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 the C:\biochemHH_work in the first line with the path to your working directory, and run the following code in Windows CMD to copy example scripts into your working directory. A working directory folder will be created if it does not exist.

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 given mutation notations

"""
Six types of variations are supported:
    1-aa substitution, e.g.,    R13A or 13A
    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 by '_' to form a notation, e.g., '_13A_28del_90~91insE'
"""

from biochemHH import GBparser

notations = ['_13A_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')

Six types of notations are supported, to be joined A detailed Demonstration_of_batch_mode_cloning_design.pdf and an example input pUCv2-cat.gb is 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

from biochemHH import StructureHH

# ........................................ Duplicate a structure
# The script will download '5AXN.cif' from RCSB database if it does not exist in the working directory
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')