Python bpd Examples

Example #1

File: generate_conect_lines_for_whole_pdb_with_functions.py Project: bkotryna/PDB_file_editing

def get_all_atoms():
    # read in a pdb file
    file = bpd().read_pdb('nuc_with_5FC.pdb')

    # create a dataframe that contains all atoms
    atoms = file.df['ATOM']
    atoms

    hetatm = file.df['HETATM']
    hetatm

    all_atoms = atoms.append(hetatm)
    all_atoms
    all_atoms.head(50)
    all_atoms.tail(50)

    # clean up the order - make sure atom numbers are nicely ascending
    all_atoms = all_atoms.sort_values(['atom_number'], ascending=[True])
    all_atoms
    all_atoms.head(50)
    all_atoms.tail(50)

    return (all_atoms)

Example #2

File: add_some_formyl_atoms_to_pdb.py Project: bkotryna/PDB_file_editing

# set working directory to where your input pdb file is
import sys, os
os.chdir('C:\Kotryna\Python\Lab projects\pdb file handling\Input_Output_files')
cwd = os.getcwd()
print("cwd is: ", cwd)

# import tools you'll need
import pandas as pd
from biopandas.pdb import PandasPdb as bpd
import numpy as np



# read in a pdb file
file1 = bpd().read_pdb('nuc_with_hydrogens.pdb')

# create a dataframe that contains all atoms
atoms = file1.df['ATOM']
atoms
# write atoms out to csv for reference
#atoms.to_csv("../Output_files/original_atoms.csv", encoding='utf-8', index=False)

# what are the column names
atoms.columns


#############################################
# part 2 = specific DNA chain
# get the cytosines & their C5 atoms

Example #3

"""

# set working directory to where your input pdb file is
import sys, os
os.chdir('C:\Kotryna\Python\Lab projects\pdb file handling\Input_Output_files')
cwd = os.getcwd()
print("cwd is: ", cwd)

# import tools you'll need
import pandas as pd
from biopandas.pdb import PandasPdb as bpd
import numpy as np

### make a dictionary to match atom numbers to atom names
# open pdb snippet that contains the relevant atom names & numbers
file = bpd().read_pdb('pdb_snippet_for_conect.txt')

# create a dataframe that contains all atoms
atoms = file.df['ATOM']
atoms

hetatm = file.df['HETATM']
hetatm

all_atoms = atoms.append(hetatm)
all_atoms

# extract atom numbers & names into lists
atom_numbers = all_atoms.atom_number.tolist()
atom_names = all_atoms.atom_name.tolist()
length = len(atom_numbers)

Example #4

File: testing_ground_to_generate_conect_lines.py Project: bkotryna/PDB_file_editing

# set working directory to where your input pdb file is
import sys, os
os.chdir('C:\Kotryna\Python\Lab projects\pdb file handling\Input_Output_files')
cwd = os.getcwd()
print("cwd is: ", cwd)

# import tools you'll need
import pandas as pd
from biopandas.pdb import PandasPdb as bpd
import numpy as np



# read in a pdb file
file = bpd().read_pdb('pdb_with_5FC.pdb')

# create a dataframe that contains all atoms
atoms = file.df['ATOM']
atoms

hetatm = file.df['HETATM']
hetatm

all_atoms = atoms.append(hetatm)
all_atoms

all_atoms.tail(50)


## write atoms out to csv for reference