17.1.1.9. pysisyphus.io package

17.1.1.9.1. Submodules

17.1.1.9.2. pysisyphus.io.cjson module

pysisyphus.io.cjson.geom_from_cjson(fn, **kwargs)

pysisyphus.io.cjson.parse_cjson(fn)

17.1.1.9.3. pysisyphus.io.crd module

pysisyphus.io.crd.a8(str_)

pysisyphus.io.crd.atoms_coords_to_crd_str(atoms, coords, resno=1, res='UNL1', segid=None, resid=1, ref_atoms=None, del_atoms=None)

pysisyphus.io.crd.f20(float_)

pysisyphus.io.crd.geom_from_crd(fn, **kwargs)

pysisyphus.io.crd.geom_to_crd_str(geom, **kwargs)

pysisyphus.io.crd.i10(int_)

17.1.1.9.4. pysisyphus.io.hdf5 module

pysisyphus.io.hdf5.get_h5_group(fn, group_name, data_model=None, reset=False)

Return (and create if neccesary) group with given name and data model.

pysisyphus.io.hdf5.init_h5_group(f, group_name, data_model)

Create group with given name and data model.

pysisyphus.io.hdf5.resize_h5_group(group, max_cycles)

Increase size of first dimension of datasets in the given group.

17.1.1.9.5. pysisyphus.io.hessian module

pysisyphus.io.hessian.geom_from_hessian(h5_fn, **geom_kwargs)

pysisyphus.io.hessian.save_hessian(h5_fn, geom, cart_hessian=None, energy=None, mult=None)

pysisyphus.io.hessian.save_third_deriv(h5_fn, geom, third_deriv_result, H_mw, H_proj)

17.1.1.9.6. pysisyphus.io.mol2 module

pysisyphus.io.mol2.dict_to_mol2_string(as_dict)

pysisyphus.io.mol2.geom_from_mol2(text, **kwargs)

pysisyphus.io.mol2.render_xyz(xyz)

17.1.1.9.7. pysisyphus.io.molden module

pysisyphus.io.molden.geoms_from_molden(fn, **kwargs)

pysisyphus.io.molden.parse_mo(mo_lines)

pysisyphus.io.molden.parse_molden_atoms(data)

17.1.1.9.8. pysisyphus.io.pdb module

pysisyphus.io.pdb.atoms_coords_to_pdb_str(atoms, coords, fragments=None, resname='', conect=True)

pysisyphus.io.pdb.geom_from_pdb(fn, **kwargs)

pysisyphus.io.pdb.geom_to_pdb_str(geom, detect_fragments=False, **kwargs)

pysisyphus.io.pdb.get_conect_lines(atoms, coords)

pysisyphus.io.pdb.get_parser(widths)

pysisyphus.io.pdb.parse_atom_name(name)

17.1.1.9.9. pysisyphus.io.pubchem module

pysisyphus.io.pubchem.cid_from_name(name)

pysisyphus.io.pubchem.geom_from_pubchem_name(name, **kwargs)

pysisyphus.io.pubchem.sdf_from_cid(cid)

17.1.1.9.10. pysisyphus.io.sdf module

pysisyphus.io.sdf.geom_from_sdf(text, **kwargs)

pysisyphus.io.sdf.parse_coord_line(line)

pysisyphus.io.sdf.parse_sdf(text)

17.1.1.9.11. pysisyphus.io.xyz module

pysisyphus.io.xyz.geom_from_xyz(fn, **kwargs)

pysisyphus.io.xyz.geoms_from_inline_xyz(inline_xyz, **kwargs)

pysisyphus.io.xyz.geoms_from_xyz(fn, **kwargs)

17.1.1.9.12. pysisyphus.io.zmat module

class pysisyphus.io.zmat.ZLine(atom, rind, r, aind, a, dind, d)

Bases: tuple

a

Alias for field number 4

aind

Alias for field number 3

atom

Alias for field number 0

d

Alias for field number 6

dind

Alias for field number 5

r

Alias for field number 2

rind

Alias for field number 1

pysisyphus.io.zmat.geom_from_zmat(zmat, atoms=None, coords3d=None, geom=None, start_at=None, drop_dummy=True, **geom_kwargs)

Adapted from https://github.com/robashaw/geomConvert by Robert Shaw.

pysisyphus.io.zmat.geom_from_zmat_fn(fn, **geom_kwargs)

pysisyphus.io.zmat.geom_from_zmat_str(text, coord_type='cart', coord_kwargs=None)

pysisyphus.io.zmat.zmat_from_fn(fn)

pysisyphus.io.zmat.zmat_from_str(text)

17.1.1.9.13. Module contents

pysisyphus.io.geom_from_cjson(fn, **kwargs)

pysisyphus.io.geom_from_crd(fn, **kwargs)

pysisyphus.io.geom_from_cube(inp, *args, **kwargs)

pysisyphus.io.geom_from_fchk(inp, *args, **kwargs)

pysisyphus.io.geom_from_hessian(h5_fn, **geom_kwargs)

pysisyphus.io.geom_from_mol2(text, **kwargs)

pysisyphus.io.geom_from_pdb(fn, **kwargs)

pysisyphus.io.geom_from_pubchem_name(name, **kwargs)

pysisyphus.io.geom_from_qcschema(qcschema, **geom_kwargs)

pysisyphus.io.geom_from_zmat(zmat, atoms=None, coords3d=None, geom=None, start_at=None, drop_dummy=True, **geom_kwargs)

Adapted from https://github.com/robashaw/geomConvert by Robert Shaw.

pysisyphus.io.geoms_from_molden(fn, **kwargs)

pysisyphus.io.geoms_from_xyz(fn, **kwargs)

pysisyphus.io.save_hessian(h5_fn, geom, cart_hessian=None, energy=None, mult=None)

pysisyphus.io.save_third_deriv(h5_fn, geom, third_deriv_result, H_mw, H_proj)