns

polymer names

getAtomResidueNames(atom, name)

Get the residue names for this atom.

Parameters
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
Return type

list

Returns

polymer names

getAtomResidueNames(atom, name)

Get the residue names for this atom.

Parameters
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