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 ( 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...

Installation

pip install ConsurfDB-client-API

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

Author

This package was written by Matteo Ferla |