Chemical Data Processing Library C++ API - Version 1.1.1
Chem/ControlParameterDefault.hpp
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1 /*
2  * ControlParameterDefault.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_CONTROLPARAMETERDEFAULT_HPP
30 #define CDPL_CHEM_CONTROLPARAMETERDEFAULT_HPP
31 
32 #include <string>
33 #include <cstddef>
34 
35 #include "CDPL/Chem/APIPrefix.hpp"
37 
38 
39 namespace CDPL
40 {
41 
42  namespace Chem
43  {
44 
48  namespace ControlParameterDefault
49  {
50 
54  extern CDPL_CHEM_API const bool STRICT_ERROR_CHECKING;
55 
59  extern CDPL_CHEM_API const bool ORDINARY_HYDROGEN_DEPLETE;
60 
65 
69  extern CDPL_CHEM_API const bool CHECK_LINE_LENGTH;
70 
74  extern CDPL_CHEM_API const bool JME_SEPARATE_COMPONENTS;
75 
79  extern CDPL_CHEM_API const std::string RECORD_SEPARATOR;
80 
84  extern CDPL_CHEM_API const std::string INCHI_INPUT_OPTIONS;
85 
89  extern CDPL_CHEM_API const std::string INCHI_OUTPUT_OPTIONS;
90 
94  extern CDPL_CHEM_API const std::size_t COORDINATES_DIMENSION;
95 
99  extern CDPL_CHEM_API const bool MDL_IGNORE_PARITY;
100 
104  extern CDPL_CHEM_API const bool MDL_TRIM_STRINGS;
105 
109  extern CDPL_CHEM_API const bool MDL_TRIM_LINES;
110 
114  extern CDPL_CHEM_API const bool MDL_TRUNCATE_STRINGS;
115 
119  extern CDPL_CHEM_API const bool MDL_TRUNCATE_LINES;
120 
124  extern CDPL_CHEM_API const bool MDL_UPDATE_TIMESTAMP;
125 
129  extern CDPL_CHEM_API const unsigned int MDL_CTAB_VERSION;
130 
135 
140 
144  extern CDPL_CHEM_API const std::string MDL_CONF_ENERGY_SD_TAG;
145 
149  extern CDPL_CHEM_API const unsigned int MDL_RXN_FILE_VERSION;
150 
154  extern CDPL_CHEM_API const std::string SMILES_RECORD_FORMAT;
155 
159  extern CDPL_CHEM_API const bool SMILES_WRITE_CANONICAL_FORM;
160 
164  extern CDPL_CHEM_API const bool SMILES_WRITE_KEKULE_FORM;
165 
169  extern CDPL_CHEM_API const bool SMILES_WRITE_ATOM_STEREO;
170 
174  extern CDPL_CHEM_API const bool SMILES_WRITE_BOND_STEREO;
175 
180 
184  extern CDPL_CHEM_API const std::size_t SMILES_MIN_STEREO_BOND_RING_SIZE;
185 
189  extern CDPL_CHEM_API const bool SMILES_WRITE_ISOTOPE;
190 
196 
202 
206  extern CDPL_CHEM_API const bool SMILES_WRITE_SINGLE_BONDS;
207 
211  extern CDPL_CHEM_API const bool SMILES_WRITE_AROMATIC_BONDS;
212 
216  extern CDPL_CHEM_API const bool SMILES_NO_ORGANIC_SUBSET;
217 
221  extern CDPL_CHEM_API const bool MULTI_CONF_IMPORT;
222 
226  extern CDPL_CHEM_API const bool MULTI_CONF_EXPORT;
227 
233 
238 
239  extern CDPL_CHEM_API const std::string CONF_INDEX_NAME_SUFFIX_PATTERN;
240 
242 
244 
246 
247  extern CDPL_CHEM_API const bool MOL2_CALC_FORMAL_CHARGES;
248 
249  extern CDPL_CHEM_API const unsigned int MOL2_CHARGE_TYPE;
250 
251  extern CDPL_CHEM_API const unsigned int MOL2_MOLECULE_TYPE;
252 
253  extern CDPL_CHEM_API const bool MOL2_OUTPUT_SUBSTRUCTURES;
254 
255  extern CDPL_CHEM_API const bool XYZ_COMMENT_IS_NAME;
256 
257  extern CDPL_CHEM_API const bool XYZ_PERCEIVE_CONNECTIVITY;
258 
259  extern CDPL_CHEM_API const bool XYZ_PERCEIVE_BOND_ORDERS;
260 
261  extern CDPL_CHEM_API const bool XYZ_CALC_FORMAL_CHARGES;
262 
263  } // namespace ControlParameterDefault
264  } // namespace Chem
265 } // namespace CDPL
266 
267 #endif // CDPL_CHEM_CONTROLPARAMETERDEFAULT_HPP
CDPL::Chem::ControlParameterDefault::MULTI_CONF_INPUT_PROCESSOR
CDPL_CHEM_API const MultiConfMoleculeInputProcessor::SharedPointer MULTI_CONF_INPUT_PROCESSOR
Default setting (= pointer to Chem::DefaultMultiConfMoleculeInputProcessor instance) for the control-...
CDPL::Chem::ControlParameterDefault::XYZ_CALC_FORMAL_CHARGES
CDPL_CHEM_API const bool XYZ_CALC_FORMAL_CHARGES
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_RING_BOND_STEREO
CDPL_CHEM_API const bool SMILES_WRITE_RING_BOND_STEREO
Default setting (= true) for the control-parameter Chem::ControlParameter::SMILES_WRITE_RING_BOND_STE...
CDPL::Chem::ControlParameterDefault::MDL_TRUNCATE_STRINGS
CDPL_CHEM_API const bool MDL_TRUNCATE_STRINGS
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_TRUNCATE_STRINGS.
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CHEM_API.
CDPL::Chem::ControlParameterDefault::MDL_TRUNCATE_LINES
CDPL_CHEM_API const bool MDL_TRUNCATE_LINES
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_TRUNCATE_LINES.
CDPL_CHEM_API
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Chem::ControlParameterDefault::MDL_TRIM_STRINGS
CDPL_CHEM_API const bool MDL_TRIM_STRINGS
Default setting (= true) for the control-parameter Chem::ControlParameter::MDL_TRIM_STRINGS.
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_CANONICAL_FORM
CDPL_CHEM_API const bool SMILES_WRITE_CANONICAL_FORM
Default setting (= false) for the control-parameter Chem::ControlParameter::SMILES_WRITE_CANONICAL_FO...
CDPL::Chem::ControlParameterDefault::MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD
CDPL_CHEM_API const bool MDL_OUTPUT_CONF_ENERGY_TO_ENERGY_FIELD
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_TO...
CDPL::Chem::ControlParameterDefault::MDL_RXN_FILE_VERSION
CDPL_CHEM_API const unsigned int MDL_RXN_FILE_VERSION
Default setting (= MDLDataFormatVersion::UNDEF) for the control-parameter Chem::ControlParameter::MDL...
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_ISOTOPE
CDPL_CHEM_API const bool SMILES_WRITE_ISOTOPE
Default setting (= true) for the control-parameter Chem::ControlParameter::SMILES_WRITE_ISOTOPE.
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_BOND_STEREO
CDPL_CHEM_API const bool SMILES_WRITE_BOND_STEREO
Default setting (= true) for the control-parameter Chem::ControlParameter::SMILES_WRITE_BOND_STEREO.
CDPL::Chem::ControlParameterDefault::MDL_CTAB_VERSION
CDPL_CHEM_API const unsigned int MDL_CTAB_VERSION
Default setting (= MDLDataFormatVersion::UNDEF) for the control-parameter Chem::ControlParameter::MDL...
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_AROMATIC_BONDS
CDPL_CHEM_API const bool SMILES_WRITE_AROMATIC_BONDS
Default setting (= false) for the control-parameter Chem::ControlParameter::SMILES_WRITE_AROMATIC_BON...
CDPL::Chem::ControlParameterDefault::MDL_UPDATE_TIMESTAMP
CDPL_CHEM_API const bool MDL_UPDATE_TIMESTAMP
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_UPDATE_TIMESTAMP.
CDPL::Chem::ControlParameterDefault::SMILES_MOL_WRITE_ATOM_MAPPING_ID
CDPL_CHEM_API const bool SMILES_MOL_WRITE_ATOM_MAPPING_ID
Default setting (= false) for the control-parameter Chem::ControlParameter::SMILES_WRITE_ATOM_MAPPING...
CDPL::Chem::MultiConfMoleculeInputProcessor::SharedPointer
std::shared_ptr< MultiConfMoleculeInputProcessor > SharedPointer
A reference-counted smart pointer [SHPTR] for dynamically allocated MultiConfMoleculeInputProcessor i...
Definition: MultiConfMoleculeInputProcessor.hpp:56
CDPL::Chem::ControlParameterDefault::BOND_MEMBER_SWAP_STEREO_FIX
CDPL_CHEM_API const bool BOND_MEMBER_SWAP_STEREO_FIX
Default setting (= true) for the control-parameter Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FI...
CDPL::Chem::ControlParameterDefault::MOL2_CHARGE_TYPE
CDPL_CHEM_API const unsigned int MOL2_CHARGE_TYPE
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_SINGLE_BONDS
CDPL_CHEM_API const bool SMILES_WRITE_SINGLE_BONDS
Default setting (= false) for the control-parameter Chem::ControlParameter::SMILES_WRITE_SINGLE_BONDS...
CDPL::Chem::ControlParameterDefault::INCHI_OUTPUT_OPTIONS
CDPL_CHEM_API const std::string INCHI_OUTPUT_OPTIONS
Default setting (= "/WarnOnEmptyStructure /AuxNone /NEWPSOFF") for the control-parameter Chem::Contro...
CDPL::Chem::ControlParameterDefault::CDF_WRITE_SINGLE_PRECISION_FLOATS
CDPL_CHEM_API const bool CDF_WRITE_SINGLE_PRECISION_FLOATS
CDPL::Chem::ControlParameterDefault::MULTI_CONF_IMPORT
CDPL_CHEM_API const bool MULTI_CONF_IMPORT
Default setting (= true) for the control-parameter Chem::ControlParameter::MULTI_CONF_IMPORT.
CDPL::Chem::ControlParameterDefault::MULTI_CONF_EXPORT
CDPL_CHEM_API const bool MULTI_CONF_EXPORT
Default setting (= true) for the control-parameter Chem::ControlParameter::MULTI_CONF_EXPORT.
CDPL::Chem::ControlParameterDefault::JME_SEPARATE_COMPONENTS
CDPL_CHEM_API const bool JME_SEPARATE_COMPONENTS
Default setting (= true) for the control-parameter Chem::ControlParameter::JME_SEPARATE_COMPONENTS.
CDPL::Chem::ControlParameterDefault::MOL2_OUTPUT_SUBSTRUCTURES
CDPL_CHEM_API const bool MOL2_OUTPUT_SUBSTRUCTURES
CDPL::Chem::ControlParameterDefault::XYZ_PERCEIVE_CONNECTIVITY
CDPL_CHEM_API const bool XYZ_PERCEIVE_CONNECTIVITY
CDPL::Chem::ControlParameterDefault::XYZ_PERCEIVE_BOND_ORDERS
CDPL_CHEM_API const bool XYZ_PERCEIVE_BOND_ORDERS
CDPL::Chem::ControlParameterDefault::STRICT_ERROR_CHECKING
CDPL_CHEM_API const bool STRICT_ERROR_CHECKING
Default setting (= false) for the control-parameter Chem::ControlParameter::STRICT_ERROR_CHECKING.
CDPL::Chem::ControlParameterDefault::CHECK_LINE_LENGTH
CDPL_CHEM_API const bool CHECK_LINE_LENGTH
Default setting (= false) for the control-parameter Chem::ControlParameter::CHECK_LINE_LENGTH.
CDPL::Chem::ControlParameterDefault::MDL_IGNORE_PARITY
CDPL_CHEM_API const bool MDL_IGNORE_PARITY
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_IGNORE_PARITY.
CDPL::Chem::ControlParameterDefault::ORDINARY_HYDROGEN_DEPLETE
CDPL_CHEM_API const bool ORDINARY_HYDROGEN_DEPLETE
Default setting (= true) for the control-parameter Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE.
CDPL::Chem::ControlParameterDefault::COORDINATES_DIMENSION
CDPL_CHEM_API const std::size_t COORDINATES_DIMENSION
Default setting (= 1) for the control-parameter Chem::ControlParameter::COORDINATES_DIMENSION.
CDPL::Chem::ControlParameterDefault::SMILES_MIN_STEREO_BOND_RING_SIZE
CDPL_CHEM_API const std::size_t SMILES_MIN_STEREO_BOND_RING_SIZE
Default setting (= 8) for the control-parameter Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_S...
CDPL::Chem::ControlParameterDefault::SMILES_RECORD_FORMAT
CDPL_CHEM_API const std::string SMILES_RECORD_FORMAT
Default setting (= "S") for the control-parameter Chem::ControlParameter::SMILES_RECORD_FORMAT.
CDPL::Chem::ControlParameterDefault::MOL2_ENABLE_AROMATIC_BOND_TYPES
CDPL_CHEM_API const bool MOL2_ENABLE_AROMATIC_BOND_TYPES
CDPL::Chem::ControlParameterDefault::OUTPUT_CONF_ENERGY_AS_COMMENT
CDPL_CHEM_API const bool OUTPUT_CONF_ENERGY_AS_COMMENT
Default setting (= false) for the control-parameter Chem::ControlParameter::OUTPUT_CONF_ENERGY_AS_COM...
CDPL::Chem::ControlParameterDefault::INCHI_INPUT_OPTIONS
CDPL_CHEM_API const std::string INCHI_INPUT_OPTIONS
Default setting (= "") for the control-parameter Chem::ControlParameter::INCHI_INPUT_OPTIONS.
CDPL::Chem::ControlParameterDefault::SMILES_RXN_WRITE_ATOM_MAPPING_ID
CDPL_CHEM_API const bool SMILES_RXN_WRITE_ATOM_MAPPING_ID
Default setting (= true) for the control-parameter Chem::ControlParameter::SMILES_WRITE_ATOM_MAPPING_...
CDPL::Chem::ControlParameterDefault::MOL2_MOLECULE_TYPE
CDPL_CHEM_API const unsigned int MOL2_MOLECULE_TYPE
CDPL::Chem::ControlParameterDefault::MOL2_CALC_FORMAL_CHARGES
CDPL_CHEM_API const bool MOL2_CALC_FORMAL_CHARGES
CDPL::Chem::ControlParameterDefault::SMILES_NO_ORGANIC_SUBSET
CDPL_CHEM_API const bool SMILES_NO_ORGANIC_SUBSET
Default setting (= false) for the control-parameter Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET.
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_ATOM_STEREO
CDPL_CHEM_API const bool SMILES_WRITE_ATOM_STEREO
Default setting (= true) for the control-parameter Chem::ControlParameter::SMILES_WRITE_ATOM_STEREO.
CDPL::Chem::ControlParameterDefault::MOL2_ENABLE_EXTENDED_ATOM_TYPES
CDPL_CHEM_API const bool MOL2_ENABLE_EXTENDED_ATOM_TYPES
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::Chem::ControlParameterDefault::MDL_CONF_ENERGY_SD_TAG
CDPL_CHEM_API const std::string MDL_CONF_ENERGY_SD_TAG
Default setting (= "<Energy>") for the control-parameter Chem::ControlParameter::MDL_CONF_ENERGY_SD_T...
CDPL::Chem::ControlParameterDefault::MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY
CDPL_CHEM_API const bool MDL_OUTPUT_CONF_ENERGY_AS_SD_ENTRY
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_OUTPUT_CONF_ENERGY_AS...
CDPL::Chem::ControlParameterDefault::CONF_INDEX_NAME_SUFFIX_PATTERN
CDPL_CHEM_API const std::string CONF_INDEX_NAME_SUFFIX_PATTERN
CDPL::Chem::ControlParameterDefault::MDL_TRIM_LINES
CDPL_CHEM_API const bool MDL_TRIM_LINES
Default setting (= false) for the control-parameter Chem::ControlParameter::MDL_TRIM_LINES.
CDPL::Chem::ControlParameterDefault::SMILES_WRITE_KEKULE_FORM
CDPL_CHEM_API const bool SMILES_WRITE_KEKULE_FORM
Default setting (= false) for the control-parameter Chem::ControlParameter::SMILES_WRITE_KEKULE_FORM.
MultiConfMoleculeInputProcessor.hpp
Definition of the class CDPL::Chem::MultiConfMoleculeInputProcessor.
CDPL::Chem::ControlParameterDefault::RECORD_SEPARATOR
CDPL_CHEM_API const std::string RECORD_SEPARATOR
Default setting (= "\n") for the control-parameter Chem::ControlParameter::RECORD_SEPARATOR.
CDPL::Chem::ControlParameterDefault::XYZ_COMMENT_IS_NAME
CDPL_CHEM_API const bool XYZ_COMMENT_IS_NAME