/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h is in librdkit-dev 201603.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 | //
// Copyright (C) 2003-2015 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef _RD_GASTEIGERPARAMS_H
#define _RD_GASTEIGERPARAMS_H
#include <RDGeneral/types.h>
#include <RDGeneral/Exceptions.h>
#include <string>
#include <map>
namespace RDKit {
extern std::string paramData;
extern std::string additionalParamData;
// this is a constant used during the iteration procedure for the hydrogen atoms
// for the remaining atoms it is computed on the fly
const double IONXH = 20.02;
const double DAMP_SCALE = 0.5;
const double DAMP = 0.5;
class GasteigerParams {
/* \brief Container for all the partial charge paramters
*
* It is filled by the paramData string defined in GasteigerParams.cpp
* The main data member is a STL map that take a pair<std::string,
*std::string>
* of element name and mode (hybridization or bonding mode) and return a
*vector
* of three parameters, used int eh ierative partial charges euqlization
*procedure
*/
public:
static const GasteigerParams *getParams(const std::string ¶mData = "");
~GasteigerParams() { d_paramMap.clear(); }
DOUBLE_VECT getParams(std::string elem, std::string mode,
bool throwOnFailure = false) const {
std::pair<std::string, std::string> query(elem, mode);
std::map<std::pair<std::string, std::string>, DOUBLE_VECT>::const_iterator
iter;
iter = d_paramMap.find(query);
if (iter != d_paramMap.end()) {
return iter->second;
} else {
if (throwOnFailure) {
std::string message =
"ERROR: No Gasteiger Partial Charge parameters for Element: ";
message += elem;
message += " Mode: ";
message += mode;
throw ValueErrorException(message);
} else {
iter =
d_paramMap.find(std::make_pair(std::string("X"), std::string("*")));
if (iter != d_paramMap.end()) {
return iter->second;
} else {
std::string message =
"ERROR: Default Gasteiger Partial Charge parameters are missing";
throw ValueErrorException(message);
}
}
}
}
GasteigerParams(std::string paramData = "");
private:
std::map<std::pair<std::string, std::string>, DOUBLE_VECT> d_paramMap;
static class GasteigerParams *ds_instance;
};
};
#endif
|