add gdb parsing

qcelemental/molparse/from_string.py

@@ -1,6 +1,6 @@
 import pprint
 import re
-from typing import Dict, Tuple, Union
+from typing import Any, Dict, Tuple, Union
 
 from ..exceptions import ChoicesError, MoleculeFormatError, ValidationError
 from ..util import filter_comments, provenance_stamp
@@ -135,6 +135,25 @@ def from_string(
  -----
  <number of atoms> is pattern-matched but ignored.
 
+ gdb
+ ---
+
+ +-------------+------------------------------------------------------------------------------------+
+ | Line | Content https://www.nature.com/articles/sdata201422/tables/3 |
+ +=============+====================================================================================+
+ | 1 | <number of atoms>, nat |
+ +-------------+------------------------------------------------------------------------------------+
+ | 2 | Scalar properties (see https://www.nature.com/articles/sdata201422/tables/4) |
+ +-------------+------------------------------------------------------------------------------------+
+ | 3,...,nat+2 | Element type, coordinate (x, y, z, in Å), Mulliken partial charges (in e) on atoms |
+ +-------------+------------------------------------------------------------------------------------+
+ | nat+3 | Harmonic vibrational frequencies (3nat−5 or 3nat-6, in cm−1) |
+ +-------------+------------------------------------------------------------------------------------+
+ | nat+4 | SMILES strings from GDB-17 and from B3LYP relaxation |
+ +-------------+------------------------------------------------------------------------------------+
+ | nat+5 | InChI strings for Corina and B3LYP geometries |
+ +-------------+------------------------------------------------------------------------------------+
+
  psi4 - Psi4 molecule {...} format
  ---------------------------------
 
@@ -178,11 +197,11 @@ def from_string(
  # << 1 >> str-->str -- discard comments
  molstr = filter_comments(molstr.strip())
 
- def parse_as_xyz_ish(molstr, strict):
+ def parse_as_xyz_ish(molstr, strict, gdb):
  molinit = {}
 
  # << 2 >> str-->dict -- process atoms, units[, chg, mult]
- molstr, processed = _filter_xyz(molstr, strict=strict)
+ molstr, processed = _filter_xyz(molstr, strict=strict, gdb=gdb)
  molinit.update(processed)
 
  if molstr:
@@ -219,17 +238,20 @@ def parse_as_psi4_ish(molstr, unsettled):
  return molstr, molinit
 
  if dtype == "xyz":
- molstr, molinit = parse_as_xyz_ish(molstr, strict=True)
+ molstr, molinit = parse_as_xyz_ish(molstr, strict=True, gdb=False)
 
  elif dtype == "xyz+":
- molstr, molinit = parse_as_xyz_ish(molstr, strict=False)
+ molstr, molinit = parse_as_xyz_ish(molstr, strict=False, gdb=False)
 
  elif dtype == "psi4":
  molstr, molinit = parse_as_psi4_ish(molstr, unsettled=False)
 
  elif dtype == "psi4+":
  molstr, molinit = parse_as_psi4_ish(molstr, unsettled=True)
 
+ elif dtype == "gdb":
+ molstr, molinit = parse_as_xyz_ish(molstr, strict=True, gdb=True)
+
  elif dtype is None:
  dtype = "[psi4, xyz, xyz+, psi4+]" # for error message
  try:
@@ -239,14 +261,14 @@ def parse_as_psi4_ish(molstr, unsettled):
  min_error_length = len(str(e))
  min_error = e
  try:
- molstr, molinit = parse_as_xyz_ish(molstr, strict=True)
+ molstr, molinit = parse_as_xyz_ish(molstr, strict=True, gdb=False)
  dtype = "xyz"
  except MoleculeFormatError as e:
  if len(str(e)) < min_error_length:
  min_error_length = len(str(e))
  min_error = e
  try:
- molstr, molinit = parse_as_xyz_ish(molstr, strict=False)
+ molstr, molinit = parse_as_xyz_ish(molstr, strict=False, gdb=False)
  dtype = "xyz+"
  except MoleculeFormatError as e:
  if len(str(e)) < min_error_length:
@@ -680,19 +702,27 @@ def process_variable(matchobj):
  r"\A" + r"(?P<nucleus>" + NUCLEUS + r")" + SEP + CARTXYZ + r"\Z", re.IGNORECASE | re.VERBOSE
 )
 
+xyz2_gdb = re.compile(r"\A" + r"gdb\d*" + SEP + r"(\d+)" + r"(" + SEP + NUMBER + r")*", re.IGNORECASE | re.VERBOSE)
+atom_cartesian_strict_gdb = re.compile(
+ r"\A" + r"(?P<nucleus>" + SIMPLENUCLEUS + r")" + SEP + CARTXYZ + SEP + NUMBER + r"\Z", re.IGNORECASE | re.VERBOSE
+)
+reNUMBER = r"(?x:" + NUMBER + ")"
+
 
-def _filter_xyz(string, strict):
+def _filter_xyz(string: str, *, strict: bool, gdb: bool) -> Tuple[str, Dict[str, Any]]:
  r"""Handle extracting atom, units, and chg/mult lines from `string`.
 
  Parameters
  ----------
- strict : bool
+ strict
  Whether to enforce a strict XYZ file format or to allow units, chg/mult,
  and add'l atom info.
+ gdb
+ Whether to expect GDB format with extra properties info.
 
  Returns
  -------
- str, dict
+ Tuple[str, Dict[str, Any]]
  Returns first a subset of `string` containing the unmatched contents.
  These are generally input violations unless handled by a subsequent
  processing function.
@@ -733,8 +763,32 @@ def process_atom_cartesian(matchobj):
  processed["geom"] = []
  processed["elbl"] = []
 
- if strict:
- for iln, line in enumerate(string.split("\n")):
+ splitstring = string.strip().split("\n")
+
+ if gdb:
+ for iln, line in enumerate(splitstring):
+ line = line.strip()
+ if iln == 0:
+ line = re.sub(xyz1strict, "", line)
+ elif iln == 1:
+ line = re.sub(xyz2_gdb, "", line)
+ elif iln == (len(splitstring) - 3):
+ nfr = 3 * (iln - 2) - 6
+ freqs = re.split(reNUMBER, line)
+ freqs = [float(fr) for fr in freqs if fr.strip()]
+ if len(freqs) == nfr or len(freqs) == nfr - 1:
+ line = ""
+ elif iln == (len(splitstring) - 2):
+ line = ""
+ elif iln == (len(splitstring) - 1):
+ line = ""
+ else:
+ line = re.sub(atom_cartesian_strict_gdb, process_atom_cartesian, line)
+ if line:
+ reconstitute.append(line)
+
+ elif strict:
+ for iln, line in enumerate(splitstring):
  line = line.strip()
  if iln == 0:
  line = re.sub(xyz1strict, "", line)
@@ -745,7 +799,7 @@ def process_atom_cartesian(matchobj):
  if line:
  reconstitute.append(line)
  else:
- for iln, line in enumerate(string.split("\n")):
+ for iln, line in enumerate(splitstring):
  line = line.strip()
  if iln == 0:
  line = re.sub(xyz1, process_bohrang, line)