schrodinger.application.msv.gui.custom_family module

exception schrodinger.application.msv.gui.custom_family.MissingAnnotationsError

Bases: Exception

__init__(*args, **kwargs)
args
with_traceback()

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

class schrodinger.application.msv.gui.custom_family.CustomFamily(title: str, aln: schrodinger.protein.alignment.ProteinAlignment, annotation: schrodinger.models.jsonable.CustomAnnotation, file_path: Optional[str] = None)

Bases: tuple

Information about a custom family read from a custom family FASTA file.

Variables

  • title – The name of the custom annotation

  • aln – The reference alignment for the family. If this family contains a custom annotations, it will be set for all residues of all sequences.

  • annotation – Information about the custom annotation. Will be None if the FASTA file didn’t contain any custom annotation values.

  • file_path – file path of the loaded custom fasta

title: str

Alias for field number 0

aln: schrodinger.protein.alignment.ProteinAlignment

Alias for field number 1

annotation: schrodinger.models.jsonable.CustomAnnotation

Alias for field number 2

file_path: str

Alias for field number 3

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

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.

class schrodinger.application.msv.gui.custom_family.CustomFamilyFastaReader

Bases: schrodinger.application.msv.seqio.FastaAlignmentReader

Reads in custom family FASTA files. These files should be formatted as follow:

  • The first line should start with “>Title: ” and specify the family name, e.g. “>Title: My Family Name”. If this line is not given, the filename will be used for the title.

  • The second line should start with “>Annotation:” and contain a comma and arrow (“=>” or “->”) delimited list of annotation descriptions (i.e. tool tip values). E.g. “>Annotation: A => Domain alpha, B => Domain beta”. This information may be split into multiple lines if needed, e.g.

    >Annotation: A => Domain alpha, B => Domain beta"
>Annotation: G => Domain gamma"

  • The third line should include the annotation sequence, properly aligned with the following sequences.

The annotation description and values are required.

The remaining lines of the file should be in standard FASTA format and contain the reference alignment for the family.

Note that the colons after “Title” and “Annotation” are optional and that “Annotations” (with an “s”) will be accepted in place of “Annotation”.

classmethod read(file_name, AlnClass=<class 'schrodinger.protein.alignment.ProteinAlignment'>)

Loads a sequence file in FASTA format, creates sequences and appends them to alignment. Splits sequence name from the FASTA header.

Parameters

  • file_name (str) – name of input FASTA file

  • AlnClass (type) – The class of the alignment object to return

Returns

Read alignment.

Return type

AlnClass

classmethod readFromText(lines, AlnClass=<class 'schrodinger.protein.alignment.ProteinAlignment'>, default_title='Custom Family')

See parent class for method documentation.

Parameters

default_title (str) – The title to use if lines does not contain a “>Title:” line.

classmethod parseSSA(seq)

Parse a SSA sequence into a list of SSA values that can be assigned to residues’ secondary_structure property

Parameters

seq (str) – the “sequence” from the FASTA file which encodes the SSA values

Returns

a list of the SSA values. The SSA values come from schrodinger.structure. Returns None if any of the elements was invalid

Type

list(int) or NoneType

classmethod readFromStringList(strings, AlnClass=<class 'schrodinger.protein.alignment.ProteinAlignment'>)

Return an alignment object created from an iterable of sequence strings

Parameters

  • strings (Iterable of strings) – Sequences as iterable of strings (1D codes)

  • AlnClass (type) – The class of the alignment object to return

Returns

The alignment

Return type

AlnClass