Chemical Data Processing Library C++ API - Version 1.4.0
Chem/ControlParameter.hpp
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1 /*
2  * ControlParameter.hpp
3  *
4  * This file is part of the Chemical Data Processing Toolkit
5  *
6  * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
7  *
8  * This library is free software; you can redistribute it and/or
9  * modify it under the terms of the GNU Lesser General Public
10  * License as published by the Free Software Foundation; either
11  * version 2 of the License, or (at your option) any later version.
12  *
13  * This library is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16  * Lesser General Public License for more details.
17  *
18  * You should have received a copy of the GNU Lesser General Public License
19  * along with this library; see the file COPYING. If not, write to
20  * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
21  * Boston, MA 02111-1307, USA.
22  */
23 
29 #ifndef CDPL_CHEM_CONTROLPARAMETER_HPP
30 #define CDPL_CHEM_CONTROLPARAMETER_HPP
31 
32 #include "CDPL/Chem/APIPrefix.hpp"
33 
34 
35 namespace CDPL
36 {
37 
38  namespace Base
39  {
40 
41  class LookupKey;
42  }
43 
44  namespace Chem
45  {
46 
50  namespace ControlParameter
51  {
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766  } // namespace ControlParameter
767  } // namespace Chem
768 } // namespace CDPL
769 
770 #endif // CDPL_CHEM_CONTROLPARAMETER_HPP
Definition of the preprocessor macro CDPL_CHEM_API.
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
Unique lookup key for control-parameter and property values.
Definition: LookupKey.hpp:54
CDPL_CHEM_API const Base::LookupKey XYZ_PERCEIVE_BOND_ORDERS
Specifies whether to perceive bond orders from the perceived connectivity when reading XYZ data.
CDPL_CHEM_API const Base::LookupKey COORDINATES_DIMENSION
Specifies the dimension of atom coordinates.
CDPL_CHEM_API const Base::LookupKey SMILES_NO_ORGANIC_SUBSET
Specifies whether to generate SMILES strings where all atom symbols are enclosed in brackets.
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_CANONICAL_FORM
Specifies whether to generate canonical SMILES strings.
CDPL_CHEM_API const Base::LookupKey MOL2_ENABLE_AROMATIC_BOND_TYPES
Specifies whether to interpret/write the Sybyl bond type "ar" as aromatic when reading/writing Sybyl ...
CDPL_CHEM_API const Base::LookupKey BOND_MEMBER_SWAP_STEREO_FIX
Specifies whether unsupported reverse stereo bonds shall be converted to regular stereo bonds by swap...
CDPL_CHEM_API const Base::LookupKey SMILES_MOL_OUTPUT_ATOM_MAPPING_ID
Specifies whether to generate molecule SMILES strings that contain atom-atom mapping numbers.
CDPL_CHEM_API const Base::LookupKey CML_ENABLE_AROMATIC_BOND_TYPES
Specifies whether to interpret/write CML's aromatic bond type "a" when reading/writing CML data.
CDPL_CHEM_API const Base::LookupKey MDL_UPDATE_TIMESTAMP
Specifies whether to update the timestamp of Mol- and Rxn-File header blocks when writing data in an ...
CDPL_CHEM_API const Base::LookupKey MDL_IGNORE_PARITY
Specifies whether the stereo parity of atoms shall be ignored when reading or writing data in an MDL ...
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_ELEMENT_NAMESPACE
Specifies the XML namespace URI emitted with the root element when generating CML output.
CDPL_CHEM_API const Base::LookupKey JME_SEPARATE_COMPONENTS
Specifies for the output of data in JME format whether the components of a molecular graph shall be w...
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_COMPACT_BOND_DATA
Specifies whether to use a compact (array-style) representation for bond data when generating CML out...
CDPL_CHEM_API const Base::LookupKey MDL_TRUNCATE_STRINGS
Specifies whether string values that exceed the size of an output data field may be truncated when wr...
CDPL_CHEM_API const Base::LookupKey MOL2_OUTPUT_FORMAL_CHARGES
Specifies whether to emit formal atomic charges in the partial charge column when generating Sybyl MO...
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_BOND_STEREO
Specifies whether to generate SMILES strings that include directional bonds for the definition of dou...
CDPL_CHEM_API const Base::LookupKey CHECK_LINE_LENGTH
Specifies whether to check if data lines exceed the maximum allowed line length when reading or writi...
CDPL_CHEM_API const Base::LookupKey MULTI_CONF_EXPORT
Specifies whether to write all molecule conformations on output.
CDPL_CHEM_API const Base::LookupKey INCHI_OUTPUT_OPTIONS
Specifies options for the output of InChI strings.
CDPL_CHEM_API const Base::LookupKey MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY
Specifies whether to output the energy of conformers as an MDL SD-File structure data entry when writ...
CDPL_CHEM_API const Base::LookupKey MDL_TRIM_STRINGS
Specifies whether to remove leading and trailing whitespace from string values when reading or writin...
CDPL_CHEM_API const Base::LookupKey MDL_RXN_FILE_VERSION
Specifies the desired data format version for the output of reactions in MDL Rxn- or RD-File format.
CDPL_CHEM_API const Base::LookupKey XYZ_COMMENT_IS_NAME
Specifies whether to treat the comment line of an XYZ record as the molecule name on data I/O.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_COMPACT_ATOM_DATA
Specifies whether to use a compact (array-style) representation for atom data when generating CML out...
CDPL_CHEM_API const Base::LookupKey XYZ_CALC_FORMAL_CHARGES
Specifies whether to recompute formal atomic charges after the bond perception step when reading XYZ ...
CDPL_CHEM_API const Base::LookupKey MOL2_ENABLE_EXTENDED_ATOM_TYPES
Specifies whether to enable the CDPL-specific extended Sybyl atom type set when reading/writing Sybyl...
CDPL_CHEM_API const Base::LookupKey SMILES_RECORD_FORMAT
Specifies the format of SMILES molecular graph or reaction data records.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_ATOM_PARITY
Specifies whether to emit tetrahedral atom parities when generating CML output.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_SINGLE_BOND_STEREO
Specifies whether to emit wedge/hash stereo flags for single bonds when generating CML output.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_MOLECULE_NAME
Specifies whether to emit the title attribute (molecule name) when generating CML output.
CDPL_CHEM_API const Base::LookupKey XYZ_PERCEIVE_CONNECTIVITY
Specifies whether to perceive bond connectivity from atom 3D coordinates when reading XYZ data.
CDPL_CHEM_API const Base::LookupKey MDL_TRUNCATE_LINES
Specifies whether data lines that exceed the maximum allowed line length may be truncated when writin...
CDPL_CHEM_API const Base::LookupKey CONF_INDEX_NAME_SUFFIX_PATTERN
Specifies a format pattern used to derive per-conformer molecule name suffixes from the conformer ind...
CDPL_CHEM_API const Base::LookupKey MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD
Specifies whether to output conformer energies into the energy field of the molecule header block whe...
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_STRUCTURE_DATA
Specifies whether to emit attached structure data fields when generating CML output.
CDPL_CHEM_API const Base::LookupKey MULTI_CONF_INPUT_PROCESSOR
Specifies an instance of Chem::MultiConfMoleculeInputProcessor that implements the logic of multi-con...
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_ATOM_STEREO
Specifies whether to generate SMILES strings with atom configuration specifications.
CDPL_CHEM_API const Base::LookupKey INCHI_INPUT_OPTIONS
Specifies options for the input of InChI strings.
CDPL_CHEM_API const Base::LookupKey MOL2_CHARGE_TYPE
Specifies the charge type to write to the @<TRIPOS>MOLECULE block when generating Sybyl MOL2 output (...
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_RING_BOND_STEREO
Specifies whether to generate SMILES strings that also include directional bonds for the definition o...
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_KEKULE_FORM
Specifies whether to generate SMILES strings with kekulized aromatic rings.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_XML_DECLARATION
Specifies whether to emit an XML declaration at the beginning of CML output records.
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_SINGLE_BONDS
Specifies whether to generate SMILES strings with explicit single bond specifications.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_SPIN_MULTIPLICITY
Specifies whether to emit the atom spin multiplicity when generating CML output.
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_ISOTOPE
Specifies whether to generate SMILES strings with isotopic mass specifications.
CDPL_CHEM_API const Base::LookupKey SMILES_MIN_STEREO_BOND_RING_SIZE
Specifies the minimum ring size that is required for the specification of ring double bond configurat...
CDPL_CHEM_API const Base::LookupKey MDL_TRIM_LINES
Specifies whether to remove leading and trailing whitespace from data lines when reading or writing d...
CDPL_CHEM_API const Base::LookupKey MDL_CTAB_VERSION
Specifies the desired version of the connection table data format for the output of molecular graphs ...
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_HYDROGEN_COUNT
Specifies whether to generate SMILES strings with implicit hydrogen count specifications.
CDPL_CHEM_API const Base::LookupKey RECORD_SEPARATOR
Specifies the separator for SMILES, SMARTS, JME and InChI output data records.
CDPL_CHEM_API const Base::LookupKey MOL2_MOLECULE_TYPE
Specifies the molecule type to write to the @<TRIPOS>MOLECULE block when generating Sybyl MOL2 output...
CDPL_CHEM_API const Base::LookupKey CDF_OUTPUT_SINGLE_PRECISION_FLOATS
Specifies whether floating-point values shall be output in single-precision (true) or double-precisio...
CDPL_CHEM_API const Base::LookupKey MDL_CONF_ENERGY_SD_TAG
Specifies the MDL SD-File structure data entry header used for the conformer energy.
CDPL_CHEM_API const Base::LookupKey MOL2_OUTPUT_SUBSTRUCTURES
Specifies whether to write the @<TRIPOS>SUBSTRUCTURE block when generating Sybyl MOL2 output.
CDPL_CHEM_API const Base::LookupKey MDL_ENABLE_AROMATIC_BOND_TYPES
Specifies whether to output the 'aromatic' bond type value (4) in the type field of aromatic bonds wh...
CDPL_CHEM_API const Base::LookupKey MOL2_READ_PARTIAL_AS_FORMAL_CHARGES
Specifies whether to interpret read partial charges as formal charges (obtained by rounding to the ne...
CDPL_CHEM_API const Base::LookupKey MOL2_CALC_FORMAL_CHARGES
Specifies whether to recompute formal charges from atom types when reading Sybyl MOL2 data.
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_AROMATIC_BONDS
Specifies whether to generate SMILES strings with explicit aromatic bond specifications.
CDPL_CHEM_API const Base::LookupKey OUTPUT_CONF_ENERGY_AS_COMMENT
Specifies whether to write the conformer energy into the molecule comment field (if supported by the ...
CDPL_CHEM_API const Base::LookupKey STRICT_ERROR_CHECKING
Specifies whether non-fatal recoverable I/O errors should be ignored or cause an I/O operation to fai...
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_DOUBLE_BOND_STEREO
Specifies whether to emit cis/trans descriptors for double bonds when generating CML output.
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_ISOTOPE
Specifies whether to emit the isotopic mass number of non-standard isotopes when generating CML outpu...
CDPL_CHEM_API const Base::LookupKey ORDINARY_HYDROGEN_DEPLETE
Specifies whether the calculation of a molecular property has to be performed for the ordinary hydrog...
CDPL_CHEM_API const Base::LookupKey MULTI_CONF_IMPORT
Specifies whether to check for and import multi-conformer molecules.
CDPL_CHEM_API const Base::LookupKey SMILES_RXN_OUTPUT_ATOM_MAPPING_ID
Specifies whether to generate reaction SMILES strings that contain atom-atom mapping numbers.
The namespace of the Chemical Data Processing Library.