schrodinger.application.bioluminate.protein_interaction.utils module

class schrodinger.application.bioluminate.protein_interaction.utils.Residue(chain, resname, resnum, inscode)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

chain

Alias for field number 0

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.

inscode

Alias for field number 3

resname

Alias for field number 1

resnum

Alias for field number 2

schrodinger.application.bioluminate.protein_interaction.utils.parse_resstr(resstr, resstr_re=re.compile('(?P<chain>[a-zA-Z0-9_]{1})\n    :\n    (?P<resname>.{,4})  # PDB residue names can be any string upto 4 characters\n    \\s\n    (?P<resnum>[0-9]+)\n    (?P<inscode>[A-Z]{1})?\n    ', re.VERBOSE))

Parse a residue string and return a populated Residue object.

Parameters

  • resstr (str) –

    a residue string of the form

    <chain>:<resname> <resnum><inscode>

    e.g.

    A:Gln 123H

  • resstr_re (re.Pattern) – Regular expression pattern to use for parsing. The pattern should contain chain, resname, resnum, inscode groups.

Returns

a residue object populated with information from the string

Return type

Residue

schrodinger.application.bioluminate.protein_interaction.utils.get_structure_residue(st, resstr, resstr_re=re.compile('(?P<chain>[a-zA-Z0-9_]{1})\n    :\n    (?P<resname>.{,4})  # PDB residue names can be any string upto 4 characters\n    \\s\n    (?P<resnum>[0-9]+)\n    (?P<inscode>[A-Z]{1})?\n    ', re.VERBOSE))

Return the matching residue from a structure.

Parameters

  • st (structure.Structure) – a protein structure

  • resstr (str) –

    a residue string of the form

    <chain>:<resname> <resnum><inscode>

    e.g.

    A:Gln 123H

  • resstr_re (re.Pattern) – Regular expression pattern to use for parsing. The pattern should contain chain, resname, resnum, inscode groups.

Returns

a structure residue from st matching resstr

Return type

structure._Residue

schrodinger.application.bioluminate.protein_interaction.utils.get_residue_representation(res)

Return the residue representation. :param res: Residue :type res: structure._Residue or utils.Residue :return: Residue representation. :rtype: str

schrodinger.application.bioluminate.protein_interaction.utils.get_residue_sorting_key(res_str)

Return sort key to use to sort residues. :param res_str: See parse_resstr. :type res_str: str :return: Key to use during sorting. :rtype: tuple(str, int, str)

schrodinger.application.bioluminate.protein_interaction.utils.sort_residue_pair(res1_str, res2_str)

Return sorted residue pair.

Parameters
Returns

Sorted residue pair.

Return type

tuple(str, str)