蛋白质基础组成结构

$ python3 -m pip install xponge --upgrade
Requirement already satisfied: xponge in /home/dechin/anaconda3/envs/mindspore16/lib/python3.9/site-packages (1.2.5.9)
Requirement already satisfied: NetCDF4 in /home/dechin/anaconda3/envs/mindspore16/lib/python3.9/site-packages (from xponge) (1.5.8)
Requirement already satisfied: pubchempy in /home/dechin/anaconda3/envs/mindspore16/lib/python3.9/site-packages (from xponge) (1.0.4)
Requirement already satisfied: numpy in /home/dechin/anaconda3/envs/mindspore16/lib/python3.9/site-packages (from xponge) (1.20.3)
Requirement already satisfied: cftime in /home/dechin/anaconda3/envs/mindspore16/lib/python3.9/site-packages (from NetCDF4->xponge) (1.6.0)

$ python3
Python 3.9.12 (main, Apr  5 2022, 06:56:58) 
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import Xponge
>>> import Xponge.forcefield.AMBER.ff14SB
Reference for ff14SB:
  James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling
    ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
    Journal of Chemical Theory and Computation 2015 11 (8), 3696-3713
    DOI: 10.1021/acs.jctc.5b00255

>>> Save_PDB(ALA,'ALA.pdb') # 内置了所有的氨基酸种类，注意开头结尾的氨基酸名称有所变化
>>> exit()

$ cat ALA.pdb 
REMARK   Generated By Xponge (Molecule)
ATOM      1    N ALA     1      -3.801  -7.214   0.158                   
ATOM      2    H ALA     1      -2.791  -7.214   0.158                   
ATOM      3   CA ALA     1      -4.487  -5.938   0.158                   
ATOM      4   HA ALA     1      -5.112  -5.861  -0.732                   
ATOM      5   CB ALA     1      -5.374  -5.792   1.390                   
ATOM      6  HB1 ALA     1      -4.761  -5.858   2.289                   
ATOM      7  HB2 ALA     1      -5.877  -4.826   1.363                   
ATOM      8  HB3 ALA     1      -6.118  -6.588   1.399                   
ATOM      9    C ALA     1      -3.497  -4.783   0.158                   
ATOM     10    O ALA     1      -2.287  -4.998   0.158

In [1]: import Xponge

In [2]: import Xponge.forcefield.AMBER.ff14SB
Reference for ff14SB.py:
  James A. Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E. Hauser, and Carlos Simmerling
    ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB
    Journal of Chemical Theory and Computation 2015 11 (8), 3696-3713
    DOI: 10.1021/acs.jctc.5b00255

In [3]: Save_PDB(ACE+ALA*10+NME,'multi_ALA.pdb')

def write_pdb(crd, atom_names, res_names, res_ids, pdb_name='temp.pdb'):
    """Write protein crd information into pdb format files.
    Args:
        crd(numpy.float32): The coordinates of protein atoms.
        atom_names(numpy.str_): The atom names differ from aminos.
        res_names(numpy.str_): The residue names of amino names.
        res_ids(numpy.int32): A unique mask each same residue.
        pdb_name(str): The path to save the pdb file, absolute path is suggested.
    """
    success = 1
    with open(pdb_name, 'w') as pdb:
        pdb.write('MODEL     1\n')
        for i,c in enumerate(crd[0]):
            pdb.write('ATOM'.ljust(6))
            pdb.write('{}'.format(i + 1).rjust(5))
            if len(atom_names[i])<4:
                pdb.write('  ')
                pdb.write(atom_names[i].ljust(3))
            else:
                pdb.write(' ')
                pdb.write(atom_names[i].ljust(4))
            pdb.write(res_names[i].rjust(4))
            pdb.write('A'.rjust(2))
            pdb.write('{}'.format(res_ids[i]).rjust(4))
            pdb.write('    ')
            pdb.write('{:.3f}'.format(c[0]).rjust(8))
            pdb.write('{:.3f}'.format(c[1]).rjust(8))
            pdb.write('{:.3f}'.format(c[2]).rjust(8))
            pdb.write('1.0'.rjust(6))
            pdb.write('0.0'.rjust(6))
            pdb.write('{}'.format(atom_names[i][0]).rjust(12))
            pdb.write('\n')
        pdb.write('TER\n')
        pdb.write('ENDMDL\n')
        pdb.write('END\n')
    return success