Chemical Data Processing Library C++ API - Version 1.4.0
Chem/ControlParameter.hpp
Go to the documentation of this file.
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  {
52 
65 
75 
87 
97 
116 
134 
147 
161 
173 
185 
198 
213 
220 
227 
233 
243 
257 
275 
287 
301 
316 
330 
342 
355 
371 
380 
392 
404 
416 
428 
440 
453 
466 
476 
486 
492 
498 
504 
514 
521 
528 
535 
542 
550 
556 
563 
570 
576 
583 
590 
598 
606 
614 
622 
629 
636 
643 
650 
657 
664 
671 
678 
685 
692 
699 
700  } // namespace ControlParameter
701  } // namespace Chem
702 } // namespace CDPL
703 
704 #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 [SMILES] 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 [SMILES].
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 [SMILES] 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/wrting 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 [JME] whether the components of a molecular graph shal...
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_COMPACT_BOND_DATA
Specifies whether to use CML's compact (array-style) representation for bond data on output....
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 [SMILES] that include directional bonds for the definiti...
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. Value Type: bool.
CDPL_CHEM_API const Base::LookupKey INCHI_OUTPUT_OPTIONS
Specifies options for the output of InChI strings [INCHI].
CDPL_CHEM_API const Base::LookupKey MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY
Specifies whether to write conformer energies as an SD-file entry when writing data in an MDL CTFile ...
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 an MDL Rxn- or RD-File forma...
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....
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_COMPACT_ATOM_DATA
Specifies whether to use CML's compact (array-style) representation for atom data on output....
CDPL_CHEM_API const Base::LookupKey XYZ_CALC_FORMAL_CHARGES
Specifies whether to recompute formal atomic charges after the bond perception step on XYZ input....
CDPL_CHEM_API const Base::LookupKey MOL2_ENABLE_EXTENDED_ATOM_TYPES
Specifies whether to enable the extended Sybyl atom-type set when reading/writing Sybyl MOL2 data....
CDPL_CHEM_API const Base::LookupKey SMILES_RECORD_FORMAT
Specifies the format of SMILES molecular graph or reaction data records [SMILES].
CDPL_CHEM_API const Base::LookupKey CML_OUTPUT_ATOM_PARITY
Specifies whether to encode tetrahedral atom parities when generating CML output. Value Type: bool.
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 write conformer energies into the energy field of the molecule header block when...
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 [SMILES] with atom parity specifications.
CDPL_CHEM_API const Base::LookupKey INCHI_INPUT_OPTIONS
Specifies options for the input of InChI strings [INCHI].
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 [SMILES] that also include directional bonds for the def...
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_KEKULE_FORM
Specifies whether to generate SMILES strings [SMILES] 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 [SMILES] 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. Value Type: bool.
CDPL_CHEM_API const Base::LookupKey SMILES_OUTPUT_ISOTOPE
Specifies whether to generate SMILES strings [SMILES] 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 geometries...
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 [SMILES] 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 [SMILES,...
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 written to the native CDF format are encoded in single-precis...
CDPL_CHEM_API const Base::LookupKey MDL_CONF_ENERGY_SD_TAG
Specifies the SD-file tag used for the conformer energy entry (see MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY...
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 round Sybyl partial charges to the nearest integer formal charges on Sybyl MOL2 ...
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 [SMILES] 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 on output....
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 encode 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. Value Type: bool.
CDPL_CHEM_API const Base::LookupKey SMILES_RXN_OUTPUT_ATOM_MAPPING_ID
Specifies whether to generate reaction SMILES strings [SMILES] that contain atom-atom mapping numbers...
The namespace of the Chemical Data Processing Library.