schrodinger.application.matsci.amorphous module¶

Builder classes for making amorphous cells

class schrodinger.application.matsci.amorphous.AttachmentAtoms(coupler, coupler_marker, grower, grow_marker)¶

Bases: tuple

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

__len__()¶: Return len(self).

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

coupler¶: Alias for field number 0

coupler_marker¶: Alias for field number 1

grow_marker¶: Alias for field number 3

grower¶: Alias for field number 2

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

Return first index of value.

Raises ValueError if the value is not present.

class schrodinger.application.matsci.amorphous.ConnectionInfo(missed_atom_ids, connecting_atom_ids)¶

Bases: tuple

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

__len__()¶: Return len(self).

connecting_atom_ids¶: Alias for field number 1

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.

missed_atom_ids¶: Alias for field number 0

schrodinger.application.matsci.amorphous.log_debug(msg)¶

Add a message to debug logger file.

Parameters: msg (str) – The message to debug logging

schrodinger.application.matsci.amorphous.has_head_tail_roles_marked(struct)¶

Check if a monomer is marked with the polymer head and tail role properties

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: bool
Returns: True if head and tail role atoms are marked, False if not

schrodinger.application.matsci.amorphous.mark_monomer_head_tail_ce_th(struct)¶

Find monomers marked with the Canvas method of marking head and tail - a Ce atom marks the head and tha Th atom marks the tail. Mark the Ce atom with the HEAD role and the Th atom with the TAIL role.

Parameters: struct (schrodinger.structure.Structure) – The structure to mark
Return type: bool
Returns: True if head and tail role atoms were marked, False if not

schrodinger.application.matsci.amorphous.mark_monomer_head_tail_dummy(struct)¶

Find monomers marked with the dummy atom method of marking head and tail - dummy atoms mark both the head and tail. In this case there is nothing to distinguish the two position, so mark the first dummy atom with the HEAD role and the second dummy atom with the TAIL role.

Parameters: struct (schrodinger.structure.Structure) – The structure to mark
Return type: bool
Returns: True if head and tail role atoms were marked, False if not

schrodinger.application.matsci.amorphous.mark_monomer_head_tail_rx(struct)¶

Find monomers marked with the polymer builder method of marking head and tail - the Rx atom property is used to identify atoms. The atom designated as R1 is marked as the HEAD role and the atom designated as R2 with the TAIL role.

Parameters: struct (schrodinger.structure.Structure) – The structure to mark
Return type: bool
Returns: True if head and tail role atoms were marked, False if not

schrodinger.application.matsci.amorphous.mark_monomer_head_and_tail(struct)¶

Find monomers marked with a variety of marking head and tail atoms and mark them with the polymer role property. Note that the atoms so marked will be the atoms to remove when building a polymer - the disposable H, dummy or other atom attached to the heavy atom that remains in the monomer when the polymer is built.

Parameters: struct (schrodinger.structure.Structure) – The structure to mark
Return type: bool
Returns: True if head and tail role atoms were marked, False if not

schrodinger.application.matsci.amorphous.mark_orig_atom_idx(struct)¶

Mark the original atom indexes as atom property.

Parameters: struct ('schrodinger.structure.Structure') – each atom in this structure will be marked with atom index as original atom index property.

schrodinger.application.matsci.amorphous.get_orig_atom_idx(struct)¶

Return the original atom indexes.

Parameters: struct ('schrodinger.structure.Structure' or any 'schrodinger.structure._AtomCollection') – the structure to get original atom indexes.
Return type: list of int
Returns: the original atom indexes of this atom collection.

schrodinger.application.matsci.amorphous.get_missed_atom_id_groups(struct, atom_ids)¶

Return the missed atom indexed grouped by bond connectivity.

Parameters

struct ('schrodinger.structure.Structure') – the structure to get missed atom indexes groups
atom_ids (list of int) – each int is an atom index of a missing atom in the polymerfragment.

Return type

list of list

Returns

such sublist contains atom indexes that are bonded.

schrodinger.application.matsci.amorphous.get_density(struct)¶

Calculate the density of the struct.

Parameters: struct (schrodinger.structure.Structure) – A structure with chorus_properties
Return type: float
Returns: The density of the struct in unit g/cm^3

schrodinger.application.matsci.amorphous.get_maximum_vdw_radius(struct)¶

Find the maximum VDW radius of any atom in the structure

Parameters: struct (schrodinger.structure.Structure) – The structure to check
Return type: float
Returns: The maximum VDW radius of any atom

schrodinger.application.matsci.amorphous.get_color(index)¶

Get the next color in our color rotation

Parameters: index (int) – The index in the color rotation to get. If index is greater than the number of colors, we just start over
Return type: str
Returns: A color as understood by the schrodinger.structure._StructureAtom.color property

schrodinger.application.matsci.amorphous.random_rotation(struct, centroid=None, max_rotation=6.283185307179586, no_rotation=False, rotate_velocities=False)¶

Randomly rotate struct in 3 dimensions

Parameters

struct (schrodinger.structure.Structure) – The structure to rotate
centroid (3-element numpy array) – the rotation center [x, y, z]
max_rotation (float) – The maximum rotation to perform
no_rotation (bool) – If True, do not rotate the structure
rotate_velocities (bool) – If True, besides the structure, also rotate FFIO atom velocities (if present)

Return type

list, list

Returns

Centroid and rotation matrix

schrodinger.application.matsci.amorphous.prepare_building_block(struct, index, recolor=True, preserve_res=False)¶

Do some prepwork on a component before adding them to the disordered cell

Parameters

struct (schrodinger.structure.Structure) – The structure to modify
index (int) – The index of this structure in the list of components
recolor (bool) – Whether to color the molecule a single color
preserve_res (bool) – Whether to preserve the current residue information

schrodinger.application.matsci.amorphous.detect_custom_mmffld_data(structs) → bool¶

Detect if a custom FEP charge block exists in the structure

Parameters: structs (list) – List of Structure objects to check
Return type: bool
Returns: Whether a custom FEP charge block exists in any of the strucures

schrodinger.application.matsci.amorphous.get_generic_end_structure(is_coarse_grain=False)¶

Get a single atom structure that can be used as a terminal (initiator/terminator) moiety.

Parameters: is_coarse_grain (bool) – whether the structure is coarse grain
Return type: schrodinger.structure.Structure
Returns: Structure of one single H or C atom with Br marker.

schrodinger.application.matsci.amorphous.dispersity(structs)¶

Return dispersity of the structures.

Notes with Einstein notation (duplicated index means summation): Mn = NiMi/sum(Ni); Mw = NiMiMi/NiMi Mw/Mn = sum(Ni) * NiMiMi / (NiMi)^2 When Ni = 1, Mw/Mn = len(Mi) * MiMi /(sum(Mi))^2

Parameters: structs (list of structure.Structure) – the list of structures to calculate dispersity.
Returns: dispersity over all structures
Return type: float

class schrodinger.application.matsci.amorphous.FlorySchulzDistribution(conversion=0.5, initial_num=1000, xmer=5)¶

Bases: object

Molecular weight distribution in linear step-growth homo polymers (single monomer type or equimolar quantities for two types of monomers). Collected and published by Polymer Properties Database (polymerdatabase.com)

Refs: P. J. Flory, Journal of the American Chemical Society, 58, 1877-1885 (1936) Wallace H. Carothers, Trans. Faraday Soc., Vol. 32, pp 39-49 (1936) Paul L. Flory, Principles of Polymer Chemistry, Ithaca, New york, 1953 Paul J. Flory, Chem. Rev., Vol. 39, No. 1, 137 (1946)

Story (paraphrase): Monomer conversion (p) is reactivated monomers over all initial monomers An oligomer containing x repeat units must have undergone x-1 reactions

__init__(conversion=0.5, initial_num=1000, xmer=5)¶

Parameters

conversion (float in [0, 1)) – reactivated monomers over all initial monomers
initial_num (positive int) – the initial number of monomers
xmer (positive int) – repeat unit number in a chain

polydispersity()¶

Carothers equation in step-growth polymerization, proposed by Wallace Carothers, who invented nylon in 1935.

Conditions: two monomers in equimolar quantities Ref: https://en.wikipedia.org/wiki/Carothers_equation

Returns: polydispersity according to Carothers equation for two monomers in equimolar quantities
Return type: float

xmerProbability()¶

The number probability of x-mer at the specific conversion.

Returns: The probability of a chain is x-mer long
Return type: float

moleculeNum()¶

The number of molecules (polymer, oligomer, and monomers).

Returns: the total number of molecules at the specific conversion.
Return type: float

degreeOfPolymerization()¶

Degree of polymerization at the specific conversion.

Returns: Degree of polymerization at the specific conversion.
Return type: float

setConversion(deg_of_polym=2)¶

Set the conversion based on degree of polymerization.

Parameters: dp (int) – Degree of polymerization

xmerNum()¶

The number of molecules of x-mer length at the specific conversion.

Returns: number of molecules
Return type: float

numberDistribution(mer_lim=None)¶

The number distribution: monomer length vs number probability.

Parameters: mer_lim (None or a tuple of two int) – the lower and upper limits of x-mers
Returns: monomer length, probability
Return type: 2d numpy array

weightDistribution(mer_lim=None)¶

The weight distribution: monomer length vs length-weighted probability.

Parameters: mer_lim (None or a tuple of two int) – the lower and upper limits of x-mers
Returns: monomer length, length-weighted probability
Return type: 2d numpy array

class schrodinger.application.matsci.amorphous.Box(vertices)¶

Bases: object

Class that defines the region a new structure may be placed in

X = 0¶

Y = 1¶

Z = 2¶

AXES = [0, 1, 2]¶

__init__(vertices)¶

Create a box object

Parameters: vertices (list) – A six item list that defines the min and max value of X, Y and Z. The six values in order are: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax

getMinMax(axis)¶

Get the min and max values for axis

Parameters: axis (int) – One of the class constants X, Y or Z
Return type: (float, float)
Returns: The min and max value for the requested axis

getLargestSpan()¶

Get the largest span of the box in the X, Y or Z direction

Return type: float
Returns: The largest span (delta between the min and max value)

getCentroid()¶

Get the centroid of the box

Return type: numpy.array
Returns: The centoid of the box - a numpy array of 3 items (x, y, z)

getPointInBox()¶

Get a point in a random position in the box

Return type: list
Returns: [x, y, z] coordinates of a random point in the box

isPointInBox(point)¶

Is the given point inside the box

Parameters: point (iterable) – An iterable of length 3 floats that gives the x, y and z values of the point in question
Return type: bool
Returns: Whether the point falls within the box

getTranslationToBox(point)¶

Return a vector that translates the mirror image of a point inside the box

Parameters: point (iterable) – An iterable of length 3 floats that gives the x, y and z values of the point in question
Return type: list
Returns: A list of 3 floats that gives the x, y and z coordinates of the mirror image of point that lies within the box

isValidPoint(point)¶: Check if point is a valid point - the default implementation just returns True. Subclasses may use this to weed out points that violate custom box conditions

class schrodinger.application.matsci.amorphous.BoxWithInnerHull(hull, *args, **kwargs)¶

Bases: schrodinger.application.matsci.amorphous.Box

A cubic Box object that contains an inner non-cubic region that limits the valid volume for the components to be placed in.

__init__(hull, *args, **kwargs)¶

Create a BoxWithInnerHull object

Parameters: hull (scipy.spatial.Delaunay) – The convex hull defining the region of space the components are allowed to be placed in

See parent class for additional documentation

isPointInBox(point, *args)¶

Overrides the parent method to check to see if the given point is also inside the hull

Parameters: point (iterable) – An iterable of length 3 floats that gives the x, y and z values of the point in question
Return type: bool
Returns: Whether the point falls within the box

isPointInHull(point)¶

Check to see if the point is inside the hull

Parameters: point (iterable) – An iterable of length 3 floats that gives the x, y and z values of the point in question
Return type: bool
Returns: Whether the point falls within the hull

getPointInBox(max_attempts=1000)¶

Overrides the parent class to get a point that is inside the hull rather than just in the box

Parameters: max_attempts (int) – Maximum number of attempts to try to find a point that is both inside the box and the hull
Return type: list
Returns: List of three floats that give the xyz coordinates of a point in the hull
Raises: ScaffoldError – If a point can’t be found inside the hull

isValidPoint(point)¶

Overrides the parent method to check to make sure the point is inside the hull

Parameters: point (iterable) – An iterable of length 3 floats that gives the x, y and z values of the point in question
Return type: bool
Returns: Whether the point is inside the hull

AXES = [0, 1, 2]¶

X = 0¶

Y = 1¶

Z = 2¶

getCentroid()¶

Get the centroid of the box

Return type: numpy.array
Returns: The centoid of the box - a numpy array of 3 items (x, y, z)

getLargestSpan()¶

Get the largest span of the box in the X, Y or Z direction

Return type: float
Returns: The largest span (delta between the min and max value)

getMinMax(axis)¶

Get the min and max values for axis

Parameters: axis (int) – One of the class constants X, Y or Z
Return type: (float, float)
Returns: The min and max value for the requested axis

getTranslationToBox(point)¶

Return a vector that translates the mirror image of a point inside the box

Parameters: point (iterable) – An iterable of length 3 floats that gives the x, y and z values of the point in question
Return type: list
Returns: A list of 3 floats that gives the x, y and z coordinates of the mirror image of point that lies within the box

exception schrodinger.application.matsci.amorphous.ScaffoldError¶

Bases: ValueError

Class for errors involving the scaffold input

__init__(*args, **kwargs)¶

args¶

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

class schrodinger.application.matsci.amorphous.Scaffold(struct=None, volume=None, seed=None)¶

Bases: object

A Scaffold is a structure that occupies space in a cluster of molecules but is not considered part of the system itself. Scaffolds could be: 1) A nanoparticle that has an amorphous system surrounding it or a protein surrounded by a box of water molecules, 2) A container such as a zeolyte or nanotube that holds an amorphous system within it, 3) a surface upon which a disordered system is laid down.

__init__(struct=None, volume=None, seed=None)¶

Create a Scaffold object

Parameters

struct (schrodinger.structure.Structure or None) – The scaffold structure, or None if there is no scaffold for the cell.
seed (int) – Random seed

property volume¶

Get scaffold volume.

Return type: float
Returns: Scaffold volume in Angstrom

static approximateVolume(input_struct, vdw_scale=1.0, seed=None, sphere_radius=None, sphere_origin=None, sphere_quadrant=None, buffer_len=2, return_ratio=False, use_standard_nuclear_orientation=True, free_volume=False)¶

Computes the approximate volume of the scaffold molecule using a Monte Carlo sampling algorithm. The alogorithm: 1a) define a box or sphere that fully encloses the structure 1b) optionally specify that a sphere quandrant be used 2) randomly pick a point inside the shape 3) check if the point lies inside the VDW radius of an atom 4) iterate over steps 2 & 3 a bunch 5) The volume is shape_volume * fraction of points inside VDW radii

Parameters

vdw_scale (float) – The VdW scale factor to apply to VdW radii when checking to see if a point is “inside” an atom
seed (int or None) – the seed for random, if None then random is not re-seeded
sphere_radius (float) – specifies to sample points in a sphere of this radius in Angstrom rather than the default which uses the smallest enclosing box
sphere_origin (numpy.array) – the origin in Angstrom of the sphere used if sampling points in a sphere
sphere_quadrant (None or str) – restrict sphere sampling to a quadrant specified as a key of ORDINAL_DIRECTIONS
buffer_len (float) – a shape buffer lengths in Angstrom
return_ratio (bool) – whether to return the hit ratio as a percent
use_standard_nuclear_orientation (bool) – if True then the copy of the input structure will be rotated to a standard orientation prior to calculating the volume
free_volume (bool) – use this option to return the free volume

Return type

float or float, float

Returns

The approximate volume of a molecule (or free volume) in Angstrom^3 followed by the hit (or miss) ratio if return_ratio is used

Note

This is expensive, so is only done at class initialization. After that, call getExcludedVolume to obtain the cached volume.

getNewCell()¶

Return a new structure that contains the scaffold molecule. If there is scaffold structure, the returned structure is empty

Return type: schrodinger.structure.Structure
Returns: A structure object that is either empty or contains the scaffold structure, depending on whether a scaffold structure exists or not.

getExcludedVolume()¶

Get the amount of volume the scaffold occupies

Return type: bool
Returns: The volume computed by approximateVolume when this object was created.

defineBox(volume)¶

The default implementation is to define a cube with all sides equal that is centered on the scaffold centroid.

Parameters: volume (float) – The volume of the desired cube
Return type: Box
Returns: The Box object for this scaffold

addPBCProperties(struct, volume)¶

Add periodic boundary condition properties to the structure. This method overwrites any existing periodic boundary condition properties, including Desmond chorus and PDB space group properties.

Parameters

struct (schrodinger.structure.Structure) – The structure to add the properties to
volume (float) – The volume of the cubic periodic boundary condition

addDesmondPBC(struct, ax, ay=0.0, az=0.0, bx=0.0, by=None, bz=0.0, cx=0.0, cy=0.0, cz=None)¶

Add properties to the structure that define the periodic boundary condition in the way Desmond wants it defined.

Parameters

struct (schrodinger.structure.Structure) – The structure to add the properties to
ax (float) – The value of the ax box property
ay (float) – The value of the ay box property. Defaults to 0.
az (float) – The value of the az box property. Defaults to 0.
bx (float) – The value of the bx box property. Defaults to 0.
by (float) – The value of the by box property. If not given, this value is set the same as ax.
bz (float) – The value of the bz box property. Defaults to 0.
cx (float) – The value of the cx box property. Defaults to 0.
cy (float) – The value of the cy box property. Defaults to 0.
cz (float) – The value of the cz box property. If not given, this value is set the same as ax.

addSpaceGroupPBC(struct, aval, bval, cval, alpha=90.0, beta=90.0, gamma=90.0, space_group='P 1')¶

Add properties to the structure that define the periodic boundary condition in the way Crystal wants it defined.

Parameters

struct (schrodinger.structure.Structure) – The structure to add the properties to
side (float) – The length of one side of the cubic periodic boundary condition

getPBCMinMaxes()¶

Get the length of one side of the periodic boundary condition

Parameters: cell (schrodinger.structure.Structure) – The current cell with structures that have already been placed
Return type: list
Returns: A six item list that defines the min and max value of X, Y and Z. The six values in order are: Xmin, Ymin, Zmin, Xmax, Ymax, Zmax. If not PBC box has been created, a list of all 0.0 is returned

getPointInBox()¶

Get a point in a random position in the box

Return type: list
Returns: [x, y, z] coordinates of a random point in the box

class schrodinger.application.matsci.amorphous.BuilderWithClashDetection(basename='cell', backend=None, logger=None, color=None, vdw_scale=1.0)¶

Bases: object

The base class for the amorphous builder classes

__init__(basename='cell', backend=None, logger=None, color=None, vdw_scale=1.0)¶

Create a Builder object

Parameters

basename (str) – The base name for structure files created by this builder
backend (schrodinger.job.jobcontrol._Backend) – The job control backend we are running under, or None if not running under a backend
logger (logging.Logger) – The logger for this builder
color (str or None) – Set to module constant COLOR_BY_MOLECULE to color the structures in the cell by molecule
vdw_scale (float) – Scale factor for VdW radii during clash detection

log(msg, level=20)¶

Log a message

Parameters

msg (str) – The message to log
level (logging constant) – A log level constant from the logging module such as INFO, WARNING, ERROR…

buildingBlocksHaveRings()¶

Override in subclasses to check if any of the building blocks have rings. If none do, it will be a waste of time to look for them in the larger structure.

Return type: bool
Returns: If any of the building blocks have rings

findRings(struct)¶

Find all the rings in the provided structure. Since ring-finding is expensive, its best to pre-calculate them once. Since the coordinates of the ring don’t matter, we can use these rings over and over as long as the atom numbering doesn’t change.

Parameters: struct (schrodinger.structure.Structure) – The structure to find the rings for
Return type: list
Returns: List of schrodinger.structure._Ring objects in the given structure.

findRingSpears(ring_struct, spear_struct=None, rings=None, ring_based=True, pbc=None)¶

Find all cases where a bond spears a ring

Parameters

ring_struct (schrodinger.structure.Structure) – The structure containing the rings
spear_struct (schrodinger.structure.Structure) – The structure containing the atoms that might spear the rings. If not provided, ring_struct will be used.
rings (list) – Each item of the list is a schrodinger.structure._Ring object. This is the list returned by the findRings() method. If not provided, they will be calculated on the fly - which takes considerable time. If findRingSpears will be run more than once on the same structure (even if the geometry changes), the rings should be precalculated via findRings and passed in via this parameter.
ring_based (bool) – Whether the returned dictionary should contain keys that are atom indexes of the speared ring (True), or of the bond spearing the ring (False)
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors

Return type

dict

Returns

If ring_based=True, keys are an atom index of one of the atoms in the speared ring, and values are the atom index of one of the atoms in the spearing bond. If ring_based=False, the keys/values are flipped.

removeIgnoredClashes(all_clashes, ignored_clashes)¶

Get only those clashes that are not ignored.

Parameters

all_clashes (dict) – All found clashes
ignored_clashes (dict) – Clashes that should be ignored

Return type

dict

Returns

Those clashes in all_clashes that are not in ignored_clashes. Keys are atom indexes, values are all the atom indexes that clash with that atom

getInfraStructure(struct)¶

Get an infrastructure Structure object and an associated bitset struct.atom_total long

Parameters: struct (schrodinger.structure.Structure) – The python module Structure object
Return type: tuple
Returns: First item of the tuple is a schrodinger.infra.structure.Structure object. Second item is a bitset that is struct.atom_total long

getClashes(struct1, cutoff, struct2=None, pbc=None, check_14=False)¶

Find clashes - either intrastructure if struct2 is None, or interstructure if struct2 is not None.

Parameters

struct (schrodinger.structure.Structure) – The structure for intrastructure clashes or the first structure for interstructure clashes
cutoff (float) – The cutoff for finding clashes. This value is multipied times the sum of the VDW radii of the two atoms. If the distance is less than this scaled VDW radii sum, a clash exists
struct2 (schrodinger.structure.Structure) – The second structure for interstructure clashes
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
check_14 (bool) – If False, the atom pairs separated by 3 covalent bonds are excluded for clash check.

Return type

dict

Returns

keys are atom indexes in struct1 (or struct2 if defined), and values are all the atom indexes in struct1 that clash with that atom

checkForIntraStructureClashes(struct, scale=None, pbc=None, rings=None)¶

Check for any intrastructure clashes

Parameters

struct (schrodinger.structure.Structure) – The structure for intrastructure clashes
scale (float) – The cutoff for finding clashes. This value is multipied times the sum of the VDW radii of the two atoms. If the distance is less than this scaled VDW radii sum, a clash exists
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
rings (list) – The precalculated rings returned by findRings() on the structure. If not supplied, they will be calculated on the fly.

Return type

dict

Returns

keys are atom indexes, and values are all the atom indexes that clash with that atom. A clash may come from two atoms too close together, or a ring that is speared by a bond.

static countClashes(clashes)¶

Count the total number of clashes

Parameters: clashes (dict) – keys are atom indexes, values are all the atom indexes that clash with that atom

colorByMolecule(struct)¶

Color each molecule in struct a different color

Parameters: struct (schrodinger.structure.Structure) – The structure to color

schrodinger.application.matsci.amorphous.nearest_rotatable_bonds(struct, rings, backbone_atom_id, side_atom_ids, pre_atom_prop='b_matsci_polymer_branch_atom', atom_prop='b_matsci_polymer_head_atom')¶

Search the side groups of one atom and find the ‘first neighbor’ rotatable bonds.

Parameters

struct (schrodinger.structure.Structure) – structure to search bonds
rings (list) – List of ring atom index lists
backbone_atom_id (int) – the atom id of one backbone atom
side_atom_ids (list) – list of atom ids of the side groups for the backbone_atom
pre_atom_prop (str) – the property to be set True for the atom in the rotatable bonds that is closer to the backbone_atom_id
atom_prop (str) – the property to be set True for the atom in the rotatable bonds that is deeper in side group

Return type

list of tuple

Returns

each tuple is two atom indexes, indicating ‘first neighbor’ rotatable bonds in side groups for one atoms

class schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin¶

Bases: object

A mixin for classes that uses in-cell polymer grow method.

setRingsForOneMol(new_init_frag, ringnum)¶

Create _Ring objects for each fragment in one molecule.

Parameters

new_init_frag (PolymerFragment) – the first fragment containing initiator
ringnum (int) – the total number of rings of all molecules in cell

placeOneIniInCell(frag, new_chain=True)¶

Place a new or dead chain fragment containing initiator into the cell. If new_chain=True, randomly pick a position in cell; make sure the position is away from pre-existing initiators; check contact of the newly added fragments against all pre-existing atoms. If contact exists, randomly pick anothor position. If new_chain=False, find a random position in the largest void in cell; check contact; if contact exists, loop over all the gridded positions in the largest void.

Parameters

frag (PolymerFragment) – the first fragment containing initiator
new_chain (bool) – if True, the fragment is from a new chain; else, the fragment is from a dead chain.

Return type

bool

Returns

True, if the initiator fragment is successfully placed in cell

initiateMultiMols(frags, grid_mids, margins, indexes)¶

Place multiple initiators of the fragments into the cell.

Parameters

frags (list of PolymerFragment) – the first fragments containing initiators
grid_mids (list) – middle points on a grid layout
margins (list) – the margin between two middle points
indexes (list) – the available grid indexes

Returns

the fragment failed to be placed

Return type

list of PolymerFragment

getGrids(diameter)¶

Get the grid points for placing initiators

Parameters: diameter (float) – the diameter of the largest initiator
Returns: grid points, margins in three dims, available grid indexes
Return type: dict, list, list

getPositions(num, grid_mids, margins, indexes)¶

Get positions based on grid with randomness

Parameters

num (int) – the number of position requested
grid_mids (dict) – the grid middle points
margins (list of float) – the margins for grid points in each dimension. Intentionally design this room so that initiators can translationally move away from the grid mid points.
indexes (list) – the available grid indexes

Returns

list of random points

Return type

list

growFragmentCell(density, avdw_scale)¶

Make a single attempt at building the cell by growing polymer fragments.

Parameters

density (float) – The density of the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs

Return type

schrodinger.structure.Structure or None

Returns

The built cell, or None if an error occurred

initTangledMethod(density)¶

Initialize some attributes for the tangled method.

Parameters: density (float) – the density of the cell

setCellsForTangledChain()¶: Set cells for tangle chain method.

copyAllStructsIntoCell()¶: Copy all structures into the cell, but the bitsets are off. Deepcopy fragments.

preparePbcAndParams(avdw_scale)¶

Prepare pbc, contact parameters, max distance for distance cell.

Parameters: avdw_scale (float) – The VDW scale factor for clash cutoffs

setSubstrateSpearRings()¶: Set Spear Rings for the substrate.

setVolGraphAndBitset()¶: Set volume graph and bitset.

setIniFragsOnebyOne(ini_frags)¶

Set the initiator fragments one by one.

Parameters: ini_frags (list of 'PolymerFragments') – the initiators of some components to be placed into the cell and grow later.

setIniFrags(ini_frags)¶

Set the initiator fragments in batch mode.

Parameters: ini_frags (list of 'PolymerFragments') – the initiators of some components to be placed into the cell and grow later.

getIniDiameter(frags)¶

Get the largest diameters of the initiators by computing the longest span between any pairs of atoms.

Parameters: frags (list of 'PolymerFragments') – list for fragments to be placed in
Returns: the largest diameters of the initiators
Return type: float

getAllComponents()¶

Get all components to be placed in the cell. Volume, fragment number, and replica number for each component are used to divide all component into several groups.

Returns: Large, soft, and fewer fragments first
Return type: list of ‘PolymerFragment’ lists

static indexChanges(values, threshold=10.0, reverse=False)¶

Use the threshold as the ratio criterion to index the sudden change in the sorted sequence.

Parameters

values (list of floats) – input values to divide
threshold (float) – the ratio criterion to identify the sudden change
reverse (bool) – If True, smaller values are grouped with smaller indexes. Otherwise larger values are grouped with smaller indexes.

Returns

indexes are the group tokens

Return type

list of int

setDistanceCell()¶: Set DistanceCell for the clash check of current fragment.

writeDihedralDis(file_name='tmp_dis.txt')¶: Write the dihedral angle distribution of the structures in cell.

relocateFailedMol(pre_frag, frags_in_one_mol, tried_per_mol, undo_crystal_links=False)¶

Place one failed molecule back into the cell.

Parameters

pre_frag ({PolymerFragment}) – the ini fragment of one polymer
frags_in_one_mol (list of {PolymerFragment}) – polymer fragment of this polymer within one polymer
tried_per_mol (int) – failed trial number
undo_crystal_links (bool) – whether to unlink the chain from the crystals

Return type

bool

Returns

True, if successfully placed the ini fragment back

hasClashes()¶

Check whether current fragment has clashes and speared rings with pre-existing structure.

Return type: bool
Returns: True, if has clashes

removeFinishedPolymer()¶: Remove frags_by_mols that have no polymer fragments and update finished polymer number.

bitSetOn(frag)¶

Set on the pre-existing atom bitset according to atom ids in the fragment; record rings and spear_rings according to rings in the fragment.

Parameters: frag (PolymerFragment) – the polymer fragment providing the atom ids

bitSetOff(bitset, frag)¶

Set the bitset off according to the atom ids in the fragment; remove rings and spear_rings according to rings in the fragment.

Parameters

bitset (Bitset) – the bitset to set
frag (PolymerFragment) – the polymer fragment providing the atom ids

getPosition(new_chain)¶

Find random positions in the cell according to the following rules. If new_chain=True, randomly pick a position in cell that is away from pre-existing initiators. If new_chain=False, randomly loop over all the gridded positions in the largest void in cell.

Parameters: new_chain (bool) – if True, the fragment is from a new chain; else, the fragment is from a dead chain.
Return type: generator
Returns: a generator of [x, y, z], a random position in cell. The generator is empty if no position could be found

getRandGridXYZ()¶

Get xyz iterator of random grid points in the largest void.

Return type: generator of list
Returns: Each item of the generator is [x, y, z], a random position in cell. The generator is empty if there are no voids

getRandXYZ(max_num=2000, max_failed_num=2000)¶

Return a random point in the space and no other initiators and scaffold within a pre-defined raduis.

Parameters

max_num (int) – max number of xyz position returned
max_failed_num (int) – max number of attemps when finding points self.r_per_ini_frag away from scaffold and other initiator atoms.

Return type

generator of list

Returns

Each item of the generator is [x, y, z], a random position in cell. The generator is empty if no point can be found

deleteOtherBranches(pre_frag, frags_in_one_mol)¶

Remove the fragments from the next_frags pool and set off the bitset of moved fragments.

Parameters

pre_frag (PolymerFragment) – the branching parent polymer fragment
frags_in_one_mol (list of PolymerFragment) – the pool of PolymerFragment to be grown

setPolymerFragments(vdw_scale)¶

Set polymer fragments for tangled chain method.

Parameters: avdw_scale (float) – The VDW scale factor for clash cutoffs

getPolymerFragments(vdw_scale, get_rigid=False, restore_template=None)¶

Break polymers (if needed), prepare them, and return the corresponding PolymerFragments objects.

Parameters

avdw_scale (float) – The VDW scale factor for clash cutoffs
get_rigid (bool) – If True, pick those marked as rigid bodies. If False, skip those marked as rigid bodies.
restore_template (bool or None) – Whether to restore the template polymer to the original one. If None, the template will be restored unless in debug mode.

Return type

list of ‘PolymerFragments’

Returns

Each item contains fragment information for one molecule.

class schrodinger.application.matsci.amorphous.AmorphousCellBuilder(scaffold=None, system=True, population=1, composition=None, density=0.5, amorphous_vdw_scale=1.0, obey='density', tries_per_dc=5, tries_per_mol=5, title='', allow_increased_density=True, forcefield='OPLS_2005', grow=False, dihe_temperature=None, grow_together=False, recolor=False, preserve_res=True, split_components=False, wam_type=None, **kwargs)¶

Bases: schrodinger.application.matsci.amorphous.BuilderWithClashDetection, schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin

Builder for an amorphous cell

__init__(scaffold=None, system=True, population=1, composition=None, density=0.5, amorphous_vdw_scale=1.0, obey='density', tries_per_dc=5, tries_per_mol=5, title='', allow_increased_density=True, forcefield='OPLS_2005', grow=False, dihe_temperature=None, grow_together=False, recolor=False, preserve_res=True, split_components=False, wam_type=None, **kwargs)¶

Create an AmorphousCellBuilder object

Parameters

Scaffold (Scaffold) – The Scaffold object for the cell to use that defines the molecule the cell should be built around (or inside or on top of)
system (bool) – Whether a Desmond system should be built with the final amorphous cell
population (int) – The number of molecules to include in the amorphous cell
composition (list) – A list of the same length and order as structs which gives the number of structures of each component
density (float) – The initial target density for building the cell. Does not include the scaffold volume or mass
amorphous_vdw_scale (float) – The initial VdW scale factor to use when looking for clashes in the amorphous cell
obey (str) – A module constant indicating which initial target to keep constant when trying to build an amorphous cell - either OBEY_DENSITY to keep the density constant, OBEY_CLASH to keep the VdW scale factor constant, or OBEY_BOTH to keep both constant. The latter will prevent the builder from relaxing one of these constraints to find a cell without clashes.
tries_per_dc (int) – The number of tries to make a cell at a given density and VdW clash scale factor before relaxing the parameter that is not specified by obey
tries_per_mol (int) – The number of times to try placing a molecule in the cell without clases before scrapping the cell and starting over
title (str) – The title to give the final cell structure
allow_increased_density (bool) – If True and obey=OBEY_CLASH, allow attempts to build cells at increasing density as long as a cell was built successfully
forcefield (str) – The name of the force field to use. The default is ‘OPLS_2005’.
grow (bool) – whether grow polymers via self-avoiding random walk
dihe_temperature (float, or None) – the temperature to calculate dihedral angle distribution
grow_together (bool) – Grow all the molecules together if True
recolor (bool) – Whether to recolor the components so that each molecule of the same component is the same color
preserve_res (bool) – Whether to preserve the current residue information
split_components (bool) – Whether to split system in components in the system build
wam_type (int or None) – One of the enums defined in workflow_action_menu.h if the results should have a Workflow Action Menu in Maestro

See the parent class for additional keyword documentation

setDensityIncreaseAllowed(is_allowed)¶

Set whether increased cell densities can be attempted after a successful cell is built using OBEY_CLASH

Parameters: is_allowed (bool) – Whether increased density attempts can be tried

build(generate_only=False, center=True)¶

Build the cell and do all the post-processing

Parameters

generate_only (bool) – Only generate the cell, do not write it to a file, write final density, or attempt to create a Desmond system with it
center (bool) – Center the structure in the PBC unit cell, assuming the cell has its origin at 0, 0, 0

Return type

schrodinger.structure.Structure or None

Returns

The created structure or None if no structure was found

postTreatBuiltCell(cell)¶

The default implementation of this does nothing, but subclasses can use this method to modify the raw cell immediately after the last structure is added to it but before any other processing (such as centering, coloring, writing out or building a Desmond system)

Parameters: cell (schrodinger.structure.Structure) – The built cell
Return type: schrodinger.structure.Structure
Returns: The modified cell

buildCell(density, avdw_scale)¶

Make a single attempt at building the cell.

Parameters

density (float) – The density of the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs

Return type

schrodinger.structure.Structure or None

Returns

The built cell, or None if an error occurred

buildCellDriver()¶

Driver function for cell building. Tries multiple cells until one succeeds. Adjust initial parameters to try to create more dense or tighter class cells as needed.

Return type: schrodinger.structure.Structure or None
Returns: The built cell, or None if an error occurred

prepareTangledChainBlocks(vdw_scale, vdw_min)¶

Break structures into polymer fragments and handle vdw scale adjustment.

Parameters

vdw_scale (float) – the vdw scale to check clashes.
vdw_min (float or None) – If float, this is the minimum allowable vdw scale after adjustment. If None, don’t allow vdw adjustment.

Return type

float or None

Returns

If float, this is the vdw scale.

getBuildingBlocks(number)¶

Get the structures to place into the amorphous cell. Must be overridden in the subclass to produce structures

Parameters: number (int) – The number of structures to return
Return type: list
Returns: list of schrodinger.structure.Structure objects to place into the cell

rotateRigidBodyCell(density, avdw_scale)¶

Make a single attempt at building the cell by random placing and rotating rigid structures.

Parameters

density (float) – The density of the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs

Return type

schrodinger.structure.Structure or None

Returns

The built cell, or None if an error occurred

placeStructureInCell(cell, struct, avdw_scale, no_rotation=False, rotate_velocities=False)¶

Place a structure in the cell. Make multiple rotations and translations to try to find a spot that the structure fits in with no clashes

Parameters

cell (schrodinger.structure.Structure) – The current cell with structures that have already been placed
struct (schrodinger.structure.Structure) – The structure to attempt to place into the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs
no_rotation (bool) – If True, do not rotate the structure
rotate_velocities (bool) – If True, besides the structure, also rotate FFIO atom velocities (if present)

Return type

bool

Returns

Whether the structure was placed in the cell successfully

duplicateRings(original_rings, new_struct)¶

Take a list of _Ring objects referenced to one structure and convert to a list of _Ring objects referenced to a new structure. This is much faster than finding rings in the new structure. It is implied that the new and old structure have identical bonding.

Parameters

original_rings (iterable of _Ring objects) – The _Ring objects to duplicate
new_struct – schrodinger.structure.Structure
new_struct – The new structure the ring objects should reference

Return type

list

Returns

List of schrodinger.structure._Ring objects that reference atoms in new_structure

locateAndRotate(struct, no_rotation=False, rotate_velocities=False)¶

Randomly rotate a copy of struct and translate it to a position in the cell

Parameters

struct (schrodinger.structure.Structure) – The structure to attempt to place into the cell
no_rotation (bool) – If True, do not rotate the structure
rotate_velocities (bool) – If True, besides the structure, also rotate FFIO atom velocities (if present)

Return type

schrodinger.structure.Structure

Returns

A copy of struct that has been randomly rotated and translated

adjustACellDensity(density, down=True)¶

Adjust the cell density up or down - the amount it is adjusted depends on its current value and the direction it is being adjusted

Parameters

density (float) – The current cell density
down (bool) – Whether to adjust the density down (or up if False)

Return type

float

Returns

The adjusted density

adjustACellClashVDWScale(avdw_scale, down=True)¶

Adjust the cell clash scaling up or down - the amount it is adjusted depends on its current value and the direction it is being adjusted

Parameters

avdw_scale (float) – The current clash vdw scale factor
down (bool) – Whether to adjust the scale factor down (or up if False)

Return type

float

Returns

The adjusted scale factor

checkForClashes(cell, candidate, avdw_scale, raw_clashes, cell_rings, candidate_rings)¶

Check for clashes between the candidate structure and structures already within the cell, and also intrastructure clashes within the candiate that are the result of the periodic boundary condition. If intrastructure clashes are found, interstructure clashes are not checked for.

Parameters

cell (schrodinger.structure.Structure) – The current cell with structures that have already been placed
candidate (schrodinger.structure.Structure) – The structure to attempt to place into the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs
raw_clashes (dict) – Those clashes that exist in the candidate without accounting for the PBC
cell_rings (list) – Each item of the list is a schrodinger.structure._Ring object returned by the findRings() method.
candidate_rings (list) – Each item of the list is a schrodinger.structure._Ring object returned by the findRings() method.

Return type

dict

Returns

Any clashes found. Keys are atom indexes values are all the atom indexes that clash with that atom

checkForInterStructureClashes(cell, candidate, avdw_scale, pbc, cell_rings, candidate_rings)¶

Check for clashes of the structure with other structures in the cell, including the periodic boundary condition. Also check for ring spears. The first check that finds clashes will return those clashes and no more checks will be made.

Parameters

cell (schrodinger.structure.Structure) – The current cell with structures that have already been placed
candidate (schrodinger.structure.Structure) – The structure to attempt to place into the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
cell_rings (list) – Each item of the list is a schrodinger.structure._Ring object returned by the findRings() method.
candidate_rings (list) – Each item of the list is a schrodinger.structure._Ring object returned by the findRings() method.

Return type

dict

Returns

Any clashes found. Keys are atom indexes values are all the atom indexes that clash with that atom

getPBCSide(cell)¶

Get the length of one side of the periodic boundary condition

Parameters: cell (schrodinger.structure.Structure) – The current cell with structures that have already been placed
Return type: float
Returns: The length of one side of the periodic boundary condition. 0 is returned if no PBC has been set on the cell

getNewCellStructure(volume)¶

Get a new, empty structure with the periodic boundary condition set

Parameters: volume (float) – The desired volume of the periodic boundary condition
Return type: schrodinger.structure.Structure
Returns: The structure to add the properties to

getDesiredVolume(structures, density, num_per_chain=None)¶

Get the volume of a cube that will have the given density when the given structures are placed entirely inside it

Parameters

structures (list) – The list of structures to be placed into the box
density (float) – The desired density (g/cm3)
num_per_chain (list of int) – The number of each structure. If provided, this list must be of the same length as the above structure list

Return type

float

Returns

The desired box side

bitSetOff(bitset, frag)¶

Set the bitset off according to the atom ids in the fragment; remove rings and spear_rings according to rings in the fragment.

Parameters

bitset (Bitset) – the bitset to set
frag (PolymerFragment) – the polymer fragment providing the atom ids

bitSetOn(frag)¶

Set on the pre-existing atom bitset according to atom ids in the fragment; record rings and spear_rings according to rings in the fragment.

Parameters: frag (PolymerFragment) – the polymer fragment providing the atom ids

buildingBlocksHaveRings()¶

Override in subclasses to check if any of the building blocks have rings. If none do, it will be a waste of time to look for them in the larger structure.

Return type: bool
Returns: If any of the building blocks have rings

checkForIntraStructureClashes(struct, scale=None, pbc=None, rings=None)¶

Check for any intrastructure clashes

Parameters

struct (schrodinger.structure.Structure) – The structure for intrastructure clashes
scale (float) – The cutoff for finding clashes. This value is multipied times the sum of the VDW radii of the two atoms. If the distance is less than this scaled VDW radii sum, a clash exists
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
rings (list) – The precalculated rings returned by findRings() on the structure. If not supplied, they will be calculated on the fly.

Return type

dict

Returns

keys are atom indexes, and values are all the atom indexes that clash with that atom. A clash may come from two atoms too close together, or a ring that is speared by a bond.

colorByMolecule(struct)¶

Color each molecule in struct a different color

Parameters: struct (schrodinger.structure.Structure) – The structure to color

copyAllStructsIntoCell()¶: Copy all structures into the cell, but the bitsets are off. Deepcopy fragments.

static countClashes(clashes)¶

Count the total number of clashes

Parameters: clashes (dict) – keys are atom indexes, values are all the atom indexes that clash with that atom

deleteOtherBranches(pre_frag, frags_in_one_mol)¶

Remove the fragments from the next_frags pool and set off the bitset of moved fragments.

Parameters

pre_frag (PolymerFragment) – the branching parent polymer fragment
frags_in_one_mol (list of PolymerFragment) – the pool of PolymerFragment to be grown

findRingSpears(ring_struct, spear_struct=None, rings=None, ring_based=True, pbc=None)¶

Find all cases where a bond spears a ring

Parameters

ring_struct (schrodinger.structure.Structure) – The structure containing the rings
spear_struct (schrodinger.structure.Structure) – The structure containing the atoms that might spear the rings. If not provided, ring_struct will be used.
rings (list) – Each item of the list is a schrodinger.structure._Ring object. This is the list returned by the findRings() method. If not provided, they will be calculated on the fly - which takes considerable time. If findRingSpears will be run more than once on the same structure (even if the geometry changes), the rings should be precalculated via findRings and passed in via this parameter.
ring_based (bool) – Whether the returned dictionary should contain keys that are atom indexes of the speared ring (True), or of the bond spearing the ring (False)
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors

Return type

dict

Returns

If ring_based=True, keys are an atom index of one of the atoms in the speared ring, and values are the atom index of one of the atoms in the spearing bond. If ring_based=False, the keys/values are flipped.

findRings(struct)¶

Find all the rings in the provided structure. Since ring-finding is expensive, its best to pre-calculate them once. Since the coordinates of the ring don’t matter, we can use these rings over and over as long as the atom numbering doesn’t change.

Parameters: struct (schrodinger.structure.Structure) – The structure to find the rings for
Return type: list
Returns: List of schrodinger.structure._Ring objects in the given structure.

getAllComponents()¶

Get all components to be placed in the cell. Volume, fragment number, and replica number for each component are used to divide all component into several groups.

Returns: Large, soft, and fewer fragments first
Return type: list of ‘PolymerFragment’ lists

getClashes(struct1, cutoff, struct2=None, pbc=None, check_14=False)¶

Find clashes - either intrastructure if struct2 is None, or interstructure if struct2 is not None.

Parameters

struct (schrodinger.structure.Structure) – The structure for intrastructure clashes or the first structure for interstructure clashes
cutoff (float) – The cutoff for finding clashes. This value is multipied times the sum of the VDW radii of the two atoms. If the distance is less than this scaled VDW radii sum, a clash exists
struct2 (schrodinger.structure.Structure) – The second structure for interstructure clashes
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
check_14 (bool) – If False, the atom pairs separated by 3 covalent bonds are excluded for clash check.

Return type

dict

Returns

keys are atom indexes in struct1 (or struct2 if defined), and values are all the atom indexes in struct1 that clash with that atom

getGrids(diameter)¶

Get the grid points for placing initiators

Parameters: diameter (float) – the diameter of the largest initiator
Returns: grid points, margins in three dims, available grid indexes
Return type: dict, list, list

getInfraStructure(struct)¶

Get an infrastructure Structure object and an associated bitset struct.atom_total long

Parameters: struct (schrodinger.structure.Structure) – The python module Structure object
Return type: tuple
Returns: First item of the tuple is a schrodinger.infra.structure.Structure object. Second item is a bitset that is struct.atom_total long

getIniDiameter(frags)¶

Get the largest diameters of the initiators by computing the longest span between any pairs of atoms.

Parameters: frags (list of 'PolymerFragments') – list for fragments to be placed in
Returns: the largest diameters of the initiators
Return type: float

getPolymerFragments(vdw_scale, get_rigid=False, restore_template=None)¶

Break polymers (if needed), prepare them, and return the corresponding PolymerFragments objects.

Parameters

avdw_scale (float) – The VDW scale factor for clash cutoffs
get_rigid (bool) – If True, pick those marked as rigid bodies. If False, skip those marked as rigid bodies.
restore_template (bool or None) – Whether to restore the template polymer to the original one. If None, the template will be restored unless in debug mode.

Return type

list of ‘PolymerFragments’

Returns

Each item contains fragment information for one molecule.

getPosition(new_chain)¶

Find random positions in the cell according to the following rules. If new_chain=True, randomly pick a position in cell that is away from pre-existing initiators. If new_chain=False, randomly loop over all the gridded positions in the largest void in cell.

Parameters: new_chain (bool) – if True, the fragment is from a new chain; else, the fragment is from a dead chain.
Return type: generator
Returns: a generator of [x, y, z], a random position in cell. The generator is empty if no position could be found

getPositions(num, grid_mids, margins, indexes)¶

Get positions based on grid with randomness

Parameters

num (int) – the number of position requested
grid_mids (dict) – the grid middle points
margins (list of float) – the margins for grid points in each dimension. Intentionally design this room so that initiators can translationally move away from the grid mid points.
indexes (list) – the available grid indexes

Returns

list of random points

Return type

list

getRandGridXYZ()¶

Get xyz iterator of random grid points in the largest void.

Return type: generator of list
Returns: Each item of the generator is [x, y, z], a random position in cell. The generator is empty if there are no voids

getRandXYZ(max_num=2000, max_failed_num=2000)¶

Return a random point in the space and no other initiators and scaffold within a pre-defined raduis.

Parameters

max_num (int) – max number of xyz position returned
max_failed_num (int) – max number of attemps when finding points self.r_per_ini_frag away from scaffold and other initiator atoms.

Return type

generator of list

Returns

Each item of the generator is [x, y, z], a random position in cell. The generator is empty if no point can be found

growFragmentCell(density, avdw_scale)¶

Make a single attempt at building the cell by growing polymer fragments.

Parameters

density (float) – The density of the cell
avdw_scale (float) – The VDW scale factor for clash cutoffs

Return type

schrodinger.structure.Structure or None

Returns

The built cell, or None if an error occurred

hasClashes()¶

Check whether current fragment has clashes and speared rings with pre-existing structure.

Return type: bool
Returns: True, if has clashes

static indexChanges(values, threshold=10.0, reverse=False)¶

Use the threshold as the ratio criterion to index the sudden change in the sorted sequence.

Parameters

values (list of floats) – input values to divide
threshold (float) – the ratio criterion to identify the sudden change
reverse (bool) – If True, smaller values are grouped with smaller indexes. Otherwise larger values are grouped with smaller indexes.

Returns

indexes are the group tokens

Return type

list of int

initTangledMethod(density)¶

Initialize some attributes for the tangled method.

Parameters: density (float) – the density of the cell

initiateMultiMols(frags, grid_mids, margins, indexes)¶

Place multiple initiators of the fragments into the cell.

Parameters

frags (list of PolymerFragment) – the first fragments containing initiators
grid_mids (list) – middle points on a grid layout
margins (list) – the margin between two middle points
indexes (list) – the available grid indexes

Returns

the fragment failed to be placed

Return type

list of PolymerFragment

log(msg, level=20)¶

Log a message

Parameters

msg (str) – The message to log
level (logging constant) – A log level constant from the logging module such as INFO, WARNING, ERROR…

placeOneIniInCell(frag, new_chain=True)¶

Place a new or dead chain fragment containing initiator into the cell. If new_chain=True, randomly pick a position in cell; make sure the position is away from pre-existing initiators; check contact of the newly added fragments against all pre-existing atoms. If contact exists, randomly pick anothor position. If new_chain=False, find a random position in the largest void in cell; check contact; if contact exists, loop over all the gridded positions in the largest void.

Parameters

frag (PolymerFragment) – the first fragment containing initiator
new_chain (bool) – if True, the fragment is from a new chain; else, the fragment is from a dead chain.

Return type

bool

Returns

True, if the initiator fragment is successfully placed in cell

preparePbcAndParams(avdw_scale)¶

Prepare pbc, contact parameters, max distance for distance cell.

Parameters: avdw_scale (float) – The VDW scale factor for clash cutoffs

relocateFailedMol(pre_frag, frags_in_one_mol, tried_per_mol, undo_crystal_links=False)¶

Place one failed molecule back into the cell.

Parameters

pre_frag ({PolymerFragment}) – the ini fragment of one polymer
frags_in_one_mol (list of {PolymerFragment}) – polymer fragment of this polymer within one polymer
tried_per_mol (int) – failed trial number
undo_crystal_links (bool) – whether to unlink the chain from the crystals

Return type

bool

Returns

True, if successfully placed the ini fragment back

removeFinishedPolymer()¶: Remove frags_by_mols that have no polymer fragments and update finished polymer number.

removeIgnoredClashes(all_clashes, ignored_clashes)¶

Get only those clashes that are not ignored.

Parameters

all_clashes (dict) – All found clashes
ignored_clashes (dict) – Clashes that should be ignored

Return type

dict

Returns

Those clashes in all_clashes that are not in ignored_clashes. Keys are atom indexes, values are all the atom indexes that clash with that atom

setCellsForTangledChain()¶: Set cells for tangle chain method.

setDistanceCell()¶: Set DistanceCell for the clash check of current fragment.

setIniFrags(ini_frags)¶

Set the initiator fragments in batch mode.

Parameters: ini_frags (list of 'PolymerFragments') – the initiators of some components to be placed into the cell and grow later.

setIniFragsOnebyOne(ini_frags)¶

Set the initiator fragments one by one.

Parameters: ini_frags (list of 'PolymerFragments') – the initiators of some components to be placed into the cell and grow later.

setPolymerFragments(vdw_scale)¶

Set polymer fragments for tangled chain method.

Parameters: avdw_scale (float) – The VDW scale factor for clash cutoffs

setRingsForOneMol(new_init_frag, ringnum)¶

Create _Ring objects for each fragment in one molecule.

Parameters

new_init_frag (PolymerFragment) – the first fragment containing initiator
ringnum (int) – the total number of rings of all molecules in cell

setSubstrateSpearRings()¶: Set Spear Rings for the substrate.

setVolGraphAndBitset()¶: Set volume graph and bitset.

writeDihedralDis(file_name='tmp_dis.txt')¶: Write the dihedral angle distribution of the structures in cell.

class schrodinger.application.matsci.amorphous.EnergySurface(orig_dihe_values)¶

Bases: object

Calculate energy surface, and dihedral angle probability distrubtion.

__init__(orig_dihe_values)¶

Save original dihedral values and initialize energy.

Parameters: orig_dihe_values (list of float) – The original dihedral values

setUniformDistribution()¶: Set uniform distribution.

setBoltzmannDistribution(struct, dihedral, forcefield_num, force_constant, beta)¶

Calculate torsion energy surface. If any energies on the surface are invalid, set uniform distribution. If all are valid, set Boltzmann distribution

Parameters

struct ({schrodinger.Structure.structure}) – the local structure for dihedral angle energy surface
dihedral (list of int) – the 4 ints are the atom ids of target dihedral angle
forcefield_num (int) – the mmffld integer for the given forcefield
force_constant (float) – the energy constant for torsion restraints
beta (float) – 1/kT to get Boltzmann factor (E / kT)

exception schrodinger.application.matsci.amorphous.RotationError¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

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

class schrodinger.application.matsci.amorphous.PolymerFragments(struct, num_struct, dihedral_min=0.0, dihedral_max=360.0, dihedral_num=73, dihedral_exclude=False, only_backbone=False, vdw_scale=1.0, forcefield='OPLS_2005', temperature=None, pop_local_clash=True, logger=None, indexing='0')¶

Bases: schrodinger.application.matsci.amorphous.BuilderWithClashDetection

Save the struct and break it into fragments.

LETTER_NUM = 26¶

__init__(struct, num_struct, dihedral_min=0.0, dihedral_max=360.0, dihedral_num=73, dihedral_exclude=False, only_backbone=False, vdw_scale=1.0, forcefield='OPLS_2005', temperature=None, pop_local_clash=True, logger=None, indexing='0')¶

Prepare infomation for in-cell grow of one single polymer chain.

Parameters

struct (schrodinger.structure.Structure) – the structure to be breaked into fragments
num_struct (int) – copy the struct by num_struct times when placing them into the cell
dihedral_min (float) – lower limit of dihedral angle
dihedral_max (float) – upper limit of dihedral angle
dihedral_num (int) – the number of dihedral values
dihedral_exclude (bool) – (0, dihedral_min) and (dihedral_max, 360) are used as dihedral angle range, if True.
only_backbone (bool) – only the rotatable bonds in backbone is considered
vdw_scale (float) – VDW scale factor to use
forcefield (str) – The name of the force field to use. The default is ‘OPLS_2005’.
temperature (float, or None) – the temperature to calculate dihedral angle distribution using boltzmann factor. If None, a uniform distribution is used.
pop_local_clash (bool) – whether remove dihedral angle values that lead to local clashes
logger (logging.Logger) – logger for output info
indexing (str) – the indexing based on compositions and molecules

setDiheInit()¶: Set descrete dihedral values.

breakIntoFragments(is_rigid=False, restore_template=True)¶

Break polymer into fragments.

Parameters

is_rigid (bool) – set the molecule as one fragment.
restore_template (bool) – restore the template polymer to the original one.

checkAndmarkPolymerProp()¶

Check the struct and mark with necessary polymer properties.

Return type: bool
Returns: True, if the structure is successfully marked with polymer properties.

setLocalStructs()¶: Set the local structures.

setAsOneFragment()¶: Set the whole molecule as one fragment.

setAllfragments()¶: Set all fragments.

saveLocalStructs()¶: Save local structs and update dihedrals according to the atom ids in newly saved local structs.

popLocalClashes()¶: Try dihedral value one by one for the target torsion in local structs, and eliminate those leading to inevitable local clashes by incomplete conformer search of local structs.

torsionEnergySurf(force_constant=10.0, temperature=300.0)¶

Sample torsion energy surface for local structs, and initialize the dihedral angle distribution using Boltzmann distribution.

Parameters

force_constant (float) – the energy constant for torsion restraints
temperature (float, or None) – the temperature to calculate dihedral angle distribution

extractWithMap(struct, indices, copy_props=False)¶

Return a new structure object which contains the atoms of the current structure that appear in the specified list and a dict which maps atom ids in current structure to those in newly fextracted substructure.

Parameters

struct (structure.Structure) – the structure to extract substructs from
indices (list of int) – the ids of atoms to be extracted
copy_props (bool) – whether to copy the structure level property

Return type

structure.Structure, dict

Returns

substructure, dict mapping to atom ids in substructure

getCapperTerminator(is_coarse_grain)¶

Get a terminator moiety to cap the atom in a broken bond.

Parameters: is_coarse_grain (bool) – whether the structure is coarse grain
Return type: Terminator
Returns: terminator moiety of one single H or C atom with Br marker.

findNeighborFrags(separated_bond_num=2)¶

Search for and save neighboring fragments for each fragment. For any fragments, the bond between dihe 2nd and 3rd atoms is rotatable. If any other fragments has any atoms that are within separated_bond_num bonds away from the dihe 2nd and 3rd atoms of one certain fragment, they are considered neighbor fragments of that fragment.

Parameters: separated_bond_num (int) – criteria for defining neighbor fragments

setLocalStructAtomIds()¶: Set the local struct atom ids and end atom ids defined by neighbor fragments.

isCgPolymer()¶

Coarse grain particles of one type are considerred as one type of polymer residue. If one cg structure has INI, TRM, and others as residues, consider it built from polymer builder, assuming all bonds between particles are rotatable.

Return type: bool
Returns: True, if the cg structure is originally from polymer builder and prepared properly.

renumberResGetM2PMap(monomer_orig_idx_prop='i_matsci_polymer_monomer_orig_atom_idx')¶

Loop over all the residues and create mapping from atom id in residue to that in polymer.

Parameters: monomer_orig_idx_prop (str) – The atom property to define the original atom index

updateAllAtomIndexMaps()¶: Get information from previous polymer build for polymer grow in cell.

setInitiatorResidue()¶: Save the residue containing the polymer initiator.

setResidueConnectivity(moiety, residue_num)¶

Create mapping from connected resnum pair to connected atom pair.

Parameters

moiety (schrodinger.structure.Structure) – one moiety used to construct part of the polymer
residue_num (int) – residue num

setBackboneAndSideGroup(moiety, residue_num)¶

Update backbone and side group maps.

Parameters

moiety (schrodinger.structure.Structure) – one moiety used to construct part of the polymer
residue_num (int) – residue num

setPathtoBranchingAtom(moiety_bb_to_marked_end, residue_num)¶

Update maps for the path between backbone atom to atom branching point.

Parameters

moiety_bb_to_marked_end (dict) – Keys are backbone atom indexes, values are dictionaries with keys being the branching atom and values being the path between backbone atom and branching atom
residue_num (int) – residue num

setRotatableBond(moiety_rotatable_bonds, residue_num)¶

Update maps for the path between backbone atom to atom branching point.

Parameters

moiety_rotatable_bonds (list of tuple) – (atom 1, atom 2) between which bond is rotatable
residue_num (int) – residue num

createFragForInitiator()¶: Create the the first polymer fragment from the initiator and append the following children of it.

getInitiatorSubBackbone(sub_backbone, dihe_3rd)¶

Return a list of atom ids: the last two atoms are bonded and the last bonds with the dihe 3rd atom.

Parameters

sub_backbone (list) – the last two atoms are bound and the last one binds with the dihe 3rd atom.
dihe_3rd (int) – the 3rd atom in a dihedral

finishPolymerFrags()¶: Generate all polymer fragments from the first generation fragment containing INT and the following generation fragments.

appendMissedFrags()¶: When polymer fragments don’t find all the atoms in the original structure, this methods first groups them by bond connections and appends each group to a found fragment.

getConnectionInfos(missed_atom_id_groups, all_missed_atom_ids)¶

Return the connecting atoms, which belong to the atoms in the found fragment and connect to the missed atoms.

Parameters

missed_atom_id_groups (list of list) – each sublist has missed atoms connected by covalent bonds.
all_missed_atom_ids (list of int) – a flat list of all missed atom indexes

Return type

list of set

Returns

each set has the connecting atoms, which belong to the found atoms in the fragment and are connected to the missed atoms.

assignRingAtomIds()¶: Assign ring atom indexes to each fragment.

structToOriginByFrag()¶: Move the structure so the centroid of the fragment is at the origin.

getFragCentroid(struct, frag)¶

Calculate the centroid of polymer fragment.

Parameters

frag (Polymerfragment) – polymer structure to get atom positions from
frag – The polymer fragment to get atom ids from

Return type

list

Returns

the centroid of polymer fragment

getDelNextResnumByResnum(cur_resnum)¶

Given resnum, find all the connected residues and atoms. Delete the connectivity from current residue to next residue and the connectivity from next residue to current residue.

Parameters

cur_resnum (int) – the residue number which the atom id belongs to
del_connection (bool) – del the connection from current atom and residue to the connected atom and residue

Return type

iterator to generate int, [int, int]

Returns

the connected residue number, [atom id, connected atom id]

delConnectivity(cur_resnum, next_resnum, atom_id, next_atom_id)¶

Delete the connectivity from current residue to next residue and the connectivity from next residue to current residue.

Parameters

cur_resnum (int) – the residue number which the current atom id belongs to
next_resnum (int) – the residue number which the connected atom id belongs to
atom_id (int) – the atom id from which other connections are searched
next_atom_id (int) – one connected atom id

createEndSubFragment(cur_frag, dihe_3rd_resnum, sub_backbone, dihe_4th_resnum, dihe_4th_atom_id, append_to_frag=None, last_created_frag=False)¶

Create one child PolymerFragment or append atoms to append_to_frag.

Parameters

cur_frag (PolymerFragment) – current polymer fragment
dihe_3rd_resnum (int) – the resnum of the 3rd atom in dihedral
sub_backbone (list of int) – the backbone whose last atom (dihedral 3rd) will be connected to new fragment
dihe_4th_resnum (int) – a guess of the resnum of the 4th atom in res
dihe_4th_atom_id (int or None) – the 4th atom of dihedral, if int; None, if the 4th atom is in the adjacent res
append_to_frag (PolymerFragment or None) – if None, the found ‘branching’ is new polymer fragment, and new PolymerFragment is created with dihedral_4th_atom. if not None, the found ‘branching’ is part of the old polymer fragment and no new PolymerFragment is created. Add dihedral_4th_atom to old polymer fragment.
last_created_frag (bool) – if True, will not return fragment

Return type

PolymerFragment or None

Returns

the newly created PolymerFragment, or None if atoms are appended to append_to_frag fragment

addBranchingAtoms(cur_frag)¶

Append extra dihedral 4th atoms for branching. Add to the parent of cur_frag instead of cur_frag, if the current fragment and new branch share the 1st, 2nd, and 3rd atoms in a dihedral angle.

Parameters: cur_frag (PolymerFragment) – branching points will be added to the this fragment

resBackbone(resnum, atom_id)¶

Given residue number and starting atom id, return the short backbone path (from the starting atom id to the end) and set head/tail using dictionary.

Parameters

resnum (int) – the residue number
atom_id (int) – backbone path starts from this atom id

Return type

list of int

Returns

the atom ids of backbone from atom_id to the other end

continueResBackbone(atom_id)¶

Return rest of the backbone path continuing from the atom_id.

Parameters: atom_id (int) – atom id of the starting point
Return type: list
Returns: the atom ids of backbone from atom_id to the other end

bondedAtomIdInSameRes(atom_id)¶

Find the atom id of a neighbor atom within the same residue.

Parameters: atom_id (int) – atom id
Return type: int or None
Returns: the atom id of a neighbor atom in the same residue

getDelNextResnumByAtomID(atom_id)¶

Given atom id, find all the connected residues and atoms. Delete the connectivity from current residue to next residue and the connectivity from next residue to current residue.

Parameters

atom_id (int) – the atom id from which all connections are returned
del_connection (bool) – del the connection from current atom and residue to the connected atom and residue

Return type

iterator to generate int, [int, int]

Returns

the connected residue number, [atom id, connected atom id]

isAllAtomPolymer()¶

Each polymer built by polymer has one INI, TRM, and at least one MOMONOMER; each atom in polymer has MONOMER_ORIG_ATOM_IDX_PROP property; residues from the same moiety should have same number of atoms.

Return type: bool
Returns: True, if the structure is built using polymer builder.

breakIntoMols()¶

Make a copy of the template polymer and break the structure into molecules serving as INI, TRM, and Monomer.

Return type: {schrodinger.Structure.structure}, int
Returns: the structure copy broken into molecules serving as a moiety, atom id of one atom in INI

static findHeadTail(struct, atom_ids=None, source=None, set_style=False)¶

Find the head and tail atoms of the longest path. If multiple longest paths are found, rank those longest paths by the head atom ids and then tail atom ids. Choose the longest path with the smallest head/tail atom ids.

Parameters

struct ("schrodinger.structure.Structure") – the structure to find head and tail
atom_ids (atom ids of the target molecule. If None, all the atoms in the struct are used.) – list of int or None
source (bool) – node (head atom index), Starting node for path. If not specified, compute shortest path lengths using all nodes as source nodes.
set_style – Mark the head, tail, and backbone atoms

Return type

int, int

Returns

atom ids for head and tail atoms

setAndMarkResidues()¶

Break the molecule into fragments by rotatable bonds and set each fragment as one residue.

Return type: bool
Returns: True, if struct_copy has more than one molecule, serving as INI, TRM, and Monomers

setResProperties(residue_name, atom_indexes, residue_number)¶

Reassign atom properties so that atoms of atom_indexes are treated as one residue with proper MONOMER_ORIG_ATOM_IDX_PROP.

NOTE: MONOMER_ORIG_ATOM_IDX_PROP MODIFIED BASED ON ATOMS IN RESIDUE

Parameters

residue_name (str) – the residue name for atoms in this residue
atom_indexes (list of int) – the atom ids for atoms in one residue
residue_number (int) – the residue number for atom_indexes

extractMoieties()¶: Extract residue structures in a polymer and save one for each residue type.

updateOrigAtomIdx()¶: Update the MONOMER_ORIG_ATOM_IDX_PROP property in each polymer atom with the atom index of atoms in moiety_structs set by setResProperties().

markMoietiesProps()¶

Copy and add additional properties to moiety_structs to pass the validations in Moieties. However, these properties are not used, since polymer is already built.

Parameters: polymer (schrodinger.structure.Structure) – structure of a polymer

buildingBlocksHaveRings()¶

Override in subclasses to check if any of the building blocks have rings. If none do, it will be a waste of time to look for them in the larger structure.

Return type: bool
Returns: If any of the building blocks have rings

checkForIntraStructureClashes(struct, scale=None, pbc=None, rings=None)¶

Check for any intrastructure clashes

Parameters

struct (schrodinger.structure.Structure) – The structure for intrastructure clashes
scale (float) – The cutoff for finding clashes. This value is multipied times the sum of the VDW radii of the two atoms. If the distance is less than this scaled VDW radii sum, a clash exists
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
rings (list) – The precalculated rings returned by findRings() on the structure. If not supplied, they will be calculated on the fly.

Return type

dict

Returns

keys are atom indexes, and values are all the atom indexes that clash with that atom. A clash may come from two atoms too close together, or a ring that is speared by a bond.

colorByMolecule(struct)¶

Color each molecule in struct a different color

Parameters: struct (schrodinger.structure.Structure) – The structure to color

static countClashes(clashes)¶

Count the total number of clashes

Parameters: clashes (dict) – keys are atom indexes, values are all the atom indexes that clash with that atom

findRingSpears(ring_struct, spear_struct=None, rings=None, ring_based=True, pbc=None)¶

Find all cases where a bond spears a ring

Parameters

ring_struct (schrodinger.structure.Structure) – The structure containing the rings
spear_struct (schrodinger.structure.Structure) – The structure containing the atoms that might spear the rings. If not provided, ring_struct will be used.
rings (list) – Each item of the list is a schrodinger.structure._Ring object. This is the list returned by the findRings() method. If not provided, they will be calculated on the fly - which takes considerable time. If findRingSpears will be run more than once on the same structure (even if the geometry changes), the rings should be precalculated via findRings and passed in via this parameter.
ring_based (bool) – Whether the returned dictionary should contain keys that are atom indexes of the speared ring (True), or of the bond spearing the ring (False)
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors

Return type

dict

Returns

If ring_based=True, keys are an atom index of one of the atoms in the speared ring, and values are the atom index of one of the atoms in the spearing bond. If ring_based=False, the keys/values are flipped.

findRings(struct)¶

Find all the rings in the provided structure. Since ring-finding is expensive, its best to pre-calculate them once. Since the coordinates of the ring don’t matter, we can use these rings over and over as long as the atom numbering doesn’t change.

Parameters: struct (schrodinger.structure.Structure) – The structure to find the rings for
Return type: list
Returns: List of schrodinger.structure._Ring objects in the given structure.

getClashes(struct1, cutoff, struct2=None, pbc=None, check_14=False)¶

Find clashes - either intrastructure if struct2 is None, or interstructure if struct2 is not None.

Parameters

struct (schrodinger.structure.Structure) – The structure for intrastructure clashes or the first structure for interstructure clashes
cutoff (float) – The cutoff for finding clashes. This value is multipied times the sum of the VDW radii of the two atoms. If the distance is less than this scaled VDW radii sum, a clash exists
struct2 (schrodinger.structure.Structure) – The second structure for interstructure clashes
pbc (None, infrastructure.PBC, or list) – If periodic boundary conditions should be used, provide either an infrastructure.PBC object or the parameters to construct one. Allowed constructors: * a, b, c : box lengths * a, b, c, alpha, beta, gamma box : box lengths and angles * ax, ay, az, bx, by, bz, cx, cy, cz : box vectors
check_14 (bool) – If False, the atom pairs separated by 3 covalent bonds are excluded for clash check.

Return type

dict

Returns

keys are atom indexes in struct1 (or struct2 if defined), and values are all the atom indexes in struct1 that clash with that atom

getInfraStructure(struct)¶

Get an infrastructure Structure object and an associated bitset struct.atom_total long

Parameters: struct (schrodinger.structure.Structure) – The python module Structure object
Return type: tuple
Returns: First item of the tuple is a schrodinger.infra.structure.Structure object. Second item is a bitset that is struct.atom_total long

log(msg, level=20)¶

Log a message

Parameters

msg (str) – The message to log
level (logging constant) – A log level constant from the logging module such as INFO, WARNING, ERROR…

removeIgnoredClashes(all_clashes, ignored_clashes)¶

Get only those clashes that are not ignored.

Parameters

all_clashes (dict) – All found clashes
ignored_clashes (dict) – Clashes that should be ignored

Return type

dict

Returns

Those clashes in all_clashes that are not in ignored_clashes. Keys are atom indexes, values are all the atom indexes that clash with that atom

class schrodinger.application.matsci.amorphous.PolymerFragment(resnum, generation, pre_frag=None, is_branching=False, pre_backbone=None, template_frag=None, molnum=None, template_polymer=None)¶

Bases: object

__init__(resnum, generation, pre_frag=None, is_branching=False, pre_backbone=None, template_frag=None, molnum=None, template_polymer=None)¶

PolymerFragment class stores the connectivity, dihedral angle, and anthoer other information for tangled chain method.

Parameters

resnum (int) – the resnum of the 3rd atom in dihedral angle
generation (int) – the generation of the fragment
pre_frag (PolymerFragment) – The parent fragment
is_branching (bool) – True, if current fragment has more than children
pre_backbone (list of int) – the last atom in pre_backbone is the 3rd dihedral atom
template_frag (PolymerFragment or None) – the polymer fragment to be copied
molnum (int) – molecule number
template_polymer (schrodinger.structure.Structure) – the structure of one polymer chain

preDeepCopy(original_frag, molnum)¶

Deep copy the fragment attributes except those linking different fragments.

Parameters

original_frag (PolymerFragment) – Polymerfragment object to be copied
molnum (int) – molecule number

deepCopy(molnum)¶

Deep copy the fragment class from the INI fragment.

Parameters: molnum (int) – molecule number
Return type: PolymerFragment
Returns: new INI fragment directing to all copied fragments

setDihedrals(dihe_init)¶

Set the dihedral angle pool and rand for each fragment. dihedral angle pool and rand are lists of possible dihedral angles. When the polymer chain grows, move to next polymer fragment and set the dihedral angle using a value randomly picked from rand; When the polymer growing site dies, move to previous polymer fragment, pop up the used dihedral angle from the pool, and randomly pick a new one from the left dihedral values in pool.

Parameters: dihe_init (list of floats) – list of possible dihedral angles

markSidegroupFrag()¶: Mark the side group polymer fragment, if the 3rd atom in the dihedral angle is in side group (not backbone atom).

resetFragDihedralPool()¶: Reset the dihedral angle pool of all following fragment according to rand in each fragment.

fragments(include_self=True)¶

Yield the first fragment of next_frags and append the children of that fragment to next_frags for recursion.

Parameters: include_self (bool) – If True, loop over itself and all child fragments. If False, only loop over its child polymer fragments.
Return type: iterator to generate PolymerFragment
Returns: one child polymer fragment

adjustAtomIds(pre_atomnum)¶

Adjust atom ids in PolymerFragment when multipe chains are added into the cell.

Parameters: pre_atomnum (int) – number of atoms before adding current molecule

markBranchingFrag()¶: Mark the branching fragments.

getDiheValues()¶

Get the possbile dihedral values of current fragment.

Return type: list
Returns: all polymer dihedral vaules

schrodinger.application.matsci.amorphous.assign_markers(residue_struct, polym=None)¶

Find and add marker atoms to the extracted structures.

Parameters

residue_struct (schrodinger.structure.Structure) – The structure to add the markers to
polym (schrodinger.structure.Structure) – If provided, the corresponding head/tail atoms are located in this reference structure, and the position of Br is determined by bonding and residue informations

exception schrodinger.application.matsci.amorphous.VolumeMemoryError¶

Bases: Exception

__init__(*args, **kwargs)¶

args¶

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

class schrodinger.application.matsci.amorphous.LowMemoryVolGraph¶

Bases: object

This class mimics a networkx graph for the XYZVolumeGraph class. It has only minimal networkx functionality. It is necessary because networkx graphs are giant memory hogs and can’t be used for even moderately-sized sparse grid graphs. This class takes a tiny fraction - a few percent or so - of the memory for an equivalent networkx graph.

__init__()¶: Create a LowMemoryVolGraph instance

__len__()¶

The length of the graph is just the number of nodes

Return type: int
Returns: The number of nodes in the graph

checkMemoryLimit()¶

Check that the amount of memory used is not approaching the total memory available

Raises: VolumeMemoryError – If the amount of memory used is too large compared to the total system memory

addNode(node)¶

Add a new node to the graph.

Parameters: node (tuple (or hashable, sortable object)) – The node to add

addEdge(node1, node2)¶

Add a new edge (a connection between two nodes) to the graph

Parameters

node1 (tuple (or hashable, sortable object)) – One of the nodes to create the edge between. Node order does not matter.
node2 (tuple (or hashable, sortable object)) – The other node to create the edge between. Node order does not matter.

Raises

KeyError – If one of the nodes is not found in the graph

removeNode(node)¶

Remove a node from the graph. Also removes all edges attached to this node

Parameters: node (tuple (or hashable, sortable object)) – The node to remove
Raises: KeyError – If one of the nodes is not found in the graph

removeEdge(node1, node2)¶

Remove an edge (a connection between two nodes) from the graph. The nodes are not removed.

Parameters

node1 (tuple (or hashable, sortable object)) – One of the nodes for the existing edge. Node order does not matter.
node2 (tuple (or hashable, sortable object)) – The other node to for the existing edge. Node order does not matter.

Raises

KeyError – If one of the nodes is not found in the graph

nodes()¶

A generator over all the nodes in the graph

Return type: node type
Returns: Iterates over each node in the graph

edges()¶

A generator over all edges in the graph

Return type: (node, node)
Returns: Iterates over each pair of connected nodes. Nodes are returned in sort order.

blobs()¶

A generator for all the blobs (groups of connected nodes) in the graph

Return type: set
Returns: Iterates over blobs. Blobs are returned in order of largest to smallest

degree(node)¶

Return the number of edges for the node

Parameters: node (tuple (or hashable, sortable object)) – The node to check
Return type: int
Returns: The number of edges for a node
Raises: KeyError – If the node is not found in the graph

class schrodinger.application.matsci.amorphous.XYZVolumeGraph(struct, spacing=2.0, scaffold=None)¶

Bases: object

Create a networkx graph to search the voids in structure.

__init__(struct, spacing=2.0, scaffold=None)¶

Create networkx graph based on the structure PBC or coordinates.

Parameters

struct (schrodinger.structure.Structure) – The structure to compute the graph over
spacing (float) – The approximate spacing (Angstroms) between graph nodes. The actual grid spacing will be adjusted in each direction to ensure uniform grid point distribution, and the actual spacing used in each direction can be found in the self.xyz_spacings list
scaffold (Scaffold or None) – a structure that occupies space as a cluster of molecules.

defineBoxFromScaffold(scaffold)¶

Define the grid box as the scaffold box size

Parameters: scaffold (Scaffold) – a structure that occupies space as a cluster of molecules.

defineBoxFromPBC()¶: Define the box from the PBC. This method works for triclinic cells by virtue of creating a hull that can be used to eliminate grid points outside the arbitrary-shaped PBC region.

defineBoxFromNonPBCStruct()¶: Define a box that encompasses the structure, including the VDW radii of the extreme atoms

getNodeXYZ(node)¶

Convert networkx node (tuple of X, Y, Z index) to XYZ coordinates

Parameters: node (tuple) – the node to convert
Return type: tuple
Returns: A tuple of x, y z coordinates in Angstroms

static getDistanceCellDistance(struct, probe)¶

Get the distance that will be used as the cutoff for atoms close to a point

Parameters

struct (schrodinger.structure.Structure) – The structure that will be checked
probe (float) – The probe radius that will be used

Return type

float

Returns

The distance cutoff that will be used

locateVoids(atom_ids=None, vdw_scale=1.0, probe=0.0, logger=None)¶

Remove all nodes that overlap a bitset-on atom (all atoms by default) in current structure. And connect all grid points that are part of the same void.

Parameters

atom_ids (set or None) – if not None, only check clashes for atoms in this set
vdw_scale (float) – VDW scale factor to use
probe (float) – A radius to add to each atom’s vdw radius in order to determine whether the atom encompasses a point or not. This is the thought equivalent of rolling a ball around the vdw surface of the atoms and tracing out the center of the ball.
logger (Logger) – If given, progress will be logged using this object

Raises

VolumeMemoryError – If memory usage grows too large

bondRemainingNodes()¶

Connect each node with its neighbor nodes that remain in the graph. Nodes that differ by 1 in 1 coordinate are considered neighbors. Any PBC is also accounted for so that neighboring nodes on the opposite side of the cell are also bonded.

Raises: VolumeMemoryError – If memory usage grows too large

static gridNeighbors(node, num_xyz, pbc)¶

A generator over all potential node values for the neighbors of the given node. The nodes may or may not exist in the graph. Neighbors are considered to have one of x, y or z values that differs by exactly 1 and both other values are the same. The PBC is used to connect neighbors on opposite edges of the cell.

Parameters

node (tuple) – the node to get the neighbors for
num_xyz (list) – The number of grid points in the x, y and z directions
pbc (schrodinger.infra.structure.PBC or None) – The PBC if one exists

Return type

tuple

Returns

Iterates over potential (x, y, z) neighbors of the given node.

static getNeighborCoordVal(node, delta, coord, numpts, pbc)¶

Get the (x, y, z) tuple for a neighbor of node that differs by delta in coord. (x, y, z) is modified based on the PBC if necessary

Parameters

node (tuple) – the node to convert
delta (int) – How much the coord value differs from the given node. Typically 1 or -1 to give a neighboring node.
coord (int) – 0, 1 or 2 for the x, y or z direction
numpts (int) – The number of grid points in the coord direction
pbc (schrodinger.infra.structure.PBC or None) – The PBC if one exists

Return type

tuple or None

Returns

The (x, y, z) tuple formed by modifying coord of node by delta, or None if there is no pbc and the modified coord would be outside 0:numpts-1

voids()¶

A generator that returns groups of connected nodes that define voids in the structure.

Return type: tuple
Returns: Each returned value is a set of nodes that are all connected and define a void blob. The sets are returned in order of size, largest to smallest

getLargestVoid()¶

Get the largest void.

Return type: tuple or None
Returns: The set of nodes that form the largest void in the structure. None is returned if there are no voids.

getSurfaceNodes(blob)¶

Get a list of nodes in blob that have fewer than 6 connections

Parameters: blob (set) – The set of nodes to search for surface nodes in
Return type: list
Returns: Each item of the list is a node that has fewer than 6 connections

getBuriedNode(blob)¶

A generator that returns nodes that is buried inside the blob of connected nodes. Buried nodes have lots of connections to other nodes.

Parameters: blob (a set of tuples) – Each item of the set is a node
Return type: tuple
Returns: The buried node

getBuriedXYZ(blob)¶

Like getBuriedNode but return the xyz coordinates.

Parameters: blob (a set of tuples) – Each item of the set is a node
Return type: tuple
Returns: A tuple of x, y z coordinates in Angstroms

schrodinger.application.matsci.amorphous.find_attached_atom_index(struct, mark_index, prop=None, propval=True)¶

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters

struct (schrodinger.structure.Structure) – The structure to search for the atom
mark_index (int) – The index of the atom that we want to find an atom attached to.
prop (str) – An atom property name
propval – The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Return type

int

Returns

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

schrodinger.application.matsci.amorphous.get_other_item(two_list, item)¶

In a two item list, return the item that isn’t the one passed in

Parameters

two_list (list) – A list two items long
item – One of the items from two_list

Returns

The item in two_list that is not the one passed in

schrodinger.application.matsci.amorphous.propagate_chain_data_from_atom(struct, chain_atom)¶

Set the chain data for all atoms in struct to the same data as found on atom

Parameters

struct (schrodinger.structure.Structure) – The structure to set atom properties on
chain_atom (schrodinger.structure._StructureAtom) – The atom object to take the chain information from. Might not be from the same structure object as struct

schrodinger.application.matsci.amorphous.get_random_nonzero_to_one()¶

Get a random float: 0 > x >= 1

Return type: float
Returns: A floating point number in the range (0, 1]

class schrodinger.application.matsci.amorphous.TorsionAngler(options, minimum_steps=5, max_stepsize=15.0)¶

Bases: object

Class to handle cycling a structure though a series of torsion values

__init__(options, minimum_steps=5, max_stepsize=15.0)¶

Create a TorsionAngler object

Parameters

options (argparse.Namespace) – Object with dihedral_min and dihedral_max properties that describe the minimum and maximum allowed dihedral angles
minimum_steps – The minimum steps to take. The actual number of steps may be larger if the allowed range of torsions is greather than max_stepsize*minimum_steps.
max_stepsize (float) – The largest number of degrees to move the torsion per step.

setData(struct, torsion_atoms)¶

Set the structure to operate on and the 4 atoms involved in the torsion

Parameters

struct (schrodinger.structure.Structure) – The struct containing the torsion to rotate
torsion_atoms (list) – A four int list, each int is the atom index of an atom in the torsion, in the order A-B-C-D, where B-C is the bond that rotates when the torsion changes.

getTorsionValueInRange()¶

Get a value for the torsion that falls within the specified range. The user may have supplied 150-210, but the measured value might be -170 instead of 190. Convert the measured value to fall within the range.

Return type: float
Returns: The torsion value converted to fall within the range specified for the min/max of the torsion values.

rotomers()¶

A generator for structures that step the torsion through the desired values.

Return type: schrodinger.structure.Structure
Returns: Each yield gives the structure with the specified torsion marched through the specified values.

incrementTorsionValue()¶: Sets the torsion property to the next value to try for a dihedral as we rotate it through its allowed range.

exception schrodinger.application.matsci.amorphous.MoietyError¶

Bases: Exception

Raised if there is an error in creating a Moiety subclass object

__init__(*args, **kwargs)¶

args¶

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

exception schrodinger.application.matsci.amorphous.InitiationError¶

Bases: Exception

Raised if there is an error in initiating the amorphous cell.

__init__(*args, **kwargs)¶

args¶

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

class schrodinger.application.matsci.amorphous.BaseMoiety(struct, markers=None, name=None)¶

Bases: object

Base class for all polymer units - initiator, terminator, cascader, monomers

bond_length_cache = {}¶

RX_PROP = 'i_matsci_rx'¶

COUPLER_AT_ORIGIN = True¶

__init__(struct, markers=None, name=None)¶

Create a BaseMoiety object

Parameters

struct (schrodinger.structure.Structure) – The structure of this Moiety
markers (list) – A list of the indexes of the Rx atoms. If not supplied, information will be read from the structure properties

findAttachedAtomIndex(mark_index, prop=None, propval=True)¶

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters

mark_index (int) – The index of the atom that we want to find an atom attached to.
prop (str) – An atom property name
propval – The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Return type

int

Returns

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

moveHeadToOrigin()¶: Move the structure so that the head atom is at the origin

alignToVector(struct, current_vector, vector)¶

Rotate the structure so that the current_vector is aligned to a new vector

Parameters

struct (schrodinger.structure.Structure) – The structure to rotate. The coordinates of this structure will be modified by this method
current_vector (list) – The current vector that will be aligned to the new vector
vector (list) – The new vector that current_vector should be aligned to

Returns

There is no return value, the structure is modified directly

Return type

schrodinger.structure.Structure

Raises

ValueError – If either vector has zero magnitude

getStructureForCoupling(orientation, location=None, vector=None, remove_marker=True, residue_number=None, mark_bond=False)¶

Get the appropriate structure to couple to the existing unit

Parameters

orientation (str) – Should be the HEADFIRST or TAILFIRST constant, indicates which end of the moiety will bind
location (list) – XYZ coordinates that the coupling atom (head or tail depending on orientation) should be moved to (moving the rest of this moiety with it)
vector (list) – The vector that the coupler-coupling marker vector should be aligned to
remove_marker (bool) – Whether the marker atom should be removed.
residue_number (int or None) – If not None, the resnum property of every atom in the returned structure will be set to this value and the residue name will be assigned.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

(schrodinger.structure.Structure, AttachementAtoms)

Returns

A copy of the structure of this moiety rotated and translated as requested so that it can bind in the specified orientation. An AttachedAtoms tuple that gives the coupler, grower and marker indexes for this structure.

markHeadTailLabels(grower, coupler)¶

Mark the atom unique label based on element, monomer lettter, and ‘Head or Tail’ orientation.

Parameters

grower ('structure.Structure.Atom') – the atom connecting chain
coupler ('structure.Structure.Atom') – the atom waiting for other coming monomer

getBondLength(atom1, atom2, cg_bond_factor=1)¶

Get the desired bond length between the grower atom of the existing unit and the coupling atom of this moiety

Parameters

atom1 (_StructureAtom) – One of the atoms to form a bond in between.
atom2 (_StructureAtom) – The other atoms to form a bond in between.
cg_bond_factor (float) – The pre-factor to calcuate the bond length based on the particle radius.

Return type

float

Returns

The desired bond distance

determineCouplerLocation(xyz, vector, bond_length)¶

Figure out the XYZ coordinates where the coupler atom should go

Parameters

xyz (list) – The XYZ coordinates of the grower atom
vector (list) – The desired bond vector for coupling (goes from grower->coupler)
bond_length (float) – the bond length between grower and coupler

Return type

list

Returns

The XYZ coordinates where the coupler atom should be placed

addToChain(chain, grower, grow_marker, orientation, remove_marker=True, set_residue_data=False, propagate_chain_data=False, chain_namer=None, mark_bond=False)¶

Bind this moiety to an existing chain

The grower, grow_marker, coupler and coupler_marker are defined so that the binding occurs like this:

chain-grower coupler_marker

grow_marker coupler-this_moiety

goes to:

chain-grower

coupler-this_moiety

Parameters

chain (schrodinger.structure.Structure) – The existing chain to add this moiety to
grower (int) – The index of the atom in the existing chain that this moiety should bond with
grow_marker (int) – The index of the Rx atom that marks the attachment point - the grower->grow_marker bond vector indicates the desired grower->coupler bond vector.
orientation (str) – Whether this moiety should add head first or tail first. Should be a module HEADFIRST or TAILFIRST constant.
remove_marker (bool) – Whether the chains grower_marker atom should be removed. Set to False if adding multiple moieties and you don’t want existing atom numbers to change during the process.
set_residue_data (bool) – Whether to set the residue number property for all atoms added by this method to 1 greater than the residue number of the grow atom on the passed in chain. If False, no residue numbers will be set. A residue name is also assigned if this value is True.
propagate_chain_data (bool) – Whether to set the chain data for all atoms added by this method to the same chain information as the grow atom on the passed in chain. If False or the grower atom contains no chain information, this will not be done. This parameter is used if the added moiety should have the same chain information as the existing moiety. See also the chain_namer parameter.
chain_namer (function) – A function that should be called with the structure that will be added to chain. The purpose of this function should be to add chain name data to the added structure. Supply this function if the moiety to be added is a full chain. If the moiety to be added is just another monomer, terminator, etc during the building of a single chain, do not supply this function. This parameter is used if the added moiety should have different chain information from the existing moiety, and it is up to the chain_namer function to set that data. See also the propagate_chain_data paramter.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

tuple(AttachmentAtoms, dict)

Returns

First item is the updated attachment atoms with coupler atom, the new grower atom and the new grow marker. Second item is dictionary with updated atom indices after removing markers where keys are atom numbers before deleting, and value for each is the new atom number, or None if that atom was deleted.

markBond(chain, grower, coupler)¶

Mark the directional bond from grower to coupler.

Parameters

chain ('structure.Structure') – the structure whose bond is to be marked
grower (int) – the core atom connecting to the just added monomer
coupler (int) – the just added monomer’s atom connecting to the core

findBackbone2BranchingPoint(exclude_markers)¶

Find the branching point and the shortest path to the nearest atom in backbone_path_indexes. The branching point may have multiple branches connected to, but only one single pair of [backbone atom][branching atom] = [path with ends] is recorded.

Parameters: exclude_markers (list of int) – the atom ids of markers to be excluded

classmethod write(filename, struct, markers, name, classname=None)¶

Write the structure out to a file, tagging it with properties in such a way that the driver will recognize when reading the structure in

Parameters

filename (str) – The path to the file
struct (schrodinger.structure.Structure) – The structure to write
markers (list) – A list of the indexes of the Rx atoms.
name (str) – The name to use for the title of the structure
classname (str) – The chemical class of this moiety. If not supplied, the actual python class name will be used since those are typically the same as the chemical class.

checkRequiredProperties(struct, propexps)¶

Check to see if the structure has the desired properties set on it

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

readFromStructure(struct, propexps=None)¶

Read the data for this moiety from the structure object and check to make sure all the required properties are set

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

findSideGroup()¶: Find and mark the side group atoms. The side group is any heavy atom not part of the backbone and any hydrogen attached to one of those heavy atoms. Note that IUPAC specifically states that a “sidechain” is an oligomer or polymer, while a “side group” is a non-oligomer/polymer. So monomers have side groups, not sidechains.

finalizeSideGroup()¶: Find atoms in backbone (marked as BACKBONE_ATOM_PROP) but not in the shortest path (backbone_path_indexes) and then treat these atoms along with their side groups as the side groups of certain atom in shortest path (backbone_path_indexes)

markBackboneAtom(index)¶

Mark the atom as a backbone atom and make sure that if the atom is in a ring that all atoms in the ring are marked as backbone

Parameters: index (int) – The index of the atom to mark

setAsFragment()¶: Set backbone path and side atoms for Initiator and Terminator. Only the atom connected to R1 group is treated as backbone path; all the rest real atoms are treated as side groups.

findRotatableBonds()¶: Find rotatable bond along the backbone path.

class schrodinger.application.matsci.amorphous.Terminator(struct, markers=None, name=None)¶

Bases: schrodinger.application.matsci.amorphous.BaseMoiety

A unit that terminates a chain

Note that the concept of an “Terminator” can be a bit fungible. It can either be the actual terminator moiety that ends a polymer chain, or it may be an already built chain that will be tacked on to some initiation point.

__init__(struct, markers=None, name=None)¶

Create a Terminator object

Terminators drawn by the user as:: R1-stuff
And stored as:: marker-head-stuff

where marker is the R1 atom, head is the atom it is bound to, and stuff is everything else.

Parameters

struct (schrodinger.structure.Structure) – The structure of this Moiety
markers (list) – A list of the indexes of the Rx atoms
name (str) – The name of this moiety - gets added to each atom as an atom property

findHead()¶: Find and store the index of the head atom

getNextStructure(*args)¶: Get a copy of this structure to add to a chain

getCouplerAtom(*args)¶: Get the coupler (head) atom

getCouplerAndGrower(*args)¶

Get the coupler and grower atoms and markers. The latter is None because Terminators have no grow points

Return type: AttachmentAtoms
Returns: The atoms indexes of the coupler, grower and marker atoms

getPDBName()¶: Get a PDB residue-like name for this moiety

COUPLER_AT_ORIGIN = True¶

RX_PROP = 'i_matsci_rx'¶

addToChain(chain, grower, grow_marker, orientation, remove_marker=True, set_residue_data=False, propagate_chain_data=False, chain_namer=None, mark_bond=False)¶

Bind this moiety to an existing chain

The grower, grow_marker, coupler and coupler_marker are defined so that the binding occurs like this:

chain-grower coupler_marker

grow_marker coupler-this_moiety

goes to:

chain-grower

coupler-this_moiety

Parameters

chain (schrodinger.structure.Structure) – The existing chain to add this moiety to
grower (int) – The index of the atom in the existing chain that this moiety should bond with
grow_marker (int) – The index of the Rx atom that marks the attachment point - the grower->grow_marker bond vector indicates the desired grower->coupler bond vector.
orientation (str) – Whether this moiety should add head first or tail first. Should be a module HEADFIRST or TAILFIRST constant.
remove_marker (bool) – Whether the chains grower_marker atom should be removed. Set to False if adding multiple moieties and you don’t want existing atom numbers to change during the process.
set_residue_data (bool) – Whether to set the residue number property for all atoms added by this method to 1 greater than the residue number of the grow atom on the passed in chain. If False, no residue numbers will be set. A residue name is also assigned if this value is True.
propagate_chain_data (bool) – Whether to set the chain data for all atoms added by this method to the same chain information as the grow atom on the passed in chain. If False or the grower atom contains no chain information, this will not be done. This parameter is used if the added moiety should have the same chain information as the existing moiety. See also the chain_namer parameter.
chain_namer (function) – A function that should be called with the structure that will be added to chain. The purpose of this function should be to add chain name data to the added structure. Supply this function if the moiety to be added is a full chain. If the moiety to be added is just another monomer, terminator, etc during the building of a single chain, do not supply this function. This parameter is used if the added moiety should have different chain information from the existing moiety, and it is up to the chain_namer function to set that data. See also the propagate_chain_data paramter.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

tuple(AttachmentAtoms, dict)

Returns

First item is the updated attachment atoms with coupler atom, the new grower atom and the new grow marker. Second item is dictionary with updated atom indices after removing markers where keys are atom numbers before deleting, and value for each is the new atom number, or None if that atom was deleted.

alignToVector(struct, current_vector, vector)¶

Rotate the structure so that the current_vector is aligned to a new vector

Parameters

struct (schrodinger.structure.Structure) – The structure to rotate. The coordinates of this structure will be modified by this method
current_vector (list) – The current vector that will be aligned to the new vector
vector (list) – The new vector that current_vector should be aligned to

Returns

There is no return value, the structure is modified directly

Return type

schrodinger.structure.Structure

Raises

ValueError – If either vector has zero magnitude

bond_length_cache = {}¶

checkRequiredProperties(struct, propexps)¶

Check to see if the structure has the desired properties set on it

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

determineCouplerLocation(xyz, vector, bond_length)¶

Figure out the XYZ coordinates where the coupler atom should go

Parameters

xyz (list) – The XYZ coordinates of the grower atom
vector (list) – The desired bond vector for coupling (goes from grower->coupler)
bond_length (float) – the bond length between grower and coupler

Return type

list

Returns

The XYZ coordinates where the coupler atom should be placed

finalizeSideGroup()¶: Find atoms in backbone (marked as BACKBONE_ATOM_PROP) but not in the shortest path (backbone_path_indexes) and then treat these atoms along with their side groups as the side groups of certain atom in shortest path (backbone_path_indexes)

findAttachedAtomIndex(mark_index, prop=None, propval=True)¶

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters

mark_index (int) – The index of the atom that we want to find an atom attached to.
prop (str) – An atom property name
propval – The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Return type

int

Returns

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

findBackbone2BranchingPoint(exclude_markers)¶

Find the branching point and the shortest path to the nearest atom in backbone_path_indexes. The branching point may have multiple branches connected to, but only one single pair of [backbone atom][branching atom] = [path with ends] is recorded.

Parameters: exclude_markers (list of int) – the atom ids of markers to be excluded

findRotatableBonds()¶: Find rotatable bond along the backbone path.

findSideGroup()¶: Find and mark the side group atoms. The side group is any heavy atom not part of the backbone and any hydrogen attached to one of those heavy atoms. Note that IUPAC specifically states that a “sidechain” is an oligomer or polymer, while a “side group” is a non-oligomer/polymer. So monomers have side groups, not sidechains.

getBondLength(atom1, atom2, cg_bond_factor=1)¶

Get the desired bond length between the grower atom of the existing unit and the coupling atom of this moiety

Parameters

atom1 (_StructureAtom) – One of the atoms to form a bond in between.
atom2 (_StructureAtom) – The other atoms to form a bond in between.
cg_bond_factor (float) – The pre-factor to calcuate the bond length based on the particle radius.

Return type

float

Returns

The desired bond distance

getStructureForCoupling(orientation, location=None, vector=None, remove_marker=True, residue_number=None, mark_bond=False)¶

Get the appropriate structure to couple to the existing unit

Parameters

orientation (str) – Should be the HEADFIRST or TAILFIRST constant, indicates which end of the moiety will bind
location (list) – XYZ coordinates that the coupling atom (head or tail depending on orientation) should be moved to (moving the rest of this moiety with it)
vector (list) – The vector that the coupler-coupling marker vector should be aligned to
remove_marker (bool) – Whether the marker atom should be removed.
residue_number (int or None) – If not None, the resnum property of every atom in the returned structure will be set to this value and the residue name will be assigned.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

(schrodinger.structure.Structure, AttachementAtoms)

Returns

A copy of the structure of this moiety rotated and translated as requested so that it can bind in the specified orientation. An AttachedAtoms tuple that gives the coupler, grower and marker indexes for this structure.

markBackboneAtom(index)¶

Mark the atom as a backbone atom and make sure that if the atom is in a ring that all atoms in the ring are marked as backbone

Parameters: index (int) – The index of the atom to mark

markBond(chain, grower, coupler)¶

Mark the directional bond from grower to coupler.

Parameters

chain ('structure.Structure') – the structure whose bond is to be marked
grower (int) – the core atom connecting to the just added monomer
coupler (int) – the just added monomer’s atom connecting to the core

markHeadTailLabels(grower, coupler)¶

Mark the atom unique label based on element, monomer lettter, and ‘Head or Tail’ orientation.

Parameters

grower ('structure.Structure.Atom') – the atom connecting chain
coupler ('structure.Structure.Atom') – the atom waiting for other coming monomer

moveHeadToOrigin()¶: Move the structure so that the head atom is at the origin

readFromStructure(struct, propexps=None)¶

Read the data for this moiety from the structure object and check to make sure all the required properties are set

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

setAsFragment()¶: Set backbone path and side atoms for Initiator and Terminator. Only the atom connected to R1 group is treated as backbone path; all the rest real atoms are treated as side groups.

classmethod write(filename, struct, markers, name, classname=None)¶

Write the structure out to a file, tagging it with properties in such a way that the driver will recognize when reading the structure in

Parameters

filename (str) – The path to the file
struct (schrodinger.structure.Structure) – The structure to write
markers (list) – A list of the indexes of the Rx atoms.
name (str) – The name to use for the title of the structure
classname (str) – The chemical class of this moiety. If not supplied, the actual python class name will be used since those are typically the same as the chemical class.

class schrodinger.application.matsci.amorphous.Cascader(*args, **kwargs)¶

Bases: schrodinger.application.matsci.amorphous.Terminator

A group that ends a chain but starts multiple new chains

Cascaders are drawn as:

    R2
    |
R1-stuff-R2

and stored as:

          cascader
              |
marker-head-stuff-cascader

where cascader is an atom property added to the R2 marker atoms

__init__(*args, **kwargs)¶

Create a Terminator object

Terminators drawn by the user as:: R1-stuff
And stored as:: marker-head-stuff

where marker is the R1 atom, head is the atom it is bound to, and stuff is everything else.

Parameters

struct (schrodinger.structure.Structure) – The structure of this Moiety
markers (list) – A list of the indexes of the Rx atoms
name (str) – The name of this moiety - gets added to each atom as an atom property

findBackbone()¶

Find the set of atoms that creates the shortest distance (number of bonds) between the head and each cascade points. These are considered backbone atoms.

Backbone atoms are marked with a backbone atom property.

findHead()¶: Find the head atom, but also mark cascader atoms that will start new points

readFromStructure(struct)¶

Overrides the parent method to add and read Cascader-specific properties.

See the parent class method for documentation

classmethod write(generations, filename, struct, *args)¶

Over-ride the parent class method to add generations as a property to the structure.

Parameters: generations (int) – The number of cascade generations allowed

See the parent class method for documentation

getPDBName()¶: Get a PDB residue-like Name for this moiety

setAsFragment()¶: Prepare Cascader information for in-cell grow.

COUPLER_AT_ORIGIN = True¶

RX_PROP = 'i_matsci_rx'¶

addToChain(chain, grower, grow_marker, orientation, remove_marker=True, set_residue_data=False, propagate_chain_data=False, chain_namer=None, mark_bond=False)¶

Bind this moiety to an existing chain

The grower, grow_marker, coupler and coupler_marker are defined so that the binding occurs like this:

chain-grower coupler_marker

grow_marker coupler-this_moiety

goes to:

chain-grower

coupler-this_moiety

Parameters

chain (schrodinger.structure.Structure) – The existing chain to add this moiety to
grower (int) – The index of the atom in the existing chain that this moiety should bond with
grow_marker (int) – The index of the Rx atom that marks the attachment point - the grower->grow_marker bond vector indicates the desired grower->coupler bond vector.
orientation (str) – Whether this moiety should add head first or tail first. Should be a module HEADFIRST or TAILFIRST constant.
remove_marker (bool) – Whether the chains grower_marker atom should be removed. Set to False if adding multiple moieties and you don’t want existing atom numbers to change during the process.
set_residue_data (bool) – Whether to set the residue number property for all atoms added by this method to 1 greater than the residue number of the grow atom on the passed in chain. If False, no residue numbers will be set. A residue name is also assigned if this value is True.
propagate_chain_data (bool) – Whether to set the chain data for all atoms added by this method to the same chain information as the grow atom on the passed in chain. If False or the grower atom contains no chain information, this will not be done. This parameter is used if the added moiety should have the same chain information as the existing moiety. See also the chain_namer parameter.
chain_namer (function) – A function that should be called with the structure that will be added to chain. The purpose of this function should be to add chain name data to the added structure. Supply this function if the moiety to be added is a full chain. If the moiety to be added is just another monomer, terminator, etc during the building of a single chain, do not supply this function. This parameter is used if the added moiety should have different chain information from the existing moiety, and it is up to the chain_namer function to set that data. See also the propagate_chain_data paramter.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

tuple(AttachmentAtoms, dict)

Returns

First item is the updated attachment atoms with coupler atom, the new grower atom and the new grow marker. Second item is dictionary with updated atom indices after removing markers where keys are atom numbers before deleting, and value for each is the new atom number, or None if that atom was deleted.

alignToVector(struct, current_vector, vector)¶

Rotate the structure so that the current_vector is aligned to a new vector

Parameters

struct (schrodinger.structure.Structure) – The structure to rotate. The coordinates of this structure will be modified by this method
current_vector (list) – The current vector that will be aligned to the new vector
vector (list) – The new vector that current_vector should be aligned to

Returns

There is no return value, the structure is modified directly

Return type

schrodinger.structure.Structure

Raises

ValueError – If either vector has zero magnitude

bond_length_cache = {}¶

checkRequiredProperties(struct, propexps)¶

Check to see if the structure has the desired properties set on it

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

determineCouplerLocation(xyz, vector, bond_length)¶

Figure out the XYZ coordinates where the coupler atom should go

Parameters

xyz (list) – The XYZ coordinates of the grower atom
vector (list) – The desired bond vector for coupling (goes from grower->coupler)
bond_length (float) – the bond length between grower and coupler

Return type

list

Returns

The XYZ coordinates where the coupler atom should be placed

finalizeSideGroup()¶: Find atoms in backbone (marked as BACKBONE_ATOM_PROP) but not in the shortest path (backbone_path_indexes) and then treat these atoms along with their side groups as the side groups of certain atom in shortest path (backbone_path_indexes)

findAttachedAtomIndex(mark_index, prop=None, propval=True)¶

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters

mark_index (int) – The index of the atom that we want to find an atom attached to.
prop (str) – An atom property name
propval – The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Return type

int

Returns

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

findBackbone2BranchingPoint(exclude_markers)¶

Find the branching point and the shortest path to the nearest atom in backbone_path_indexes. The branching point may have multiple branches connected to, but only one single pair of [backbone atom][branching atom] = [path with ends] is recorded.

Parameters: exclude_markers (list of int) – the atom ids of markers to be excluded

findRotatableBonds()¶: Find rotatable bond along the backbone path.

findSideGroup()¶: Find and mark the side group atoms. The side group is any heavy atom not part of the backbone and any hydrogen attached to one of those heavy atoms. Note that IUPAC specifically states that a “sidechain” is an oligomer or polymer, while a “side group” is a non-oligomer/polymer. So monomers have side groups, not sidechains.

getBondLength(atom1, atom2, cg_bond_factor=1)¶

Get the desired bond length between the grower atom of the existing unit and the coupling atom of this moiety

Parameters

atom1 (_StructureAtom) – One of the atoms to form a bond in between.
atom2 (_StructureAtom) – The other atoms to form a bond in between.
cg_bond_factor (float) – The pre-factor to calcuate the bond length based on the particle radius.

Return type

float

Returns

The desired bond distance

getCouplerAndGrower(*args)¶

Get the coupler and grower atoms and markers. The latter is None because Terminators have no grow points

Return type: AttachmentAtoms
Returns: The atoms indexes of the coupler, grower and marker atoms

getCouplerAtom(*args)¶: Get the coupler (head) atom

getNextStructure(*args)¶: Get a copy of this structure to add to a chain

getStructureForCoupling(orientation, location=None, vector=None, remove_marker=True, residue_number=None, mark_bond=False)¶

Get the appropriate structure to couple to the existing unit

Parameters

orientation (str) – Should be the HEADFIRST or TAILFIRST constant, indicates which end of the moiety will bind
location (list) – XYZ coordinates that the coupling atom (head or tail depending on orientation) should be moved to (moving the rest of this moiety with it)
vector (list) – The vector that the coupler-coupling marker vector should be aligned to
remove_marker (bool) – Whether the marker atom should be removed.
residue_number (int or None) – If not None, the resnum property of every atom in the returned structure will be set to this value and the residue name will be assigned.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

(schrodinger.structure.Structure, AttachementAtoms)

Returns

A copy of the structure of this moiety rotated and translated as requested so that it can bind in the specified orientation. An AttachedAtoms tuple that gives the coupler, grower and marker indexes for this structure.

markBackboneAtom(index)¶

Mark the atom as a backbone atom and make sure that if the atom is in a ring that all atoms in the ring are marked as backbone

Parameters: index (int) – The index of the atom to mark

markBond(chain, grower, coupler)¶

Mark the directional bond from grower to coupler.

Parameters

chain ('structure.Structure') – the structure whose bond is to be marked
grower (int) – the core atom connecting to the just added monomer
coupler (int) – the just added monomer’s atom connecting to the core

markHeadTailLabels(grower, coupler)¶

Mark the atom unique label based on element, monomer lettter, and ‘Head or Tail’ orientation.

Parameters

grower ('structure.Structure.Atom') – the atom connecting chain
coupler ('structure.Structure.Atom') – the atom waiting for other coming monomer

moveHeadToOrigin()¶: Move the structure so that the head atom is at the origin

class schrodinger.application.matsci.amorphous.Initiator(*args, **kwargs)¶

Bases: schrodinger.application.matsci.amorphous.BaseMoiety

A group that starts the whole polymer off - can have multiple grow points, which means that multiple chains will radiate from this group (a dendrimer).

Note that the concept of an “Initiator” can be a bit fungible. It can either be the actual intiator moiety that starts the whole polymer, or it may be a partially built polymer that still needs additional chains added to it.

__init__(*args, **kwargs)¶

Overrides the parent init method to allow the parial_polymer keyword parameter.

Parameters: partial_polymer (bool) – If True, this Initiator is actually a partially built polymer that is going to just act like an initiator.

completePolymer(chain_terminator, chain_namer, clash_fixer)¶

Tack on an existing chain to each grow point

Parameters

chain_terminator (Terminator) – A Terminator object that stores the existing chain to add
chain_namer (function) – A function that should be called on each chain that will be added to the existing polymer. The purpose of this function should be to add chain name data to the added structure.
clash_fixer (function) – A function to call on the polymer when any new chain is added in order to fix any clashes caused by the new chain

fillBranchPoints(chain_terminator, chain_branch_points, chain_namer, clash_fixer)¶

Tack on an existing chain to each of our branch points - each point has a percent chance of getting a chain added to it as long as its generation is less than the generation limit

Parameters

chain_terminator (Terminator) – A Terminator object that stores the existing chain to add
chain_branch_points (list) – A list of atom indexes in the chain_terminator structure that are branch points
chain_namer (function) – A function that should be called on each chain that will be added to the existing polymer. The purpose of this function should be to add chain name data to the added structure.
clash_fixer (function) – A function to call on the polymer when any new chain is added in order to fix any clashes caused by the new chain

Return type

(schrodinger.structure.Structure, int)

Returns

The new polymer structure with additional branching, plus the number of new branches that were added

getPDBName()¶: Get a PDB residue-like Name for this moiety

COUPLER_AT_ORIGIN = True¶

RX_PROP = 'i_matsci_rx'¶

addToChain(chain, grower, grow_marker, orientation, remove_marker=True, set_residue_data=False, propagate_chain_data=False, chain_namer=None, mark_bond=False)¶

Bind this moiety to an existing chain

The grower, grow_marker, coupler and coupler_marker are defined so that the binding occurs like this:

chain-grower coupler_marker

grow_marker coupler-this_moiety

goes to:

chain-grower

coupler-this_moiety

Parameters

chain (schrodinger.structure.Structure) – The existing chain to add this moiety to
grower (int) – The index of the atom in the existing chain that this moiety should bond with
grow_marker (int) – The index of the Rx atom that marks the attachment point - the grower->grow_marker bond vector indicates the desired grower->coupler bond vector.
orientation (str) – Whether this moiety should add head first or tail first. Should be a module HEADFIRST or TAILFIRST constant.
remove_marker (bool) – Whether the chains grower_marker atom should be removed. Set to False if adding multiple moieties and you don’t want existing atom numbers to change during the process.
set_residue_data (bool) – Whether to set the residue number property for all atoms added by this method to 1 greater than the residue number of the grow atom on the passed in chain. If False, no residue numbers will be set. A residue name is also assigned if this value is True.
propagate_chain_data (bool) – Whether to set the chain data for all atoms added by this method to the same chain information as the grow atom on the passed in chain. If False or the grower atom contains no chain information, this will not be done. This parameter is used if the added moiety should have the same chain information as the existing moiety. See also the chain_namer parameter.
chain_namer (function) – A function that should be called with the structure that will be added to chain. The purpose of this function should be to add chain name data to the added structure. Supply this function if the moiety to be added is a full chain. If the moiety to be added is just another monomer, terminator, etc during the building of a single chain, do not supply this function. This parameter is used if the added moiety should have different chain information from the existing moiety, and it is up to the chain_namer function to set that data. See also the propagate_chain_data paramter.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

tuple(AttachmentAtoms, dict)

Returns

First item is the updated attachment atoms with coupler atom, the new grower atom and the new grow marker. Second item is dictionary with updated atom indices after removing markers where keys are atom numbers before deleting, and value for each is the new atom number, or None if that atom was deleted.

alignToVector(struct, current_vector, vector)¶

Rotate the structure so that the current_vector is aligned to a new vector

Parameters

struct (schrodinger.structure.Structure) – The structure to rotate. The coordinates of this structure will be modified by this method
current_vector (list) – The current vector that will be aligned to the new vector
vector (list) – The new vector that current_vector should be aligned to

Returns

There is no return value, the structure is modified directly

Return type

schrodinger.structure.Structure

Raises

ValueError – If either vector has zero magnitude

bond_length_cache = {}¶

checkRequiredProperties(struct, propexps)¶

Check to see if the structure has the desired properties set on it

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

determineCouplerLocation(xyz, vector, bond_length)¶

Figure out the XYZ coordinates where the coupler atom should go

Parameters

xyz (list) – The XYZ coordinates of the grower atom
vector (list) – The desired bond vector for coupling (goes from grower->coupler)
bond_length (float) – the bond length between grower and coupler

Return type

list

Returns

The XYZ coordinates where the coupler atom should be placed

finalizeSideGroup()¶: Find atoms in backbone (marked as BACKBONE_ATOM_PROP) but not in the shortest path (backbone_path_indexes) and then treat these atoms along with their side groups as the side groups of certain atom in shortest path (backbone_path_indexes)

findAttachedAtomIndex(mark_index, prop=None, propval=True)¶

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters

mark_index (int) – The index of the atom that we want to find an atom attached to.
prop (str) – An atom property name
propval – The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Return type

int

Returns

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

findBackbone2BranchingPoint(exclude_markers)¶

Find the branching point and the shortest path to the nearest atom in backbone_path_indexes. The branching point may have multiple branches connected to, but only one single pair of [backbone atom][branching atom] = [path with ends] is recorded.

Parameters: exclude_markers (list of int) – the atom ids of markers to be excluded

findRotatableBonds()¶: Find rotatable bond along the backbone path.

findSideGroup()¶: Find and mark the side group atoms. The side group is any heavy atom not part of the backbone and any hydrogen attached to one of those heavy atoms. Note that IUPAC specifically states that a “sidechain” is an oligomer or polymer, while a “side group” is a non-oligomer/polymer. So monomers have side groups, not sidechains.

getBondLength(atom1, atom2, cg_bond_factor=1)¶

Get the desired bond length between the grower atom of the existing unit and the coupling atom of this moiety

Parameters

atom1 (_StructureAtom) – One of the atoms to form a bond in between.
atom2 (_StructureAtom) – The other atoms to form a bond in between.
cg_bond_factor (float) – The pre-factor to calcuate the bond length based on the particle radius.

Return type

float

Returns

The desired bond distance

getStructureForCoupling(orientation, location=None, vector=None, remove_marker=True, residue_number=None, mark_bond=False)¶

Get the appropriate structure to couple to the existing unit

Parameters

orientation (str) – Should be the HEADFIRST or TAILFIRST constant, indicates which end of the moiety will bind
location (list) – XYZ coordinates that the coupling atom (head or tail depending on orientation) should be moved to (moving the rest of this moiety with it)
vector (list) – The vector that the coupler-coupling marker vector should be aligned to
remove_marker (bool) – Whether the marker atom should be removed.
residue_number (int or None) – If not None, the resnum property of every atom in the returned structure will be set to this value and the residue name will be assigned.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

(schrodinger.structure.Structure, AttachementAtoms)

Returns

A copy of the structure of this moiety rotated and translated as requested so that it can bind in the specified orientation. An AttachedAtoms tuple that gives the coupler, grower and marker indexes for this structure.

markBackboneAtom(index)¶

Mark the atom as a backbone atom and make sure that if the atom is in a ring that all atoms in the ring are marked as backbone

Parameters: index (int) – The index of the atom to mark

markBond(chain, grower, coupler)¶

Mark the directional bond from grower to coupler.

Parameters

chain ('structure.Structure') – the structure whose bond is to be marked
grower (int) – the core atom connecting to the just added monomer
coupler (int) – the just added monomer’s atom connecting to the core

markHeadTailLabels(grower, coupler)¶

Mark the atom unique label based on element, monomer lettter, and ‘Head or Tail’ orientation.

Parameters

grower ('structure.Structure.Atom') – the atom connecting chain
coupler ('structure.Structure.Atom') – the atom waiting for other coming monomer

moveHeadToOrigin()¶: Move the structure so that the head atom is at the origin

readFromStructure(struct, propexps=None)¶

Read the data for this moiety from the structure object and check to make sure all the required properties are set

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

setAsFragment()¶: Set backbone path and side atoms for Initiator and Terminator. Only the atom connected to R1 group is treated as backbone path; all the rest real atoms are treated as side groups.

classmethod write(filename, struct, markers, name, classname=None)¶

Write the structure out to a file, tagging it with properties in such a way that the driver will recognize when reading the structure in

Parameters

filename (str) – The path to the file
struct (schrodinger.structure.Structure) – The structure to write
markers (list) – A list of the indexes of the Rx atoms.
name (str) – The name to use for the title of the structure
classname (str) – The chemical class of this moiety. If not supplied, the actual python class name will be used since those are typically the same as the chemical class.

class schrodinger.application.matsci.amorphous.Monomer(struct)¶

Bases: schrodinger.application.matsci.amorphous.BaseMoiety

The repeating unit that makes up the polymer chain

__init__(struct)¶

Create a Monomer object

Monomers drawn by the user as:: R1-stuff-R2
And stored as:: marker1-head-stuff-tail-marker2

where marker1 is the R1 atom, head is the atom it is bound to, marker2 is the R2 atom and tail is the atom it is bound to, and stuff is everything else.

setAllTransBackbone()¶: Set all the backbone dihedrals to 180

hasChirality()¶

Check if this monomer has a chiral backbone

Return type: bool
Returns: Whether the backbone has a chiral atom

findHeadTailBranch()¶: Find and mark the head, tail and any branching atoms

findBackbone()¶

Find the set of atoms that creates the shortest distance (number of bonds) between the head and tail atoms. This is the monomer backbone.

Backbone atoms are marked with a backbone atom property

findRingSideGroup(struct, terminator_indexes, root_index)¶

Return a list of atoms bound to root_index (and recursively all atoms bound to those atoms, ad infinitum). terminator_indexes is a set of atoms that terminate the group - when a terminator atom is encountered, the group stops growing in that direction. Unlike Structure.getMovingAtoms or buildcomplex.find_atoms_to_remove, this method gracefully handles cases where terminator atoms and group atoms share the same ring. Imagine naphthalene:

If root_index=6 and terminator_indexes={1}, all other atoms will become part of the same group as 6 - because there is a path all the way around the outer ring that bypasses 1 going clockwise from 6.

If root_index=6 and terminator_indexes={1,2}, then only atoms 6, 5, 4, 3 will be members of the group, because both atoms 1 and 2 terminate the group.

root_index is always part of the group

Parameters

struct (schrodinger.structure.Structure) – The structure to use
terminator_indexes (set of int) – The indexes of the atoms that terminate the group.
root_index (int) – The index of the first atom in the group. All neighbors of this atom that are not terminator atoms will be added to the list.

Return type

list

Returns

A list of all atoms recursively bound to the root atom, including root_index itself but not including any atom in terminator_indexes

alignOnXAxis()¶: Align the monomer so the head is at the origin and the backbone is aligned to the +X axis

flipTailFirst()¶: Flip the structure so the tail is on the origin and the backbone is aligned to the +X axis

setDirecional()¶: Set whether the monomer has directional properties.

setupTacticity()¶: Store both R and S structures for the monomer so we don’t have to keep inverting the chirality when needed. This takes a miniscule amount of effort, since it is only done once per monomer type

getNextStructure(orientation)¶

Get the next monomer structure with the given orientation. “Next” in this case takes into account the chirality of the previous structure - for syntactic polymers, the monomers alternate chirality.

Parameters: orientation (str) – HEADFIRST or TAILFIRST constants
Return type: schrodinger.structure.Structure
Returns: The next structure to use for this monomer

getCouplerAndGrower(orientation)¶

Get the coupler, coupler_marker, grower and grow_marker atoms for this monomer

Parameters: orientation (str) – HEADFIRST or TAILFIRST constants
Return type: AttachmentAtoms
Returns: The atoms indexes of the coupler, grower and marker atoms. Which one is the head and which is the tail depends on orientation.

getCouplerAtom(orientation)¶

Get the coupler atom.

Parameters: orientation (str) – HEADFIRST or TAILFIRST constants
Return type: _StructureAtom
Returns: The coupler atom Whether this is the head and or the tail depends on orientation.

isBrancher()¶

Is this monomer a braching monomer?

Return type: bool
Returns: Whether this monomer is a branching monomer

isLadder()¶

Is this monomer a braching monomer?

Return type: bool
Returns: Whether this monomer is a branching monomer

static addPropsToStructure(struct, letter, markers, name, tacticity, branching_percent, branching_max_gen, all_trans)¶

Add properties to the structure that the driver will need as input

Parameters

struct (schrodinger.structure.Structure) – The structure to add the properties to
letter (str) – The one-character code for this monomer
markers (list of int) – Atom indexes of the marker atoms
name (str) – The title to use
tacticity (str) – One of the TACTICITY module constants specifying the tacticity for this monomer
branching_percent (float) – The % chance to branch for this monomer
branching_max_gen (int) – The maximum branching generations for this monomer
all_trans (bool) – Whether the intra-monomer backbone dihedrals should be all set to 180.

classmethod write(filename, struct, *args)¶

Write out the structure

Parameters

filename (str) – The path to the file
struct (schrodinger.structure.Structure) – The structure to write out

See the addPropsToStructure method for additional argument documentation

readFromStructure(struct)¶

Overrides the parent method to add and read Monomer-specific properties.

See the parent class method for documentation

getPDBName()¶: Get a PDB residue-like Name for this moiety

setAsFragment()¶: Prepare monomer information for in-cell grow.

breakTemplatePolymer()¶

Copy the original moieties to tmp_moieties and break the monomers into small new monomers according to rotatable bonds in side group.

Return type: list of {Monomer}
Returns: the small monomer moieties that replace the old large one

findBondsToBreak()¶

Search the side groups of all backbone atoms and find the ‘first neighbor’ rotatable bonds.

Return type: list of tuple
Returns: ‘first neighbor’ rotable bonds in side groups for all backbone atoms

stripSideStructs(struct_copy, pdbres)¶

Strip the sub structures in side groups and form new monomers from these sub structures.

Parameters

struct_copy (schrodinger.structure.Structure) – the structure copy with ‘first neighbor’ rotatable bonds deleted.
pdbres (str) – the name of the residue to strip side structs from

getNewResidueName(is_finished_moiety)¶

Generate the residue name for new sub structure.

Parameters: is_finished_moiety (bool) – whether the new sub structure contains the backbone of the parent monomer
Return type: str
Returns: residue name for new sub structure

getFirstTmpResname()¶

The resname of the first temporary moiety in self.tmp_moieties list.

Parameters: resname (str) – residue name of a moiety

updateTemplatePolymerResidue(struct, pdbres, resname)¶

Update the residue number and name for the atoms in template polymer for the newly added residue.

Parameters

struct (schrodinger.structure.Structure) – the new sub struct to form new monomer
pdbres (str) – name of the parent residue
resname (str) – residue name of the new sub struct

getMonosaccharideType()¶

Get the monosaccharide type for this monomer, if any

Return type: str
Returns: The monosaccharide type, or None if the monomer is not a monosaccharide

COUPLER_AT_ORIGIN = True¶

RX_PROP = 'i_matsci_rx'¶

addToChain(chain, grower, grow_marker, orientation, remove_marker=True, set_residue_data=False, propagate_chain_data=False, chain_namer=None, mark_bond=False)¶

Bind this moiety to an existing chain

The grower, grow_marker, coupler and coupler_marker are defined so that the binding occurs like this:

chain-grower coupler_marker

grow_marker coupler-this_moiety

goes to:

chain-grower

coupler-this_moiety

Parameters

chain (schrodinger.structure.Structure) – The existing chain to add this moiety to
grower (int) – The index of the atom in the existing chain that this moiety should bond with
grow_marker (int) – The index of the Rx atom that marks the attachment point - the grower->grow_marker bond vector indicates the desired grower->coupler bond vector.
orientation (str) – Whether this moiety should add head first or tail first. Should be a module HEADFIRST or TAILFIRST constant.
remove_marker (bool) – Whether the chains grower_marker atom should be removed. Set to False if adding multiple moieties and you don’t want existing atom numbers to change during the process.
set_residue_data (bool) – Whether to set the residue number property for all atoms added by this method to 1 greater than the residue number of the grow atom on the passed in chain. If False, no residue numbers will be set. A residue name is also assigned if this value is True.
propagate_chain_data (bool) – Whether to set the chain data for all atoms added by this method to the same chain information as the grow atom on the passed in chain. If False or the grower atom contains no chain information, this will not be done. This parameter is used if the added moiety should have the same chain information as the existing moiety. See also the chain_namer parameter.
chain_namer (function) – A function that should be called with the structure that will be added to chain. The purpose of this function should be to add chain name data to the added structure. Supply this function if the moiety to be added is a full chain. If the moiety to be added is just another monomer, terminator, etc during the building of a single chain, do not supply this function. This parameter is used if the added moiety should have different chain information from the existing moiety, and it is up to the chain_namer function to set that data. See also the propagate_chain_data paramter.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

tuple(AttachmentAtoms, dict)

Returns

First item is the updated attachment atoms with coupler atom, the new grower atom and the new grow marker. Second item is dictionary with updated atom indices after removing markers where keys are atom numbers before deleting, and value for each is the new atom number, or None if that atom was deleted.

alignToVector(struct, current_vector, vector)¶

Rotate the structure so that the current_vector is aligned to a new vector

Parameters

struct (schrodinger.structure.Structure) – The structure to rotate. The coordinates of this structure will be modified by this method
current_vector (list) – The current vector that will be aligned to the new vector
vector (list) – The new vector that current_vector should be aligned to

Returns

There is no return value, the structure is modified directly

Return type

schrodinger.structure.Structure

Raises

ValueError – If either vector has zero magnitude

bond_length_cache = {}¶

checkRequiredProperties(struct, propexps)¶

Check to see if the structure has the desired properties set on it

Parameters

struct (schrodinger.structure.Structure) – The structure to check
propexps (list of tuple) – (property string, explanation of what the property is) for each structure property to check

determineCouplerLocation(xyz, vector, bond_length)¶

Figure out the XYZ coordinates where the coupler atom should go

Parameters

xyz (list) – The XYZ coordinates of the grower atom
vector (list) – The desired bond vector for coupling (goes from grower->coupler)
bond_length (float) – the bond length between grower and coupler

Return type

list

Returns

The XYZ coordinates where the coupler atom should be placed

finalizeSideGroup()¶: Find atoms in backbone (marked as BACKBONE_ATOM_PROP) but not in the shortest path (backbone_path_indexes) and then treat these atoms along with their side groups as the side groups of certain atom in shortest path (backbone_path_indexes)

findAttachedAtomIndex(mark_index, prop=None, propval=True)¶

Find the index of the atom attached to the atom with the given index, optionally setting a property/value on that atom

Parameters

mark_index (int) – The index of the atom that we want to find an atom attached to.
prop (str) – An atom property name
propval – The value to set prop to on the found attached atom. The type of this object depends on the type of property being set

Return type

int

Returns

The index of an atom attached to the mark_index atom. If more than one atom is attached to mark_index atom, the first one is returned.

findBackbone2BranchingPoint(exclude_markers)¶

Find the branching point and the shortest path to the nearest atom in backbone_path_indexes. The branching point may have multiple branches connected to, but only one single pair of [backbone atom][branching atom] = [path with ends] is recorded.

Parameters: exclude_markers (list of int) – the atom ids of markers to be excluded

findRotatableBonds()¶: Find rotatable bond along the backbone path.

findSideGroup()¶: Find and mark the side group atoms. The side group is any heavy atom not part of the backbone and any hydrogen attached to one of those heavy atoms. Note that IUPAC specifically states that a “sidechain” is an oligomer or polymer, while a “side group” is a non-oligomer/polymer. So monomers have side groups, not sidechains.

getBondLength(atom1, atom2, cg_bond_factor=1)¶

Get the desired bond length between the grower atom of the existing unit and the coupling atom of this moiety

Parameters

atom1 (_StructureAtom) – One of the atoms to form a bond in between.
atom2 (_StructureAtom) – The other atoms to form a bond in between.
cg_bond_factor (float) – The pre-factor to calcuate the bond length based on the particle radius.

Return type

float

Returns

The desired bond distance

getStructureForCoupling(orientation, location=None, vector=None, remove_marker=True, residue_number=None, mark_bond=False)¶

Get the appropriate structure to couple to the existing unit

Parameters

orientation (str) – Should be the HEADFIRST or TAILFIRST constant, indicates which end of the moiety will bind
location (list) – XYZ coordinates that the coupling atom (head or tail depending on orientation) should be moved to (moving the rest of this moiety with it)
vector (list) – The vector that the coupler-coupling marker vector should be aligned to
remove_marker (bool) – Whether the marker atom should be removed.
residue_number (int or None) – If not None, the resnum property of every atom in the returned structure will be set to this value and the residue name will be assigned.
mark_bond (bool) – If True, the created bond between two monomers is marked

Return type

(schrodinger.structure.Structure, AttachementAtoms)

Returns

A copy of the structure of this moiety rotated and translated as requested so that it can bind in the specified orientation. An AttachedAtoms tuple that gives the coupler, grower and marker indexes for this structure.

markBackboneAtom(index)¶

Mark the atom as a backbone atom and make sure that if the atom is in a ring that all atoms in the ring are marked as backbone

Parameters: index (int) – The index of the atom to mark

markBond(chain, grower, coupler)¶

Mark the directional bond from grower to coupler.

Parameters

chain ('structure.Structure') – the structure whose bond is to be marked
grower (int) – the core atom connecting to the just added monomer
coupler (int) – the just added monomer’s atom connecting to the core

markHeadTailLabels(grower, coupler)¶

Mark the atom unique label based on element, monomer lettter, and ‘Head or Tail’ orientation.

Parameters

grower ('structure.Structure.Atom') – the atom connecting chain
coupler ('structure.Structure.Atom') – the atom waiting for other coming monomer

moveHeadToOrigin()¶: Move the structure so that the head atom is at the origin

schrodinger.application.matsci.amorphous.remove_stale_props(st)¶

Remove stale properties from the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure from which to remove the stale properties

class schrodinger.application.matsci.amorphous.Moieties(filename, structs=None, one_letter=True, simple=False, monomer_class=<class 'schrodinger.application.matsci.amorphous.Monomer'>)¶

Bases: object

A holder and manager for the various moieties that make up the polymer

__init__(filename, structs=None, one_letter=True, simple=False, monomer_class=<class 'schrodinger.application.matsci.amorphous.Monomer'>)¶

Create a Moieties object

Parameters

filename (str) – The path to the file that holds the moiety structures
structs (list) – List of structure moiety
one_letter (If True, the monomer letter must a one letter code) – bool
simple (bool) – If True, use the simplified input rules - initiator/terminator need not be specified, structures not marked with MOIETY_PROP are considered monomers, etc.
monomer_class (Monomer) – The class to use for monomers

handleSimpleInput(untyped_monomers)¶

Fill out any required moiety information that was not supplied due to the simplified input format

Parameters: untyped_monomers (list) – Structures that were not typed in the input file so need to have monomer codes assigned to them.

findSimpleHeadTailMarkers(struct)¶

Find the atoms that mark the head and tail atoms for monomers that did not have these marked on input. The “marker” atom is the one that is bonded to the head or tail and gets deleted when joining monomers.

For now, a simple algorithm is used that finds the longest bond path in the structure and uses that, preferably one terminated with H atoms in case of ties.

Parameters: struct (schrodinger.structure.Structure) – The monomer structure
Return type: list
Returns: First item is the index of the head atom marker, the second item is the index of the tail atom marker

findMarkHeadTailMarkers(struct)¶

Find atoms that were marked via the Mark Head and Tail panel

Parameters: struct (schrodinger.Structure) – The structure to search
Return type: list or None
Returns: First item is the index of the head atom marker, the second item is the index of the tail atom marker. In this case, the “marker” is a hydrogen atom attached to the Head/Tail atom and is the atom that should be deleted when joining monomers. None is returned if no acceptable markers were found.

hasCascader()¶

Has a cascader been defined?

Return type: bool
Returns: Whether a cascader was defined

hasBrancher()¶

Has a brancher been defined?

Return type: bool
Returns: Whether a brancher was defined

hasLadder()¶

Return True if ladder monomers are found.

Return type: bool
Returns: Ladder monomers exist

singleR1Atom(end_moieties=None)¶

Whether each end moiety has one single R1 atom.

Parameters: end_moieties (list) – the end moieties to check against.
Returns: True if each end moiety has one single R1 atom
Return type: bool

hasRings()¶

Do any moieties have rings?

Return type: bool
Returns: Whether any of the moieties have rings

getMonomer(letter)¶

Get the monomer with the given one-letter code

Parameters: letter (str) – The one-letter code for the desired monomer
Return type: Monomer
Returns: The monomer with the given one-letter code

getMoiety(letter)¶

Get the get one single moiety based on ‘INI’, ‘TRM’, ‘CAS’ or monomer one-letter code.

Parameters: letter (str) – The one-letter code for the desired monomer
Return type: Monomer, Initiator, Cascader, or Terminator
Returns: the initiator, cascader, terminat or one nonomer find by the one letter code

getOneLetterCodes()¶

Get all the allowed one-letter codes

Return type: list
Returns: All the defined one-letter codes

checkValidOneLetterCodes(codes)¶

Check that all the codes in the given string are valid

Parameters: codes (str) – A string with a series of one-letter codes
Return type: bool
Returns: Whether all the one-letter codes are associated with a Monomer

checkValidWeights(weights)¶

Validate the given weights

Parameters: weights (dict) – Keys are one-letter codes, values are integer weights for that monomer in a random copolymer
Return type: bool
Returns: Whether all the one-letter codes in weights are valid

getCascadeGenerations()¶

Get the number of cascade generations

Return type: int
Returns: The number of cascade generations (0 if none)

getAllMoietyNames()¶

Get the names of all Moieties - initiator, terminator, monomers, etc.

Return type: list
Returns: A list of all moiety names. Monomers first, then initiator, terminator and cascader (if defined)