biochemHH

biochemHH is a Python package supporting experimental protein engineering. It contains tools for cloning design, structure analysis, and structural file (GB, CIF) editing.

1. Create a new Python environment

Create a new Python environment (Python version >= 3.12).

2. Install the package

Activate the environment and run the following code:

pip install biochemHH==0.0.6

3. Copy example files to your working directory

Activate the environment, replace C:\biochemHH_work in the first line with your desired working directory, and run the code in Windows CMD. The folder will be created if it does not exist, and the example files will be copied into it.

set "WORKDIR=C:\biochemHH_work"

python -c "import biochemHH,pathlib,shutil; p=pathlib.Path(biochemHH.__file__).parent; d=pathlib.Path(r'%WORKDIR%'); d.mkdir(parents=True,exist_ok=True); [shutil.copy2(f,d/f.name) for n in ('example_input','example_script') for f in (p/n).rglob('*') if f.is_file() and f.suffix.lower() in ('.pdf','.gb','.py','.csv')]; print('Copied all matching files to',d)"

Notes:

• It is recommended to install PyMOL for protein visualization.
• All input/output files will be read from/written to your working directory. Move output files elsewhere after completion to avoid overwriting them.

4. Examples

4.1 Batch-mode cloning design

"""
Six types of variations are supported:
	1-aa substitution, e.g.,    _R13A
	1-aa deletion, e.g.,        _28del
	1-aa insertion, e.g.,       _90~91insE
	multi insertions, e.g.,     _101~102insEAT
	multi deletion, e.g.,       _130~135del
	deletion & insertion, e.g., _140~142delinsAAG'
	Multiple variations can be joined to form a notation for a plasmid.
"""

from biochemHH import GBparser

notations = ['_R13A_28del_90~91insE',       		# the first plasmid
	'_101~102insEAT_130~135del_140~142delinsAAG',   # the second plasmid 
	]

GBparser.cloning_design_wrapper_1(
	base_filename='pUCv2-cat',	
	feature_select='cat',		# a gene is annotated 'cat' in 'pUCv2-cat.gb' file
	notations=notations,
	species='ecoli',
	plasmid_prefix='pL-',
	oligo_prefix='Oz')

A detailed Demonstration_of_batch_mode_cloning_design.pdf and an example input pUCv2-cat.gb have been copied into your working directory in step 3.

4.2 Analyze noncovalent interactions

""" 
To specify a target_string:
	A:      A chain all residues
	P2:     P chain resi 2
	B1~23:  B chain resi 1~23
	These can be joined by space, forming target_string =  "A P2 B1~23"

To specify the chain to analyze against (coi):
	coi = ['A', 'B']    # analyze the target against all residues in chain A and B
	coi = []            # analyze the target against all residues in all chains
"""

from biochemHH import StructureHH

StructureHH.Shell_analyses_II( '8OV6.cif' ,
                               target_string='C501 B52~55',
                               coi=[],
                               exclude_van_der_waals=False,
                               exclude_intrachain_van_der_waals=False,
                               exclude_intrachain_noncovalent_bonds=False,
                               exclude_water=False
                               )

4.3 Structure file (CIF, PDB) editing

"""
If '5AXN.cif' does not already exist in the working directory, either command will automatically download it from RCSB database.
"""

from biochemHH import StructureHH

# ........................................ Duplicate a structure
StructureHH.copy_structure_file('5AXN.cif', new_filename = '5AXNcopy.pdb')


# ........................................ Rename chains
StructureHH.rename_chains('5AXN.cif', initial_chain_id=['A', 'B'], new_chain_id=['C', 'D'], new_filename = '5AXNedit.cif')	# The example rename chain 'A' -> 'C', chain 'B' -> 'D' respectively.


# ........................................ Delete chains
StructureHH.delete_chains('5AXN.cif', chains_to_remove = ['B','P'], new_filename = '5AXNedit.cif')


# ........................................ Edit chain: retain a list of residues
StructureHH.chain_shrinking('5AXN.cif', chain = 'A', resi_to_retain = range(10,200), new_filename='5AXNedit.cif')


# ........................................ Edit chain: remove a list of residues
StructureHH.chain_shrinking('5AXN.cif', chain='A', resi_to_remove = range(10,200), new_filename='5AXNedit.cif')


# ........................................ Duplicate a residue
StructureHH.duplicate_residue( '5AXN.cif', initial_chain_resi = ['A', 304], new_filename='5AXNedit.cif', verbose = True)

# ........................................ Edit residue: re-assign and rename
StructureHH.edit_residue('5AXN.cif', initial_chain_resi = ['A', 304], new_chain_resi = ['L', 1], new_resname = 'LIG', new_filename = '5AXNedit.cif')


# ........................................ Edit residue: remove certain atoms
StructureHH.edit_residue('5AXN.cif', initial_chain_resi = ['A', 304], remove_atoms = ["O2'", "O3'"], new_filename = '5AXNedit.cif')


# ........................................ ATOM to HETATM (some AI tools only consider HETATM as ligand)
StructureHH.atom_to_hetatm('5AXN.cif', chain_id = 'P', new_filename='5AXNedit.cif')