source: src/Actions/FragmentationAction/FragmentationAction.def@ ce70d25

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Last change on this file since ce70d25 was 0f5956, checked in by Frederik Heber <heber@…>, 8 years ago

Added "parse-state-files" option to fragment-molecule which is off by default.

  • this prevents accidental parsing of stale keysets, adjacency, or orderatsite files. These hard to find errors ever and again cause failing fragmentation because e.g. some hydrogen is suddenly in the keysets although hydrogens are excluded.
  • Property mode set to 100644
File size: 2.8 KB
Line 
1/*
2 * FragmentationAction.def
3 *
4 * Created on: Aug 26, 2010
5 * Author: heber
6 */
7
8// all includes and forward declarations necessary for non-integral types below
9#include <boost/assign.hpp>
10#include <string>
11#include <vector>
12
13#include "Parameters/Validators/DummyValidator.hpp"
14#include "Parameters/Validators/GenericValidators.hpp"
15#include "Parameters/Validators/RangeValidator.hpp"
16#include "Parameters/Validators/STLVectorValidator.hpp"
17#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
18#include "Parameters/Validators/Specific/ParserTypeValidator.hpp"
19
20// i.e. there is an integer with variable name Z that can be found in
21// ValueStorage by the token "Z" -> first column: int, Z, "Z"
22// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
23#define paramtypes (std::string)(double)(int)(bool)(bool)(std::vector<std::string>)(unsigned int)(unsigned int)(bool)(bool)
24#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")("grid-level")("inter-order")("DoCyclesFull")("parse-state-files")
25#define paramdescriptions ("prefix of each fragment file")("distance in space up to which fragments are combined")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")("resolution of density sampling multigrid")("up to which order distinct fragments are combined")("always calculate (aromatic) rings fully, even beyond desired order")("whether to parse keysets, orderatsite, adjacency from state files")
26#define paramdefaults (PARAM_DEFAULT("BondFragment"))(PARAM_DEFAULT(3.))(PARAM_DEFAULT(3))(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(NOPARAM_DEFAULT)(PARAM_DEFAULT(5))(PARAM_DEFAULT(0))(PARAM_DEFAULT(false))(PARAM_DEFAULT(false))
27#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)(level)(InterOrder)(DoCyclesFull)(ParseStateFiles)
28#define paramvalids \
29(DummyValidator< std::string >()) \
30(BoxLengthValidator()) \
31(DummyValidator< int >()) \
32(DummyValidator< bool >()) \
33(DummyValidator< bool >()) \
34(STLVectorValidator< std::vector<std::string> >(0, 10, ParserTypeValidator())) \
35(RangeValidator< unsigned int >(1, 10)) \
36(DummyValidator< unsigned int >()) \
37(DummyValidator< bool >()) \
38(DummyValidator< bool >())
39
40#undef statetypes
41#undef statereferences
42
43// some defines for all the names, you may use ACTION, STATE and PARAMS
44#define CATEGORY Fragmentation
45#define MENUNAME "fragmentation"
46#define MENUPOSITION 3
47#define ACTIONNAME Fragmentation
48#define TOKEN "fragment-molecule"
49
50// finally the information stored in the ActionTrait specialization
51#define DESCRIPTION "create for a given molecule into fragments up to given order"
52#define SHORTFORM "f"
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