ConsurfDB-client-API 1.0

Python3 client API for ConsurfDB

Description from GitHub readme.md:

Python3 client API for ConsurfDB

Consurf-DB is a web server developed by the group of Prof. Nir Ben-Tal which provides PDB structures with the b-factors remapped to residue conservation scores as determined by their rate4site.

This unofficial Python3 module queries this server and performs several operations.

This was formerly a part of the Venus backend (:octocat: michelanglo-protein), but I (MF) moved it out as it may be useful for others.

PS. Like all APIs, especially the unofficial ones, do not abuse the server...

Usage

Get and parse consurfDB data.

from consurfDB import ConsurfDB
cp = ConsurfDB.from_web('1UBQ', 'A')

The grades file data is in cp.data and can be made into a pandas dataframe: It takes ~1.7 seconds to fetch a grades file off the web. Do simply ignore the unsafe SSL warning (changing ConsurfDB.REQUEST_VERIFY_SETTING to True, will result in failure).

One can also run it from a grades file:

from consurfDB import ConsurfDB
cp = ConsurfDB.from_filename('grades.txt')

Data is in self.data, which is a dict of MET1:A to dict of values. See the type dictionary ResidueDataType for details.

from consurfDB import ResidueDataType
help(ResidueDataType)

One can make a pandas dataframe from it.

grades : pd.DataFrame = cp.to_pandas()

If a residue appears in SEQPOS but no ATOM records are present, they will be like cp.data['___1:A']. The key is the 3LATOM field, this is ATOM numbering, while POS is the SEQPOS numbering. apply_offset_from_swissmodel uses the latter and makes both Uniprot numbering.

Also can add a consurf conservation to a PyRosetta pose in place.

pose : pyrosetta.Pose = ... # noqa
cp.add_bfactor_to_pose(pose)

Or a pymol object

also, if chain number differs, e.g. V in consurf grades file and A in pose:

cp.remap_chains({'B': 'A'})

Likewise with offset.

If the Uniprot id is known, the offset can be taken from Swissmodel

cp.apply_offset_from_swissmodel(uniprot, code, chain)

Potentially support multi-chain operations, but not tested.

cp = ConsurfDB.merge([cp1, cp2, cp3]) # noqa

Dump of attributes and methods:

• Consurf.REQUEST_VERIFY_SETTING
• Consurf.ResidueDataType
• Consurf.add_bfactor_to_pose
• Consurf.add_bfactor_to_pymol
• Consurf.add_bfactor_via_pymol
• Consurf.align
• Consurf.apply_offset_by_alignment
• Consurf.apply_offset_from_swissmodel
• Consurf.assert_reply
• Consurf.fetch
• Consurf.from_filename
• Consurf.from_web
• Consurf.get_color
• Consurf.get_conscore
• Consurf.get_consurf_chain
• Consurf.get_key
• Consurf.get_offset_by_alignment
• Consurf.get_offset_from_swissmodel
• Consurf.get_offset_vector_by_alignment
• Consurf.get_residue_chain
• Consurf.get_residue_index
• Consurf.get_residue_name
• Consurf.get_variety
• Consurf.keys
• Consurf.log
• Consurf.merge
• Consurf.offset_atom
• Consurf.offset_seqpos
• Consurf.parse
• Consurf.read
• Consurf.remap_chains
• Consurf.sequence
• Consurf.to_pandas