rubabel 0.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -0,0 +1,337 @@
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+ ************************************************************
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+ OpenBabel
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+ ************************************************************
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+ to_angle_data: -1
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+ to_atom_class_data: -1
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+ to_chiral_data: -1
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+ to_comment_data: -1
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+ to_conformer_data: -1
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+ to_external_bond_data: -1
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+ to_grid_data: -1
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+ to_matrix_data: -1
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+ to_nasa_thermo_data: -1
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+ to_pair_data: -1
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+ to_rate_data: -1
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+ to_rotamer_list: -1
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+ to_rotation_data: -1
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+ to_serial_nums: -1
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+ to_set_data: -1
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+ to_symmetry_data: -1
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+ to_torsion_data: -1
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+ to_unit_cell: -1
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+ to_vector_data: -1
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+ to_vibration_data: -1
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+ to_virtual_bond: -1
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+ double_multiply: -1
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+ double_add: -1
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+ double_modulus: -1
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+ rotate_coords: -1
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+ calc_rms: -1
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+ <<: -1
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+ +: -1
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+ -: -1
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+ /: -1
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+ *: -1
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+ dot: -1
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+ cross: -1
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+ vector_angle: -1
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+ calc_torsion_angle: -1
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+ point_2plane_signed: -1
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+ point_2plane: -1
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+ point_2plane_angle: -1
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+ point_2line: -1
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+ VZero: 0
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+ VX: 0
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+ VY: 0
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+ VZ: 0
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+ obrelease_version: -1
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+ obErrorLog: 0
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+ obErrorLog=: 1
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+ Residue: 0
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+ Residue=: 1
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+ ElemDesc: 0
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+ ElemDesc=: 1
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+ ResNo: 0
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+ ResNo=: 1
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+ ElemNo: 0
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+ ElemNo=: 1
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+ throw_error: -1
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+ cartesian_to_internal: -1
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+ internal_to_cartesian: -1
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+ new_extension: -1
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+ etab: 0
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+ etab=: 1
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+ ttab: 0
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+ ttab=: 1
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+ isotab: 0
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+ isotab=: 1
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+ aromtyper: 0
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+ aromtyper=: 1
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+ atomtyper: 0
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+ atomtyper=: 1
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+ chainsparser: 0
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+ chainsparser=: 1
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+ resdat: 0
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+ resdat=: 1
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+ NoId: 0
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+ get_rmat: -1
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+ ob_make_rmat: -1
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+ qtrfit: -1
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+ superimpose: -1
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+ compare_ring_size: -1
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+ smarts_lex_replace: -1
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+ AliasDataType: 0
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+ tanimoto: -1
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+ ***[OpenBabel::VectorUnsignedInt NO METHODS]***
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+ ***[OpenBabel::VectorInt NO METHODS]***
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+ ***[OpenBabel::Iterator NO METHODS]***
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+ ***[OpenBabel::ConstIterator NO METHODS]***
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+ ***[OpenBabel::GCVALUE NO METHODS]***
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+ ***[OpenBabel::OBTorsion NO METHODS]***
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+ ***[OpenBabel::OBSymmetryData NO METHODS]***
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+ ***[OpenBabel::OBConformerData NO METHODS]***
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+ ***[OpenBabel::OBUnitCell NO METHODS]***
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+ ***[OpenBabel::OBRingData NO METHODS]***
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+ ***[OpenBabel::OBVirtualBond NO METHODS]***
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+ ***[OpenBabel::OBSetData NO METHODS]***
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+ ***[OpenBabel::OBPairData NO METHODS]***
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+ ***[OpenBabel::OBExternalBondData NO METHODS]***
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+ ***[OpenBabel::OBExternalBond NO METHODS]***
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+ ***[OpenBabel::OBCommentData NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBAtom
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+ ************************************************************
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+ class_description: -1
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+ ***[OpenBabel::OBInternalCoord NO METHODS]***
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+ ***[OpenBabel::LineSearchType NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBDescriptor
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+ ************************************************************
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+ default: -1
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+ find_type: -1
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+ filter_compare: -1
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+ add_properties: -1
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+ delete_properties: -1
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+ get_values: -1
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+ get_identifier: -1
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+ get_plugin: -1
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+ list_as_vector: -1
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+ list: -1
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+ list_as_string: -1
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+ first_line: -1
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+ begin: -1
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+ end: -1
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+ ***[OpenBabel::FastSearchIndexer NO METHODS]***
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+ ***[OpenBabel::FastSearch NO METHODS]***
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+ ***[OpenBabel::FptIndexHeader NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBFingerprint
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+ ************************************************************
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+ default: -1
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+ find_type: -1
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+ tanimoto: -1
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+ getbitsperint: -1
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+ find_fingerprint: -1
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+ get_plugin: -1
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+ list_as_vector: -1
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+ list: -1
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+ list_as_string: -1
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+ first_line: -1
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+ begin: -1
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+ end: -1
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+ ***[OpenBabel::OBAtomClassData NO METHODS]***
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+ ************************************************************
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+ OpenBabel::AliasData
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+ ************************************************************
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+ revert_to_alias_form: -1
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+ ***[OpenBabel::OBMolRingIter NO METHODS]***
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+ ***[OpenBabel::OBMolPairIter NO METHODS]***
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+ ***[OpenBabel::OBMolTorsionIter NO METHODS]***
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+ ***[OpenBabel::OBMolAngleIter NO METHODS]***
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+ ***[OpenBabel::OBResidueAtomIter NO METHODS]***
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+ ***[OpenBabel::OBResidueIter NO METHODS]***
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+ ***[OpenBabel::OBAtomBondIter NO METHODS]***
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+ ***[OpenBabel::OBAtomAtomIter NO METHODS]***
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+ ***[OpenBabel::OBMolBondIter NO METHODS]***
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+ ***[OpenBabel::OBMolBondBFSIter NO METHODS]***
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+ ***[OpenBabel::OBMolAtomBFSIter NO METHODS]***
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+ ***[OpenBabel::OBMolAtomDFSIter NO METHODS]***
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+ ***[OpenBabel::OBMolAtomIter NO METHODS]***
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+ ***[OpenBabel::OBRotamerList NO METHODS]***
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+ ***[OpenBabel::OBRotorKeys NO METHODS]***
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+ ***[OpenBabel::RotorDigit NO METHODS]***
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+ ***[OpenBabel::OBRotorList NO METHODS]***
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+ ***[OpenBabel::OBRotor NO METHODS]***
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+ ***[OpenBabel::OBRotorRules NO METHODS]***
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+ ***[OpenBabel::OBRotorRule NO METHODS]***
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+ ***[OpenBabel::OBBitVec NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBOp
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+ ************************************************************
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+ default: -1
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+ find_type: -1
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+ op_options: -1
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+ do_ops: -1
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+ get_plugin: -1
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+ list_as_vector: -1
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+ list: -1
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+ list_as_string: -1
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+ first_line: -1
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+ begin: -1
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+ end: -1
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+ ************************************************************
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+ OpenBabel::OBBuilder
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+ ************************************************************
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+ get_new_bond_vector: -1
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+ connect: -1
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+ swap: -1
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+ correct_stereo_bonds: -1
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+ correct_stereo_atoms: -1
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+ is_spiro_atom: -1
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+ get_fragment: -1
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+ add_nbrs: -1
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+ ************************************************************
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+ OpenBabel::OBForceField
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+ ************************************************************
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+ default: -1
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+ find_type: -1
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+ find_force_field: -1
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+ ignore_calculation: -1
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+ vector_bond_derivative: -1
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+ vector_distance_derivative: -1
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+ vector_length_derivative: -1
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+ vector_angle_derivative: -1
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+ vector_oopderivative: -1
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+ vector_torsion_derivative: -1
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+ vector_subtract: -1
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+ vector_add: -1
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+ vector_divide: -1
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+ vector_multiply: -1
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+ vector_self_multiply: -1
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+ vector_normalize: -1
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+ vector_copy: -1
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+ vector_length: -1
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+ vector_distance: -1
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+ vector_angle: -1
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+ vector_torsion: -1
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+ vector_oop: -1
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+ vector_clear: -1
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+ vector_dot: -1
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+ vector_cross: -1
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+ print_vector: -1
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+ get_plugin: -1
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+ list_as_vector: -1
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+ list: -1
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+ list_as_string: -1
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+ first_line: -1
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+ begin: -1
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+ end: -1
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+ ***[OpenBabel::OBFFConstraints NO METHODS]***
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+ ***[OpenBabel::OBFFConstraint NO METHODS]***
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+ ***[OpenBabel::OBFFCalculation4 NO METHODS]***
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+ ***[OpenBabel::OBFFCalculation3 NO METHODS]***
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+ ***[OpenBabel::OBFFCalculation2 NO METHODS]***
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+ ***[OpenBabel::OBFFParameter NO METHODS]***
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+ ***[OpenBabel::OBSSMatch NO METHODS]***
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+ ***[OpenBabel::OBSmartsMatcher NO METHODS]***
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+ ***[OpenBabel::OBSmartsPattern NO METHODS]***
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+ ***[OpenBabel::OBRTree NO METHODS]***
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+ ***[OpenBabel::OBRingSearch NO METHODS]***
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+ ***[OpenBabel::OBRing NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBMol
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+ ************************************************************
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+ class_description: -1
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+ ************************************************************
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+ OpenBabel::OBBond
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+ ************************************************************
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+ class_description: -1
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+ ************************************************************
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+ OpenBabel::OBResidue
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+ ************************************************************
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+ class_description: -1
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+ ************************************************************
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+ OpenBabel::OBConversion
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+ ************************************************************
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+ register_format: -1
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+ find_format: -1
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+ format_from_ext: -1
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+ format_from_mime: -1
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+ get_next_format: -1
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+ description: -1
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+ register_option_param: -1
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+ get_option_params: -1
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+ get_default_format: -1
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+ ************************************************************
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+ OpenBabel::OBFormat
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+ ************************************************************
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+ default: -1
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+ find_type: -1
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+ format_from_mime: -1
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+ get_plugin: -1
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+ list_as_vector: -1
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+ list: -1
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+ list_as_string: -1
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+ first_line: -1
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+ begin: -1
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+ end: -1
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+ ***[OpenBabel::ObLogBuf NO METHODS]***
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+ ***[OpenBabel::OBMessageHandler NO METHODS]***
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+ ***[OpenBabel::OBError NO METHODS]***
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+ ***[OpenBabel::Stringbuf NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBPlugin
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+ ************************************************************
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+ get_plugin: -1
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+ list_as_vector: -1
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+ list: -1
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+ list_as_string: -1
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+ first_line: -1
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+ begin: -1
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+ end: -1
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+ ***[OpenBabel::CharPtrLess NO METHODS]***
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+ ***[OpenBabel::Dummy NO METHODS]***
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+ ***[OpenBabel::OBGridData NO METHODS]***
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+ ***[OpenBabel::OBMatrixData NO METHODS]***
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+ ***[OpenBabel::OBVectorData NO METHODS]***
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+ ***[OpenBabel::OBRotationData NO METHODS]***
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+ ***[OpenBabel::OBElectronicTransitionData NO METHODS]***
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+ ***[OpenBabel::OBOrbitalData NO METHODS]***
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+ ***[OpenBabel::OBOrbital NO METHODS]***
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+ ***[OpenBabel::OBDOSData NO METHODS]***
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+ ***[OpenBabel::OBVibrationData NO METHODS]***
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+ ***[OpenBabel::OBSerialNums NO METHODS]***
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+ ***[OpenBabel::OBChiralData NO METHODS]***
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+ ***[OpenBabel::OBAngleData NO METHODS]***
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+ ***[OpenBabel::OBAngle NO METHODS]***
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+ ***[OpenBabel::OBTorsionData NO METHODS]***
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+ ************************************************************
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+ OpenBabel::OBBase
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+ ************************************************************
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+ class_description: -1
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+ ***[OpenBabel::OBGenericData NO METHODS]***
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+ ************************************************************
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+ OpenBabel::Matrix3x3
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+ ************************************************************
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+ jacobi: -1
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+ ***[OpenBabel::Vector3 NO METHODS]***
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+ ***[OpenBabel::OBSqrtTbl NO METHODS]***
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+ ***[OpenBabel::OBStopwatch NO METHODS]***
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+ ***[OpenBabel::OBRandom NO METHODS]***
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+ ***[OpenBabel::DoubleType NO METHODS]***
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+ ***[OpenBabel::OBResidueData NO METHODS]***
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+ ***[OpenBabel::OBTypeTable NO METHODS]***
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+ ***[OpenBabel::OBIsotopeTable NO METHODS]***
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+ ***[OpenBabel::OBElementTable NO METHODS]***
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+ ***[OpenBabel::OBElement NO METHODS]***
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+ ***[OpenBabel::OBGlobalDataBase NO METHODS]***
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+ ***[OpenBabel::VectorpOBGenericData NO METHODS]***
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+ ***[OpenBabel::VectorpOBRing NO METHODS]***
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+ ***[OpenBabel::VectorOBRing NO METHODS]***
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+ ***[OpenBabel::VectorOBResidue NO METHODS]***
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+ ***[OpenBabel::VectorOBBond NO METHODS]***
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+ ***[OpenBabel::VectorOBMol NO METHODS]***
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+ ***[OpenBabel::VectorVector3 NO METHODS]***
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+ ***[OpenBabel::VectorString NO METHODS]***
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+ ***[OpenBabel::VectorDouble NO METHODS]***
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+ ***[OpenBabel::VectorVInt NO METHODS]***
@@ -0,0 +1,145 @@
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+ Visit=
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+ Visit
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+ duplicate
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+ set_idx
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+ set_id
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+ set_hyb
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+ set_atomic_num
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+ set_isotope
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+ set_implicit_valence
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+ increment_implicit_valence
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+ decrement_implicit_valence
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+ set_formal_charge
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+ set_spin_multiplicity
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+ set_type
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+ set_partial_charge
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+ set_coord_ptr
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+ set_vector
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+ set_residue
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+ set_parent
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+ set_aromatic
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+ unset_aromatic
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+ set_clockwise_stereo
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+ set_anti_clockwise_stereo
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+ set_positive_stereo
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+ set_negative_stereo
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+ unset_stereo
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+ set_in_ring
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+ set_chiral
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+ clear_coord_ptr
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+ get_formal_charge
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+ get_atomic_num
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+ get_isotope
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+ get_spin_multiplicity
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+ get_atomic_mass
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+ get_exact_mass
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+ get_idx
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+ get_index
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+ get_id
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+ get_coordinate_idx
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+ get_cidx
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+ get_valence
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+ get_hyb
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+ get_implicit_valence
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+ get_hvy_valence
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+ get_hetero_valence
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+ get_type
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+ get_x
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+ get_y
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+ get_z
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+ x
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+ y
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+ z
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+ get_coordinate
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+ get_vector
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+ get_partial_charge
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+ get_residue
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+ get_parent
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+ get_new_bond_vector
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+ get_bond
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+ get_next_atom
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+ begin_bonds
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+ end_bonds
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+ begin_bond
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+ next_bond
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+ begin_nbr_atom
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+ next_nbr_atom
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+ get_distance
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+ get_angle
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+ new_residue
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+ add_residue
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+ delete_residue
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+ add_bond
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+ insert_bond
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+ delete_bond
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+ clear_bond
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+ hto_methyl
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+ set_hyb_and_geom
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+ force_no_h
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+ has_no_hforced
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+ force_impl_h
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+ has_impl_hforced
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+ count_free_oxygens
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+ implicit_hydrogen_count
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+ explicit_hydrogen_count
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+ member_of_ring_count
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+ member_of_ring_size
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+ count_ring_bonds
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+ smallest_bond_angle
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+ average_bond_angle
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+ bosum
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+ kbosum
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+ has_residue
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+ is_hydrogen
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+ is_carbon
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+ is_nitrogen
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+ is_oxygen
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+ is_sulfur
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+ is_phosphorus
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+ is_aromatic
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+ is_in_ring
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+ is_in_ring_size
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+ is_heteroatom
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+ is_not_cor_h
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+ is_connected
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+ is_one_three
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+ is_one_four
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+ is_carboxyl_oxygen
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+ is_phosphate_oxygen
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+ is_sulfate_oxygen
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+ is_nitro_oxygen
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+ is_amide_nitrogen
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+ is_polar_hydrogen
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+ is_non_polar_hydrogen
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+ is_aromatic_noxide
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+ is_chiral
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+ is_axial
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+ is_clockwise
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+ is_anti_clockwise
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+ is_positive_stereo
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+ is_negative_stereo
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+ has_chirality_specified
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+ has_chiral_volume
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+ is_hbond_acceptor
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+ is_hbond_donor
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+ is_hbond_donor_h
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+ has_alpha_beta_unsat
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+ has_bond_of_order
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+ count_bonds_of_order
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+ has_non_single_bond
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+ has_single_bond
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+ has_double_bond
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+ has_aromatic_bond
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+ matches_smarts
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+ clear
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+ do_transformations
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+ get_title
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+ set_title
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+ has_data
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+ delete_data
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+ clone_data
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+ data_size
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+ get_all_data
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+ get_data
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+ begin_data
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+ end_data