schrodinger.application.matsci.msutils module

Utility functions and classes for MatSci workflows.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.msutils.remove_properties(struct, props=None, matches=None, atom_props=None, atom_matches=None)

Remove all the matching structure and atom properties. No error is thrown if the given properties do not actually exist on the structure.

Parameters:
  • props (list) – A list of structure properties to delete
  • matches (list) – Remove all structure properties whose name contains any of these strings
  • atom_props (list) – A list of atom properties to delete
  • atom_matches (list) – Remove all atom properties whose name contains any of these strings
schrodinger.application.matsci.msutils.remove_atom_property(struct, prop)

Delete atom property from all atoms in a structure (structure will be modified).

Parameters:
  • struct (structure.Structure) – Structure object to be modified
  • prop (str) – Atom property to be removed
schrodinger.application.matsci.msutils.has_atom_property(struct, prop)

Check if structure has any atom with the property set.

Parameters:
  • structure.Structure – Input structure
  • str – Property name
Raises:
  • KeyError – If property name doesn’t start with: s_, r_, i_, b_
  • mm.MmException – If unexpected error occurred
Return bool:

True of property is present, False otherwise
schrodinger.application.matsci.msutils.roundup(inp)

Round away from zero (to +/-infinity).

Parameters:inp (float or numpy.array) – value to be rounded
Return type:float or numpy.array
Returns:Rounded value
schrodinger.application.matsci.msutils.getstr(ret)

Convert binary string (or other data) to str.

Parameters:ret (binary_type or any other type convertable to str) – Value to be converted to str
Return type:str
Returns:Value converted to str
schrodinger.application.matsci.msutils.sig_fig_round(value, significant_figure=5)
Parameters:
  • value (float) – change the significant figures of this value
  • significant_figure (int) – significant figure of the displayed value
Return type:

str
Returns:

str representation of a number with proper significant figures
schrodinger.application.matsci.msutils.get_significant_figures(number)

Get significant digits of a number

Parameters:number (float or int or str) – number to find significant digits
Return type:int
Returns:number of significant digits
schrodinger.application.matsci.msutils.set_significant_figures(number, sig_fig)

Set significant digits of a number

Parameters:
  • number (float or int) – number to set significant digits
  • sig_fig (int) – number of significant digits
Return type:

float
Returns:

number with desired significant digits
schrodinger.application.matsci.msutils.get_project_group_hierarchy(st=None, row=None)

Return the project group hierarchy for the given structure or row.

Parameters:
Raises:

ValueError – if there is an issue
Return type:

list
Returns:

the hierarchy (outermost to innermost)
schrodinger.application.matsci.msutils.set_project_group_hierarchy(st, hierarchy, collapsed=False)

Set the project group hierarchy for the given structure.

Parameters:
  • st (schrodinger.structure.Structure) – the structure
  • hierarchy (list) – the hierarchy (outermost to innermost)
  • collapsed (bool) – Whether the group should initially be collapsed
schrodinger.application.matsci.msutils.get_matsci_user_data_dir()

Get the absolute path to the user’s local MatSci data directory for storing custom templates, protocols, etc. Directory is created if it doesn’t exist.

Return type:str
Returns:The absolute path the Materials Science data parent directory
schrodinger.application.matsci.msutils.structure_reader(filename, log=None)

Read structures from a file until the end or the first structure with an error.

Parameters:
  • filename (str) – filename
  • log (function) – Log function, if None, nothing is called
Yield schrodinger.structure.Structure:
 

Next structure in the file
schrodinger.application.matsci.msutils.is_dummy_atom(atom)

Return True if the given atom is a dummy atom.

Parameters:atom (schrodinger.structure._StructureAtom) – the atom
Return type:bool
Returns:return True if the given atom is a dummy atom
schrodinger.application.matsci.msutils.add_or_update_bond_order(ct, atom1, atom2, bond_order)

Create a new bond, or update the existing bond order of this bond.

Return type:schrodinger.structure._Bond
schrodinger.application.matsci.msutils.add_or_update_bond_type(ct, atom1, atom2, bond_type)

Create a new bond, or update the existing bond type of this bond.

Return type:schrodinger.structure._Bond
schrodinger.application.matsci.msutils.polyfit(xdata, ydata, degree)

Fit a polynomial of rang degree to data.

Parameters:
  • xdata (numpy.array) – X data
  • ydata (numpy.array) – Y data
  • degree (int) – Degree of the fitting polynomial
Return type:

numpy.array, float
Returns:

Fitting coefficients, coefficient of determination (R^2)
schrodinger.application.matsci.msutils.trim_str(text, max_len, suffix='...')

Trim the string to approximately max_len. Add a suffix if the string is longer than max_len.

Parameters:
  • text – String to trim
  • max_len (int) – Max length of the string
  • suffix (str) – Suffix to add if the string is to be trimmed
Return str:

Trimmed string
schrodinger.application.matsci.msutils.mmlewis_apply()

Context manager that initializes mm and returns mm.mmlews_apply method.

Yield:mm.mmlewis_apply method.

Example usage:

with msutils.mmlewis_apply() as lewis_apply:
assert lewis_apply(struct) is None
schrodinger.application.matsci.msutils.get_disorder_groups(struct)

Get atoms that have s_cif_disorder_group set and occupancies are not 0 or 1.

Parameters:structure.Structure – Input structure
Return type:dict or None
Returns:Dict with keys disorder group labels, values list of atom indices or None if nothing is present in the structure
schrodinger.application.matsci.msutils.get_atom_ffio_velocity(atom)

Get FFIO atom velocities.

Parameters:atom (structure._StructureAtom) – Input atom
Return numpy.array:
 Array of velocities
schrodinger.application.matsci.msutils.set_atom_ffio_velocity(atom, velocity)

Set FFIO atom velocities.

Parameters:
schrodinger.application.matsci.msutils.get_unique_name(new_name, existing_names)

Add a suffix to new_name to make a unique name if it already exists in existing_names.

Parameters:
  • new_name (str) – The new name
  • existing_names (list) – Existing names
Return type:

str
Returns:

The unique version of new_name
schrodinger.application.matsci.msutils.setting_to_bool(string, empty_is_false=True)

Convert a yes/no/true/false/1/0/on/off type string to a Python boolean

Parameters:
  • string (str) – The string to convert
  • empty_is_false – If the string is empty or None, return False
Return type:

bool
Returns:

True if the string is a “true”-y word (TRUE, true, t, yes, on, 1, etc), False if it is a “false”-y word (FALSE, false, f, no, off, 0).
Raises:
  • ValueError – If the string cannot be interpreted in a True/False manner
  • AttributeError – If something other than a string is passed in
schrodinger.application.matsci.msutils.get_ordered_polymer_backbone(struct, backbone_path, remove_side_chain)

Backbone of a polymer chain should follow H–TH–TH–T format, where backbone starts with head and ends with tail.

Parameters:
  • struct (schrodinger.structure.Structure) – The structure to find backbone atoms in.
  • backbone_path (list) – list of atom indexes in the backbone
  • remove_side_chain (bool) – If true it will remove the side chain atoms from the backbone in the start and end.
Return list:

list of atom indexes in the backbone such that first atom is always a head.
schrodinger.application.matsci.msutils.get_ordered_backbone_atoms(struct)

Return dictionary of backbone atoms for each molecule in the structure.

Parameters:struct (schrodinger.structure.Structure) – The structure to find backbone atoms in.
Return dict(list):
 the key of the dictionary is molecule number and the value is the list of backbone atoms
schrodinger.application.matsci.msutils.flatten(alist, afunc=None)

Flatten the given list into a set.

Parameters:
  • alist (list) – elements contain iterable data
  • afunc (function or None) – function used to extract iterable data from the given list elements or None if there isn’t one
Return type:

set
Returns:

a flattened set of data from the given list