Coverage for /builds/kinetik161/ase/ase/io/sdf.py: 100.00%

1"""Reads chemical data in SDF format (wraps the molfile format). 

2 

3See https://en.wikipedia.org/wiki/Chemical_table_file#SDF 

4""" 

5from typing import TextIO 

6 

7from ase.atoms import Atoms 

8from ase.utils import reader 

9 

10 

11def get_num_atoms_sdf_v2000(first_line: str) -> int: 

12 """Parse the first line extracting the number of atoms. 

13 

14 The V2000 dialect uses a fixed field length of 3, which means there 

15 won't be space between the numbers if there are 100+ atoms, and 

16 the format doesn't support 1000+ atoms at all. 

17 

18 http://biotech.fyicenter.com/1000024_SDF_File_Format_Specification.html 

19 """ 

20 return int(first_line[0:3]) # first three characters 

21 

22 

23@reader 

24def read_sdf(file_obj: TextIO) -> Atoms: 

25 """Read the sdf data and compose the corresponding Atoms object.""" 

26 lines = file_obj.readlines() 

27 # first three lines header 

28 del lines[:3] 

29 

30 num_atoms = get_num_atoms_sdf_v2000(lines.pop(0)) 

31 positions = [] 

32 symbols = [] 

33 for line in lines[:num_atoms]: 

34 x, y, z, symbol = line.split()[:4] 

35 symbols.append(symbol) 

36 positions.append((float(x), float(y), float(z))) 

37 return Atoms(symbols=symbols, positions=positions)