计算两个蛋白或小分子之间的RMSD

# Root-mean-square deviation (RMSD) for proteins and/or ligands
# in PDB files.
#class Pdb(object):""" Object that allows operations with protein files in PDB format. """def __init__(self, file_cont = [], pdb_code = ""):self.cont = []self.atom = []self.hetatm = []self.fileloc = ""if isinstance(file_cont, list):self.cont = file_cont[:]elif isinstance(file_cont, str):try:with open(file_cont, 'r') as pdb_file:self.cont = [row.strip() for row in pdb_file.read().split('\n') if row.strip()]except FileNotFoundError as err:print(err)if self.cont:self.atom = [row for row in self.cont if row.startswith('ATOM')]self.hetatm = [row for row in self.cont if row.startswith('HETATM')]self.conect = [row for row in self.cont if row.startswith('CONECT')]def rmsd(self, sec_molecule, ligand=False, atoms="no_h"):"""Calculates the Root Mean Square Deviation (RMSD) between twoprotein or ligand molecules in PDB format.Requires that both molecules have the same number of atoms in thesame numerical order.Keyword arguments:sec_molecule (PdbObj): the second molecule as PdbObj object.ligand (bool): If true, calculates the RMSD between twoligand molecules (based on HETATM entries), else RMSDbetween two protein molecules (ATOM entries) is calculated.hydrogen (bool): If True, hydrogen atoms will be included in theRMSD calculation.atoms (string) [all/c/no_h/ca]: "all" includes all atoms in the RMSD calculation,"c" only considers carbon atoms, "no_h" considers all but hydrogen atoms,and "ca" compares only C-alpha protein atoms.Returns:Calculated RMSD value as float or None if RMSD not becalculated."""rmsd = Noneif not ligand:coords1, coords2 = self.atom, sec_molecule.atomelse:coords1, coords2 = self.hetatm, sec_molecule.hetatmif atoms == "c":coords1 = [row for row in coords1 if row[77:].startswith('C')]coords2 = [row for row in coords2 if row[77:].startswith('C')]elif atoms == "no_h":coords1 = [row for row in coords1 if not row[77:].startswith('H')]coords2 = [row for row in coords2 if not row[77:].startswith('H')]elif atoms == "ca":coords1 = self.calpha()coords2 = sec_molecule.calpha()if all((coords1, coords2, len(coords1) == len(coords2))):total = 0for (i, j) in zip(coords1, coords2):total += ( float(i[30:38]) - float(j[30:38]) )**2 +\( float(i[38:46]) - float(j[38:46]) )**2 +\( float(i[46:54]) - float(j[46:54]) )**2      rmsd = round(( total / len(coords1) )**0.5, 4)return rmsdif __name__ == '__main__':import argparseparser = argparse.ArgumentParser(description='The RMSD measures the average distance between atoms \n'\'of 2 protein or ligand structures.\n'\'By default, all atoms but hydrogen atoms of the protein are included in the RMSD calculation.\n'\'NOTE: Both structures must contain the same number of atoms in similar order.',epilog='Example:\n'\'rmsd.py ~/Desktop/pdb1.pdb ~/Desktop/pdb2.pdb\n'\'0.7377',formatter_class=argparse.RawTextHelpFormatter)parser.add_argument('PDBfile1')parser.add_argument('PDBfile2')parser.add_argument('-l', '--ligand', action='store_true', help='Calculates RMSD between ligand (HETATM) atoms.')parser.add_argument('-c', '--carbon', action='store_true', help='Calculates the RMSD between carbon atoms only.')parser.add_argument('-ca', '--calpha', action='store_true', help='Calculates the RMSD between alpha-carbon atoms only.')parser.add_argument('-v', '--version', action='version', version='rmsd v. 1.0')args = parser.parse_args()pdb1 = Pdb(args.PDBfile1)pdb2 = Pdb(args.PDBfile2)if args.carbon and args.calpha:print('\nERROR: Please provide EITHER -c OR -ca, not both.\n')parser.print_help()quit()if args.ligand and args.carbon:print(pdb1.rmsd(sec_molecule=pdb2, ligand=True, atoms="c"))elif args.ligand and args.calpha:print(pdb1.calpha())print(pdb1.rmsd(sec_molecule=pdb2, ligand=True, atoms="ca"))elif args.ligand:print(pdb1.rmsd(sec_molecule=pdb2, ligand=True, atoms="no_h"))elif args.calpha:print(pdb1.rmsd(sec_molecule=pdb2, ligand=False, atoms="ca"))elif args.carbon:print(pdb1.rmsd(sec_molecule=pdb2, ligand=False, atoms="c"))else:print(pdb1.rmsd(sec_molecule=pdb2, ligand=False, atoms="no_h"))
if __name__ == '__main__':pass## python rmsd.py protein1.pdb protein2.pdb

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计算两个蛋白或小分子之间的RMSD

计算两个蛋白或小分子之间的RMSD

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