PDBParser

Briefs

PDBParser facilitates the conversion between PDB files and Structure objects. It primarily offers two functions: get_structure() for converting a PDB file into a Structure object, and save_structure() for performing the inverse operation.

Input/Output

PDBParser.get_structure()

Input

path

Specifies the file path of the PDB file.

How to obtain

PDB files can be downloaded from the Protein Data Bank or acquired from experimental results.

Output

Structure()

Returns the constructed Structure object.

Tip

PDBParser fixes missing chain identifiers. For example, polymer PDB files generated by AMBER often lack chain IDs.

Arguments

Click to see more details

path

Path to the PDB file. (See PDBParser.get_structure() section)

model

Index of the model to select if the file contains multiple models. The index starts from 0 (default: 0). Assume that “MODEL” tags appear in order in the file.

Determine if there are multiple models by looking for “MODEL {number}” and “ENDMDL” tags in the PDB file, or by using protein visualization tools such as PyMOL or UCSF Chimera.

add_solvent_list

List used to categorize residues, this parameter allows for the inclusion of additional solvent names. For example, add_solvent_list=["DMS", "ACT"]

Solvents are recognized by matching the names in these lists within non-polypeptide chains:

chem.RD_SOLVENT_LIST + add_solvent_list

RD_SOLVENT_LIST includes common water aliases such as HOH and WAT. (RD_SOLVENT_LIST: List[str] = ["HOH", "WAT"])

add_ligand_list

List sed to categorize residues, this parameter adds additional names for ligands. This change will only affect the original RD_NON_LIGAND_LIST.

For example, add_ligand_list=["EDO", "FAD", "NAD"]

Ligands are identified by names not matching those in these lists within non-polypeptide chains:

1. chem.RD_SOLVENT_LIST + add_solvent_list

RD_SOLVENT_LIST includes common water aliases such as HOH and WAT. (RD_SOLVENT_LIST:  List[str] = ["HOH", "WAT"])

2. chem.RD_NON_LIGAND_LIST - add_ligand_list

RD_NON_LIGAND_LIST includes common co-crystallized ligands found in solvents, including CL (CHLORIDE ION), EDO (1,2-ETHANEDIOL), GOL (GLYCEROL), and EOH (ETHANOL). ("RD_NON_LIGAND_LIST: List[str] = ["CL", "EDO", "GOL", "EOH"]")

*Solvent list have higher pirority

remove_trash

Option to remove trash ligands, defined by chem.RD_NON_LIGAND_LIST - add_ligand_list, can be set to either remove_trash=True or remove_trash=False, default value is True.

give_idx_map

Option to return a tuple of (Structure, idx_change_mapper), can be set to either give_idx_map=True or give_idx_map=False, default value is Flase.

The mapping is a dictionary: {(old_chain_id, old_residue_id): (new_chain_id, new_residue_id), ... }

allow_multichain_in_atom

Used for resolving chain id, can be set to either allow_multichain_in_atom=True or allow_multichain_in_atom=False, default value is Flase.

When set to True, it allows multiple chain IDs to appear within the same chain that consists of ATOM records. Although this conflicts with the standard PDB file format definition, it is useful for resolving chain IDs of multi-chain PDB files exported by PyMOL2.

Example Code

• Generate a Structure objects from a simple PDB file

In this example, we use PDBParser to process a single-chain, single-model PDB file. We aim to import the PDB file as a Structure object.

How input is prepared

For PDBParser.get_structure(), need to prepare:

path

The file path of the PDB file. In this example, the PDB file was downloaded from the Protein Data Bank with the ID “8K4Z” and is named "./8k4z.pdb". (See PDBParser.get_structure() section)

add_solvent_list

According to the PDB file, if you want to prevent the chloride ion from being discarded as trash, you can categorize the chloride ion (named “CL” in the PDB file) as a solvent.

add_ligand_list

According to the PDB file, if you want to prevent the chloride ion from being discarded as trash, you can categorize the chloride ion (named “CL” in the PDB file) as a ligand.

from enzy_htp.structure import PDBParser

test_A="./8k4z.pdb"
test_A_struc1 = PDBParser.get_structure(path=test_A,
                                       add_solvent_list=["CL"], #In this way, the CL will not be treated as trash.
                                       remove_trash=True)

test_A_struc2 = PDBParser.get_structure(path=test_A,
                                       add_ligand_list=["CL"], #In this way, the CL will not be treated as trash.
                                       remove_trash=True)

PDBParser.save_structure()

Input

outfile

Path for saving the Structure() object as a string.

How to obtain

Define the save path as a string, e.g., outfile='./save_pro.pdb'.

stru

The Structure() object to be saved.

How to obtain

(See PDBParser.get_structure() section)

Output

str()

Path where the Structure() was saved, returned as a string.

Arguments

Click to see more details

outfile

Path for saving the Structure() object as a string. (See PDBParser.save_structure() section)

stru

The Structure() object to be saved. (See PDBParser.save_structure() section)

if_renumber

Determines whether to renumber atoms starting from 1, can be set to either if_renumber=True or if_renumber=False, default value is True.

if_fix_atomname

Determines whether atom names should be adjusted to conform to PDB conventions, can be set to either if_fix_atomname=True or if_fix_atomname=False. The default value is True, which ensures that atom names are automatically converted to the standard PDB format.

Example Code

• Save a Structure objects to a PDB file

In this example, we use PDBParser to export Structure object as a new PDB file.

How input is prepared

For PDBParser.save_structure(), need to prepare:

outfile

The path to save the Structure object as a string. In this example, we save the structure as "./2v7m_new.pdb"

stru

The Structure() object obtained from PDBParser.get_structure() (See PDBParser.get_structure() section)

from enzy_htp.structure import PDBParser

test_A="./2v7m.pdb"
test_A_struc = PDBParser.get_structure(path=test_A)
test_A_saved_path = PDBParser.save_structure(outfile="./2v7m_new.pdb",
                                             stru=test_A_struc)
print(test_A_saved_path) #./2v7m_new.pdb

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Author: Xingyu Ouyang <ouyangxingyu913@gmail.com>