RDKit: GasteigerParams.h Source File

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GasteigerParams.h
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1//
2// Copyright (C) 2003-2015 Rational Discovery LLC
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <RDGeneral/export.h>
11#ifndef _RD_GASTEIGERPARAMS_H
12#define _RD_GASTEIGERPARAMS_H
13
14#include <RDGeneral/types.h>
15#include <RDGeneral/Exceptions.h>
16#include <string>
17#include <map>
18
19namespace RDKit {
20extern std::string paramData;
21extern std::string additionalParamData;
22
23// this is a constant used during the iteration procedure for the hydrogen atoms
24// for the remaining atoms it is computed on the fly
25 const double IONXH = 20.02;
26
27 const double DAMP_SCALE = 0.5;
28 const double DAMP = 0.5;
29
30 class RDKIT_PARTIALCHARGES_EXPORT GasteigerParams {
31 /* \brief Container for all the partial charge parameters
32 *
33 * It is filled by the paramData string defined in GasteigerParams.cpp
34 * The main data member is a STL map that take a pair<std::string,
35 *std::string>
36 * of element name and mode (hybridization or bonding mode) and return a
37 *vector
38 * of three parameters, used in the iterative partial charges equalization
39 *procedure
40 */
41
42 public:
43 static const GasteigerParams *getParams(const std::string &paramData = "");
44
45 ~GasteigerParams() { d_paramMap.clear(); }
46
47 DOUBLE_VECT getParams(std::string elem, std::string mode,
48 bool throwOnFailure = false) const {
49 std::pair<std::string, std::string> query(elem, mode);
50 std::map<std::pair<std::string, std::string>, DOUBLE_VECT>::const_iterator
51 iter;
52 iter = d_paramMap.find(query);
53 if (iter != d_paramMap.end()) {
54 return iter->second;
55 } else {
56 if (throwOnFailure) {
57 std::string message =
58 "ERROR: No Gasteiger Partial Charge parameters for Element: ";
59 message += elem;
60 message += " Mode: ";
61 message += mode;
62 throw ValueErrorException(message);
63 } else {
64 iter =
65 d_paramMap.find(std::make_pair(std::string("X"), std::string("*")));
66 if (iter != d_paramMap.end()) {
67 return iter->second;
68 } else {
69 std::string message =
70 "ERROR: Default Gasteiger Partial Charge parameters are missing";
71 throw ValueErrorException(message);
72 }
73 }
74 }
75 }
76
77 GasteigerParams(std::string paramData = "");
78
79 private:
80 std::map<std::pair<std::string, std::string>, DOUBLE_VECT> d_paramMap;
81
82 static class GasteigerParams *ds_instance;
83};
84}; // namespace RDKit
85
86#endif
Exceptions.h
RDKit::GasteigerParams::~GasteigerParams
~GasteigerParams()
Definition GasteigerParams.h:45
RDKit::GasteigerParams::getParams
DOUBLE_VECT getParams(std::string elem, std::string mode, bool throwOnFailure=false) const
Definition GasteigerParams.h:47
RDKit::GasteigerParams::GasteigerParams
GasteigerParams(std::string paramData="")
RDKit::GasteigerParams::getParams
static const GasteigerParams * getParams(const std::string &paramData="")
ValueErrorException
Class to allow us to throw a ValueError from C++ and have it make it back to Python.
Definition Exceptions.h:40
export.h
RDKIT_PARTIALCHARGES_EXPORT
#define RDKIT_PARTIALCHARGES_EXPORT
Definition export.h:401
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::DAMP
const double DAMP
Definition GasteigerParams.h:28
RDKit::IONXH
const double IONXH
Definition GasteigerParams.h:25
RDKit::additionalParamData
std::string additionalParamData
RDKit::paramData
std::string paramData
RDKit::DAMP_SCALE
const double DAMP_SCALE
Definition GasteigerParams.h:27
RDKit::DOUBLE_VECT
std::vector< double > DOUBLE_VECT
Definition types.h:328
types.h