You are reading the documentation for version 3.0 of ProMod3.
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Parameters: |
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Returns: |
AddAlignment
(allow_multitemplate=False)¶Commandline options for alignments.
Activate everything needed to load alignments to the argument parser.
Command line arguments are then added in AssembleParser()
and the
input is post processed and checked in Parse()
.
Parameters: | allow_multitemplate (bool ) – enable support for multitemplate alignments |
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Options/arguments added:
-f/--fasta <FILE>
- Target-template alignment in FASTA format.
Target sequence is either named “trg” or “target” or the first
sequence is used. File can be plain or gzipped.-c/--clustal <FILE>
- Target-template alignment in CLUSTAL format.
Target sequence is either named “trg” or “target” or the first
sequence is used. File can be plain or gzipped.-j/--json <OBJECT>|<FILE>
- Alignments provided as JSON
file/object. File can be plain or gzipped.See here for details on the file formats.
Attributes added to the namespace returned by Parse()
:
fasta
- filled with the input of the --fasta
option, a
list
of str
(filenames).clustal
- filled with the input of the --clustal
option, a
list
of str
(filenames).json
- filled with the input of the --json
option, a
list
of str
, where each string may be a filename
or a JSON object string.alignments
- ost.AlignmentList
, same order as given.
First sequence of the alignment is the target sequence, if in doubt,
check for sequence roles TARGET
or TEMPLATE
aln_sources
- list
of str
with the original
source(s) of the alignment: may be filename(s) or JSON strings.Exit codes related to alignment input:
--json
AddFragments
()¶Commandline option for usage of Fragments
Activate everything needed to setup
promod3.modelling.FraggerHandle
objects in the argument parser.
Command line arguments are then added in AssembleParser()
and the
input is post processed and checked in Parse()
.
Options/arguments added:
-r/--use-fragments
- Boolean flag whether to setup fragger handles.Notes:
promod3.loop.StructureDB
.-s/--seqprof <FILE>
), fragments are identified based on BLOSUM62
sequence similarity.Attributes added to the namespace returned by Parse()
:
fragger_handles
- list
of
promod3.modelling.FraggerHandle
, ordered to match the target
sequences.Exit codes related to fragments input:
AddProfile
()¶Commandline options for profiles
Activate everything needed to load profiles to the argument parser.
Command line arguments are then added in AssembleParser()
and the
input is post processed and checked in Parse()
.
Options/arguments added:
-s/--seqprof <FILE>
- Sequence profile in any format readable
by the ost.io.LoadSequenceProfile()
method. Format is chosen by
file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
.pssm.gz. Consider to use
ost.bindings.hhblits.HHblits.A3MToProfile()
if you have a file
in a3m format at hand.Notes:
Attributes added to the namespace returned by Parse()
:
profiles
- list
of ost.seq.ProfileHandle
,
ordered to match the target sequences.Exit codes related to profile input:
AddStructure
(attach_views=False)¶Commandline options for structures.
Activate everything needed to load structures to the argument parser.
Command line arguments are then added in AssembleParser()
and the
input is post processed and checked in Parse()
.
Parameters: | attach_views (bool ) – if True: attach views to alignments. Requires call
to AddAlignment() . Chains for each sequence
are identified based on the sequence name of the
templates in the alignments (see
here for details). |
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Options/arguments added:
-p/--pdb <FILE>
- Structure in PDB format. File can be plain or
gzipped.-e/--entity <FILE>
- Structure in any format readable by the
ost.io.LoadEntity()
method. Format is chosen by file ending.
Recognized File Extensions: .ent, .pdb, .ent.gz, .pdb.gz, .cif, .cif.gz.Notes:
Attributes added to the namespace returned by Parse()
:
pdb
- filled with the input of the --pdb
option, a
list
of str
(filenames).entity
- filled with the input of the --entity
option, a
list
of str
(filenames).structures
- list
of ost.EntityHandle
, same
order as given.structure_sources
- list
of str
with the
original filenames of the structures.Exit codes related to alignment input:
Exit codes if attach_views = True:
AssembleParser
()¶When adding options via the Add*()
methods, call this after you
are done. Everything before just tells the parser that it should
contain those option sets but does not actually add anything.
AssembleParser()
will put everything in place, in the right order
and with the right constraints.
Parse
(args=None)¶Parse an argument string. See Add*()
methods.
Options/arguments added by default: -h/--help
shows usage.
General exit codes:
Parameters: | args (list ) – The argument string. As default sys.argv is used. |
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Returns: | Namespace filled with attributes (see Add*() methods). |
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- Parsing Command Lines