Source code for qcelemental.molparse.to_string

import collections
from typing import Any, Dict, List, Tuple, Union

import numpy as np

from ..molutil import guess_connectivity
from ..physical_constants import constants


[docs]def to_string( molrec: Dict, dtype: str, units: str = None, *, atom_format: str = None, ghost_format: str = None, width: int = 17, prec: int = 12, return_data: bool = False, ) -> Union[str, Tuple[str, Dict]]: """Format a string representation of QM molecule. Parameters ---------- molrec : Dict Psi4 json Molecule spec. dtype : str, {'xyz', 'cfour', 'nwchem', 'molpro', 'turbomole', 'qchem'} Overall string format. Note that it's possible to request variations that don't fit the dtype spec so may not be re-readable (e.g., ghost and mass in nucleus label with ``'xyz'``). 'cfour' forces nucleus label, ignoring atom_format, ghost_format units : str, optional Units in which to write string. Usually ``Angstrom`` or ``Bohr`` but may be any length unit. There is not an option to write in intrinsic/input units. For ``dtype='xyz', units='Bohr'`` where the format doesn't have a slot to specify units, "au" is added so that readable as ``dtype='xyz+'``. atom_format : str, optional General format is ``'{elem}'``. A format string that may contain fields 'elea' (-1 will be ''), 'elez', 'elem', 'mass', 'elbl' in any arrangement. For example, if a format naturally uses element symbol and you want atomic number instead with mass info, too, pass ``'{elez}@{mass}'``. See `ghost_format` for handling field 'real'. ghost_format : str, optional General format is ``'@{elem}'``. Like `atom_format`, but this formatter is used when `real=False`. To suppress ghost atoms, use `ghost_format=''`. width : int, optional Field width for formatting coordinate float. prec : int, optional Number of decimal places for formatting coordinate float. return_data : bool, optional Whether to return dictionary with additional info from the molrec that's not expressible in the string but may be of interest to the QC program. Note that field names are in QCSchema, not molrec, language. Returns ------- str String representation of the molecule. str, dict When ``return_data=True`, return additionally a dictionary keywords: key, value pairs for processing molecule info into options fields: aspects of ``qcelemental.models.Molecule`` expressed into string _or_ keywords. """ # funits, fiutau = process_units(molrec) # molrec = self.to_dict(force_units=units, np_out=True) dtype = dtype.lower() default_units = { "xyz": "Angstrom", "xyz+": "Angstrom", "nglview-sdf": "Angstrom", "cfour": "Bohr", "gamess": "Bohr", "molpro": "Bohr", "nwchem": "Bohr", "psi4": "Bohr", "qchem": "Bohr", "terachem": "Bohr", "turbomole": "Bohr", } if dtype not in default_units: raise KeyError(f"dtype '{dtype}' not understood.") # Handle units if units is None: units = default_units[dtype] if molrec["units"] == "Angstrom" and units.capitalize() == "Angstrom": factor = 1.0 elif molrec["units"] == "Angstrom" and units.capitalize() == "Bohr": if "input_units_to_au" in molrec: factor = molrec["input_units_to_au"] else: factor = 1.0 / constants.bohr2angstroms elif molrec["units"] == "Bohr" and units.capitalize() == "Angstrom": factor = constants.bohr2angstroms elif molrec["units"] == "Bohr" and units.capitalize() == "Bohr": factor = 1.0 else: factor = constants.conversion_factor(molrec["units"], units) geom = np.asarray(molrec["geom"]).reshape((-1, 3)) * factor name = molrec.get("name", formula_generator(molrec["elem"])) tagline = """auto-generated by QCElemental from molecule {}""".format(name) class Data: fields: List[str] = ["atomic_numbers", "geometry", "symbols"] keywords: Dict[str, Any] = {} _dict_attrs: List[str] = ["fields", "keywords"] def to_dict(self) -> Dict: return {attr: getattr(self, attr) for attr in self._dict_attrs} data = Data() if dtype in ["xyz", "xyz+"]: # Notes # * if units not in umap (e.g., nm), can't be read back in by from_string() atom_format = "{elem}" if atom_format is None else atom_format ghost_format = "@{elem}" if ghost_format is None else ghost_format umap = {"bohr": "au", "angstrom": ""} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) nat = len(atoms) first_line = """{} {}""".format(str(nat), umap.get(units.lower(), units.lower())) smol = [first_line.rstrip()] smol.append(f"{int(molrec['molecular_charge'])} {molrec['molecular_multiplicity']} {name}") smol.extend(atoms) elif dtype == "cfour": # Notes # * losing identity of ghost atoms. picked up again in basis formatting # * casting 'molecular_charge' to int # * no spaces at the beginning of 1st/comment line is important atom_format = "{elem}" ghost_format = "GH" # TODO handle which units valid umap = {"bohr": "bohr", "angstrom": "angstrom"} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) smol = [tagline] smol.extend(atoms) data.fields.extend(["molecular_charge", "molecular_multiplicity"]) data.keywords = { "charge": int(molrec["molecular_charge"]), "multiplicity": molrec["molecular_multiplicity"], "units": umap.get(units.lower()), "coordinates": "cartesian", } elif dtype == "molpro": atom_format = "{elem}" ghost_format = "{elem}" umap = {"bohr": "bohr", "angstrom": "angstrom"} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) smol = [] # Don't orient the molecule if asked to fix_com or fix_orientation if molrec["fix_orientation"] or molrec["fix_com"]: smol.append("{orient,noorient}") # Have no symmetry if asked to fix_symmetry if "fix_symmetry" in molrec.keys() and molrec["fix_symmetry"] == "c1": smol.append("{symmetry,nosym}") elif "fix_symmetry" not in molrec.keys(): smol.append("{symmetry,auto}") smol.append("") units_line = f"""{{{umap.get(units.lower())}}}""" geom_line = """geometry={""" end_bracket = """}""" smol.append(units_line) smol.append(geom_line) smol.extend(atoms) smol.append(end_bracket) # Write ghost atom declarations in Molpro (using dummy card) if False in molrec["real"]: ghost_line = "dummy," + ",".join([str(idx + 1) for idx, real in enumerate(molrec["real"]) if not real]) smol.append(ghost_line) smol.append(f"set,charge={molrec['molecular_charge']}") # The Molpro "spin" is the multiplicity minus one smol.append(f"set,spin={molrec['molecular_multiplicity']-1}") elif dtype == "nwchem": atom_format = "{elem}" ghost_format = "GH" # TODO handle which units valid umap = {"bohr": "bohr", "angstrom": "angstroms", "nm": "nanometers", "pm": "picometers"} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) first_line = f"""geometry units {umap.get(units.lower())}""" # noautosym nocenter # no reorienting input geometry fix_symm = molrec.get("fix_symmetry", None) symm_line = "" if fix_symm: symm_line = "symmetry {}".format(fix_symm) # not quite what Jiyoung had last_line = """end""" smol = [first_line] smol.extend(atoms) smol.append(symm_line) smol.append(last_line) data.fields.extend(["molecular_charge", "molecular_multiplicity"]) data.keywords = {"charge": int(molrec["molecular_charge"])} if molrec["molecular_multiplicity"] != 1: data.keywords["scf__nopen"] = molrec["molecular_multiplicity"] - 1 data.keywords["dft__mult"] = molrec["molecular_multiplicity"] elif dtype == "gamess": atom_format = " {elem}{elbl} {elez}" ghost_format = " {BQ} -{elez}" umap = {"bohr": "bohr", "angstrom": "angs"} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) first_line = """ $data""" second_line = f""" {tagline}""" third_line = """ C1""" last_line = """ $end""" smol = [first_line, second_line, third_line] smol.extend(atoms) smol.append(last_line) data.fields.extend(["molecular_charge", "molecular_multiplicity"]) data.keywords = { "contrl__icharg": int(molrec["molecular_charge"]), "contrl__mult": molrec["molecular_multiplicity"], "contrl__units": umap.get(units.lower()), "contrl__coord": "prinaxis", } elif dtype == "terachem": atom_format = "{elem}" ghost_format = "X{elem}" umap = {"bohr": "au", "angstrom": ""} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) first_line = f"""{len(atoms)} {umap[units.lower()]}""" smol = [first_line.rstrip(), name] smol.extend(atoms) elif dtype == "psi4": atom_format = "{elem}{elbl}" ghost_format = "Gh({elem}{elbl})" umap = {"bohr": "bohr", "angstrom": "angstrom"} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) smol = [f"""{int(molrec['molecular_charge'])} {molrec['molecular_multiplicity']}"""] split_atoms = np.split(atoms, molrec["fragment_separators"]) for ifr, fr in enumerate(split_atoms): if len(split_atoms) > 1: # harmless to include but tidier to exclude smol.extend(["--", f"{int(molrec['fragment_charges'][ifr])} {molrec['fragment_multiplicities'][ifr]}"]) smol.extend(fr.tolist()) # append units and any other non-default molecule keywords smol.append(f"units {umap[units.lower()]}") if molrec["fix_com"]: smol.append("no_com") if molrec["fix_orientation"]: smol.append("no_reorient") data.fields.extend( [ "molecular_charge", "molecular_multiplicity", "fragments", "fragment_charges", "fragment_multiplicities", "fix_com", "fix_orientation", "real", ] ) data.keywords = {} elif dtype == "turbomole": # In Turbomole coord files the coordinates come first, and the atomic # symbol comes afterwards. # Handling of ghost atoms is done in the basis section of the control # file by setting the nuclear charge of certain atoms to zero. atom_format = "{elem}" ghost_format = "{elem}" umap = {"bohr": "bohr"} umap[units.lower()] # trigger error if downstream can't handle atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2, xyze=True) atoms = [at.lower() for at in atoms] smol = ["$coord"] + atoms + ["$end"] elif dtype == "nglview-sdf": # SDF is pretty special, handle it manually if units.capitalize() != "Angstrom": raise ValueError("SDF Format must be in Angstroms") ghost_format = ghost_format or "Gh" connectivity = molrec.get("connectivity", None) if connectivity is None: bohr_geom = geom * constants.conversion_factor("Angstrom", "Bohr") connectivity = guess_connectivity(molrec["elem"], bohr_geom, default_connectivity=1) smol = [] smol.append("") smol.append("QCElemental\n") smol.append(f"{len(molrec['real']):3d} {len(connectivity):2d} 0 0 0 0 0 0 0 0 0") for real, sym, xyz in zip(molrec["real"], molrec["elem"], geom): if bool(real) is False: sym = ghost_format smol.append(f"{xyz[0]:10.4f}{xyz[1]:10.4f}{xyz[2]:10.4f}{sym:>3s} 0 0 0 0 0 0 0 0") for a1, a2, b in connectivity: smol.append(f" {(a1 + 1):2d} {(a2 + 1):2d} {int(b):1d} 0 0 0 0") elif dtype == "qchem": atom_format = "{elem}" ghost_format = "@{elem}" umap = {"bohr": True, "angstrom": False} atoms = _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, 2) first_line = "$molecule" chgmult_line = f"""{int(molrec['molecular_charge'])} {molrec['molecular_multiplicity']}""" last_line = "$end" smol = [first_line, chgmult_line] split_atoms = np.split(atoms, molrec["fragment_separators"]) for ifr, fr in enumerate(split_atoms): if len(split_atoms) > 1: smol.extend( ["--", f"""{int(molrec['fragment_charges'][ifr])} {molrec['fragment_multiplicities'][ifr]}"""] ) smol.extend(fr.tolist()) smol.append(last_line) data.fields.extend( [ "fix_com", "fix_orientation", "fragment_charges", "fragment_multiplicities", "molecular_charge", "molecular_multiplicity", "real", "units", ] ) data.keywords = { "no_reorient": molrec["fix_orientation"] or molrec["fix_com"], "input_bohr": umap[units.lower()], } if "fix_symmetry" in molrec.keys() and molrec["fix_symmetry"] == "c1": data.keywords["sym_ignore"] = True data.keywords["symmetry"] = False else: raise KeyError(f"dtype '{dtype}' not understood.") smol_ret = "\n".join(smol) + "\n" if return_data: return smol_ret, data.to_dict() else: return smol_ret
def _atoms_formatter(molrec, geom, atom_format, ghost_format, width, prec, sp, xyze=False): """Format a list of strings, one per atom from `molrec`.""" nat = geom.shape[0] fxyz = """{:>{width}.{prec}f}""" sp = """{:{sp}}""".format("", sp=sp) atoms = [] for iat in range(nat): atom = [] atominfo = { "elea": "" if molrec["elea"][iat] == -1 else molrec["elea"][iat], "elez": molrec["elez"][iat], "elem": molrec["elem"][iat], "mass": molrec["mass"][iat], "elbl": molrec["elbl"][iat], } if molrec["real"][iat]: nuc = """{:{width}}""".format(atom_format.format(**atominfo), width=width) atom.append(nuc) else: if ghost_format in ["", None]: continue else: nuc = """{:{width}}""".format(ghost_format.format(**atominfo), width=width) atom.append(nuc) atom.extend([fxyz.format(x, width=width, prec=prec) for x in geom[iat]]) if xyze: atom.append(atom.pop(0).rstrip()) atoms.append(sp.join(atom)) return atoms def formula_generator(elem): """Return simple chemical formula from element list `elem`. >>> formula_generator(['C', 'Ca', 'O', 'O', 'Ag'] AgCCaO2 """ counted = collections.Counter(elem) return "".join((el if cnt == 1 else (el + str(cnt))) for el, cnt in sorted(counted.items()))