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e08e0d16d8999a4ef9df3142268ee705a8e2d795
rdkit/Code/ForceField/MMFF/Params.cpp
Greg Landrum e08e0d16d8 first pass, using google style
2015-11-14 14:58:11 +01:00

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// $Id$
//
// Copyright (C) 2013 Paolo Tosco
//
// Copyright (C) 2004-2006 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.
//
#ifdef WIN32
#define _USE_MATH_DEFINES
#endif
#include <cmath>
#include "Params.h"
#include <iostream>
#include <sstream>
#include <RDGeneral/StreamOps.h>
#include <boost/lexical_cast.hpp>
#include <boost/tokenizer.hpp>
#include <Geometry/point.h>
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
namespace ForceFields {
namespace MMFF {
class MMFFAromCollection *MMFFAromCollection::ds_instance = NULL;
extern const boost::uint8_t defaultMMFFArom[];
MMFFAromCollection *MMFFAromCollection::getMMFFArom(
const boost::uint8_t *mmffArom) {
if (!ds_instance) {
ds_instance = new MMFFAromCollection(mmffArom);
} else if (mmffArom) {
delete ds_instance;
ds_instance = new MMFFAromCollection(mmffArom);
}
return ds_instance;
}
MMFFAromCollection::MMFFAromCollection(const boost::uint8_t *mmffArom) {
if (!mmffArom) {
mmffArom = defaultMMFFArom;
}
for (unsigned int i = 0; i < sizeof(mmffArom) / sizeof(mmffArom[0]); ++i) {
d_params.push_back(mmffArom[i]);
}
}
const boost::uint8_t defaultMMFFArom[] = {37, 38, 39, 44, 58, 59, 63, 64, 65,
66, 69, 76, 78, 79, 80, 81, 82};
class MMFFDefCollection *MMFFDefCollection::ds_instance = NULL;
extern const std::string defaultMMFFDef;
MMFFDefCollection *MMFFDefCollection::getMMFFDef(const std::string &mmffDef) {
if (!ds_instance) {
ds_instance = new MMFFDefCollection(mmffDef);
} else if (mmffDef != "") {
delete ds_instance;
ds_instance = new MMFFDefCollection(mmffDef);
}
return ds_instance;
}
MMFFDefCollection::MMFFDefCollection(std::string mmffDef) {
if (mmffDef == "") {
mmffDef = defaultMMFFDef;
}
std::istringstream inStream(mmffDef);
std::string inLine = RDKit::getLine(inStream);
unsigned int oldAtomType = 0;
unsigned int atomType;
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFDef mmffDefObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
// skip first token
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int atomType = boost::lexical_cast<unsigned int>(*token);
#else
atomType = (boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
#endif
++token;
// Level 2 (currently = Level 1, see MMFF.I page 513)
mmffDefObj.eqLevel[0] =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
// Level 3
mmffDefObj.eqLevel[1] =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
// Level 4
mmffDefObj.eqLevel[2] =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
// Level 5
mmffDefObj.eqLevel[3] =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
if (atomType != oldAtomType) {
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[atomType] = mmffDefObj;
#else
d_params.push_back(mmffDefObj);
#endif
oldAtomType = atomType;
}
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFDef =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* PRIMARY\n"
"* MMFF MMFF \n"
"*SYMBOL TYPE DEFAULT TYPES DEFINITION \n"
"*\n"
"CR 1 1 1 1 0 ALKYL CARBON \n"
"C=C 2 2 2 1 0 VINYLIC \n"
"* CSP2 2 2 2 1 0 GENERIC CSP2 \n"
"* CGD 2 2 2 1 0 GUANIDINE CARBON "
"\n"
"C=O 3 3 3 1 0 GENERAL CARBONYL "
"C \n"
"* C=N 3 3 3 1 0 C=N \n"
"* C=OR 3 3 3 1 0 KETONE OR "
"ALDEHYDE CO \n"
"* C=ON 3 3 3 1 0 AMIDE CARBONYL "
"\n"
"* COO 3 3 3 1 0 CARBOXYLIC ACID "
"OF EST \n"
"* COON 3 3 3 1 0 CARBAMATE "
"CARBONYL \n"
"* COOO 3 3 3 1 0 CARBONIC ACID "
"OR ESTER \n"
"* C=OS 3 3 3 1 0 THIOESTER, C=O "
"\n"
"* C=S 3 3 3 1 0 THIOESTER, C=S "
"\n"
"* C=SN 3 3 3 1 0 THIOAMIDE \n"
"* CSO2 3 3 3 1 0 CARBON IN >C=SO2 "
"\n"
"CSP 4 4 4 1 0 ACETYLENIC C "
"\n"
"* =C= 4 4 4 1 0 ALLENIC C \n"
"HC 5 5 5 5 0 H-C \n"
"* HSI 5 5 5 5 0 H-SI \n"
"* HP 5 5 5 5 0 H-P \n"
"OR 6 6 6 6 0 O-CSP3 \n"
"* OH2 6 6 6 6 0 OXYGEN IN H2O "
"\n"
"* OC=O 6 6 6 6 0 ESTER OR ACID "
"-O- \n"
"* OC=C 6 6 6 6 0 ENOL OR "
"PHEMOLIC O \n"
"* OC=N 6 6 6 6 0 OXYGEN IN -O-C=N "
"MOIETY\n"
"* OSO3 6 6 6 6 0 DIVALENT O "
"IN SULFATE\n"
"* OSO2 6 6 6 6 0 DIVALENT O "
"IN SULFITE\n"
"* OSO 6 6 6 6 0 PAIR OF "
"DIVALENT O ON S\n"
"* -OS 6 6 6 6 0 OTHER DIVALENT "
"O ON S\n"
"* OPO3 6 6 6 6 0 DIVALENT O "
"IN PHOSPHATE\n"
"* OPO2 6 6 6 6 0 DIVALENT O "
"IN PHOSPHITE\n"
"* OPO 6 6 6 6 0 PAIR OF "
"DIVALENT O ON P\n"
"* -OP 6 6 6 6 0 OTHER DIVALENT "
"O ON P\n"
"* -O- 6 6 6 6 0 GENERAL DIVALENT "
"OX \n"
"O=C 7 7 7 6 0 O=C, GENERIC \n"
"* O=CN 7 7 7 6 0 O=C IN AMIDES "
"\n"
"* O=CR 7 7 7 6 0 O=C IN KET, "
"ALD \n"
"* O=CO 7 7 7 6 0 O=C IN ACIDS, "
"ESTERS \n"
"* O=S 7 7 7 6 0 TERMINAL O "
"SULFOXIDES \n"
"* O=N 7 7 7 6 0 NITROSO-GROUP OXYGEN "
"\n"
"NR 8 8 8 8 0 AMINE N \n"
"N=C 9 9 9 8 0 N=C, IMINES \n"
"* N=N 9 9 9 8 0 N=N, AZO "
"COMPOUNDS \n"
"NC=O 10 10 10 8 0 N-C=O, AMIDES \n"
"* NC=S 10 10 10 8 0 N-C=S (DELOC LP) "
"\n"
"* NN=C 10 10 10 8 0 N-N=C (DELOC LP) "
"\n"
"* NN=N 10 10 10 8 0 N-N=N (DELOC LP) "
"\n"
"F 11 11 11 11 0 FLUORINE \n"
"CL 12 12 12 12 0 CHLORINE \n"
"BR 13 13 13 13 0 BROMINE \n"
"I 14 14 14 14 0 IODINE \n"
"S 15 15 15 15 0 THIOL, SULFIDE \n"
"S=C 16 16 16 15 0 S DOUBLY BONDED "
"TO C \n"
"S=O 17 17 17 15 0 SULFOXIDE S "
"\n"
"SO2 18 18 18 15 0 SULFONE S \n"
"* SO2N 18 18 18 15 0 SULFONAMIDE S "
"\n"
"* SO3 18 18 18 15 0 SULFONATE S "
"\n"
"* =SO2 18 18 18 15 0 OXYGENATED SULFONE "
"S \n"
"* SNO 18 18 18 15 0 NITROGEN ANALOG "
"OF SO2 \n"
"SI 19 19 19 19 0 SILICON \n"
"CR4R 20 20 1 1 0 C IN "
"CYCLOBUTYL \n"
"HOR 21 21 21 5 0 H-O, ALCOHOLS "
"\n"
"* HO 21 21 21 5 0 GENERAL H ON "
"O \n"
"CR3R 22 22 22 1 0 C IN "
"CYCLOPROPLY \n"
"HNR 23 23 23 5 0 H-N, AMINES \n"
"* H3N 23 23 23 5 0 H, AMMONIA \n"
"* HPYL 23 23 23 5 0 H-N IN PYRROLE "
"\n"
"* HN 23 23 23 5 0 GENERAL H-N \n"
"HOCO 24 24 24 5 0 H-O, ACIDS \n"
"* HOP 24 21 21 5 0 H-O-P, PHOS ACIDS "
"\n"
"PO4 25 25 25 25 0 PHOSPHODIESTER \n"
"* PO3 25 25 25 25 0 TETRACRD P, "
"3 OXYGENS \n"
"* PO2 25 25 25 25 0 TETRACRD P, "
"2 OXYGENS \n"
"* PO 25 25 25 25 0 TETRACRD P, "
"2 OXYGENS \n"
"* PTET 25 25 25 25 0 GENERAL TETRACRD "
"P \n"
"P 26 26 26 25 0 TRICOORDINATE P \n"
"HN=C 27 27 28 5 0 IMINE N-H \n"
"* HN=N 27 27 28 5 0 AZO N-H \n"
"HNCO 28 28 28 5 0 H-N, AMIDES \n"
"* HNCC 28 28 28 5 0 H-N, ENAMINES "
"\n"
"* HNCS 28 28 28 5 0 H-N, THIOAMIDES "
"\n"
"* HNCN 28 28 28 5 0 H-N, HN-C=N \n"
"* HNNC 28 28 28 5 0 H-N, HN-N=C \n"
"* HNNN 28 28 28 5 0 H-N, HN-N=N \n"
"* HSP2 28 28 28 5 0 GENERAL H ON "
"SP2 N \n"
"HOCC 29 29 29 5 0 H-O, ENOLS, PHENOLS "
"\n"
"* HOCN 29 29 29 5 0 H-O IN HO-C=N "
"\n"
"CE4R 30 30 2 1 0 C=C IN 4-RING "
"\n"
"HOH 31 31 31 31 0 H-OH \n"
"O2CM 32 32 7 6 0 O, CARBOXYLATE "
"ANION \n"
"* OXN 32 32 7 6 0 OXIDE ON "
"NITROHGEN \n"
"* O2N 32 32 7 6 0 NITRO-GROUP OXYGEN "
"\n"
"* O2NO 32 32 7 6 0 NITRO-GROUP IN "
"NITRATE \n"
"* O3N 32 32 7 6 0 NITRATE ANION OXYGEN "
"\n"
"* O-S 32 32 7 6 0 SINGLE TERM O "
"ON TET S \n"
"* O2S 32 32 7 6 0 SULFONES, "
"SULFONAMIDES \n"
"* O3S 32 32 7 6 0 SULFONATES, TERM "
"OX \n"
"* O4S 32 32 7 6 0 SO4(3-) \n"
"* OSMS 32 32 7 6 0 THIOSULFINATE O "
"(-1/2) \n"
"* OP 32 32 7 6 0 TERMINAL O, "
"O-P \n"
"* O2P 32 32 7 6 0 TERMINAL O, "
"O2P GROUP \n"
"* O3P 32 32 7 6 0 TERMINAL O, "
"O3P GROUP \n"
"* O4P 32 32 7 6 0 TERMINAL O, "
"PO4(-3) \n"
"* O4CL 32 32 7 6 0 TERMINAL O "
"IN CLO4(-) \n"
"HOS 33 33 21 5 0 H-O-S, SULF ACIDS "
"\n"
"NR+ 34 34 8 8 0 N+, QUATERNARY "
"N \n"
"OM 35 35 6 6 0 OXIDE OXYGEN ON "
"SP3 C \n"
"* OM2 35 35 6 6 0 OXIDE OXYGEN ON "
"SP2 C \n"
"HNR+ 36 36 36 5 0 H-N+ \n"
"* HNN+ 36 36 36 5 0 H ON "
"IMIDAZOLIUM N \n"
"* HNC+ 36 36 36 5 0 H ON "
"PROTONATED N+=C-N \n"
"* HGD+ 36 36 36 5 0 H ON "
"GUANIDINIUM N \n"
"CB 37 37 2 1 0 AROMATIC C \n"
"NPYD 38 38 9 8 0 AROMATIC N, "
"PYRIDINE \n"
"NPYL 39 39 10 8 0 AROMATIC N, "
"PYRROLE \n"
"NC=C 40 40 10 8 0 N-C=C (DELOC LP) "
"\n"
"* NC=N 40 40 10 8 0 N-C=N (DELOC LP) "
"\n"
"CO2M 41 41 3 1 0 C IN CO2- "
"ANION \n"
"* CS2M 41 41 3 1 0 THIOCARBOXYLATE C "
"\n"
"NSP 42 42 42 8 0 N TRIPLE BONDED "
"\n"
"NSO2 43 43 10 8 0 N, SULFONAMIDES "
"\n"
"STHI 44 44 16 15 0 S IN "
"THIOPHENE \n"
"NO2 45 45 10 8 0 NITRO GROUP N "
"\n"
"* NO3 45 45 10 8 0 NITRATE GROUP N "
"\n"
"N=O 46 46 9 8 0 NITROSO GROUP N "
"\n"
"NAZT 47 47 42 8 0 TERMINAL N, "
"AZIDE \n"
"NSO 48 48 9 8 0 DIVAL. N IN "
"S(N)(O) GP \n"
"O+ 49 49 6 6 0 OXONIUM (TRICOORD) "
"O \n"
"HO+ 50 50 21 5 0 H ON OXONIUM "
"OXYGEN \n"
"O=+ 51 51 7 6 0 OXENIUM OXYGEN+ \n"
"HO=+ 52 52 21 5 0 H ON OXENIUM "
"O+ \n"
"=N= 53 53 42 8 0 N TWICE DOUBLE "
"BONDED \n"
"N+=C 54 54 9 8 0 IMINIUM NITROGEN "
"\n"
"* N+=N 54 54 9 8 0 AZONIUM NITROGEN "
"\n"
"NCN+ 55 55 10 8 0 N IN +N=C-N: "
"; Q=1/2 \n"
"NGD+ 56 56 10 8 0 GUANIDINIUM N; "
"Q=1/3 \n"
"CGD+ 57 57 2 1 0 GUANIDINIUM CARBON "
"\n"
"* CNN+ 57 57 2 1 0 C IN +N=C-N "
"RESONANCE \n"
"NPD+ 58 58 10 8 0 N PYRIDINIUM "
"ION \n"
"OFUR 59 59 6 6 0 AROMATIC O, "
"FURAN \n"
"C% 60 60 4 1 0 ISONITRILE CARBON \n"
"NR% 61 61 42 8 0 ISONITRILE N "
"\n"
"NM 62 62 10 8 0 SULFONAMIDE N- \n"
"C5A 63 63 2 1 0 ALPHA AROM 5-RING "
"C \n"
"C5B 64 64 2 1 0 BETA AROM 5-RING "
"C \n"
"N5A 65 65 9 8 0 ALPHA AROM 5-RING "
"N \n"
"N5B 66 66 9 8 0 ALPHA AROM 5-RING "
"N \n"
"N2OX 67 67 9 8 0 NITROGEN IN "
"N-OXIDE \n"
"N3OX 68 68 8 8 0 NITROGEN IN "
"N-OXIDE \n"
"NPOX 69 69 9 8 0 NITROGEN IN "
"N-OXIDE \n"
"OH2 70 70 70 70 70 OXYGEN IN WATER "
"\n"
"HS 71 71 5 5 0 H-S \n"
"S2CM 72 72 16 15 0 THIOCARBOXYLATE S "
"\n"
"* S-P 72 72 16 15 0 TERMINAL SULFUR "
"ON P \n"
"* SM 72 72 16 15 0 TERMINAL SULFUR "
"ON C \n"
"* SSMO 72 72 16 15 0 TERM S, "
"THIOSULFINATE \n"
"SO2M 73 73 18 15 0 SULFUR IN "
"SULFINATE \n"
"* SSOM 73 73 18 15 0 SULFUR, THIOSULFINATE "
"\n"
"=S=O 74 74 17 15 0 SULFINYL SULFUR, "
"C=S=O \n"
"-P=C 75 75 26 25 0 P DOUBLY BONDED "
"TO C\n"
"N5M 76 76 9 8 0 NEG N IN "
"TETRAZOLE AN \n"
"CLO4 77 77 12 12 0 CHLORINE IN "
"CLO4(-) \n"
"C5 78 78 2 1 0 GENERAL AROM 5-RING "
"C \n"
"N5 79 79 9 8 0 GENERAL AROM 5-RING "
"N \n"
"CIM+ 80 80 2 1 0 C IN N-C-N, "
"IM+ ION \n"
"NIM+ 81 81 10 8 0 N IN N-C-N, "
"IM+ ION \n"
"N5AX 82 82 9 8 0 5R NITROGEN "
"IN N-OXIDE \n"
"* N5BX 82 82 9 8 0 5R NITROGEN "
"IN N-OXIDE \n"
"* N5OX 82 82 9 8 0 5R NITROGEN "
"IN N-OXIDE \n"
"FE+2 87 87 87 87 87 IRON +2 "
"CATION\n"
"FE+3 88 88 88 88 88 IRON +3 "
"CATION\n"
"F- 89 89 89 89 89 FLUORIDE ANION\n"
"CL- 90 90 90 90 90 CHLORIDE ANION\n"
"BR- 91 91 91 91 91 BROMIDE ANION\n"
"LI+ 92 92 92 92 92 LITHIUM CATION \n"
"NA+ 93 93 93 93 93 SODIUM CATION \n"
"K+ 94 94 94 94 94 POTASSIUM CATION \n"
"ZN+2 95 95 95 95 95 DIPOSITIVE ZINC "
"CATION \n"
"* ZINC 95 95 95 95 95 DIPOSITIVE ZINC "
"CATION \n"
"CA+2 96 96 96 96 96 DIPOSITIVE CALCIUM "
"CATION\n"
"CU+1 97 97 97 97 97 MONOPOSITIVE COPPER "
"CATION\n"
"CU+2 98 98 98 98 98 DIPOSITIVE COPPER "
"CATION\n"
"MG+2 99 99 99 99 99 DIPOSITIVE "
"MAGNESIUM CATION\n";
class MMFFPropCollection *MMFFPropCollection::ds_instance = NULL;
extern const std::string defaultMMFFProp;
MMFFPropCollection *MMFFPropCollection::getMMFFProp(
const std::string &mmffProp) {
if (!ds_instance) {
ds_instance = new MMFFPropCollection(mmffProp);
} else if (mmffProp != "") {
delete ds_instance;
ds_instance = new MMFFPropCollection(mmffProp);
}
return ds_instance;
}
MMFFPropCollection::MMFFPropCollection(std::string mmffProp) {
if (mmffProp == "") {
mmffProp = defaultMMFFProp;
}
std::istringstream inStream(mmffProp);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFProp mmffPropObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int atomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)boost::lexical_cast<unsigned int>(*token));
#endif
++token;
mmffPropObj.atno =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.crd =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.val =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.pilp =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.mltb =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.arom =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.linh =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
mmffPropObj.sbmb =
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token));
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[atomType] = mmffPropObj;
#else
d_params.push_back(mmffPropObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFProp =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFFPROP - MMFF atom-type properties\n"
"*\n"
"* atype aspec crd val pilp mltb arom lin sbmb\n"
"1 6 4 4 0 0 0 0 0\n"
"2 6 3 4 0 2 0 0 1\n"
"3 6 3 4 0 2 0 0 1\n"
"4 6 2 4 0 3 0 1 1\n"
"5 1 1 1 0 0 0 0 0\n"
"6 8 2 2 1 0 0 0 0\n"
"7 8 1 2 0 2 0 0 0\n"
"8 7 3 3 1 0 0 0 0\n"
"9 7 2 3 0 2 0 0 1\n"
"10 7 3 3 1 1 0 0 0\n"
"11 9 1 1 1 0 0 0 0\n"
"12 17 1 1 1 0 0 0 0\n"
"13 35 1 1 1 0 0 0 0\n"
"14 53 1 1 1 0 0 0 0\n"
"15 16 2 2 1 0 0 0 0\n"
"16 16 1 2 0 2 0 0 0\n"
"17 16 3 4 0 2 0 0 0\n"
"18 16 4 4 0 0 0 0 0\n"
"19 14 4 4 0 0 0 0 0\n"
"20 6 4 4 0 0 0 0 0\n"
"21 1 1 1 0 0 0 0 0\n"
"22 6 4 4 0 0 0 0 0\n"
"23 1 1 1 0 0 0 0 0\n"
"24 1 1 1 0 0 0 0 0\n"
"25 15 4 4 0 0 0 0 0\n"
"26 15 3 3 1 0 0 0 0\n"
"27 1 1 1 0 0 0 0 0\n"
"28 1 1 1 0 0 0 0 0\n"
"29 1 1 1 0 0 0 0 0\n"
"30 6 3 4 0 2 0 0 1\n"
"31 1 1 1 0 0 0 0 0\n"
"32 8 1 12 1 1 0 0 0\n"
"33 1 1 1 0 0 0 0 0\n"
"34 7 4 4 0 0 0 0 0\n"
"35 8 1 1 1 1 0 0 0\n"
"36 1 1 1 0 0 0 0 0\n"
"37 6 3 4 0 2 1 0 1\n"
"38 7 2 3 0 2 1 0 0\n"
"39 7 3 3 1 1 1 0 1\n"
"40 7 3 3 1 0 0 0 0\n"
"41 6 3 4 0 1 0 0 0\n"
"42 7 1 3 0 3 0 0 0\n"
"43 7 3 3 1 0 0 0 0\n"
"44 16 2 2 1 1 1 0 0\n"
"45 7 3 4 0 2 0 0 0\n"
"46 7 2 3 0 2 0 0 0\n"
"47 7 1 2 0 2 0 0 0\n"
"48 7 2 2 0 0 0 0 0\n"
"49 8 3 3 0 0 0 0 0\n"
"50 1 1 1 0 0 0 0 0\n"
"51 8 2 3 0 2 0 0 0\n"
"52 1 1 1 0 0 0 0 0\n"
"53 7 2 4 0 2 0 1 0\n"
"54 7 3 4 0 2 0 0 1\n"
"55 7 3 34 0 1 0 0 0\n"
"56 7 3 34 0 1 0 0 0\n"
"57 6 3 4 0 2 0 0 1\n"
"58 7 3 4 0 1 1 0 1\n"
"59 8 2 2 1 1 1 0 0\n"
"60 6 1 3 0 3 0 0 0\n"
"61 7 2 4 0 3 0 1 0\n"
"62 7 2 2 1 0 0 0 0\n"
"63 6 3 4 0 2 1 0 1\n"
"64 6 3 4 0 2 1 0 1\n"
"65 7 2 3 0 2 1 0 0\n"
"66 7 2 3 0 2 1 0 0\n"
"67 7 3 4 0 2 0 0 1\n"
"68 7 4 4 0 0 0 0 0\n"
"69 7 3 4 0 1 1 0 0\n"
"70 8 2 2 1 0 0 0 0\n"
"71 1 1 1 0 0 0 0 0\n"
"72 16 1 1 1 1 0 0 0\n"
"73 16 3 3 0 0 0 0 0\n"
"74 16 2 4 0 2 0 0 0\n"
"75 15 2 3 0 2 0 0 1\n"
"76 7 2 2 1 0 0 0 0\n"
"77 17 4 4 0 0 0 0 0\n"
"78 6 3 4 0 2 1 0 1\n"
"79 7 2 3 0 2 1 0 0\n"
"80 6 3 4 0 2 0 0 1\n"
"81 7 3 4 0 1 1 0 1\n"
"82 7 3 4 0 1 1 0 0\n"
"87 26 0 0 0 0 0 0 0\n"
"88 26 0 0 0 0 0 0 0\n"
"89 9 0 0 0 0 0 0 0\n"
"90 17 0 0 0 0 0 0 0\n"
"91 35 0 0 0 0 0 0 0\n"
"92 3 0 0 0 0 0 0 0\n"
"93 11 0 0 0 0 0 0 0\n"
"94 19 0 0 0 0 0 0 0\n"
"95 30 0 0 0 0 0 0 0\n"
"96 20 0 0 0 0 0 0 0\n"
"97 29 0 0 0 0 0 0 0\n"
"98 29 0 0 0 0 0 0 0\n"
"99 12 0 0 0 0 0 0 0\n";
class MMFFPBCICollection *MMFFPBCICollection::ds_instance = NULL;
extern const std::string defaultMMFFPBCI;
MMFFPBCICollection *MMFFPBCICollection::getMMFFPBCI(
const std::string &mmffPBCI) {
if (!ds_instance) {
ds_instance = new MMFFPBCICollection(mmffPBCI);
} else if (mmffPBCI != "") {
delete ds_instance;
ds_instance = new MMFFPBCICollection(mmffPBCI);
}
return ds_instance;
}
MMFFPBCICollection::MMFFPBCICollection(std::string mmffPBCI) {
if (mmffPBCI == "") {
mmffPBCI = defaultMMFFPBCI;
}
std::istringstream inStream(mmffPBCI);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFPBCI mmffPBCIObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
// IMPORTANT: skip the first field
++token;
unsigned int atomType = boost::lexical_cast<unsigned int>(*token);
#else
// IMPORTANT: skip the first two fields
++token;
#endif
++token;
mmffPBCIObj.pbci = boost::lexical_cast<double>(*token);
++token;
mmffPBCIObj.fcadj = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[atomType] = mmffPBCIObj;
#else
d_params.push_back(mmffPBCIObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFPBCI =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF Partial Bond Charge Incs and Formal-Charge Adj. Factors: "
"19-MAY-1994\n"
"*\n"
"* type pbci fcadj Origin/Comment\n"
"0 1 0.000 0.000 E94\n"
"0 2 -0.135 0.000 E94\n"
"0 3 -0.095 0.000 E94\n"
"0 4 -0.200 0.000 E94\n"
"0 5 -0.023 0.000 E94\n"
"0 6 -0.243 0.000 E94\n"
"0 7 -0.687 0.000 E94\n"
"0 8 -0.253 0.000 E94\n"
"0 9 -0.306 0.000 E94\n"
"0 10 -0.244 0.000 E94\n"
"0 11 -0.317 0.000 E94\n"
"0 12 -0.304 0.000 E94\n"
"0 13 -0.238 0.000 E94\n"
"0 14 -0.208 0.000 E94\n"
"0 15 -0.236 0.000 E94\n"
"0 16 -0.475 0.000 E94\n"
"0 17 -0.191 0.000 E94\n"
"0 18 -0.118 0.000 E94\n"
"0 19 0.094 0.000 E94\n"
"0 20 -0.019 0.000 E94\n"
"0 21 0.157 0.000 E94\n"
"0 22 -0.095 0.000 E94\n"
"0 23 0.193 0.000 E94\n"
"0 24 0.257 0.000 E94\n"
"0 25 0.012 0.000 E94\n"
"0 26 -0.142 0.000 E94\n"
"0 27 0.094 0.000 E94\n"
"0 28 0.058 0.000 E94\n"
"0 29 0.207 0.000 E94\n"
"0 30 -0.166 0.000 E94\n"
"0 31 0.161 0.000 E94\n"
"0 32 -0.732 0.500 E94\n"
"0 33 0.257 0.000 E94\n"
"0 34 -0.491 0.000 E94\n"
"0 35 -0.456 0.500 E94\n"
"0 36 -0.031 0.000 E94\n"
"0 37 -0.127 0.000 E94\n"
"0 38 -0.437 0.000 E94\n"
"0 39 -0.104 0.000 E94\n"
"0 40 -0.264 0.000 E94\n"
"0 41 0.052 0.000 E94\n"
"0 42 -0.757 0.000 E94\n"
"0 43 -0.326 0.000 E94\n"
"0 44 -0.237 0.000 E94\n"
"0 45 -0.260 0.000 E94\n"
"0 46 -0.429 0.000 E94\n"
"0 47 -0.418 0.000 E94\n"
"0 48 -0.525 0.000 E94\n"
"0 49 -0.283 0.000 E94\n"
"0 50 0.284 0.000 E94\n"
"0 51 -1.046 0.000 E94\n"
"0 52 -0.546 0.000 E94\n"
"0 53 -0.048 0.000 E94\n"
"0 54 -0.424 0.000 E94\n"
"0 55 -0.476 0.000 E94\n"
"0 56 -0.438 0.000 E94\n"
"0 57 -0.105 0.000 E94\n"
"0 58 -0.488 0.000 E94\n"
"0 59 -0.337 0.000 E94\n"
"0 60 -0.635 0.000 E94\n"
"0 61 -0.265 0.000 E94\n"
"0 62 -0.125 0.250 E94\n"
"0 63 -0.180 0.000 E94\n"
"0 64 -0.181 0.000 E94\n"
"0 65 -0.475 0.000 E94\n"
"0 66 -0.467 0.000 E94\n"
"0 67 -0.099 0.000 == 69\n"
"0 68 -0.135 0.000 E94\n"
"0 69 -0.099 0.000 E94\n"
"0 70 -0.269 0.000 E94\n"
"0 71 -0.071 0.000 E94\n"
"0 72 -0.580 0.500 E94\n"
"0 73 -0.200 0.000 E94\n"
"0 74 -0.301 0.000 E94\n"
"0 75 -0.255 0.000 E94\n"
"0 76 -0.568 0.250 E94\n"
"0 77 -0.282 0.000 E94\n"
"0 78 -0.168 0.000 E94\n"
"0 79 -0.471 0.000 == (65+66)/2\n"
"0 80 -0.144 0.000 E94\n"
"0 81 -0.514 0.000 E94\n"
"0 82 -0.099 0.000 == 69\n"
"0 83 0.000 0.000 Unused\n"
"0 84 0.000 0.000 Unused\n"
"0 85 0.000 0.000 Unused\n"
"0 86 0.000 0.000 Unused\n"
"0 87 2.000 0.000 Ionic charge\n"
"0 88 3.000 0.000 Ionic charge\n"
"0 89 -1.000 0.000 Ionic charge\n"
"0 90 -1.000 0.000 Ionic charge\n"
"0 91 -1.000 0.000 Ionic charge\n"
"0 92 1.000 0.000 Ionic charge\n"
"0 93 1.000 0.000 Ionic charge\n"
"0 94 1.000 0.000 Ionic charge\n"
"0 95 2.000 0.000 Ionic charge\n"
"0 96 2.000 0.000 Ionic charge\n"
"0 97 1.000 0.000 Ionic charge\n"
"0 98 2.000 0.000 Ionic charge\n"
"0 99 2.000 0.000 Ionic charge\n";
class MMFFChgCollection *MMFFChgCollection::ds_instance = NULL;
extern const std::string defaultMMFFChg;
MMFFChgCollection *MMFFChgCollection::getMMFFChg(const std::string &mmffChg) {
if (!ds_instance) {
ds_instance = new MMFFChgCollection(mmffChg);
} else if (mmffChg != "") {
delete ds_instance;
ds_instance = new MMFFChgCollection(mmffChg);
}
return ds_instance;
}
MMFFChgCollection::MMFFChgCollection(std::string mmffChg) {
if (mmffChg == "") {
mmffChg = defaultMMFFChg;
}
std::istringstream inStream(mmffChg);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFChg mmffChgObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int bondType = boost::lexical_cast<unsigned int>(*token);
#else
d_bondType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffChgObj.bci = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[bondType][iAtomType][jAtomType] = mmffChgObj;
#else
d_params.push_back(mmffChgObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFChg =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF BOND-CHARGE INCREMENTS - Rev: 26-OCT-94 Source: MMFF\n"
"* C94 - CORE MMFF parameter, obtained from fit to dipole moments\n"
"* #C94 - CORE MMFF parameter, either fixed or adjusted to fit \n"
"* HF/6-31G* interaction energies\n"
"* X94 - EXTD MMFF parameter, obtained from fit to dipole moments\n"
"* #X94 - EXTD MMFF parameter, fixed in the fit to dipole moments\n"
"* E94 - derived from partial bond charge increments (empirical rule)\n"
"*\n"
"* types bci Source\n"
"0 1 1 0.0000 #C94\n"
"0 1 2 -0.1382 C94\n"
"0 1 3 -0.0610 #C94\n"
"0 1 4 -0.2000 #X94\n"
"0 1 5 0.0000 #C94\n"
"0 1 6 -0.2800 #C94\n"
"0 1 8 -0.2700 #C94\n"
"0 1 9 -0.2460 #C94\n"
"0 1 10 -0.3001 C94\n"
"0 1 11 -0.3400 #C94\n"
"0 1 12 -0.2900 #C94\n"
"0 1 13 -0.2300 #X94\n"
"0 1 14 -0.1900 #X94\n"
"0 1 15 -0.2300 #C94\n"
"0 1 17 -0.1935 X94\n"
"0 1 18 -0.1052 X94\n"
"0 1 19 0.0805 X94\n"
"0 1 20 0.0000 #C94\n"
"0 1 22 -0.0950 E94\n"
"0 1 25 0.0000 #X94\n"
"0 1 26 -0.1669 X94\n"
"0 1 34 -0.5030 C94\n"
"0 1 35 -0.4274 X94\n"
"0 1 37 -0.1435 C94\n"
"0 1 39 -0.2556 C94\n"
"0 1 40 -0.3691 C94\n"
"0 1 41 0.1060 #C94\n"
"0 1 43 -0.3557 X94\n"
"0 1 45 -0.2402 X94\n"
"0 1 46 -0.3332 X94\n"
"0 1 54 -0.3461 C94\n"
"0 1 55 -0.4895 C94\n"
"0 1 56 -0.3276 C94\n"
"0 1 57 -0.1050 E94\n"
"0 1 58 -0.4880 E94\n"
"0 1 61 -0.2657 X94\n"
"0 1 62 -0.2000 #X94\n"
"0 1 63 -0.1800 E94\n"
"0 1 64 -0.1810 E94\n"
"0 1 67 -0.0990 E94\n"
"0 1 68 -0.2560 #C94\n"
"0 1 72 -0.5500 #X94\n"
"0 1 73 -0.0877 X94\n"
"0 1 75 -0.2550 E94\n"
"0 1 78 -0.1680 E94\n"
"0 1 80 -0.1440 E94\n"
"0 1 81 -0.5140 E94\n"
"0 2 2 0.0000 #C94\n"
"1 2 2 0.0000 #C94\n"
"1 2 3 -0.0144 C94\n"
"0 2 4 -0.0650 E94\n"
"1 2 4 -0.0650 E94\n"
"0 2 5 0.1500 #C94\n"
"0 2 6 -0.0767 C94\n"
"1 2 9 -0.1710 E94\n"
"0 2 10 -0.1090 E94\n"
"0 2 11 -0.1495 X94\n"
"0 2 12 -0.1400 #X94\n"
"0 2 13 -0.1100 #X94\n"
"0 2 14 -0.0900 #X94\n"
"0 2 15 -0.1010 E94\n"
"0 2 17 -0.0560 E94\n"
"0 2 18 0.0170 E94\n"
"0 2 19 0.2290 E94\n"
"0 2 20 0.1160 E94\n"
"0 2 22 0.0400 E94\n"
"0 2 25 0.1470 E94\n"
"0 2 30 -0.0310 E94\n"
"0 2 34 -0.3560 E94\n"
"0 2 35 -0.3500 #X94\n"
"1 2 37 0.0284 C94\n"
"1 2 39 0.0310 E94\n"
"0 2 40 -0.1000 #C94\n"
"0 2 41 0.2500 #C94\n"
"0 2 43 -0.1910 E94\n"
"0 2 45 -0.2044 X94\n"
"0 2 46 -0.2940 E94\n"
"0 2 55 -0.3410 E94\n"
"0 2 56 -0.3030 E94\n"
"0 2 62 -0.0500 #X94\n"
"1 2 63 -0.0450 E94\n"
"1 2 64 -0.0460 E94\n"
"1 2 67 0.0360 E94\n"
"0 2 72 -0.4500 #X94\n"
"1 2 81 -0.3790 E94\n"
"1 3 3 0.0000 #C94\n"
"1 3 4 -0.1050 E94\n"
"0 3 5 0.0600 #C94\n"
"0 3 6 -0.1500 #C94\n"
"0 3 7 -0.5700 #C94\n"
"0 3 9 -0.4500 #C94\n"
"1 3 9 -0.2110 E94\n"
"0 3 10 -0.0600 C94\n"
"0 3 11 -0.2220 E94\n"
"0 3 12 -0.2090 E94\n"
"0 3 15 -0.1410 E94\n"
"0 3 16 -0.3800 #X94\n"
"0 3 17 -0.0960 E94\n"
"0 3 18 -0.0230 E94\n"
"0 3 20 0.0530 #C94\n"
"0 3 22 0.0000 E94\n"
"0 3 25 0.1070 E94\n"
"1 3 30 -0.0710 E94\n"
"0 3 35 -0.3610 E94\n"
"1 3 37 0.0862 C94\n"
"1 3 39 -0.0090 E94\n"
"0 3 40 -0.0500 #C94\n"
"0 3 41 0.1470 E94\n"
"0 3 43 -0.2363 X94\n"
"0 3 45 -0.1650 E94\n"
"0 3 48 -0.4300 E94\n"
"0 3 51 -0.9500 #X94\n"
"0 3 53 -0.0134 X94\n"
"0 3 54 -0.4000 #C94\n"
"1 3 54 -0.3290 E94\n"
"0 3 55 -0.3810 E94\n"
"0 3 56 -0.3430 E94\n"
"1 3 57 -0.0100 E94\n"
"1 3 58 -0.3930 E94\n"
"0 3 62 -0.0300 E94\n"
"1 3 63 -0.0850 E94\n"
"1 3 64 -0.0860 E94\n"
"0 3 67 -0.0040 E94\n"
"0 3 74 -0.3190 X94\n"
"0 3 75 -0.2474 X94\n"
"1 3 78 -0.0730 E94\n"
"1 3 80 -0.0490 E94\n"
"0 4 5 0.1770 E94\n"
"0 4 6 -0.0430 E94\n"
"0 4 7 -0.4870 E94\n"
"0 4 9 -0.3000 E94\n"
"1 4 9 -0.1060 E94\n"
"0 4 10 -0.0440 E94\n"
"0 4 15 -0.0360 E94\n"
"0 4 20 0.1810 E94\n"
"0 4 22 0.1050 E94\n"
"0 4 30 0.0340 E94\n"
"1 4 37 0.0730 E94\n"
"0 4 40 -0.0640 E94\n"
"0 4 42 -0.5571 X94\n"
"0 4 43 -0.1260 E94\n"
"1 4 63 0.0200 E94\n"
"1 4 64 0.0190 E94\n"
"0 5 19 0.2000 #X94\n"
"0 5 20 0.0000 #C94\n"
"0 5 22 -0.1000 #C94\n"
"0 5 30 -0.1500 #C94\n"
"0 5 37 -0.1500 #C94\n"
"0 5 41 0.2203 C94\n"
"0 5 57 -0.1500 #C94\n"
"0 5 63 -0.1500 #C94\n"
"0 5 64 -0.1500 #C94\n"
"0 5 78 -0.1500 #C94\n"
"0 5 80 -0.1500 #C94\n"
"0 6 6 0.0000 #C94\n"
"0 6 8 -0.1000 #C94\n"
"0 6 9 -0.0630 E94\n"
"0 6 10 0.0355 C94\n"
"0 6 15 0.0070 E94\n"
"0 6 17 0.0520 E94\n"
"0 6 18 0.1837 X94\n"
"0 6 19 0.2974 X94\n"
"0 6 20 0.2579 C94\n"
"0 6 21 0.4000 #C94\n"
"0 6 22 0.1480 E94\n"
"0 6 24 0.5000 #C94\n"
"0 6 25 0.2712 X94\n"
"0 6 26 0.1010 E94\n"
"0 6 29 0.4500 #C94\n"
"0 6 30 0.0770 E94\n"
"0 6 33 0.5000 #X94\n"
"0 6 37 0.0825 C94\n"
"0 6 39 0.1390 E94\n"
"0 6 40 -0.0210 E94\n"
"0 6 41 0.2950 E94\n"
"0 6 43 -0.0830 E94\n"
"0 6 45 -0.0090 X94\n"
"0 6 54 -0.1810 E94\n"
"0 6 55 -0.2330 E94\n"
"0 6 57 0.1380 E94\n"
"0 6 58 -0.2450 E94\n"
"0 6 63 0.0630 E94\n"
"0 6 64 0.0620 E94\n"
"0 7 17 0.5000 #X94\n"
"0 7 46 0.1618 X94\n"
"0 7 74 0.5000 #X94\n"
"0 8 8 0.0000 #C94\n"
"0 8 9 -0.0530 E94\n"
"0 8 10 0.0090 E94\n"
"0 8 12 -0.0510 E94\n"
"0 8 15 0.0170 E94\n"
"0 8 17 0.0620 E94\n"
"0 8 19 0.3470 E94\n"
"0 8 20 0.2096 C94\n"
"0 8 22 0.1580 E94\n"
"0 8 23 0.3600 #C94\n"
"0 8 25 0.2679 X94\n"
"0 8 26 0.1110 E94\n"
"0 8 34 -0.2380 E94\n"
"0 8 39 0.1490 E94\n"
"0 8 40 -0.0110 E94\n"
"0 8 43 -0.0730 E94\n"
"0 8 45 -0.0070 E94\n"
"0 8 46 -0.1760 E94\n"
"0 8 55 -0.2230 E94\n"
"0 8 56 -0.1850 E94\n"
"0 9 9 0.0000 #C94\n"
"0 9 10 0.0620 E94\n"
"0 9 12 0.0020 E94\n"
"0 9 15 0.0700 E94\n"
"0 9 18 0.1880 E94\n"
"0 9 19 0.4000 E94\n"
"0 9 20 0.2870 E94\n"
"0 9 25 0.3180 E94\n"
"0 9 27 0.4000 #C94\n"
"0 9 34 -0.1850 E94\n"
"0 9 35 -0.1500 E94\n"
"1 9 37 0.1790 E94\n"
"1 9 39 0.2020 E94\n"
"0 9 40 0.0420 E94\n"
"0 9 41 0.3580 E94\n"
"0 9 45 0.0460 E94\n"
"0 9 53 0.3179 X94\n"
"0 9 54 -0.1180 E94\n"
"0 9 55 -0.1700 E94\n"
"0 9 56 -0.1320 E94\n"
"1 9 57 0.2010 E94\n"
"0 9 62 0.1810 E94\n"
"1 9 63 0.1260 E94\n"
"1 9 64 0.1250 E94\n"
"0 9 67 0.2070 E94\n"
"1 9 78 0.1380 E94\n"
"1 9 81 -0.2080 E94\n"
"0 10 10 0.0000 #C94\n"
"0 10 13 0.0060 E94\n"
"0 10 14 0.0360 E94\n"
"0 10 15 0.0080 E94\n"
"0 10 17 0.0530 E94\n"
"0 10 20 0.2250 E94\n"
"0 10 22 0.1490 E94\n"
"0 10 25 0.2560 E94\n"
"0 10 26 0.1020 E94\n"
"0 10 28 0.3700 #C94\n"
"0 10 34 -0.2470 E94\n"
"0 10 35 -0.2120 E94\n"
"0 10 37 0.1170 E94\n"
"0 10 39 0.1400 E94\n"
"0 10 40 -0.0200 E94\n"
"0 10 41 0.2960 E94\n"
"0 10 45 -0.0160 E94\n"
"0 10 63 0.0640 E94\n"
"0 10 64 0.0630 E94\n"
"0 11 20 0.2980 E94\n"
"0 11 22 0.2317 X94\n"
"0 11 25 0.3290 E94\n"
"0 11 26 0.1750 E94\n"
"0 11 37 0.1900 E94\n"
"0 11 40 0.0530 E94\n"
"0 12 15 0.0680 E94\n"
"0 12 18 0.1860 E94\n"
"0 12 19 0.3701 X94\n"
"0 12 20 0.2900 #C94\n"
"0 12 22 0.2273 X94\n"
"0 12 25 0.3160 E94\n"
"0 12 26 0.2112 X94\n"
"0 12 37 0.1770 E94\n"
"0 12 40 0.0400 E94\n"
"0 12 57 0.1990 E94\n"
"0 12 63 0.1240 E94\n"
"0 12 64 0.1230 E94\n"
"0 13 20 0.2190 E94\n"
"0 13 22 0.1430 E94\n"
"0 13 37 0.1110 E94\n"
"0 13 64 0.0570 E94\n"
"0 14 20 0.1890 E94\n"
"0 14 37 0.0810 E94\n"
"0 15 15 0.0000 #C94\n"
"0 15 18 0.1180 E94\n"
"0 15 19 0.3300 E94\n"
"0 15 20 0.2170 E94\n"
"0 15 22 0.1410 E94\n"
"0 15 25 0.2480 E94\n"
"0 15 26 0.0940 E94\n"
"0 15 30 0.0700 E94\n"
"0 15 37 0.1015 C94\n"
"0 15 40 -0.0280 E94\n"
"0 15 43 -0.0900 E94\n"
"0 15 57 0.1310 E94\n"
"0 15 63 0.0560 E94\n"
"0 15 64 0.0550 E94\n"
"0 15 71 0.1800 #C94\n"
"0 16 16 0.0000 #C94\n"
"0 17 17 0.0000 #X94\n"
"0 17 20 0.1720 E94\n"
"0 17 22 0.0960 E94\n"
"0 17 37 0.0640 E94\n"
"0 17 43 -0.1350 E94\n"
"0 18 18 0.0000 #X94\n"
"0 18 20 0.0990 E94\n"
"0 18 22 0.0230 E94\n"
"0 18 32 -0.6500 #X94\n"
"0 18 37 -0.0090 E94\n"
"0 18 39 0.0140 E94\n"
"0 18 43 -0.1380 X94\n"
"0 18 48 -0.5895 X94\n"
"0 18 55 -0.3580 E94\n"
"0 18 58 -0.3700 E94\n"
"0 18 62 0.2099 X94\n"
"0 18 63 -0.0620 E94\n"
"0 18 64 -0.0630 E94\n"
"0 18 80 -0.0260 E94\n"
"0 19 19 0.0000 #X94\n"
"0 19 20 -0.1130 E94\n"
"0 19 37 -0.2210 E94\n"
"0 19 40 -0.3580 E94\n"
"0 19 63 -0.2740 E94\n"
"0 19 75 -0.3490 E94\n"
"0 20 20 0.0000 #C94\n"
"0 20 22 -0.0760 E94\n"
"0 20 25 0.0310 E94\n"
"0 20 26 -0.1230 E94\n"
"0 20 30 -0.1380 #C94\n"
"0 20 34 -0.4720 E94\n"
"0 20 37 -0.1080 E94\n"
"0 20 40 -0.2450 E94\n"
"0 20 41 0.0710 E94\n"
"0 20 43 -0.3070 E94\n"
"0 20 45 -0.2410 E94\n"
"0 22 22 0.0000 #C94\n"
"0 22 30 -0.0710 E94\n"
"0 22 34 -0.3960 E94\n"
"0 22 37 -0.0320 E94\n"
"0 22 40 -0.1690 E94\n"
"0 22 41 0.1470 E94\n"
"0 22 43 -0.2310 E94\n"
"0 22 45 -0.1650 E94\n"
"0 23 39 -0.2700 #C94\n"
"0 23 62 -0.4000 #X94\n"
"0 23 67 -0.2920 E94\n"
"0 23 68 -0.3600 #C94\n"
"0 25 25 0.0000 #X94\n"
"0 25 32 -0.7000 #X94\n"
"0 25 37 -0.1390 E94\n"
"0 25 39 -0.1160 E94\n"
"0 25 40 -0.2760 E94\n"
"0 25 43 -0.3380 E94\n"
"0 25 57 -0.1170 E94\n"
"0 25 63 -0.1920 E94\n"
"0 25 71 -0.0362 X94\n"
"0 25 72 -0.6773 X94\n"
"0 26 26 0.0000 #X94\n"
"0 26 34 -0.3490 E94\n"
"0 26 37 0.0150 E94\n"
"0 26 40 -0.1220 E94\n"
"0 26 71 0.0960 X94\n"
"0 28 40 -0.4000 #C94\n"
"0 28 43 -0.4200 #X94\n"
"0 28 48 -0.4000 #X94\n"
"0 30 30 0.0000 #C94\n"
"0 30 40 -0.0980 E94\n"
"1 30 67 0.0670 E94\n"
"0 31 70 -0.4300 #C94\n"
"0 32 41 0.6500 #C94\n"
"0 32 45 0.5200 #X94\n"
"0 32 67 0.6330 E94\n"
"0 32 68 0.7500 #C94\n"
"0 32 69 0.7500 #C94\n"
"0 32 73 0.3500 #X94\n"
"0 32 77 0.4500 #X94\n"
"0 32 82 0.6330 E94\n"
"0 34 36 0.4500 #C94\n"
"0 34 37 0.3640 E94\n"
"0 34 43 0.1650 E94\n"
"0 35 37 0.3290 E94\n"
"0 35 63 0.2760 E94\n"
"0 36 54 -0.4000 #C94\n"
"0 36 55 -0.4500 #C94\n"
"0 36 56 -0.4500 #C94\n"
"0 36 58 -0.4570 E94\n"
"4 36 58 -0.4500 #C94\n"
"0 36 81 -0.4500 #C94\n"
"0 37 37 0.0000 #C94\n"
"1 37 37 0.0000 #C94\n"
"0 37 38 -0.3100 #C94\n"
"0 37 39 0.0230 E94\n"
"1 37 39 0.0230 E94\n"
"0 37 40 -0.1000 #C94\n"
"0 37 41 0.1790 E94\n"
"0 37 43 -0.1990 E94\n"
"0 37 45 -0.1330 E94\n"
"0 37 46 -0.3020 E94\n"
"0 37 55 -0.3490 E94\n"
"0 37 56 -0.3110 E94\n"
"1 37 57 0.0220 E94\n"
"0 37 58 -0.3610 E94\n"
"1 37 58 -0.3610 E94\n"
"4 37 58 -0.3500 #C94\n"
"0 37 61 -0.1380 E94\n"
"0 37 62 0.0020 E94\n"
"0 37 63 0.0000 #C94\n"
"1 37 63 -0.0530 E94\n"
"0 37 64 0.0000 #C94\n"
"1 37 64 -0.0540 E94\n"
"1 37 67 0.0280 E94\n"
"0 37 69 -0.0895 C94\n"
"0 37 78 -0.0410 E94\n"
"0 37 81 -0.3870 E94\n"
"1 37 81 -0.3870 E94\n"
"0 38 38 0.0000 #C94\n"
"0 38 63 0.2570 E94\n"
"0 38 64 0.2560 E94\n"
"0 38 69 0.3380 E94\n"
"0 38 78 0.2690 E94\n"
"1 39 39 0.0000 #C94\n"
"0 39 40 -0.1600 E94\n"
"0 39 45 -0.1560 E94\n"
"0 39 63 -0.1516 C94\n"
"1 39 63 -0.0760 E94\n"
"0 39 64 -0.0770 E94\n"
"1 39 64 -0.0770 E94\n"
"0 39 65 -0.4180 C94\n"
"0 39 78 -0.0640 E94\n"
"0 40 40 0.0000 #C94\n"
"0 40 45 0.0040 E94\n"
"0 40 46 -0.1650 E94\n"
"0 40 54 -0.1600 E94\n"
"0 40 63 0.0840 E94\n"
"0 40 64 0.0830 E94\n"
"0 40 78 0.0960 E94\n"
"0 41 41 0.0000 #C94\n"
"0 41 55 -0.5280 E94\n"
"0 41 62 -0.1770 E94\n"
"0 41 72 -0.5000 #X94\n"
"0 41 80 -0.1960 E94\n"
"0 42 61 0.4920 E94\n"
"0 43 43 0.0000 #X94\n"
"0 43 45 0.0660 E94\n"
"0 43 64 0.1450 E94\n"
"0 44 63 0.0400 #C94\n"
"0 44 65 -0.2207 C94\n"
"0 44 78 0.0690 E94\n"
"0 44 80 0.0930 E94\n"
"0 45 63 0.0800 E94\n"
"0 45 64 0.0790 E94\n"
"0 45 78 0.0920 E94\n"
"0 47 53 0.3700 #X94\n"
"0 49 50 0.5673 C94\n"
"0 51 52 0.5000 #X94\n"
"0 55 57 0.3544 C94\n"
"0 55 62 0.3510 E94\n"
"0 55 64 0.2950 E94\n"
"0 55 80 0.3320 E94\n"
"0 56 57 0.4000 #C94\n"
"0 56 63 0.2580 E94\n"
"0 56 80 0.2700 E94\n"
"4 57 58 -0.4000 #C94\n"
"1 57 63 -0.0750 E94\n"
"1 57 64 -0.0760 E94\n"
"0 58 63 0.3080 E94\n"
"0 58 64 0.3070 E94\n"
"0 59 63 0.1400 #C94\n"
"0 59 65 -0.1209 C94\n"
"0 59 78 0.1690 E94\n"
"0 59 80 0.1930 E94\n"
"0 59 82 0.2380 E94\n"
"0 60 61 0.3700 #X94\n"
"0 62 63 -0.0550 E94\n"
"0 62 64 -0.0560 E94\n"
"0 63 63 0.0000 #C94\n"
"1 63 63 0.0000 #C94\n"
"0 63 64 0.0000 #C94\n"
"0 63 66 -0.3381 C94\n"
"0 63 72 -0.4000 E94\n"
"0 63 78 0.0120 E94\n"
"0 63 81 -0.3340 E94\n"
"0 64 64 0.0000 #C94\n"
"0 64 65 -0.2888 C94\n"
"0 64 66 -0.2272 C94\n"
"0 64 78 0.0130 E94\n"
"0 64 81 -0.3330 E94\n"
"0 64 82 0.0820 E94\n"
"0 65 66 0.0000 #C94\n"
"0 65 78 0.3070 E94\n"
"0 65 81 -0.0390 E94\n"
"0 65 82 0.3760 E94\n"
"0 66 66 0.0000 #C94\n"
"0 66 78 0.2990 E94\n"
"0 66 81 -0.0470 E94\n"
"0 71 75 -0.0958 X94\n"
"0 72 73 0.4500 #X94\n"
"0 76 76 0.0000 #X94\n"
"0 76 78 0.4000 #X94\n"
"0 78 78 0.0000 #C94\n"
"1 78 78 0.0000 #C94\n"
"0 78 79 -0.3030 E94\n"
"0 78 81 -0.3500 #C94\n"
"0 79 81 -0.0430 E94\n"
"0 80 81 -0.4000 #C94\n";
class MMFFBondCollection *MMFFBondCollection::ds_instance = NULL;
extern const std::string defaultMMFFBond;
MMFFBondCollection *MMFFBondCollection::getMMFFBond(
const std::string &mmffBond) {
if (!ds_instance) {
ds_instance = new MMFFBondCollection(mmffBond);
} else if (mmffBond != "") {
delete ds_instance;
ds_instance = new MMFFBondCollection(mmffBond);
}
return ds_instance;
}
MMFFBondCollection::MMFFBondCollection(std::string mmffBond) {
if (mmffBond == "") {
mmffBond = defaultMMFFBond;
}
std::istringstream inStream(mmffBond);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFBond mmffBondObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int bondType = boost::lexical_cast<unsigned int>(*token);
#else
d_bondType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int atomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffBondObj.kb = boost::lexical_cast<double>(*token);
++token;
mmffBondObj.r0 = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[bondType][atomType][jAtomType] = mmffBondObj;
#else
d_params.push_back(mmffBondObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFBond =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF BOND PARAMETERS- Rev: 26-OCT-94 Source: MMFF\n"
"* C94 = CORE MMFF parameter - obtained from ab initio data\n"
"* X94 = EXTD MMFF parameter - fit to additional ab initio data\n"
"* E94 = r0 from fit to X-ray data, kb from empirical rule\n"
"* #C94 = r0 lies between C94 and E94 values, kb from empirical rule\n"
"* #X94 = r0 lies between X94 and E94 values, kb from empirical rule\n"
"* #E94 = r0 and k both from empirical rules\n"
"*\n"
"* types kb r0 Source\n"
"0 1 1 4.258 1.508 C94\n"
"0 1 2 4.539 1.482 C94\n"
"0 1 3 4.190 1.492 C94\n"
"0 1 4 4.707 1.459 X94\n"
"0 1 5 4.766 1.093 C94\n"
"0 1 6 5.047 1.418 C94\n"
"0 1 8 5.084 1.451 C94\n"
"0 1 9 4.763 1.458 C94\n"
"0 1 10 4.664 1.436 C94\n"
"0 1 11 6.011 1.360 #C94\n"
"0 1 12 2.974 1.773 C94\n"
"0 1 13 2.529 1.949 E94\n"
"0 1 14 1.706 2.090 E94\n"
"0 1 15 2.893 1.805 C94\n"
"0 1 17 2.841 1.813 X94\n"
"0 1 18 3.258 1.772 X94\n"
"0 1 19 2.866 1.830 #X94\n"
"0 1 20 4.650 1.504 C94\n"
"0 1 22 4.286 1.482 E94\n"
"0 1 25 2.980 1.810 #X94\n"
"0 1 26 2.790 1.830 #X94\n"
"0 1 34 3.844 1.480 #C94\n"
"0 1 35 7.915 1.307 X94\n"
"0 1 37 4.957 1.486 C94\n"
"0 1 39 6.114 1.445 C94\n"
"0 1 40 4.922 1.446 C94\n"
"0 1 41 3.830 1.510 #C94\n"
"0 1 43 3.971 1.472 X94\n"
"0 1 45 3.844 1.480 X94\n"
"0 1 46 3.813 1.482 X94\n"
"0 1 54 4.267 1.461 C94\n"
"0 1 55 4.646 1.454 C94\n"
"0 1 56 4.166 1.453 C94\n"
"0 1 57 4.669 1.461 E94\n"
"0 1 58 4.329 1.451 E94\n"
"0 1 61 4.845 1.424 X94\n"
"0 1 62 4.456 1.444 X94\n"
"0 1 63 4.481 1.471 E94\n"
"0 1 64 4.518 1.469 E94\n"
"0 1 67 4.188 1.459 E94\n"
"0 1 68 4.217 1.479 C94\n"
"0 1 72 2.956 1.801 X94\n"
"0 1 73 2.608 1.839 X94\n"
"0 1 75 2.547 1.858 E94\n"
"0 1 78 4.593 1.465 E94\n"
"0 1 80 4.373 1.477 E94\n"
"0 1 81 4.512 1.441 E94\n"
"0 2 2 9.505 1.333 C94\n"
"1 2 2 5.310 1.430 #C94\n"
"1 2 3 4.565 1.468 C94\n"
"0 2 4 9.538 1.297 E94\n"
"1 2 4 5.657 1.415 E94\n"
"0 2 5 5.170 1.083 C94\n"
"0 2 6 5.520 1.373 C94\n"
"1 2 9 6.385 1.360 E94\n"
"0 2 10 6.329 1.362 E94\n"
"0 2 11 6.283 1.350 #X94\n"
"0 2 12 3.390 1.720 #X94\n"
"0 2 13 3.413 1.854 E94\n"
"0 2 14 2.062 2.025 E94\n"
"0 2 15 3.896 1.720 E94\n"
"0 2 17 3.247 1.773 E94\n"
"0 2 18 3.789 1.728 E94\n"
"0 2 19 3.052 1.811 E94\n"
"0 2 20 4.593 1.465 E94\n"
"0 2 22 4.926 1.448 E94\n"
"0 2 25 3.750 1.742 E94\n"
"0 2 30 8.166 1.331 E94\n"
"0 2 34 5.207 1.407 E94\n"
"0 2 35 10.343 1.250 #X94\n"
"1 2 37 5.007 1.449 C94\n"
"1 2 39 6.164 1.368 E94\n"
"0 2 40 6.110 1.370 #C94\n"
"0 2 41 3.746 1.505 C94\n"
"0 2 43 4.928 1.420 E94\n"
"0 2 45 4.725 1.430 #X94\n"
"0 2 46 7.466 1.325 E94\n"
"0 2 55 6.164 1.368 E94\n"
"0 2 56 6.246 1.365 E94\n"
"0 2 62 7.105 1.336 X94\n"
"1 2 63 6.030 1.400 E94\n"
"1 2 64 5.754 1.411 E94\n"
"1 2 67 4.685 1.432 E94\n"
"0 2 72 4.179 1.700 #X94\n"
"1 2 81 6.357 1.361 E94\n"
"1 3 3 4.418 1.489 C94\n"
"1 3 4 5.135 1.438 E94\n"
"0 3 5 4.650 1.101 C94\n"
"0 3 6 5.801 1.355 C94\n"
"0 3 7 12.950 1.222 C94\n"
"0 3 9 10.077 1.290 C94\n"
"1 3 9 6.273 1.364 E94\n"
"0 3 10 5.829 1.369 C94\n"
"0 3 11 6.570 1.340 E94\n"
"0 3 12 3.449 1.715 E94\n"
"0 3 15 3.536 1.748 E94\n"
"0 3 16 4.735 1.665 E94\n"
"0 3 17 2.888 1.808 E94\n"
"0 3 18 3.394 1.760 E94\n"
"0 3 20 3.298 1.530 C94\n"
"0 3 22 4.593 1.465 E94\n"
"0 3 25 3.164 1.792 E94\n"
"1 3 30 4.481 1.471 E94\n"
"0 3 35 11.012 1.237 E94\n"
"1 3 37 4.488 1.457 C94\n"
"1 3 39 5.978 1.375 E94\n"
"0 3 40 6.110 1.370 #C94\n"
"0 3 41 4.286 1.482 E94\n"
"0 3 43 4.928 1.420 X94\n"
"0 3 45 4.531 1.440 E94\n"
"0 3 48 5.412 1.398 E94\n"
"0 3 51 8.562 1.290 #X94\n"
"0 3 53 7.637 1.320 #X94\n"
"0 3 54 10.333 1.280 C94\n"
"1 3 54 2.771 1.563 E94\n"
"0 3 55 4.886 1.422 E94\n"
"0 3 56 4.907 1.421 E94\n"
"1 3 57 5.492 1.422 E94\n"
"1 3 58 5.163 1.409 E94\n"
"0 3 62 7.568 1.322 E94\n"
"1 3 63 5.468 1.423 E94\n"
"1 3 64 5.288 1.431 E94\n"
"0 3 67 8.217 1.304 E94\n"
"0 3 74 5.204 1.639 X94\n"
"0 3 75 4.191 1.710 #X94\n"
"1 3 78 5.705 1.413 E94\n"
"1 3 80 6.719 1.375 E94\n"
"0 4 4 15.206 1.200 #X94\n"
"0 4 5 5.726 1.065 X94\n"
"0 4 6 7.193 1.328 E94\n"
"0 4 7 14.916 1.176 E94\n"
"0 4 9 15.589 1.172 E94\n"
"1 4 9 7.041 1.338 E94\n"
"0 4 10 6.824 1.345 E94\n"
"0 4 15 4.330 1.690 E94\n"
"0 4 20 5.178 1.436 E94\n"
"0 4 22 5.400 1.426 E94\n"
"0 4 30 10.227 1.282 E94\n"
"1 4 37 5.445 1.424 E94\n"
"0 4 42 16.582 1.160 #X94\n"
"0 4 43 6.947 1.341 E94\n"
"1 4 63 5.633 1.416 E94\n"
"1 4 64 5.492 1.422 E94\n"
"0 5 19 2.254 1.485 X94\n"
"0 5 20 4.852 1.093 C94\n"
"0 5 22 5.191 1.082 C94\n"
"0 5 30 5.176 1.086 C94\n"
"0 5 37 5.306 1.084 C94\n"
"0 5 41 3.256 1.144 C94\n"
"0 5 57 5.633 1.076 C94\n"
"0 5 63 5.531 1.080 C94\n"
"0 5 64 5.506 1.080 C94\n"
"0 5 78 5.506 1.080 C94\n"
"0 5 80 5.633 1.076 C94\n"
"0 6 6 4.088 1.449 E94\n"
"0 6 8 5.059 1.450 C94\n"
"0 6 9 4.491 1.395 E94\n"
"0 6 10 5.982 1.410 C94\n"
"0 6 15 4.757 1.661 E94\n"
"0 6 17 5.779 1.608 E94\n"
"0 6 18 5.326 1.630 #X94\n"
"0 6 19 4.661 1.660 #X94\n"
"0 6 20 5.623 1.433 C94\n"
"0 6 21 7.794 0.972 C94\n"
"0 6 22 4.556 1.433 E94\n"
"0 6 24 7.403 0.981 C94\n"
"0 6 25 5.243 1.630 #X94\n"
"0 6 26 5.481 1.618 E94\n"
"0 6 29 7.839 0.973 C94\n"
"0 6 30 9.359 1.271 E94\n"
"0 6 33 7.143 0.986 X94\n"
"0 6 37 5.614 1.376 C94\n"
"0 6 39 4.629 1.388 E94\n"
"0 6 40 4.609 1.389 E94\n"
"0 6 41 6.754 1.342 E94\n"
"0 6 43 3.937 1.426 E94\n"
"0 6 45 4.321 1.404 X94\n"
"0 6 54 5.117 1.365 E94\n"
"0 6 55 4.772 1.381 E94\n"
"0 6 57 7.128 1.330 E94\n"
"0 6 58 4.792 1.380 E94\n"
"0 6 63 7.324 1.324 E94\n"
"0 6 64 6.664 1.345 E94\n"
"0 7 17 8.770 1.500 #X94\n"
"0 7 46 9.329 1.235 X94\n"
"0 7 74 9.129 1.490 #X94\n"
"0 8 8 3.264 1.420 E94\n"
"0 8 9 4.581 1.342 E94\n"
"0 8 10 3.909 1.378 E94\n"
"0 8 12 3.371 1.761 E94\n"
"0 8 15 4.060 1.652 E94\n"
"0 8 17 3.901 1.663 E94\n"
"0 8 19 4.254 1.700 E94\n"
"0 8 20 5.107 1.456 C94\n"
"0 8 22 4.223 1.457 E94\n"
"0 8 23 6.490 1.019 C94\n"
"0 8 25 4.629 1.660 E94\n"
"0 8 26 4.027 1.699 E94\n"
"0 8 34 3.775 1.386 E94\n"
"0 8 39 3.435 1.408 E94\n"
"0 8 40 3.710 1.390 E94\n"
"0 8 43 3.977 1.374 E94\n"
"0 8 45 4.267 1.358 E94\n"
"0 8 46 5.519 1.301 E94\n"
"0 8 55 4.229 1.360 E94\n"
"0 8 56 3.995 1.373 E94\n"
"0 9 9 7.256 1.243 E94\n"
"1 9 9 3.808 1.384 E94\n"
"0 9 10 4.480 1.347 E94\n"
"0 9 12 3.635 1.739 E94\n"
"0 9 15 3.791 1.671 E94\n"
"0 9 18 4.465 1.626 E94\n"
"0 9 19 3.687 1.741 E94\n"
"0 9 20 4.401 1.447 E94\n"
"0 9 25 5.379 1.619 E94\n"
"0 9 27 6.230 1.026 C94\n"
"0 9 34 3.223 1.423 E94\n"
"0 9 35 5.095 1.366 E94\n"
"1 9 37 5.529 1.393 E94\n"
"1 9 39 4.685 1.337 E94\n"
"0 9 40 4.382 1.352 E94\n"
"0 9 41 5.650 1.388 E94\n"
"0 9 45 4.857 1.329 E94\n"
"0 9 53 7.291 1.242 X94\n"
"0 9 54 4.991 1.323 E94\n"
"0 9 55 3.825 1.383 E94\n"
"0 9 56 4.602 1.341 E94\n"
"1 9 57 6.824 1.345 E94\n"
"0 9 62 4.749 1.334 E94\n"
"1 9 63 6.824 1.345 E94\n"
"1 9 64 5.458 1.396 E94\n"
"0 9 67 6.752 1.258 E94\n"
"1 9 78 6.644 1.351 E94\n"
"1 9 81 3.909 1.378 E94\n"
"0 10 10 3.977 1.374 E94\n"
"0 10 13 3.110 1.878 E94\n"
"0 10 14 1.967 2.029 E94\n"
"0 10 15 3.593 1.686 E94\n"
"0 10 17 3.930 1.661 E94\n"
"0 10 20 4.240 1.456 E94\n"
"0 10 22 4.970 1.418 E94\n"
"0 10 25 3.820 1.714 E94\n"
"0 10 26 3.651 1.727 E94\n"
"0 10 28 6.663 1.015 C94\n"
"0 10 34 3.960 1.375 E94\n"
"0 10 35 4.898 1.375 E94\n"
"0 10 37 5.482 1.395 E94\n"
"0 10 39 4.382 1.352 E94\n"
"0 10 40 3.841 1.382 E94\n"
"0 10 41 7.466 1.325 E94\n"
"0 10 45 3.524 1.402 E94\n"
"0 10 63 6.137 1.369 E94\n"
"0 10 64 5.952 1.376 E94\n"
"0 11 20 6.339 1.348 E94\n"
"0 11 22 5.296 1.389 X94\n"
"0 11 25 6.019 1.583 E94\n"
"0 11 26 6.204 1.575 E94\n"
"0 11 37 6.511 1.342 E94\n"
"0 11 40 4.187 1.440 E94\n"
"0 12 15 2.978 2.031 E94\n"
"0 12 18 2.808 2.051 E94\n"
"0 12 19 2.838 2.050 #X94\n"
"0 12 20 2.859 1.751 C94\n"
"0 12 22 3.056 1.750 #X94\n"
"0 12 25 3.063 2.023 E94\n"
"0 12 26 2.448 2.100 #X94\n"
"0 12 37 3.378 1.721 E94\n"
"0 12 40 3.737 1.731 E94\n"
"0 12 57 3.714 1.694 E94\n"
"0 12 63 3.413 1.718 E94\n"
"0 12 64 3.649 1.699 E94\n"
"0 13 20 2.767 1.920 E94\n"
"0 13 22 2.928 1.902 E94\n"
"0 13 37 3.031 1.891 E94\n"
"0 13 64 3.031 1.891 E94\n"
"0 14 20 0.884 2.332 E94\n"
"0 14 37 1.781 2.075 E94\n"
"0 15 15 2.531 2.050 C94\n"
"0 15 18 2.214 2.094 E94\n"
"0 15 19 2.022 2.146 E94\n"
"0 15 20 2.757 1.822 E94\n"
"0 15 22 3.802 1.727 E94\n"
"0 15 25 2.319 2.112 E94\n"
"0 15 26 2.359 2.106 E94\n"
"0 15 30 3.750 1.731 E94\n"
"0 15 37 3.565 1.765 C94\n"
"0 15 40 3.859 1.666 E94\n"
"0 15 43 3.221 1.717 E94\n"
"0 15 57 3.993 1.713 E94\n"
"0 15 63 3.724 1.733 E94\n"
"0 15 64 3.548 1.747 E94\n"
"0 15 71 4.014 1.341 C94\n"
"0 17 20 2.397 1.865 E94\n"
"0 17 22 2.566 1.844 E94\n"
"0 17 37 3.098 1.787 E94\n"
"0 17 43 4.900 1.601 E94\n"
"0 18 20 3.172 1.780 E94\n"
"0 18 22 2.757 1.822 E94\n"
"0 18 32 10.748 1.450 #X94\n"
"0 18 37 3.281 1.770 X94\n"
"0 18 39 3.504 1.693 X94\n"
"0 18 43 3.301 1.710 #X94\n"
"0 18 48 6.186 1.540 X94\n"
"0 18 55 4.432 1.628 E94\n"
"0 18 58 2.568 1.783 E94\n"
"0 18 62 5.510 1.570 #X94\n"
"0 18 63 3.524 1.749 E94\n"
"0 18 64 3.856 1.723 E94\n"
"0 18 80 4.150 1.702 E94\n"
"0 19 20 2.288 1.900 E94\n"
"0 19 37 3.072 1.809 E94\n"
"0 19 40 4.470 1.686 E94\n"
"0 19 63 3.219 1.795 E94\n"
"0 19 75 1.600 2.226 E94\n"
"0 20 20 3.663 1.526 C94\n"
"0 20 22 4.251 1.484 E94\n"
"0 20 25 2.718 1.838 E94\n"
"0 20 26 2.588 1.853 E94\n"
"0 20 30 3.977 1.507 C94\n"
"0 20 34 4.171 1.460 E94\n"
"0 20 37 3.740 1.516 E94\n"
"0 20 40 4.784 1.427 E94\n"
"0 20 41 4.286 1.482 E94\n"
"0 20 43 3.737 1.487 E94\n"
"0 20 45 3.844 1.480 E94\n"
"0 22 22 3.969 1.499 C94\n"
"0 22 30 3.785 1.513 E94\n"
"0 22 34 4.103 1.464 E94\n"
"0 22 37 4.481 1.471 E94\n"
"0 22 40 4.188 1.459 E94\n"
"0 22 41 5.071 1.441 E94\n"
"0 22 43 4.070 1.466 E94\n"
"0 22 45 4.311 1.452 E94\n"
"0 23 39 7.112 1.012 C94\n"
"0 23 62 6.339 1.026 X94\n"
"0 23 67 6.610 1.019 #E94\n"
"0 23 68 5.899 1.038 C94\n"
"0 25 25 1.514 2.253 E94\n"
"0 25 32 8.296 1.510 #X94\n"
"0 25 37 3.586 1.755 E94\n"
"0 25 39 4.370 1.676 E94\n"
"0 25 40 4.629 1.660 E94\n"
"0 25 43 3.237 1.762 X94\n"
"0 25 57 4.356 1.699 E94\n"
"0 25 63 3.711 1.745 E94\n"
"0 25 71 3.001 1.411 X94\n"
"0 25 72 3.744 1.950 #X94\n"
"0 26 26 1.414 2.279 E94\n"
"0 26 34 3.395 1.748 E94\n"
"0 26 37 3.207 1.788 E94\n"
"0 26 40 4.870 1.646 E94\n"
"0 26 71 2.959 1.415 C94\n"
"0 28 40 6.576 1.018 C94\n"
"0 28 43 6.265 1.028 X94\n"
"0 28 48 6.413 1.024 X94\n"
"0 30 30 9.579 1.343 C94\n"
"1 30 30 5.355 1.428 E94\n"
"0 30 40 8.447 1.298 E94\n"
"1 30 67 5.274 1.404 E94\n"
"0 31 70 7.880 0.969 C94\n"
"0 32 41 9.756 1.261 C94\n"
"0 32 45 9.420 1.233 X94\n"
"0 32 67 7.926 1.269 E94\n"
"0 32 68 4.398 1.348 C94\n"
"0 32 69 6.098 1.261 C94\n"
"0 32 73 8.427 1.510 #X94\n"
"0 32 77 10.648 1.450 #X94\n"
"0 32 82 8.594 1.252 E94\n"
"0 34 36 6.163 1.028 C94\n"
"0 34 37 4.347 1.450 E94\n"
"0 34 43 4.401 1.351 E94\n"
"0 35 37 9.767 1.262 E94\n"
"0 35 63 12.760 1.207 E94\n"
"0 36 54 6.529 1.022 C94\n"
"0 36 55 6.744 1.014 C94\n"
"0 36 56 6.490 1.017 C94\n"
"0 36 58 6.610 1.019 #E94\n"
"0 36 81 6.980 1.016 C94\n"
"0 37 37 5.573 1.374 C94\n"
"1 37 37 5.178 1.436 E94\n"
"0 37 38 5.737 1.333 C94\n"
"0 37 39 5.978 1.375 E94\n"
"1 37 39 5.650 1.388 E94\n"
"0 37 40 6.168 1.398 C94\n"
"0 37 41 4.537 1.468 E94\n"
"0 37 43 4.764 1.428 X94\n"
"0 37 45 4.705 1.431 E94\n"
"0 37 46 6.191 1.367 E94\n"
"0 37 55 6.615 1.352 E94\n"
"0 37 56 5.055 1.414 E94\n"
"1 37 57 5.092 1.440 E94\n"
"0 37 58 7.432 1.326 E94\n"
"1 37 58 5.055 1.414 E94\n"
"0 37 61 5.724 1.385 E94\n"
"0 37 62 7.137 1.335 E94\n"
"0 37 63 6.095 1.372 C94\n"
"1 37 63 5.178 1.436 E94\n"
"0 37 64 6.161 1.379 C94\n"
"1 37 64 5.265 1.432 E94\n"
"1 37 67 4.725 1.430 E94\n"
"0 37 69 5.396 1.352 C94\n"
"0 37 78 6.719 1.375 E94\n"
"0 37 81 3.987 1.471 E94\n"
"1 37 81 4.531 1.440 E94\n"
"0 38 38 5.002 1.246 C94\n"
"0 38 63 7.299 1.330 E94\n"
"0 38 64 6.978 1.340 E94\n"
"0 38 69 5.036 1.321 E94\n"
"0 38 78 6.218 1.366 E94\n"
"0 39 40 4.101 1.367 E94\n"
"0 39 45 3.524 1.402 E94\n"
"0 39 63 6.301 1.364 C94\n"
"1 39 63 6.137 1.369 E94\n"
"0 39 64 6.357 1.361 E94\n"
"1 39 64 5.482 1.395 E94\n"
"0 39 65 5.513 1.339 C94\n"
"0 39 78 6.137 1.369 E94\n"
"0 40 40 4.248 1.359 E94\n"
"0 40 45 4.305 1.356 E94\n"
"0 40 46 4.727 1.335 E94\n"
"0 40 54 6.817 1.256 E94\n"
"0 40 63 6.733 1.348 E94\n"
"0 40 64 6.644 1.351 E94\n"
"0 40 78 5.900 1.378 E94\n"
"0 41 41 5.029 1.443 E94\n"
"0 41 55 5.577 1.391 E94\n"
"0 41 62 7.137 1.335 E94\n"
"0 41 72 4.519 1.678 X94\n"
"0 41 80 5.222 1.434 E94\n"
"0 42 61 16.223 1.087 E94\n"
"0 43 43 4.211 1.361 E94\n"
"0 43 45 3.710 1.390 E94\n"
"0 43 64 5.389 1.399 E94\n"
"0 44 63 3.589 1.717 C94\n"
"0 44 65 3.374 1.684 C94\n"
"0 44 78 3.711 1.734 E94\n"
"0 44 80 3.910 1.719 E94\n"
"0 45 63 5.119 1.411 E94\n"
"0 45 64 5.076 1.413 E94\n"
"0 45 78 5.724 1.385 E94\n"
"0 47 53 12.192 1.140 #X94\n"
"0 49 50 6.812 0.991 C94\n"
"0 51 52 7.100 0.987 X94\n"
"0 55 57 7.227 1.319 C94\n"
"0 55 62 3.977 1.374 E94\n"
"0 55 64 5.529 1.393 E94\n"
"0 55 80 7.500 1.324 E94\n"
"0 56 57 4.137 1.383 C94\n"
"0 56 63 5.900 1.378 E94\n"
"0 56 80 6.470 1.357 E94\n"
"1 57 63 5.400 1.426 E94\n"
"1 57 64 5.135 1.438 E94\n"
"0 58 63 6.794 1.346 E94\n"
"0 58 64 6.164 1.368 E94\n"
"0 59 63 5.787 1.360 C94\n"
"0 59 65 4.756 1.388 C94\n"
"0 59 78 6.127 1.364 E94\n"
"0 59 80 7.064 1.332 E94\n"
"0 59 82 3.855 1.431 E94\n"
"0 60 61 15.749 1.170 #X94\n"
"0 62 63 6.947 1.341 E94\n"
"0 62 64 6.273 1.364 E94\n"
"1 63 63 5.729 1.412 E94\n"
"0 63 64 7.118 1.377 C94\n"
"0 63 66 8.326 1.313 C94\n"
"0 63 72 4.503 1.679 E94\n"
"0 63 78 7.434 1.352 E94\n"
"0 63 81 7.778 1.316 E94\n"
"0 64 64 4.313 1.418 C94\n"
"1 64 64 4.926 1.448 E94\n"
"0 64 65 8.258 1.335 C94\n"
"0 64 66 4.456 1.369 C94\n"
"0 64 78 5.492 1.422 E94\n"
"0 64 81 5.824 1.381 E94\n"
"0 64 82 6.794 1.346 E94\n"
"0 65 66 7.243 1.323 C94\n"
"0 65 78 8.447 1.298 E94\n"
"0 65 81 5.223 1.313 E94\n"
"0 65 82 5.622 1.297 E94\n"
"0 66 66 3.874 1.368 C94\n"
"0 66 78 6.385 1.360 E94\n"
"0 66 81 3.960 1.375 E94\n"
"0 67 67 6.085 1.280 E94\n"
"0 71 75 2.852 1.423 X94\n"
"0 72 73 2.628 2.035 X94\n"
"0 76 76 4.286 1.357 X94\n"
"0 76 78 6.824 1.345 X94\n"
"0 78 78 5.573 1.374 C94\n"
"0 78 79 8.890 1.287 E94\n"
"0 78 81 5.046 1.381 C94\n"
"0 79 79 6.408 1.269 E94\n"
"0 79 81 4.305 1.356 E94\n"
"0 80 81 8.237 1.335 C94\n";
class MMFFBndkCollection *MMFFBndkCollection::ds_instance = NULL;
extern const std::string defaultMMFFBndk;
MMFFBndkCollection *MMFFBndkCollection::getMMFFBndk(
const std::string &mmffBndk) {
if (!ds_instance) {
ds_instance = new MMFFBndkCollection(mmffBndk);
} else if (mmffBndk != "") {
delete ds_instance;
ds_instance = new MMFFBndkCollection(mmffBndk);
}
return ds_instance;
}
MMFFBndkCollection::MMFFBndkCollection(std::string mmffBndk) {
if (mmffBndk == "") {
mmffBndk = defaultMMFFBndk;
}
std::istringstream inStream(mmffBndk);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFBond mmffBondObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iAtomicNum = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomicNum.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomicNum = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomicNum.push_back(
(boost::uint8_t)boost::lexical_cast<unsigned int>(*token));
#endif
++token;
mmffBondObj.r0 = boost::lexical_cast<double>(*token);
++token;
mmffBondObj.kb = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[iAtomicNum][jAtomicNum] = mmffBondObj;
#else
d_params.push_back(mmffBondObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFBndk =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF BOND LENGTH, FORCE CONSTANT DEFAULT-RULE PARAMETERS\n"
"* C94 = Fitted to ab-initio derived core MMFF force constants\n"
"* E94 = Based on Herschberg/Laurie parameterization of Badger's rule\n"
"*\n"
"* species r0(ref) kb(ref) Source\n"
"1 6 1.084 5.15 C94\n"
"1 7 1.001 7.35 C94\n"
"1 8 0.947 9.10 C94\n"
"1 9 0.92 10.6 E94\n"
"1 14 1.48 2.3 E94\n"
"1 15 1.415 2.95 C94\n"
"1 16 1.326 4.30 C94\n"
"1 17 1.28 4.3 E94\n"
"1 35 1.41 4.2 E94\n"
"1 53 1.60 2.7 E94\n"
"6 6 1.512 3.80 C94\n"
"6 7 1.439 4.55 C94\n"
"6 8 1.393 5.40 C94\n"
"6 9 1.353 6.20 C94\n"
"6 14 1.86 2.6 E94\n"
"6 15 1.84 2.7 E94\n"
"6 16 1.812 2.85 C94\n"
"6 17 1.781 2.75 C94\n"
"6 35 1.94 2.6 E94\n"
"6 53 2.16 1.4 E94\n"
"7 7 1.283 6.00 C94\n"
"7 8 1.333 5.90 C94\n"
"7 9 1.36 5.9 E94\n"
"7 14 1.74 3.7 E94\n"
"7 15 1.65 4.8 E94\n"
"7 16 1.674 3.75 C94\n"
"7 17 1.75 3.5 E94\n"
"7 35 1.90 2.9 E94\n"
"7 53 2.10 1.6 E94\n"
"8 8 1.48 3.6 E94\n"
"8 9 1.42 4.6 E94\n"
"8 14 1.63 5.2 E94\n"
"8 15 1.66 4.7 E94\n"
"8 16 1.470 9.90 C94\n"
"8 17 1.70 4.1 E94\n"
"8 35 1.85 3.4 E94\n"
"8 53 2.05 1.6 E94\n"
"9 14 1.57 6.4 E94\n"
"9 15 1.54 7.1 E94\n"
"9 16 1.55 6.9 E94\n"
"14 14 2.32 1.3 E94\n"
"14 15 2.25 1.5 E94\n"
"14 16 2.15 2.0 E94\n"
"14 17 2.02 3.1 E94\n"
"14 35 2.19 2.1 E94\n"
"14 53 2.44 1.5 E94\n"
"15 15 2.21 1.7 E94\n"
"15 16 2.10 2.4 E94\n"
"15 17 2.03 3.0 E94\n"
"15 35 2.21 2.0 E94\n"
"15 53 2.47 1.4 E94\n"
"16 16 2.052 2.50 C94\n"
"16 17 2.04 2.9 E94\n"
"16 35 2.24 1.9 E94\n"
"16 53 2.40 1.7 E94\n"
"17 17 1.99 3.5 E94\n"
"35 35 2.28 2.4 E94\n"
"53 53 2.67 1.6 E94\n";
class MMFFHerschbachLaurieCollection *
MMFFHerschbachLaurieCollection::ds_instance = NULL;
extern const std::string defaultMMFFHerschbachLaurie;
MMFFHerschbachLaurieCollection *
MMFFHerschbachLaurieCollection::getMMFFHerschbachLaurie(
const std::string &mmffHerschbachLaurie) {
if (!ds_instance) {
ds_instance = new MMFFHerschbachLaurieCollection(mmffHerschbachLaurie);
} else if (mmffHerschbachLaurie != "") {
delete ds_instance;
ds_instance = new MMFFHerschbachLaurieCollection(mmffHerschbachLaurie);
}
return ds_instance;
}
MMFFHerschbachLaurieCollection::MMFFHerschbachLaurieCollection(
std::string mmffHerschbachLaurie) {
if (mmffHerschbachLaurie == "") {
mmffHerschbachLaurie = defaultMMFFHerschbachLaurie;
}
std::istringstream inStream(mmffHerschbachLaurie);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFHerschbachLaurie mmffHerschbachLaurieObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iRow = boost::lexical_cast<unsigned int>(*token);
#else
d_iRow.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jRow = boost::lexical_cast<unsigned int>(*token);
#else
d_jRow.push_back(
(boost::uint8_t)boost::lexical_cast<unsigned int>(*token));
#endif
++token;
mmffHerschbachLaurieObj.a_ij = boost::lexical_cast<double>(*token);
++token;
mmffHerschbachLaurieObj.d_ij = boost::lexical_cast<double>(*token);
++token;
mmffHerschbachLaurieObj.dp_ij = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[iRow][jRow] = mmffHerschbachLaurieObj;
#else
d_params.push_back(mmffHerschbachLaurieObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFHerschbachLaurie =
"*Table I. Parameters for Badger's Rule.\n"
"*\n"
"* i j a_ij d_ij dp_ij\n"
"0 0 1.26 0.025 0.025\n"
"0 1 1.66 0.30 0.36\n"
"0 2 1.84 0.38 0.58\n"
"0 3 1.98 0.49 0.65\n"
"0 4 2.03 0.51 0.80\n"
"0 5 2.03 0.25 0.81\n"
"0 30 1.85 0.15 0.53\n"
"0 40 1.84 0.61 0.61\n"
"0 50 1.78 0.97 0.62\n"
"1 1 1.91 0.68 0.68\n"
"1 2 2.28 0.74 0.92\n"
"1 3 2.35 0.85 1.02\n"
"1 4 2.33 0.68 1.12\n"
"1 5 2.50 0.97 1.22\n"
"1 30 2.08 1.14 0.97\n"
"1 40 2.34 1.17 1.08\n"
"2 2 2.41 1.18 1.18\n"
"2 3 2.52 1.02 1.28\n"
"2 4 2.61 1.28 1.40\n"
"2 5 2.60 0.84 1.24\n"
"3 3 2.58 1.41 1.35\n"
"3 4 2.66 0.86 1.48\n"
"3 5 2.75 1.14 1.55\n"
"4 4 2.85 1.62 1.62\n"
"4 5 2.76 1.25 1.51\n";
class MMFFCovRadPauEleCollection *MMFFCovRadPauEleCollection::ds_instance =
NULL;
extern const std::string defaultMMFFCovRadPauEle;
MMFFCovRadPauEleCollection *MMFFCovRadPauEleCollection::getMMFFCovRadPauEle(
const std::string &mmffCovRadPauEle) {
if (!ds_instance) {
ds_instance = new MMFFCovRadPauEleCollection(mmffCovRadPauEle);
} else if (mmffCovRadPauEle != "") {
delete ds_instance;
ds_instance = new MMFFCovRadPauEleCollection(mmffCovRadPauEle);
}
return ds_instance;
}
MMFFCovRadPauEleCollection::MMFFCovRadPauEleCollection(
std::string mmffCovRadPauEle) {
if (mmffCovRadPauEle == "") {
mmffCovRadPauEle = defaultMMFFCovRadPauEle;
}
std::istringstream inStream(mmffCovRadPauEle);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFCovRadPauEle mmffCovRadPauEleObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int atomicNum = boost::lexical_cast<unsigned int>(*token);
#else
d_atomicNum.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffCovRadPauEleObj.r0 = boost::lexical_cast<double>(*token);
++token;
mmffCovRadPauEleObj.chi = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[atomicNum] = mmffCovRadPauEleObj;
#else
d_params.push_back(mmffCovRadPauEleObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFCovRadPauEle =
"* atomicNum covRad pauEle\n"
"1 0.33 2.20\n"
"3 1.34 0.97\n"
"6 0.77 2.50\n"
"7 0.73 3.07\n"
"8 0.72 3.50\n"
"9 0.74 4.12\n"
"11 1.54 1.01\n"
"12 1.30 1.23\n"
"14 1.15 1.74\n"
"15 1.09 2.06\n"
"16 1.03 2.44\n"
"17 1.01 2.83\n"
"19 1.96 0.91\n"
"20 1.74 1.04\n"
"29 1.38 1.75\n"
"30 1.31 1.66\n"
"35 1.15 2.74\n"
"53 1.33 2.21\n";
class MMFFAngleCollection *MMFFAngleCollection::ds_instance = NULL;
extern const std::string defaultMMFFAngleData[];
MMFFAngleCollection *MMFFAngleCollection::getMMFFAngle(
const std::string &mmffAngle) {
if (!ds_instance) {
ds_instance = new MMFFAngleCollection(mmffAngle);
} else if (mmffAngle != "") {
delete ds_instance;
ds_instance = new MMFFAngleCollection(mmffAngle);
}
return ds_instance;
}
MMFFAngleCollection::MMFFAngleCollection(std::string mmffAngle) {
if (mmffAngle == "") {
unsigned int i = 0;
while (defaultMMFFAngleData[i] != "EOS") {
mmffAngle += defaultMMFFAngleData[i];
++i;
}
}
std::istringstream inStream(mmffAngle);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFAngle mmffAngleObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int angleType = boost::lexical_cast<unsigned int>(*token);
#else
d_angleType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int kAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_kAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffAngleObj.ka = boost::lexical_cast<double>(*token);
++token;
mmffAngleObj.theta0 = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[angleType][iAtomType][jAtomType][kAtomType] = mmffAngleObj;
#else
d_params.push_back(mmffAngleObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
// another joy of VC++ "compiler limit: string exceeds 65535 bytes in length"
// compels us to
// break this into pieces
const std::string defaultMMFFAngleData[] = {
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF ANGLE PARAMETERS- Rev: 26-Oct-94 Source: MMFF\n"
"* C94 = CORE MMFF parameter - obtained from ab initio data\n"
"* X94 = EXTD MMFF parameter - fit to additional ab initio data\n"
"* E94 = theta0 from fit to X-ray data, ka from empirical rule\n"
"* #E94 = theta0 and ka both from empirical rules\n"
"*\n"
"* atom types ka theta0 Comment/origin\n"
"0 0 1 0 0.000 108.900 0:*-1-* MMFF DEF\n"
"0 1 1 1 0.851 109.608 C94\n"
"0 1 1 2 0.736 109.445 C94\n"
"0 1 1 3 0.777 107.517 C94\n"
"0 1 1 4 1.006 110.265 E94\n"
"0 1 1 5 0.636 110.549 C94\n"
"0 1 1 6 0.992 108.133 C94\n"
"0 1 1 8 0.777 108.290 C94\n"
"0 1 1 9 1.136 108.194 E94\n"
"0 1 1 10 1.050 109.960 C94\n"
"0 1 1 11 1.225 108.313 C94\n"
"0 1 1 12 1.056 108.679 C94\n"
"0 1 1 13 1.078 106.820 E94\n"
"0 1 1 14 0.980 109.945 E94\n"
"0 1 1 15 0.743 107.397 C94\n"
"0 1 1 17 1.089 108.578 E94\n"
"0 1 1 18 1.093 109.315 E94\n"
"0 1 1 19 0.755 115.436 E94\n"
"0 1 1 20 1.021 108.659 E94\n"
"0 1 1 22 1.001 110.125 E94\n"
"0 1 1 25 0.803 112.356 X94\n"
"0 1 1 26 0.833 109.879 E94\n"
"0 1 1 34 1.179 106.493 C94\n"
"0 1 1 37 0.756 108.617 C94\n"
"0 1 1 39 0.927 109.170 C94\n"
"0 1 1 40 1.130 108.678 E94\n"
"0 1 1 41 0.330 98.422 C94\n"
"0 1 1 43 1.135 108.019 E94\n"
"0 1 1 45 1.197 105.028 E94\n"
"0 1 1 54 1.173 106.424 E94\n"
"0 1 1 55 1.150 107.604 E94\n"
"0 1 1 56 1.199 110.371 C94\n"
"0 1 1 57 1.012 109.900 E94\n"
"0 1 1 58 1.179 106.327 E94\n"
"0 1 1 61 1.125 109.311 E94\n"
"0 1 1 63 1.006 110.058 E94\n"
"0 1 1 64 0.988 111.064 E94\n"
"0 1 1 67 1.216 104.557 E94\n"
"0 1 1 68 1.018 107.195 C94\n"
"0 1 1 73 1.160 104.658 E94\n",
"0 1 1 78 1.012 109.850 E94\n"
"0 1 1 80 0.947 113.327 E94\n"
"0 1 1 81 1.108 109.837 E94\n"
"0 2 1 2 1.113 111.453 C94\n"
"0 2 1 3 0.667 104.829 C94\n"
"0 2 1 4 1.022 109.873 E94\n"
"0 2 1 5 0.632 110.292 C94\n"
"0 2 1 6 1.074 108.699 C94\n"
"0 2 1 8 0.884 111.553 C94\n"
"0 2 1 9 1.118 109.577 E94\n"
"0 2 1 10 1.160 107.963 E94\n"
"0 2 1 11 1.192 110.419 E94\n"
"0 2 1 12 1.070 109.410 E94\n"
"0 2 1 15 1.078 109.560 E94\n"
"0 2 1 17 1.077 109.434 E94\n"
"0 2 1 18 1.188 105.110 E94\n"
"0 2 1 20 1.053 107.448 E94\n"
"0 2 1 22 0.942 114.020 E94\n"
"0 2 1 25 0.893 106.815 E94\n"
"0 2 1 26 1.029 99.065 E94\n"
"0 2 1 34 1.066 111.817 E94\n"
"0 2 1 37 0.985 111.446 E94\n"
"0 2 1 39 1.124 109.513 E94\n"
"0 2 1 40 1.149 108.270 E94\n"
"0 2 1 45 1.232 103.978 E94\n"
"0 2 1 63 0.935 114.692 E94\n"
"0 2 1 67 1.224 104.687 E94\n"
"0 3 1 3 0.974 111.746 E94\n"
"0 3 1 4 1.019 109.850 E94\n"
"0 3 1 5 0.650 108.385 C94\n"
"0 3 1 6 0.528 104.112 C94\n"
"0 3 1 8 1.197 105.837 E94\n"
"0 3 1 9 1.201 105.535 E94\n"
"0 3 1 10 0.634 102.655 C94\n"
"0 3 1 11 1.189 110.328 E94\n"
"0 3 1 12 1.136 106.064 E94\n"
"0 3 1 13 1.147 103.645 E94\n"
"0 3 1 14 1.048 106.404 E94\n"
"0 3 1 15 1.125 107.192 E94\n"
"0 3 1 17 1.092 108.602 E94\n"
"0 3 1 18 1.120 108.119 E94\n"
"0 3 1 20 0.969 111.830 E94\n"
"0 3 1 22 0.999 110.522 E94\n"
"0 3 1 26 0.742 116.555 E94\n"
"0 3 1 34 1.141 107.871 E94\n"
"0 3 1 37 1.011 109.833 E94\n"
"0 3 1 39 1.136 108.751 E94\n"
"0 3 1 40 1.174 106.941 E94\n"
"0 3 1 41 1.033 108.216 E94\n"
"0 3 1 45 1.221 104.281 E94\n"
"0 3 1 63 1.069 107.077 E94\n",
"0 3 1 64 1.028 109.186 E94\n"
"0 3 1 81 1.167 107.327 E94\n"
"0 4 1 4 0.954 114.186 E94\n"
"0 4 1 5 0.615 111.417 X94\n"
"0 4 1 6 1.273 109.977 E94\n"
"0 4 1 8 1.099 111.063 E94\n"
"0 4 1 9 1.187 106.750 E94\n"
"0 4 1 10 1.117 110.488 E94\n"
"0 4 1 13 1.021 110.047 E94\n"
"0 4 1 15 1.028 112.432 E94\n"
"0 4 1 18 1.187 105.351 E94\n"
"0 4 1 22 1.174 102.556 E94\n"
"0 4 1 26 0.853 108.999 E94\n"
"0 4 1 34 1.148 108.160 E94\n"
"0 4 1 37 0.993 111.424 E94\n"
"0 5 1 5 0.516 108.836 C94\n"
"0 5 1 6 0.781 108.577 C94\n"
"0 5 1 8 0.653 110.297 C94\n"
"0 5 1 9 0.733 109.894 C94\n"
"0 5 1 10 0.740 107.646 C94\n"
"0 5 1 11 0.875 107.897 C94\n"
"0 5 1 12 0.698 108.162 C94\n"
"0 5 1 13 0.613 106.049 E94\n"
"0 5 1 14 0.508 113.019 E94\n"
"0 5 1 15 0.576 109.609 C94\n"
"0 5 1 17 0.634 107.944 X94\n"
"0 5 1 18 0.663 106.855 X94\n"
"0 5 1 19 0.450 113.195 X94\n"
"0 5 1 20 0.706 111.000 C94\n"
"0 5 1 22 0.618 110.380 E94\n"
"0 5 1 25 0.487 109.486 X94\n"
"0 5 1 26 0.466 111.172 X94\n"
"0 5 1 34 0.872 106.224 C94\n"
"0 5 1 35 0.644 125.663 X94\n"
"0 5 1 37 0.627 109.491 C94\n"
"0 5 1 39 0.811 106.299 C94\n"
"0 5 1 40 0.719 109.870 C94\n"
"0 5 1 41 0.525 108.904 C94\n"
"0 5 1 43 0.692 109.083 X94\n"
"0 5 1 45 0.741 105.197 X94\n"
"0 5 1 46 0.719 106.735 X94\n"
"0 5 1 54 0.874 106.973 C94\n"
"0 5 1 55 0.861 108.507 C94\n"
"0 5 1 56 0.814 108.223 C94\n"
"0 5 1 57 0.626 110.420 E94\n"
"0 5 1 58 0.750 105.481 E94\n"
"0 5 1 61 0.710 109.227 X94\n"
"0 5 1 62 0.655 113.035 X94\n"
"0 5 1 63 0.621 110.467 E94\n"
"0 5 1 64 0.622 110.457 E94\n"
"0 5 1 67 0.732 106.474 E94\n",
"0 5 1 68 0.748 103.817 C94\n"
"0 5 1 72 0.547 116.576 X94\n"
"0 5 1 73 0.633 107.153 X94\n"
"0 5 1 78 0.640 109.078 E94\n"
"0 5 1 80 0.684 105.144 E94\n"
"0 5 1 81 0.721 107.870 E94\n"
"0 6 1 6 1.156 111.368 C94\n"
"0 6 1 8 1.333 112.223 E94\n"
"0 6 1 9 1.224 116.950 E94\n"
"0 6 1 10 1.432 108.568 E94\n"
"0 6 1 11 1.593 106.900 E94\n"
"0 6 1 15 1.273 112.012 E94\n"
"0 6 1 17 1.348 108.655 E94\n"
"0 6 1 19 0.906 117.214 E94\n"
"0 6 1 20 1.293 108.202 E94\n"
"0 6 1 22 1.287 108.913 E94\n"
"0 6 1 25 1.171 103.598 E94\n"
"0 6 1 26 0.888 118.433 E94\n"
"0 6 1 34 1.257 114.975 E94\n"
"0 6 1 37 0.878 107.978 C94\n"
"0 6 1 39 1.485 106.464 E94\n"
"0 6 1 40 1.371 110.779 E94\n"
"0 6 1 41 1.333 106.467 E94\n"
"0 6 1 45 1.523 104.438 E94\n"
"0 6 1 57 1.308 108.467 E94\n"
"0 6 1 63 1.351 106.535 E94\n"
"0 6 1 64 1.238 111.308 E94\n"
"0 8 1 8 1.203 110.856 E94\n"
"0 8 1 9 1.133 114.080 E94\n"
"0 8 1 10 1.258 108.683 E94\n"
"0 8 1 12 1.217 107.251 E94\n"
"0 8 1 15 1.120 112.356 E94\n"
"0 8 1 20 1.116 109.353 E94\n"
"0 8 1 25 1.143 98.698 E94\n"
"0 8 1 34 1.138 113.412 E94\n"
"0 8 1 37 1.090 110.992 E94\n"
"0 8 1 39 1.364 104.193 E94\n"
"0 8 1 40 0.964 123.962 E94\n"
"0 8 1 41 1.234 103.868 E94\n"
"0 8 1 43 1.137 113.596 E94\n"
"0 8 1 45 1.583 96.139 E94\n"
"0 8 1 57 1.038 114.266 E94\n"
"0 8 1 63 1.104 110.598 E94\n"
"0 8 1 64 1.156 108.127 E94\n"
"0 9 1 10 1.209 110.720 E94\n"
"0 9 1 12 1.173 109.152 E94\n"
"0 9 1 15 1.024 117.465 E94\n"
"0 9 1 25 1.060 102.432 E94\n"
"0 9 1 37 1.077 111.565 E94\n"
"0 9 1 40 1.084 116.728 E94\n"
"0 9 1 80 1.163 107.509 E94\n",
"0 10 1 10 1.191 111.995 E94\n"
"0 10 1 15 1.161 110.502 E94\n"
"0 10 1 17 1.269 105.509 E94\n"
"0 10 1 20 1.220 104.838 E94\n"
"0 10 1 22 1.132 109.262 E94\n"
"0 10 1 25 1.015 104.822 E94\n"
"0 10 1 37 1.107 110.423 E94\n"
"0 10 1 40 1.264 108.536 E94\n"
"0 10 1 41 1.087 110.961 E94\n"
"0 10 1 57 1.268 103.622 E94\n"
"0 11 1 11 1.638 106.081 C94\n"
"0 11 1 15 1.254 109.517 E94\n"
"0 11 1 20 1.243 107.637 E94\n"
"0 11 1 25 1.244 97.532 E94\n"
"0 11 1 34 1.338 108.669 E94\n"
"0 11 1 35 1.556 110.367 E94\n"
"0 11 1 37 1.151 112.278 E94\n"
"0 11 1 41 1.301 105.053 E94\n"
"0 11 1 45 1.550 100.991 E94\n"
"0 11 1 73 1.303 106.569 E94\n"
"0 11 1 75 0.884 114.378 E94\n"
"0 12 1 12 1.096 110.422 C94\n"
"0 12 1 15 1.146 111.064 E94\n"
"0 12 1 18 1.299 104.827 E94\n"
"0 12 1 19 0.932 108.971 E94\n"
"0 12 1 20 1.081 108.605 E94\n"
"0 12 1 22 1.097 108.028 E94\n"
"0 12 1 25 0.989 106.118 E94\n"
"0 12 1 37 1.076 109.030 E94\n"
"0 12 1 39 1.150 110.359 E94\n"
"0 12 1 45 1.353 101.430 E94\n"
"0 12 1 63 1.071 109.474 E94\n"
"0 12 1 64 1.093 108.338 E94\n"
"0 13 1 13 1.093 111.645 E94\n"
"0 13 1 20 1.084 106.534 E94\n"
"0 13 1 22 1.068 107.469 E94\n"
"0 13 1 45 1.305 101.383 E94\n"
"0 14 1 20 1.021 107.718 E94\n"
"0 15 1 15 1.147 111.896 E94\n"
"0 15 1 25 1.059 103.308 E94\n"
"0 15 1 34 1.222 107.318 E94\n"
"0 15 1 37 1.051 110.959 E94\n"
"0 15 1 40 1.149 111.005 E94\n"
"0 15 1 41 1.263 100.981 E94\n"
"0 15 1 63 1.060 110.596 E94\n"
"0 15 1 64 1.059 110.703 E94\n"
"0 15 1 73 1.289 105.029 E94\n"
"0 17 1 37 1.065 110.049 E94\n"
"0 18 1 20 1.121 107.960 E94\n"
"0 18 1 22 1.283 101.125 E94\n"
"0 18 1 37 1.203 104.390 E94\n",
"0 18 1 45 1.287 105.273 E94\n"
"0 18 1 64 1.093 109.683 E94\n"
"0 19 1 54 0.772 119.506 E94\n"
"0 20 1 20 1.229 99.084 E94\n"
"0 20 1 37 1.052 107.428 E94\n"
"0 20 1 45 1.169 106.335 E94\n"
"0 22 1 22 0.990 111.226 E94\n"
"0 22 1 25 0.885 107.293 E94\n"
"0 22 1 34 1.045 112.940 E94\n"
"0 22 1 37 1.037 108.586 E94\n"
"0 22 1 45 1.182 106.181 E94\n"
"0 25 1 25 0.551 127.138 E94\n"
"0 25 1 34 0.779 119.271 E94\n"
"0 25 1 37 0.784 113.945 E94\n"
"0 25 1 40 1.062 102.417 E94\n"
"0 25 1 58 0.916 110.234 E94\n"
"0 26 1 26 0.625 118.700 E94\n"
"0 34 1 34 1.216 109.167 E94\n"
"0 34 1 37 1.075 111.275 E94\n"
"0 34 1 41 1.048 112.238 E94\n"
"0 34 1 63 1.077 111.412 E94\n"
"0 34 1 73 1.142 110.240 E94\n"
"0 37 1 37 0.986 111.315 E94\n"
"0 37 1 40 1.129 109.188 E94\n"
"0 37 1 43 1.074 111.478 E94\n"
"0 37 1 45 1.259 102.800 E94\n"
"0 37 1 57 0.981 112.047 E94\n"
"0 37 1 64 1.175 102.239 E94\n"
"0 37 1 68 1.100 109.983 E94\n"
"0 37 1 78 1.005 110.638 E94\n"
"0 37 1 81 1.176 107.040 E94\n"
"0 39 1 39 1.260 108.547 E94\n"
"0 40 1 40 1.182 112.005 E94\n"
"0 40 1 55 1.322 105.786 E94\n"
"0 40 1 63 1.032 114.505 E94\n"
"0 40 1 64 1.000 116.376 E94\n"
"0 41 1 41 1.082 105.400 E94\n"
"0 41 1 63 1.061 107.112 E94\n"
"0 41 1 81 1.093 110.553 E94\n"
"0 45 1 45 1.391 102.088 E94\n"
"0 0 2 0 0.000 119.400 0:*-2-* MMFF DEF\n"
"1 0 2 0 0.000 118.200 0:*-2-* MMFF DEF\n"
"2 0 2 0 0.000 120.800 2::*-2-* MMFF DEF\n"
"3 0 2 0 0.000 62.600 3::*-2-* MMFF DEF\n"
"6 0 2 0 0.000 60.500 6:*-2-* MMFF DEF\n"
"0 1 2 1 0.752 118.043 C94\n"
"0 1 2 2 0.672 122.141 C94\n"
"1 1 2 2 0.684 116.929 C94\n"
"1 1 2 3 0.698 116.104 C94\n"
"0 1 2 4 0.828 125.045 E94\n"
"1 1 2 4 0.846 121.613 E94\n",
"0 1 2 5 0.446 120.108 C94\n"
"0 1 2 6 1.160 115.518 E94\n"
"0 1 2 10 1.015 116.707 E94\n"
"0 1 2 12 0.983 115.343 E94\n"
"0 1 2 13 0.964 115.395 E94\n"
"0 1 2 15 0.939 119.465 E94\n"
"0 1 2 17 0.883 121.868 E94\n"
"0 1 2 18 0.961 117.918 E94\n"
"0 1 2 20 0.880 118.310 E94\n"
"0 1 2 22 0.873 119.114 E94\n"
"0 1 2 30 0.826 124.605 E94\n"
"1 1 2 37 0.721 116.064 C94\n"
"0 1 2 40 0.982 118.515 E94\n"
"0 1 2 45 1.121 109.921 E94\n"
"0 1 2 56 1.006 117.192 E94\n"
"1 1 2 63 0.768 127.945 E94\n"
"1 1 2 64 0.966 113.884 E94\n"
"1 1 2 67 1.115 110.185 E94\n"
"1 2 2 2 0.747 121.550 C94\n"
"2 2 2 2 0.796 126.284 E94\n"
"6 2 2 2 0.173 60.549 E94\n"
"1 2 2 3 0.545 111.297 C94\n"
"2 2 2 3 0.893 118.456 E94\n"
"5 2 2 3 0.184 59.145 E94\n"
"1 2 2 4 0.902 121.053 E94\n"
"2 2 2 4 0.889 119.794 E94\n"
"0 2 2 5 0.535 121.004 C94\n"
"1 2 2 5 0.463 118.442 C94\n"
"0 2 2 6 1.117 121.267 C94\n"
"1 2 2 6 1.204 114.538 E94\n"
"1 2 2 9 0.960 123.536 E94\n"
"2 2 2 9 1.045 116.273 E94\n"
"0 2 2 10 1.003 120.828 E94\n"
"1 2 2 10 1.026 117.324 E94\n"
"0 2 2 11 1.089 119.100 X94\n"
"1 2 2 11 1.090 116.828 E94\n"
"0 2 2 12 0.931 120.132 X94\n"
"1 2 2 12 0.957 117.526 E94\n"
"0 2 2 13 0.867 122.717 E94\n"
"0 2 2 14 0.818 122.584 E94\n"
"1 2 2 14 0.819 122.344 E94\n"
"0 2 2 15 0.931 121.553 E94\n"
"1 2 2 15 0.949 119.466 E94\n"
"0 2 2 17 0.977 117.167 E94\n"
"0 2 2 18 1.044 114.561 E94\n"
"0 2 2 19 0.668 124.721 E94\n"
"0 2 2 20 0.931 117.784 E94\n"
"0 2 2 22 0.809 126.820 E94\n"
"3 2 2 22 0.149 66.165 E94\n"
"0 2 2 25 0.700 123.830 E94\n"
"0 2 2 34 1.066 116.151 E94\n",
"0 2 2 35 0.911 137.103 X94\n"
"1 2 2 37 0.598 117.508 C94\n"
"2 2 2 37 0.817 124.229 E94\n"
"1 2 2 39 0.976 122.360 E94\n"
"0 2 2 40 0.773 126.830 C94\n"
"1 2 2 40 0.976 120.132 E94\n"
"0 2 2 41 0.432 110.442 C94\n"
"0 2 2 43 1.144 111.808 E94\n"
"0 2 2 45 1.194 109.231 X94\n"
"1 2 2 45 1.062 113.984 E94\n"
"0 2 2 46 1.005 121.534 E94\n"
"0 2 2 55 0.995 121.154 E94\n"
"0 2 2 56 1.234 108.879 E94\n"
"0 2 2 62 0.808 135.269 X94\n"
"1 2 2 63 0.948 118.277 E94\n"
"1 2 2 64 0.866 123.528 E94\n"
"2 2 2 64 0.859 121.998 E94\n"
"1 2 2 67 1.132 112.136 E94\n"
"0 2 2 72 0.770 134.269 X94\n"
"1 2 2 81 1.078 116.541 E94\n"
"2 3 2 3 0.853 120.370 E94\n"
"2 3 2 4 0.878 119.739 E94\n"
"1 3 2 5 0.487 117.291 C94\n"
"1 3 2 6 1.142 116.738 E94\n"
"2 3 2 9 1.005 117.648 E94\n"
"1 3 2 10 1.039 115.698 E94\n"
"1 3 2 11 1.150 112.876 E94\n"
"1 3 2 12 0.997 114.732 E94\n"
"1 3 2 13 0.946 116.643 E94\n"
"1 3 2 14 0.891 117.111 E94\n"
"1 3 2 15 1.023 114.635 E94\n"
"1 3 2 20 0.870 119.265 E94\n"
"1 3 2 22 0.816 123.510 E94\n"
"1 3 2 30 1.025 112.209 E94\n"
"1 3 2 34 1.099 111.723 E94\n"
"1 3 2 35 1.141 118.767 E94\n"
"2 3 2 37 0.868 119.758 E94\n"
"1 3 2 40 1.024 116.408 E94\n"
"1 3 2 41 0.855 119.505 E94\n"
"1 3 2 43 1.046 114.257 E94\n"
"1 3 2 45 1.077 112.401 E94\n"
"1 3 2 46 1.066 114.841 E94\n"
"2 4 2 4 0.832 124.158 E94\n"
"0 4 2 5 0.573 121.000 #E94\n"
"1 4 2 5 0.545 120.000 #E94\n"
"2 4 2 9 0.973 120.845 E94\n"
"1 4 2 15 0.906 122.447 E94\n"
"1 4 2 18 0.947 119.537 E94\n"
"1 4 2 30 0.819 126.938 E94\n"
"2 4 2 37 0.864 121.093 E94\n"
"1 4 2 40 1.083 114.355 E94\n",
"1 4 2 45 1.158 109.426 E94\n"
"2 4 2 63 0.860 122.442 E94\n"
"0 5 2 5 0.365 119.523 C94\n"
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"1 5 2 9 0.643 117.000 #E94\n"
"0 5 2 10 0.667 114.859 E94\n"
"0 5 2 11 0.795 108.186 X94\n"
"0 5 2 12 0.622 110.650 X94\n"
"0 5 2 13 0.566 113.513 E94\n"
"0 5 2 15 0.546 119.562 E94\n"
"0 5 2 17 0.492 124.000 #E94\n"
"0 5 2 18 0.548 119.053 E94\n"
"0 5 2 22 0.534 120.000 #E94\n"
"0 5 2 25 0.395 124.000 #E94\n"
"0 5 2 30 0.572 120.000 #E94\n"
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"1 5 2 37 0.491 117.423 C94\n"
"1 5 2 39 0.655 115.724 E94\n"
"0 5 2 40 0.568 112.322 C94\n"
"0 5 2 41 0.294 123.706 C94\n"
"0 5 2 45 0.728 107.774 X94\n"
"0 5 2 55 0.651 116.000 #E94\n"
"0 5 2 62 0.568 125.344 X94\n"
"1 5 2 63 0.550 120.000 #E94\n"
"1 5 2 64 0.546 120.000 #E94\n"
"0 5 2 72 0.531 122.009 X94\n"
"1 5 2 81 0.665 115.000 #E94\n"
"1 6 2 9 1.214 120.520 E94\n"
"0 6 2 10 1.311 115.921 E94\n"
"0 6 2 22 1.080 120.560 E94\n"
"0 6 2 35 1.172 132.391 E94\n"
"1 6 2 37 1.198 114.441 E94\n"
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"0 10 2 25 1.144 100.818 E94\n"
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"0 12 2 45 1.076 115.543 E94\n"
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"1 15 2 37 1.007 115.757 E94\n"
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"0 22 2 22 0.841 122.108 E94\n"
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"1 35 2 37 0.991 128.032 E94\n"
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"0 40 2 56 1.072 120.987 E94\n"
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"0 0 3 0 0.000 117.300 0:*-3-* MMFF DEF\n"
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"8 0 3 0 0.000 88.900 7:*-3-* MMFF DEF\n"
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"0 1 3 54 1.135 111.322 E94\n"
"1 1 3 58 1.162 108.129 E94\n",
"0 1 3 62 1.119 111.523 E94\n"
"1 1 3 63 0.909 117.001 E94\n"
"1 1 3 64 0.887 118.253 E94\n"
"0 1 3 67 1.142 110.666 E94\n"
"0 1 3 74 1.010 116.851 X94\n"
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"2 2 3 2 0.976 112.562 E94\n"
"6 2 3 2 0.157 62.792 E94\n"
"2 2 3 3 0.957 113.239 E94\n"
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"1 2 3 15 1.057 112.105 E94\n"
"1 2 3 16 0.881 124.850 E94\n"
"1 2 3 22 0.969 113.027 E94\n"
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"1 2 3 43 1.105 111.169 E94\n"
"1 2 3 53 1.082 114.032 E94\n"
"1 2 3 54 1.012 118.588 E94\n"
"1 2 3 55 1.186 107.278 E94\n"
"1 2 3 56 1.151 108.909 E94\n"
"2 2 3 63 0.918 116.947 E94\n"
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"1 2 3 67 1.022 117.597 E94\n"
"2 3 3 3 0.822 121.775 E94\n"
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"0 5 3 53 0.644 118.000 #E94\n"
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"1 5 3 64 0.566 117.000 #E94\n"
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"1 9 3 9 1.119 120.094 E94\n"
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"1 40 3 64 1.145 110.889 E94\n"
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"0 45 3 53 1.382 105.849 E94\n"
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"2 64 3 64 0.989 113.280 E94\n"
"0 0 4 0 0.000 180.000 0:*-4-* MMFF DEF\n"
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"0 2 4 2 0.442 180.000 E94\n"
"1 2 4 4 0.432 180.000 E94\n"
"0 2 4 30 0.444 180.000 E94\n"
"1 2 4 42 0.474 180.000 E94\n"
"1 3 4 4 0.427 180.000 E94\n"
"1 3 4 42 0.469 180.000 E94\n"
"0 4 4 5 0.281 180.000 E94\n"
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"0 4 4 10 0.486 180.000 E94\n"
"1 4 4 37 0.430 180.000 E94\n"
"0 7 4 9 0.648 180.000 E94\n"
"1 9 4 42 0.537 180.000 E94\n"
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"0 20 4 42 0.469 180.000 E94\n"
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"1 37 4 42 0.472 180.000 E94\n"
"0 42 4 43 0.541 180.000 E94\n"
"1 42 4 63 0.474 180.000 E94\n"
"1 42 4 64 0.473 180.000 E94\n"
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"0 25 6 37 1.099 115.923 E94\n"
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"0 37 6 37 1.462 108.967 E94\n"
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"0 0 43 0 0.000 113.300 0:*-43-* MMFF DEF\n"
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"0 0 46 0 0.000 111.000 0:*-46-* MMFF DEF\n"
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"0 1 58 37 1.003 119.236 E94\n"
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"0 65 59 78 1.644 107.142 E94\n"
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"0 0 64 0 0.000 121.400 0:*-64-* MMFF DEF\n"
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"1 37 64 65 0.942 122.866 E94\n"
"0 37 64 66 0.845 130.337 E94\n"
"0 37 64 78 0.706 135.432 E94\n"
"0 37 64 81 0.917 124.856 E94\n"
"0 37 64 82 0.946 123.684 E94\n"
"1 37 64 82 1.000 119.086 E94\n"
"0 38 64 63 0.988 121.242 E94\n"
"0 38 64 64 0.858 129.014 E94\n"
"0 38 64 65 0.989 127.335 E94\n"
"0 38 64 66 1.022 124.454 E94\n"
"0 39 64 64 1.086 114.312 E94\n"
"0 39 64 65 1.060 122.481 E94\n"
"1 39 64 65 1.204 114.188 E94\n"
"1 39 64 66 1.170 115.157 E94\n"
"0 40 64 63 0.948 123.538 E94\n"
"0 40 64 64 0.928 123.853 E94\n"
"0 40 64 65 0.958 129.125 E94\n"
"0 40 64 81 1.035 123.154 E94\n"
"0 40 64 82 1.183 115.934 E94\n"
"0 43 64 63 0.885 126.749 E94\n"
"0 43 64 64 0.898 124.876 E94\n"
"0 43 64 65 1.024 123.706 E94\n"
"0 43 64 66 1.017 123.409 E94\n"
"0 45 64 63 0.981 120.063 E94\n"
"0 45 64 64 0.921 123.014 E94\n"
"0 45 64 65 1.276 110.521 E94\n"
"0 45 64 66 1.199 113.371 E94\n"
"0 55 64 64 0.907 124.405 E94\n"
"0 55 64 65 1.002 125.220 E94\n"
"1 57 64 65 1.020 117.950 E94\n"
"1 57 64 66 0.959 121.017 E94\n"
"0 58 64 63 1.075 115.646 E94\n"
"0 58 64 64 0.815 131.812 E94\n"
"0 58 64 66 0.978 126.562 E94\n"
"0 62 64 64 0.885 126.560 E94\n"
"0 62 64 65 1.073 121.703 E94\n"
"0 63 64 64 0.866 108.239 C94\n"
"1 63 64 64 0.827 124.584 E94\n"
"0 63 64 66 1.038 111.621 C94\n"
"0 63 64 78 1.172 105.176 E94\n"
"0 63 64 81 1.164 110.895 E94\n"
"0 63 64 82 1.395 101.902 E94\n"
"0 64 64 64 0.967 115.037 E94\n"
"0 64 64 65 0.916 113.570 C94\n"
"1 64 64 66 1.003 118.067 E94\n",
"0 64 64 78 1.194 103.479 E94\n"
"0 64 64 82 1.210 108.553 E94\n"
"0 65 64 66 1.055 115.369 C94\n"
"0 65 64 81 1.168 116.240 E94\n"
"0 66 64 66 0.932 129.624 E94\n"
"0 0 65 0 0.000 104.500 0:*-65-* MMFF DEF\n"
"0 39 65 64 1.738 101.550 C94\n"
"0 39 65 66 1.589 106.360 C94\n"
"0 39 65 82 1.740 101.208 E94\n"
"0 44 65 64 1.430 103.829 C94\n"
"0 44 65 66 1.366 110.552 E94\n"
"0 44 65 78 1.419 104.213 E94\n"
"0 59 65 64 1.788 103.452 C94\n"
"0 59 65 81 1.774 104.872 E94\n"
"0 0 66 0 0.000 106.900 0:*-66-* MMFF DEF\n"
"0 63 66 64 1.206 103.779 C94\n"
"0 63 66 66 1.406 106.735 C94\n"
"0 63 66 78 1.339 105.365 E94\n"
"0 63 66 81 1.408 106.806 E94\n"
"0 64 66 65 1.709 107.658 C94\n"
"0 65 66 66 1.932 111.306 C94\n"
"0 0 67 0 0.000 119.900 0:*-67-* MMFF DEF\n"
"1 0 67 0 0.000 116.600 1:*-67-* MMFF DEF\n"
"0 1 67 3 0.982 120.683 E94\n"
"0 1 67 9 1.178 115.581 E94\n"
"0 1 67 32 1.233 119.589 E94\n"
"0 1 67 67 1.257 111.574 E94\n"
"1 2 67 32 1.118 126.320 E94\n"
"1 2 67 67 1.231 113.438 E94\n"
"0 3 67 23 0.567 128.000 #E94\n"
"0 3 67 32 1.290 120.945 E94\n"
"1 3 67 37 1.122 113.631 E94\n"
"1 9 67 30 1.142 118.899 E94\n"
"0 9 67 32 1.325 125.531 E94\n"
"1 9 67 37 1.186 115.979 E94\n"
"0 23 67 32 0.805 120.000 #E94\n"
"1 30 67 32 1.370 114.854 E94\n"
"1 32 67 37 1.240 120.019 E94\n"
"0 32 67 67 1.504 117.327 E94\n"
"1 37 67 67 1.310 110.017 E94\n"
"0 0 68 0 0.000 108.800 0:*-68-* MMFF DEF\n"
"0 1 68 1 1.159 108.238 C94\n"
"0 1 68 23 0.772 107.200 C94\n"
"0 1 68 32 0.958 110.757 C94\n"
"0 23 68 23 0.650 104.892 C94\n"
"0 23 68 32 0.659 112.977 C94\n"
"0 0 69 0 0.000 120.300 0:*-69-* MMFF DEF\n"
"0 32 69 37 1.123 121.777 C94\n"
"0 32 69 38 1.486 117.217 E94\n"
"0 37 69 37 1.223 116.447 C94\n"
"0 38 69 38 1.122 125.930 E94\n"
"0 31 70 31 0.658 103.978 C94\n"
"0 0 73 0 0.000 106.600 0:*-73-* MMFF DEF\n"
"0 1 73 32 1.590 100.180 X94\n"
"0 1 73 72 1.481 96.166 X94\n"
"0 32 73 32 1.665 115.012 X94\n"
"0 32 73 72 1.326 115.134 X94\n"
"0 0 74 0 0.000 113.000 0:*-74-* MMFF DEF\n"
"0 3 74 7 1.357 113.010 X94\n"
"0 0 75 0 0.000 94.900 0:*-75-* MMFF DEF\n"
"0 1 75 3 1.138 96.779 E94\n"
"0 3 75 19 1.044 91.970 E94\n"
"0 3 75 71 0.729 95.899 X94\n"
"0 0 76 0 0.000 107.600 0:*-76-* MMFF DEF\n"
"0 76 76 76 1.434 109.889 X94\n"
"0 76 76 78 1.493 103.519 X94\n"
"0 78 76 78 1.235 109.421 E94\n"
"0 0 77 0 0.000 109.500 0:*-77-* MMFF DEF\n"
"0 32 77 32 1.652 109.472 X94\n"
"0 0 78 0 0.000 121.900 0:*-78-* MMFF DEF\n"
"1 0 78 0 0.000 126.100 1:*-78-* MMFF DEF\n"
"0 1 78 78 0.744 130.960 E94\n"
"0 1 78 81 0.938 121.477 E94\n"
"1 3 78 78 0.827 125.468 E94\n"
"1 3 78 81 0.922 123.748 E94\n"
"0 5 78 76 0.584 123.407 X94\n"
"0 5 78 78 0.546 128.000 C94\n"
"0 5 78 79 0.617 122.000 #E94\n"
"0 5 78 81 0.542 109.881 C94\n"
"1 9 78 78 0.863 129.501 E94\n"
"1 9 78 81 0.991 125.857 E94\n"
"0 37 78 76 0.770 137.282 E94\n"
"0 37 78 78 0.803 128.249 E94\n"
"0 37 78 81 0.864 128.714 E94\n"
"0 38 78 78 0.844 130.617 E94\n"
"0 38 78 81 1.023 123.532 E94\n"
"0 39 78 64 0.734 138.714 E94\n"
"0 39 78 78 1.202 109.426 E94\n"
"0 40 78 76 0.930 130.150 E94\n"
"0 40 78 78 0.778 135.746 E94\n"
"0 40 78 81 1.058 121.251 E94\n"
"0 44 78 63 0.677 141.902 E94\n"
"0 44 78 64 0.663 142.589 E94\n"
"0 44 78 66 0.816 134.701 E94\n"
"0 44 78 78 1.089 111.702 E94\n"
"0 45 78 76 1.199 114.467 E94\n"
"0 45 78 78 0.915 125.050 E94\n"
"0 45 78 81 1.216 112.926 E94\n"
"0 59 78 64 0.963 128.471 E94\n"
"0 59 78 65 1.097 128.375 E94\n"
"0 59 78 78 1.443 105.916 E94\n"
"0 63 78 64 0.942 117.779 E94\n"
"0 64 78 65 0.835 131.530 E94\n"
"0 64 78 78 1.038 111.834 E94\n"
"0 66 78 78 1.030 118.376 E94\n"
"0 76 78 76 1.245 113.179 X94\n"
"0 76 78 78 1.159 111.900 E94\n"
"0 78 78 78 1.336 99.459 E94\n"
"0 78 78 81 1.302 105.130 C94\n"
"0 79 78 81 1.217 114.792 E94\n"
"0 0 79 0 0.000 103.400 0:*-79-* MMFF DEF\n"
"0 78 79 81 1.569 102.043 E94\n"
"0 79 79 81 1.625 104.857 E94\n"
"0 0 80 0 0.000 121.900 0:*-80-* MMFF DEF\n"
"1 0 80 0 0.000 128.200 1:*-80-* MMFF DEF\n"
"0 1 80 81 0.864 127.147 E94\n"
"1 3 80 81 0.886 128.181 E94\n"
"0 5 80 81 0.651 125.682 C94\n"
"0 18 80 81 1.032 120.869 E94\n"
"0 41 80 81 0.909 125.057 E94\n"
"0 44 80 55 0.918 127.755 E94\n"
"0 44 80 81 1.184 112.411 E94\n"
"0 55 80 59 1.254 120.263 E94\n"
"0 55 80 81 0.991 127.612 E94\n"
"0 56 80 81 1.003 126.038 E94\n"
"0 59 80 81 1.439 112.030 E94\n"
"0 81 80 81 1.205 108.609 C94\n"
"0 0 81 0 0.000 119.500 0:*-81-* MMFF DEF\n"
"0 1 81 63 0.996 120.129 E94\n"
"0 1 81 64 0.978 119.970 E94\n"
"0 1 81 78 0.879 126.535 E94\n"
"0 1 81 79 1.144 116.113 E94\n"
"0 1 81 80 0.895 126.324 E94\n"
"1 2 81 78 0.927 125.080 E94\n"
"1 2 81 80 0.895 128.399 E94\n"
"1 9 81 78 1.015 124.270 E94\n"
"1 9 81 80 1.106 120.028 E94\n"
"0 36 81 64 0.522 130.295 E94\n"
"0 36 81 66 0.583 128.738 E94\n"
"0 36 81 78 0.578 124.658 C94\n"
"0 36 81 80 0.575 124.787 C94\n"
"0 37 81 64 0.929 122.408 E94\n"
"1 37 81 64 0.983 119.722 E94\n"
"0 37 81 65 1.184 114.158 E94\n"
"1 37 81 65 1.281 110.477 E94\n"
"1 37 81 78 0.884 126.208 E94\n"
"1 37 81 80 0.940 123.333 E94\n"
"0 63 81 64 1.115 114.945 E94\n"
"0 64 81 65 1.075 122.099 E94\n"
"0 64 81 80 1.143 113.176 E94\n"
"0 66 81 80 1.067 122.250 E94\n"
"0 78 81 80 0.957 110.556 C94\n"
"0 79 81 80 1.379 107.936 E94\n"
"0 32 82 59 1.666 114.660 E94\n"
"0 32 82 64 1.075 131.706 E94\n"
"0 32 82 65 1.238 129.293 E94\n"
"0 59 82 64 1.563 105.660 E94\n"
"0 64 82 65 1.281 112.955 E94\n",
"EOS"};
class MMFFStbnCollection *MMFFStbnCollection::ds_instance = NULL;
extern const std::string defaultMMFFStbn;
MMFFStbnCollection *MMFFStbnCollection::getMMFFStbn(
const std::string &mmffStbn) {
if (!ds_instance) {
ds_instance = new MMFFStbnCollection(mmffStbn);
} else if (mmffStbn != "") {
delete ds_instance;
ds_instance = new MMFFStbnCollection(mmffStbn);
}
return ds_instance;
}
MMFFStbnCollection::MMFFStbnCollection(std::string mmffStbn) {
if (mmffStbn == "") {
mmffStbn = defaultMMFFStbn;
}
std::istringstream inStream(mmffStbn);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFStbn mmffStbnObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int stretchBendType = boost::lexical_cast<unsigned int>(*token);
#else
d_stretchBendType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int kAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_kAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffStbnObj.kbaIJK = boost::lexical_cast<double>(*token);
++token;
mmffStbnObj.kbaKJI = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[stretchBendType][iAtomType][jAtomType][kAtomType] = mmffStbnObj;
#else
d_params.push_back(mmffStbnObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFStbn =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF STRETCH-BEND PARAMETERS- Rev: 23-FEB-93 Source: MMFF\n"
"* C94 - CORE MMFF parameter, from fits to HF/6-31G* 2nd D's\n"
"* X94 - EXTD MMFF parameter, also from fits to HF/6-31G* 2nd D's\n"
"*\n"
"* types I, J, K kbaIJK kbaKJI Source\n"
"0 1 1 1 0.206 0.206 C94\n"
"0 1 1 2 0.136 0.197 C94\n"
"0 1 1 3 0.211 0.092 C94\n"
"0 1 1 5 0.227 0.070 C94\n"
"0 1 1 6 0.173 0.417 C94\n"
"0 1 1 8 0.136 0.282 C94\n"
"0 1 1 10 0.187 0.338 C94\n"
"0 1 1 11 0.209 0.633 C94\n"
"0 1 1 12 0.176 0.386 C94\n"
"0 1 1 15 0.139 0.217 C94\n"
"0 1 1 34 0.236 0.436 C94\n"
"0 1 1 37 0.152 0.260 C94\n"
"0 1 1 39 0.144 0.595 C94\n"
"0 1 1 41 0.122 0.051 C94\n"
"0 1 1 56 0.262 0.451 C94\n"
"0 1 1 68 0.186 0.125 C94\n"
"0 2 1 2 0.282 0.282 C94\n"
"0 2 1 3 0.206 0.022 C94\n"
"0 2 1 5 0.234 0.088 C94\n"
"0 2 1 6 0.183 0.387 C94\n"
"0 2 1 8 0.214 0.363 C94\n"
"0 3 1 5 0.157 0.115 C94\n"
"0 3 1 6 -0.036 0.456 C94\n"
"0 3 1 10 0.038 0.195 C94\n"
"0 5 1 5 0.115 0.115 C94\n"
"0 5 1 6 0.013 0.436 C94\n"
"0 5 1 8 0.027 0.358 C94\n"
"0 5 1 9 0.040 0.418 C94\n"
"0 5 1 10 0.043 0.261 C94\n"
"0 5 1 11 0.003 0.452 C94\n"
"0 5 1 12 -0.018 0.380 C94\n"
"0 5 1 15 0.018 0.255 C94\n"
"0 5 1 18 0.121 0.218 X94\n"
"0 5 1 20 0.069 0.327 C94\n"
"0 5 1 22 0.055 0.267 X94\n"
"0 5 1 34 -0.003 0.342 C94\n"
"0 5 1 37 0.074 0.287 C94\n"
"0 5 1 39 0.092 0.607 C94\n"
"0 5 1 40 0.023 0.335 C94\n"
"0 5 1 41 0.093 0.118 C94\n"
"0 5 1 54 0.016 0.343 C94\n"
"0 5 1 55 0.030 0.397 C94\n"
"0 5 1 56 0.031 0.384 C94\n"
"0 5 1 68 0.041 0.216 C94\n"
"0 6 1 6 0.320 0.320 C94\n"
"0 6 1 37 0.310 0.160 C94\n"
"0 11 1 11 0.586 0.586 C94\n"
"0 12 1 12 0.508 0.508 C94\n"
"0 1 2 1 0.250 0.250 C94\n"
"0 1 2 2 0.203 0.207 C94\n"
"2 1 2 2 0.222 0.269 C94\n"
"2 1 2 3 0.244 0.292 C94\n"
"0 1 2 5 0.215 0.128 C94\n"
"2 1 2 37 0.246 0.260 C94\n"
"1 2 2 2 0.250 0.219 C94\n"
"2 2 2 3 0.155 0.112 C94\n"
"0 2 2 5 0.207 0.157 C94\n"
"1 2 2 5 0.267 0.159 C94\n"
"0 2 2 6 0.118 0.576 C94\n"
"2 2 2 37 0.143 0.172 C94\n"
"0 2 2 40 0.289 0.390 C94\n"
"0 2 2 41 0.191 -0.047 C94\n"
"1 3 2 5 0.264 0.156 C94\n"
"0 5 2 5 0.140 0.140 C94\n"
"0 5 2 6 0.213 0.502 C94\n"
"2 5 2 37 0.153 0.288 C94\n"
"0 5 2 40 0.070 0.463 C94\n"
"0 5 2 41 0.191 0.005 C94\n"
"0 1 3 1 0.358 0.358 C94\n"
"2 1 3 2 0.246 0.409 C94\n"
"2 1 3 3 0.303 0.145 C94\n"
"0 1 3 5 0.321 0.183 C94\n"
"0 1 3 6 0.338 0.732 C94\n"
"0 1 3 7 0.154 0.856 C94\n"
"0 1 3 10 0.223 0.732 C94\n"
"2 1 3 37 0.217 0.207 C94\n"
"1 2 3 5 0.407 0.159 C94\n"
"1 2 3 6 0.429 0.473 C94\n"
"1 2 3 7 0.214 0.794 C94\n"
"1 2 3 9 0.227 0.610 C94\n"
"1 2 3 10 0.298 0.600 C94\n"
"1 3 3 5 0.251 0.133 C94\n"
"1 3 3 6 0.066 0.668 C94\n"
"1 3 3 7 -0.093 0.866 C94\n"
"0 5 3 5 0.126 0.126 C94\n"
"0 5 3 6 0.174 0.734 C94\n"
"0 5 3 7 0.032 0.805 C94\n"
"0 5 3 9 0.037 0.669 C94\n"
"0 5 3 10 0.169 0.619 C94\n"
"0 5 3 40 0.087 0.685 C94\n"
"0 5 3 54 0.098 0.210 C94\n"
"0 6 3 7 0.494 0.578 C94\n"
"4 6 3 20 1.179 0.752 X94\n"
"2 6 3 37 0.350 0.175 C94\n"
"0 7 3 10 0.771 0.353 C94\n"
"0 7 3 20 0.865 -0.181 C94\n"
"2 7 3 37 0.707 0.007 C94\n"
"0 9 3 40 0.680 0.260 C94\n"
"0 10 3 10 1.050 1.050 C94\n"
"4 20 3 20 0.536 0.536 C94\n"
"0 40 3 40 0.482 0.482 C94\n"
"0 1 6 1 0.309 0.309 C94\n"
"0 1 6 2 0.157 0.375 C94\n"
"0 1 6 3 -0.153 0.252 C94\n"
"0 1 6 21 0.256 0.143 C94\n"
"0 1 6 37 0.163 0.375 C94\n"
"0 2 6 3 -0.228 0.052 C94\n"
"0 2 6 29 0.259 0.163 C94\n"
"4 3 6 20 0.456 0.379 X94\n"
"0 3 6 24 0.215 0.064 C94\n"
"0 3 6 37 -0.225 -0.320 C94\n"
"0 8 6 21 0.304 0.055 C94\n"
"0 10 6 21 0.419 0.158 C94\n"
"0 18 6 33 0.309 0.120 X94\n"
"4 20 6 20 0.739 0.739 C94\n"
"0 29 6 37 0.130 0.241 C94\n"
"0 31 6 31 0.227 0.227 X94\n"
"0 1 8 1 0.312 0.312 C94\n"
"0 1 8 6 0.212 0.354 C94\n"
"0 1 8 23 0.309 0.135 C94\n"
"0 6 8 23 0.418 0.020 C94\n"
"4 20 8 20 0.653 0.653 C94\n"
"0 20 8 23 0.128 0.122 C94\n"
"0 23 8 23 0.190 0.190 C94\n"
"0 1 9 3 0.326 0.580 C94\n"
"0 3 9 27 0.464 0.222 C94\n"
"0 1 10 1 0.063 0.063 C94\n"
"0 1 10 3 -0.021 0.340 C94\n"
"0 1 10 6 -0.024 0.374 C94\n"
"0 1 10 28 0.155 -0.051 C94\n"
"0 3 10 3 -0.219 -0.219 C94\n"
"0 3 10 6 0.497 0.513 C94\n"
"0 3 10 28 0.137 0.066 C94\n"
"0 28 10 28 0.081 0.081 C94\n"
"0 1 15 1 0.125 0.125 C94\n"
"0 1 15 15 0.012 0.238 C94\n"
"0 1 15 37 0.048 0.229 C94\n"
"0 1 15 71 0.080 -0.012 C94\n"
"0 15 15 71 0.172 -0.068 C94\n"
"0 37 15 71 0.187 -0.027 C94\n"
"0 71 15 71 0.045 0.045 C94\n"
"0 1 18 1 0.023 0.023 X94\n"
"0 1 18 6 0.003 0.213 X94\n"
"0 1 18 32 -0.091 0.390 X94\n"
"0 1 18 43 -0.008 0.607 X94\n"
"0 6 18 6 0.088 0.088 X94\n"
"0 6 18 32 0.123 0.369 X94\n"
"0 32 18 32 0.404 0.404 X94\n"
"0 32 18 43 0.384 0.281 X94\n"
"0 43 18 43 0.428 0.428 X94\n"
"0 1 20 5 0.290 0.098 C94\n"
"0 1 20 20 0.179 0.004 C94\n"
"0 3 20 5 -0.049 0.171 C94\n"
"4 3 20 20 0.607 0.437 C94\n"
"0 5 20 5 0.182 0.182 C94\n"
"0 5 20 6 0.051 0.312 C94\n"
"0 5 20 8 0.072 0.226 C94\n"
"0 5 20 12 0.014 0.597 C94\n"
"0 5 20 20 0.101 0.079 C94\n"
"0 5 20 30 0.108 0.123 C94\n"
"4 6 20 20 0.823 0.396 C94\n"
"4 8 20 20 0.701 0.369 C94\n"
"0 12 20 20 0.310 0.000 C94\n"
"4 20 20 20 0.283 0.283 C94\n"
"4 20 20 30 0.340 0.529 C94\n"
"0 1 22 5 0.067 0.174 X94\n"
"0 1 22 22 0.199 0.039 X94\n"
"0 5 22 5 0.254 0.254 C94\n"
"0 5 22 22 0.181 0.108 C94\n"
"5 22 22 22 0.000 0.000 C94\n"
"0 5 26 5 -0.121 -0.121 X94\n"
"0 5 30 20 0.251 0.007 C94\n"
"0 5 30 30 0.267 0.054 C94\n"
"4 20 30 30 0.413 0.705 C94\n"
"0 1 34 1 0.202 0.202 C94\n"
"0 1 34 36 0.160 -0.009 C94\n"
"0 36 34 36 0.087 0.087 C94\n"
"0 1 37 37 0.485 0.311 C94\n"
"1 2 37 37 0.321 0.235 C94\n"
"1 3 37 37 0.179 0.217 C94\n"
"0 5 37 37 0.279 0.250 C94\n"
"0 5 37 38 0.267 0.389 C94\n"
"0 5 37 63 0.216 0.434 C94\n"
"0 5 37 64 0.167 0.364 C94\n"
"0 5 37 69 0.273 0.391 C94\n"
"0 6 37 37 0.830 0.339 C94\n"
"0 15 37 37 0.650 0.259 C94\n"
"0 37 37 37 -0.411 -0.411 C94\n"
"0 37 37 38 -0.424 -0.466 C94\n"
"0 37 37 40 0.429 0.901 C94\n"
"0 37 37 63 -0.173 -0.215 C94\n"
"0 37 37 64 -0.229 -0.229 C94\n"
"0 37 37 69 -0.244 -0.555 C94\n"
"0 38 37 38 -0.516 -0.516 C94\n"
"0 37 38 37 -0.342 -0.342 C94\n"
"0 37 38 38 -0.164 -1.130 C94\n"
"0 1 39 63 0.313 0.500 C94\n"
"0 23 39 63 -0.131 0.422 C94\n"
"0 23 39 65 -0.122 0.281 C94\n"
"0 63 39 63 0.469 0.469 C94\n"
"0 63 39 65 0.741 0.506 C94\n"
"0 65 39 65 0.706 0.706 C94\n"
"0 1 40 28 0.238 0.091 C94\n"
"0 1 40 37 0.153 0.590 C94\n"
"0 2 40 28 0.342 0.156 C94\n"
"0 3 40 28 0.228 0.104 C94\n"
"0 28 40 28 0.094 0.094 C94\n"
"0 28 40 37 0.186 0.423 C94\n"
"0 1 41 32 0.503 0.943 C94\n"
"0 2 41 32 0.594 0.969 C94\n"
"0 5 41 32 0.276 0.852 C94\n"
"0 32 41 32 0.652 0.652 C94\n"
"0 18 43 23 0.377 0.057 X94\n"
"0 23 43 23 0.082 0.082 X94\n"
"0 63 44 63 0.591 0.591 C94\n"
"0 63 44 65 0.857 0.978 C94\n"
"0 50 49 50 0.072 0.072 C94\n"
"0 1 54 3 0.192 -0.051 C94\n"
"0 1 54 36 0.240 0.079 C94\n"
"0 3 54 36 0.005 0.127 C94\n"
"0 36 54 36 0.148 0.148 C94\n"
"0 1 55 36 0.189 0.033 C94\n"
"0 1 55 57 0.166 0.211 C94\n"
"0 36 55 36 0.106 0.106 C94\n"
"0 36 55 57 0.093 0.080 C94\n"
"0 1 56 36 0.211 -0.040 C94\n"
"0 1 56 57 0.026 0.386 C94\n"
"0 36 56 36 0.101 0.101 C94\n"
"0 36 56 57 0.108 0.068 C94\n"
"0 5 57 55 0.043 0.420 C94\n"
"0 55 57 55 0.125 0.125 C94\n"
"0 56 57 56 0.431 0.431 C94\n"
"0 58 57 58 0.732 0.732 C94\n"
"0 63 59 63 0.497 0.497 C94\n"
"0 63 59 65 0.723 0.874 C94\n"
"0 5 63 39 0.009 0.654 C94\n"
"0 5 63 44 -0.015 0.446 C94\n"
"0 5 63 59 0.067 0.588 C94\n"
"0 5 63 64 0.055 0.370 C94\n"
"0 5 63 66 0.110 0.464 C94\n"
"0 37 63 39 0.178 0.523 C94\n"
"0 37 63 64 -0.045 0.497 C94\n"
"0 39 63 64 0.422 0.409 C94\n"
"0 39 63 66 0.436 0.525 C94\n"
"0 44 63 64 0.581 0.426 C94\n"
"0 44 63 66 0.542 0.365 C94\n"
"0 59 63 64 0.852 0.332 C94\n"
"0 59 63 66 0.775 0.300 C94\n"
"0 5 64 63 0.086 0.345 C94\n"
"0 5 64 64 0.085 0.369 C94\n"
"0 5 64 65 0.051 0.436 C94\n"
"0 5 64 66 0.113 0.452 C94\n"
"0 37 64 63 0.059 0.299 C94\n"
"0 37 64 64 0.277 0.377 C94\n"
"0 63 64 64 0.206 0.030 C94\n"
"0 63 64 66 0.171 0.078 C94\n"
"0 64 64 65 0.079 0.403 C94\n"
"0 65 64 66 0.406 0.066 C94\n"
"0 39 65 64 0.528 0.644 C94\n"
"0 39 65 66 0.397 0.258 C94\n"
"0 44 65 64 0.816 0.543 C94\n"
"0 59 65 64 1.177 0.594 C94\n"
"0 63 66 64 0.213 -0.173 C94\n"
"0 63 66 66 0.234 0.077 C94\n"
"0 64 66 65 -0.149 0.383 C94\n"
"0 65 66 66 0.199 0.101 C94\n"
"0 1 68 1 0.217 0.217 C94\n"
"0 1 68 23 0.285 0.050 C94\n"
"0 1 68 32 -0.047 0.503 C94\n"
"0 23 68 23 0.145 0.145 C94\n"
"0 23 68 32 -0.182 0.504 C94\n"
"0 32 69 37 1.018 0.418 C94\n"
"0 37 69 37 -0.169 -0.169 C94\n"
"0 31 70 31 0.210 0.210 C94\n"
"0 5 78 78 0.279 0.250 C94\n"
"0 5 78 81 0.083 0.250 C94\n"
"0 78 78 81 -0.398 0.314 C94\n"
"0 5 80 81 -0.101 0.691 C94\n"
"0 81 80 81 0.732 0.732 C94\n"
"0 36 81 78 0.021 0.368 C94\n"
"0 36 81 80 0.018 0.422 C94\n"
"0 78 81 80 0.366 0.419 C94\n";
class MMFFDfsbCollection *MMFFDfsbCollection::ds_instance = NULL;
extern const std::string defaultMMFFDfsb;
MMFFDfsbCollection *MMFFDfsbCollection::getMMFFDfsb(
const std::string &mmffDfsb) {
if (!ds_instance) {
ds_instance = new MMFFDfsbCollection(mmffDfsb);
} else if (mmffDfsb != "") {
delete ds_instance;
ds_instance = new MMFFDfsbCollection(mmffDfsb);
}
return ds_instance;
}
MMFFDfsbCollection::MMFFDfsbCollection(std::string mmffDfsb) {
if (mmffDfsb == "") {
mmffDfsb = defaultMMFFDfsb;
}
std::istringstream inStream(mmffDfsb);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFStbn mmffStbnObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
unsigned int iAtomicNum = boost::lexical_cast<unsigned int>(*token);
++token;
unsigned int jAtomicNum = boost::lexical_cast<unsigned int>(*token);
++token;
unsigned int kAtomicNum = boost::lexical_cast<unsigned int>(*token);
++token;
mmffStbnObj.kbaIJK = boost::lexical_cast<double>(*token);
++token;
mmffStbnObj.kbaKJI = boost::lexical_cast<double>(*token);
++token;
d_params[iAtomicNum][jAtomicNum][kAtomicNum] = mmffStbnObj;
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFDfsb =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF Default Stretch-Bend Parameters\n"
"* Row in \n"
"* Periodic Table \n"
"* IR JR KR F(I_J,K) F(K_J,I)\n"
"0 1 0 0.15 0.15\n"
"0 1 1 0.10 0.30\n"
"0 1 2 0.05 0.35\n"
"0 1 3 0.05 0.35\n"
"0 1 4 0.05 0.35\n"
"0 2 0 0.00 0.00\n"
"0 2 1 0.00 0.15\n"
"0 2 2 0.00 0.15\n"
"0 2 3 0.00 0.15\n"
"0 2 4 0.00 0.15\n"
"1 1 1 0.30 0.30\n"
"1 1 2 0.30 0.50\n"
"1 1 3 0.30 0.50\n"
"1 1 4 0.30 0.50\n"
"2 1 2 0.50 0.50\n"
"2 1 3 0.50 0.50\n"
"2 1 4 0.50 0.50\n"
"3 1 3 0.50 0.50\n"
"3 1 4 0.50 0.50\n"
"4 1 4 0.50 0.50\n"
"1 2 1 0.30 0.30\n"
"1 2 2 0.25 0.25\n"
"1 2 3 0.25 0.25\n"
"1 2 4 0.25 0.25\n"
"2 2 2 0.25 0.25\n"
"2 2 3 0.25 0.25\n"
"2 2 4 0.25 0.25\n"
"3 2 3 0.25 0.25\n"
"3 2 4 0.25 0.25\n"
"4 2 4 0.25 0.25\n";
class MMFFOopCollection *MMFFOopCollection::ds_instance[2] = {NULL, NULL};
extern const std::string defaultMMFFOop;
extern const std::string defaultMMFFsOop;
MMFFOopCollection *MMFFOopCollection::getMMFFOop(const bool isMMFFs,
const std::string &mmffOop) {
unsigned int i = (isMMFFs ? 1 : 0);
if (!ds_instance[i]) {
ds_instance[i] = new MMFFOopCollection(isMMFFs, mmffOop);
} else if (mmffOop != "") {
delete ds_instance[i];
ds_instance[i] = new MMFFOopCollection(isMMFFs, mmffOop);
}
return ds_instance[i];
}
MMFFOopCollection::MMFFOopCollection(const bool isMMFFs, std::string mmffOop) {
if (mmffOop == "") {
mmffOop = (isMMFFs ? defaultMMFFsOop : defaultMMFFOop);
}
std::istringstream inStream(mmffOop);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFOop mmffOopObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int kAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_kAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int lAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_lAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffOopObj.koop = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[iAtomType][jAtomType][kAtomType][lAtomType] = mmffOopObj;
#else
d_params.push_back(mmffOopObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFOop =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF OUT-OF-PLANE PARAMETERS- Rev: 15-OCT-93 Source: MMFF\n"
"* C94 - CORE MMFF parameter, from fits to HF/6-31G* 2nd D's\n"
"* #C94 - Value adjusted from CORE MMFF93 value\n"
"*\n"
"* MMFF atom types koop Source\n"
"0 2 0 0 0.020 *-2-*-* C94 DEF\n"
"1 2 1 2 0.030 C94\n"
"1 2 2 2 0.027 C94\n"
"1 2 2 3 0.026 C94\n"
"1 2 2 5 0.013 C94\n"
"1 2 2 37 0.032 C94\n"
"2 2 2 5 0.013 C94\n"
"2 2 3 5 0.012 C94\n"
"2 2 5 5 0.006 C94\n"
"2 2 5 6 0.027 C94\n"
"2 2 5 37 0.017 C94\n"
"2 2 5 40 0.012 C94\n"
"2 2 5 41 0.008 C94\n"
"0 3 0 0 0.130 *-3-*-* C94 DEF\n"
"1 3 1 7 0.146 C94\n"
"1 3 2 7 0.138 C94\n"
"1 3 3 7 0.134 C94\n"
"1 3 5 7 0.122 C94\n"
"1 3 6 7 0.141 C94\n"
"1 3 7 10 0.129 C94\n"
"1 3 7 37 0.138 C94\n"
"2 3 5 7 0.113 C94\n"
"2 3 5 9 0.081 C94\n"
"2 3 6 7 0.127 C94\n"
"2 3 7 10 0.116 C94\n"
"3 3 5 7 0.113 C94\n"
"3 3 6 7 0.127 C94\n"
"5 3 5 7 0.103 C94\n"
"5 3 5 9 0.074 C94\n"
"5 3 5 54 0.078 C94\n"
"5 3 6 7 0.119 C94\n"
"5 3 7 10 0.102 C94\n"
"5 3 9 40 0.067 C94\n"
"6 3 7 37 0.127 C94\n"
"7 3 10 10 0.113 C94\n"
"7 3 20 20 0.151 C94\n"
"9 3 40 40 0.057 C94\n"
"0 8 0 0 0.000 *-8-*-* C94 DEF\n"
"0 10 0 0 -0.020 *-10-*-* C94 DEF\n"
"1 10 1 3 -0.02 #C94 (C93=-0.034)\n"
"1 10 3 6 -0.033 C94\n"
"1 10 3 28 -0.02 #C94 (C93=-0.030)\n"
"3 10 3 28 -0.030 C94\n"
"3 10 28 28 -0.019 C94\n"
"0 17 0 0 0.000 *-17-*-* E94 DEF\n"
"0 26 0 0 0.000 *-26-*-* CE4 DEF\n"
"0 30 0 0 0.010 *-30-*-* C94 DEF\n"
"5 30 20 30 0.008 C94\n"
"0 37 0 0 0.035 *-37-*-* C94 DEF\n"
"1 37 37 37 0.040 C94\n"
"2 37 37 37 0.031 C94\n"
"3 37 37 37 0.027 C94\n"
"5 37 37 37 0.015 C94\n"
"5 37 37 38 0.046 C94\n"
"5 37 37 63 0.008 C94\n"
"5 37 37 64 0.012 C94\n"
"5 37 37 69 0.016 C94\n"
"5 37 38 38 0.084 C94\n"
"6 37 37 37 0.048 C94\n"
"15 37 37 37 0.025 C94\n"
"37 37 37 40 0.046 C94\n"
"0 39 0 0 0.020 *-39-*-* C94 DEF\n"
"1 39 63 63 0.012 C94\n"
"23 39 63 63 -0.014 C94\n"
"23 39 63 65 0.021 C94\n"
"23 39 65 65 0.062 C94\n"
"0 40 0 0 -0.005 *-40-*-* C94 DEF\n"
"1 40 28 37 -0.006 C94\n"
"2 40 28 28 -0.007 C94\n"
"3 40 28 28 -0.007 C94\n"
"28 40 28 37 0.004 C94\n"
"0 41 0 0 0.180 *-41-*-* C94 DEF\n"
"1 41 32 32 0.178 C94\n"
"2 41 32 32 0.161 C94\n"
"5 41 32 32 0.158 C94\n"
"0 43 0 0 0.000 *-43-*-* E94 DEF\n"
"0 45 0 0 0.150 *-45-*-* E94 DEF\n"
"0 49 0 0 0.000 *-49-*-* E94 DEF\n"
"50 49 50 50 0.000 #C94\n"
"0 54 0 0 0.020 *-54-*-* C94 DEF\n"
"1 54 3 36 0.016 C94\n"
"3 54 36 36 0.018 C94\n"
"0 55 0 0 0.020 *-55-*-* C94 DEF\n"
"1 55 36 57 0.020 #C94\n"
"36 55 36 57 0.020 #C94\n"
"0 56 0 0 0.020 *-56-*-* C94 DEF\n"
"1 56 36 57 0.020 #C94\n"
"36 56 36 57 0.020 #C94\n"
"0 57 0 0 0.080 *-57-*-* C94 DEF\n"
"5 57 55 55 0.038 C94\n"
"56 57 56 56 0.158 C94\n"
"0 58 0 0 0.025 *-58-*-* E94 DEF\n"
"0 63 0 0 0.050 *-63-*-* C94 DEF\n"
"5 63 39 64 0.019 C94\n"
"5 63 39 66 0.068 C94\n"
"5 63 44 64 0.014 C94\n"
"5 63 44 66 0.055 C94\n"
"5 63 59 64 0.033 C94\n"
"5 63 59 66 0.085 C94\n"
"37 63 39 64 0.010 C94\n"
"0 64 0 0 0.040 *-64-*-* C94 DEF\n"
"5 64 63 64 0.006 C94\n"
"5 64 63 66 0.043 C94\n"
"5 64 64 65 0.052 C94\n"
"5 64 65 66 0.094 C94\n"
"37 64 63 64 -0.011 C94\n"
"0 67 0 0 0.070 *-67-*-* E94 DEF\n"
"0 69 0 0 0.070 *-69-*-* C94 DEF\n"
"32 69 37 37 0.067 C94\n"
"0 73 0 0 0.000 *-73-*-* E94 DEF\n"
"0 78 0 0 0.045 *-78-*-* C94 DEF\n"
"5 78 78 81 0.046 C94\n"
"0 80 0 0 0.080 *-80-*-* C94 DEF\n"
"5 80 81 81 0.057 C94\n"
"0 81 0 0 0.025 *-81-*-* C94 DEF\n"
"36 81 78 80 0.016 C94\n"
"0 82 0 0 0.000 *-82-*-* E94 DEF\n";
const std::string defaultMMFFsOop =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF94s OUT-OF-PLANE PARAMETERS\n"
"* C94 - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's\n"
"* C94S - CORE MMFF94s parameter,adjusted to promote planarity\n"
"* #C94 - Value adjusted from CORE MMFF94 value\n"
"*\n"
"* MMFF atom types koop Source\n"
"0 2 0 0 0.020 *-2-*-* C94 DEF\n"
"1 2 1 2 0.030 C94\n"
"1 2 2 2 0.027 C94\n"
"1 2 2 3 0.026 C94\n"
"1 2 2 5 0.013 C94\n"
"1 2 2 37 0.032 C94\n"
"2 2 2 5 0.013 C94\n"
"2 2 3 5 0.012 C94\n"
"2 2 5 5 0.006 C94\n"
"2 2 5 6 0.027 C94\n"
"2 2 5 37 0.017 C94\n"
"2 2 5 40 0.012 C94\n"
"2 2 5 41 0.008 C94\n"
"0 3 0 0 0.130 *-3-*-* C94 DEF\n"
"1 3 1 7 0.146 C94\n"
"1 3 2 7 0.138 C94\n"
"1 3 3 7 0.134 C94\n"
"1 3 5 7 0.122 C94\n"
"1 3 6 7 0.141 C94\n"
"1 3 7 10 0.129 C94\n"
"1 3 7 37 0.138 C94\n"
"2 3 5 7 0.113 C94\n"
"2 3 5 9 0.081 C94\n"
"2 3 6 7 0.127 C94\n"
"2 3 7 10 0.116 C94\n"
"3 3 5 7 0.113 C94\n"
"3 3 6 7 0.127 C94\n"
"5 3 5 7 0.103 C94\n"
"5 3 5 9 0.074 C94\n"
"5 3 5 54 0.078 C94\n"
"5 3 6 7 0.119 C94\n"
"5 3 7 10 0.102 C94\n"
"5 3 9 40 0.067 C94\n"
"6 3 7 37 0.127 C94\n"
"7 3 10 10 0.113 C94\n"
"7 3 20 20 0.151 C94\n"
"9 3 40 40 0.057 C94\n"
"0 8 0 0 0.000 *-8-*-* C94 DEF\n"
"0 10 0 0 0.015 *-10-*-* C94S DEF\n"
"1 10 1 3 0.015 C94S\n"
"1 10 3 6 0.015 C94\n"
"1 10 3 28 0.015 C94S\n"
"3 10 3 28 0.015 C94S\n"
"3 10 28 28 0.015 C94S\n"
"0 17 0 0 0.000 *-17-*-* E94 DEF\n"
"0 26 0 0 0.000 *-26-*-* CE4 DEF\n"
"0 30 0 0 0.010 *-30-*-* C94 DEF\n"
"5 30 20 30 0.008 C94\n"
"0 37 0 0 0.035 *-37-*-* C94 DEF\n"
"1 37 37 37 0.040 C94\n"
"2 37 37 37 0.031 C94\n"
"3 37 37 37 0.027 C94\n"
"5 37 37 37 0.015 C94\n"
"5 37 37 38 0.046 C94\n"
"5 37 37 63 0.008 C94\n"
"5 37 37 64 0.012 C94\n"
"5 37 37 69 0.016 C94\n"
"5 37 38 38 0.084 C94\n"
"6 37 37 37 0.048 C94\n"
"15 37 37 37 0.025 C94\n"
"37 37 37 40 0.046 C94\n"
"0 39 0 0 0.020 *-39-*-* C94 DEF\n"
"1 39 63 63 0.012 C94\n"
"23 39 63 63 -0.014 C94\n"
"23 39 63 65 0.021 C94\n"
"23 39 65 65 0.062 C94\n"
"0 40 0 0 0.030 *-40-*-* C94S DEF\n"
"1 40 28 37 0.030 C94S\n"
"2 40 28 28 0.030 C94S\n"
"3 40 28 28 0.030 C94S\n"
"28 40 28 37 0.030 C94S\n"
"0 41 0 0 0.180 *-41-*-* C94 DEF\n"
"1 41 32 32 0.178 C94\n"
"2 41 32 32 0.161 C94\n"
"5 41 32 32 0.158 C94\n"
"0 43 0 0 0.000 *-43-*-* E94 DEF\n"
"0 45 0 0 0.150 *-45-*-* E94 DEF\n"
"0 49 0 0 0.000 *-49-*-* E94 DEF\n"
"50 49 50 50 0.000 #C94\n"
"0 54 0 0 0.020 *-54-*-* C94 DEF\n"
"1 54 3 36 0.016 C94\n"
"3 54 36 36 0.018 C94\n"
"0 55 0 0 0.020 *-55-*-* C94 DEF\n"
"1 55 36 57 0.020 #C94\n"
"36 55 36 57 0.020 #C94\n"
"0 56 0 0 0.020 *-56-*-* C94 DEF\n"
"1 56 36 57 0.020 #C94\n"
"36 56 36 57 0.020 #C94\n"
"0 57 0 0 0.080 *-57-*-* C94 DEF\n"
"5 57 55 55 0.038 C94\n"
"56 57 56 56 0.158 C94\n"
"0 58 0 0 0.025 *-58-*-* E94 DEF\n"
"0 63 0 0 0.050 *-63-*-* C94 DEF\n"
"5 63 39 64 0.019 C94\n"
"5 63 39 66 0.068 C94\n"
"5 63 44 64 0.014 C94\n"
"5 63 44 66 0.055 C94\n"
"5 63 59 64 0.033 C94\n"
"5 63 59 66 0.085 C94\n"
"37 63 39 64 0.010 C94\n"
"0 64 0 0 0.040 *-64-*-* C94 DEF\n"
"5 64 63 64 0.006 C94\n"
"5 64 63 66 0.043 C94\n"
"5 64 64 65 0.052 C94\n"
"5 64 65 66 0.094 C94\n"
"37 64 63 64 -0.011 C94\n"
"0 67 0 0 0.070 *-67-*-* E94 DEF\n"
"0 69 0 0 0.070 *-69-*-* C94 DEF\n"
"32 69 37 37 0.067 C94\n"
"0 73 0 0 0.000 *-73-*-* E94 DEF\n"
"0 78 0 0 0.045 *-78-*-* C94 DEF\n"
"5 78 78 81 0.046 C94\n"
"0 80 0 0 0.080 *-80-*-* C94 DEF\n"
"5 80 81 81 0.057 C94\n"
"0 81 0 0 0.025 *-81-*-* C94 DEF\n"
"36 81 78 80 0.016 C94\n"
"0 82 0 0 0.000 *-82-*-* E94 DEF\n";
class MMFFTorCollection *MMFFTorCollection::ds_instance[2] = {NULL, NULL};
extern const std::string defaultMMFFTor;
extern const std::string defaultMMFFsTor;
MMFFTorCollection *MMFFTorCollection::getMMFFTor(const bool isMMFFs,
const std::string &mmffTor) {
unsigned int i = (isMMFFs ? 1 : 0);
if (!ds_instance[i]) {
ds_instance[i] = new MMFFTorCollection(isMMFFs, mmffTor);
} else if (mmffTor != "") {
delete ds_instance[i];
ds_instance[i] = new MMFFTorCollection(isMMFFs, mmffTor);
}
return ds_instance[i];
}
MMFFTorCollection::MMFFTorCollection(const bool isMMFFs, std::string mmffTor) {
if (mmffTor == "") {
mmffTor = (isMMFFs ? defaultMMFFsTor : defaultMMFFTor);
}
std::istringstream inStream(mmffTor);
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
MMFFTor mmffTorObj;
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int torType = boost::lexical_cast<unsigned int>(*token);
#else
d_torType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int iAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_iAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int jAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_jAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int kAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_kAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int lAtomType = boost::lexical_cast<unsigned int>(*token);
#else
d_lAtomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffTorObj.V1 = boost::lexical_cast<double>(*token);
++token;
mmffTorObj.V2 = boost::lexical_cast<double>(*token);
++token;
mmffTorObj.V3 = boost::lexical_cast<double>(*token);
++token;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[torType][iAtomType][jAtomType][kAtomType][lAtomType] =
mmffTorObj;
#else
d_params.push_back(mmffTorObj);
#endif
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFTor =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF TORSION PARAMETERS- Rev: 26-OCT-94 Source: MMFF\n"
"* C94 - CORE MMFF parameter - from fits to conformational energies\n"
"* X94 - EXTD MMFF parameter - also from fits to conformational E's\n"
"* E94 - EXTD MMFF parameter - from empirical rule\n"
"* #E94 - Adjusted from empirical rule value\n"
"*\n"
"* atom types V1 V2 V3 Source\n"
"0 0 1 1 0 0.000 0.000 0.300 C94 "
"0:*-1-1-* Def\n"
"5 0 1 1 0 0.200 -0.800 1.500 C94 "
"5:*-1-1-* Def\n"
"0 1 1 1 1 0.103 0.681 0.332 C94\n"
"5 1 1 1 1 0.144 -0.547 1.126 C94\n"
"0 1 1 1 2 -0.295 0.438 0.584 C94\n"
"0 1 1 1 3 0.066 -0.156 0.143 C94\n"
"0 1 1 1 5 0.639 -0.630 0.264 C94\n"
"0 1 1 1 6 -0.688 1.757 0.477 C94\n"
"5 1 1 1 6 0.000 0.000 0.054 C94\n"
"0 1 1 1 8 -1.420 -0.092 1.101 C94\n"
"5 1 1 1 8 0.000 -0.158 0.323 C94\n"
"0 1 1 1 11 0.593 0.662 1.120 C94\n"
"0 1 1 1 12 -0.678 0.417 0.624 C94\n"
"0 1 1 1 15 -0.714 0.698 0.000 C94\n"
"0 1 1 1 34 -0.647 0.550 0.590 C94\n"
"0 2 1 1 5 0.321 -0.411 0.144 C94\n"
"0 3 1 1 3 0.443 0.000 -1.140 C94\n"
"0 3 1 1 5 -0.256 0.058 0.000 C94\n"
"0 3 1 1 6 -0.679 -0.029 0.000 C94\n"
"0 5 1 1 5 0.284 -1.386 0.314 C94\n"
"0 5 1 1 6 -0.654 1.072 0.279 C94\n"
"0 5 1 1 8 -0.744 -1.235 0.337 C94\n"
"0 5 1 1 10 0.000 0.000 0.427 C94\n"
"0 5 1 1 11 0.000 0.516 0.291 C94\n"
"0 5 1 1 12 0.678 -0.602 0.398 C94\n"
"0 5 1 1 15 1.142 -0.644 0.367 C94\n"
"0 5 1 1 25 0.000 0.000 0.295 X94\n"
"0 5 1 1 34 0.692 -0.530 0.278 C94\n"
"0 5 1 1 37 0.000 0.000 0.389 C94\n"
"0 5 1 1 39 0.000 0.000 0.278 C94\n"
"0 5 1 1 41 0.000 0.000 -0.141 C94\n"
"0 5 1 1 56 0.000 0.000 0.324 C94\n"
"0 5 1 1 68 0.000 0.000 0.136 C94\n"
"0 6 1 1 6 0.408 1.397 0.961 C94\n"
"5 6 1 1 6 0.313 -1.035 1.631 C94\n"
"0 8 1 1 8 1.055 0.834 0.000 C94\n"
"0 11 1 1 11 -0.387 -0.543 1.405 C94\n"
"0 12 1 1 12 0.000 0.000 0.893 C94\n"
"0 15 1 1 15 -0.177 0.000 0.049 C94\n"
"0 0 1 2 0 0.000 0.000 0.000 C94 "
"0:*-1-2-* Def\n"
"2 0 1 2 0 0.000 0.000 0.000 E94 "
"2:*1-2-* Def\n"
"5 0 1 2 0 0.000 0.000 0.000 C94 "
"5:*-1-2-* Def\n"
"0 0 1 2 2 0.000 0.000 -0.650 C94 "
"0:*-1-2=2 Def\n"
"5 0 1 2 2 0.000 0.000 -0.650 C94 "
"5:*-1-2=2 Def\n"
"0 1 1 2 1 0.419 0.296 0.282 C94\n"
"0 1 1 2 2 -0.494 0.274 -0.630 C94\n"
"0 1 1 2 5 0.075 0.000 0.358 C94\n"
"0 2 1 2 2 -0.293 0.115 -0.508 C94\n"
"0 2 1 2 5 0.301 0.104 0.507 C94\n"
"0 3 1 2 1 0.565 -0.554 0.234 C94\n"
"0 3 1 2 2 -0.577 -0.482 -0.427 C94\n"
"0 3 1 2 5 0.082 0.000 0.123 C94\n"
"0 5 1 2 1 0.000 -0.184 0.220 C94\n"
"0 5 1 2 2 0.501 -0.410 -0.535 C94\n"
"2 5 1 2 2 0.000 0.000 0.055 C94\n"
"2 5 1 2 3 0.000 0.000 -0.108 C94\n"
"0 5 1 2 5 -0.523 -0.228 0.208 C94\n"
"2 5 1 2 37 0.000 0.000 0.000 C94\n"
"0 6 1 2 1 -0.467 0.000 0.490 C94\n"
"0 6 1 2 2 0.425 0.168 -0.875 C94\n"
"0 6 1 2 5 0.000 0.136 0.396 C94\n"
"0 8 1 2 1 -0.504 0.371 0.557 C94\n"
"0 8 1 2 2 0.541 0.539 -1.009 C94\n"
"0 8 1 2 5 0.000 0.204 0.464 C94\n"
"0 0 1 3 0 0.000 0.400 0.300 C94 "
"0:*-1-3-* Def\n"
"2 0 1 3 0 0.000 0.500 0.350 C94 "
"2:*-1-3-* Def\n"
"5 0 1 3 0 0.000 0.000 0.000 E94 "
"5:*1-3-* Def\n"
"0 0 1 3 1 0.000 0.000 0.550 C94 "
"0:*-1-3-1 Def\n"
"0 0 1 3 5 0.000 0.200 0.700 C94 "
"0:*-1-3-5 Def\n"
"0 0 1 3 7 0.000 0.400 0.400 C94 "
"0:*-1-3-7 Def\n"
"0 1 1 3 1 0.103 0.177 0.545 C94\n"
"0 1 1 3 5 -0.072 0.316 0.674 C94\n"
"0 1 1 3 6 -0.117 -0.333 0.202 C94\n"
"0 1 1 3 7 0.825 0.139 0.325 C94\n"
"0 1 1 3 10 -0.927 1.112 1.388 C94\n"
"0 2 1 3 5 0.663 -0.167 0.426 C94\n"
"0 2 1 3 7 -0.758 0.112 0.563 C94\n"
"0 5 1 3 1 -0.073 0.085 0.531 C94\n"
"2 5 1 3 2 0.000 0.000 0.115 C94\n"
"2 5 1 3 3 0.000 0.000 0.446 C94\n"
"0 5 1 3 5 -0.822 0.501 1.008 C94\n"
"0 5 1 3 6 0.000 -0.624 0.330 C94\n"
"0 5 1 3 7 0.659 -1.407 0.308 C94\n"
"0 5 1 3 10 -0.412 0.693 0.087 C94\n"
"2 5 1 3 37 0.000 0.000 0.056 C94\n"
"0 5 1 3 43 0.000 1.027 0.360 X94\n"
"0 5 1 3 51 0.000 1.543 0.350 X94\n"
"0 5 1 3 53 0.000 0.501 0.000 X94\n"
"0 5 1 3 74 0.000 0.513 -0.344 X94\n"
"0 5 1 3 75 0.000 0.511 -0.186 X94\n"
"0 6 1 3 6 0.447 0.652 0.318 C94\n"
"0 6 1 3 7 -0.395 0.730 -0.139 C94\n"
"0 10 1 3 7 0.338 2.772 2.145 C94\n"
"0 10 1 3 10 0.548 0.000 1.795 C94\n"
"0 0 1 4 0 0.000 0.000 0.000 C94 "
"0:*-1-4-* Def\n"
"0 0 1 6 0 0.000 0.000 0.200 C94 "
"0:*-1-6-* Def\n"
"5 0 1 6 0 0.000 -0.200 0.400 C94 "
"5:*-1-6-* Def\n"
"0 1 1 6 1 -0.681 0.755 0.755 C94\n"
"5 1 1 6 1 0.000 0.243 -0.596 C94\n"
"0 1 1 6 3 -0.547 0.000 0.320 C94\n"
"0 1 1 6 21 0.000 0.270 0.237 C94\n"
"0 2 1 6 21 0.102 0.460 -0.128 C94\n"
"0 3 1 6 21 -1.652 -1.660 0.283 C94\n"
"0 5 1 6 1 0.571 0.319 0.570 C94\n"
"0 5 1 6 2 0.000 0.000 0.306 C94\n"
"0 5 1 6 3 0.572 0.000 -0.304 C94\n"
"0 5 1 6 21 0.596 -0.276 0.346 C94\n"
"0 5 1 6 25 0.000 0.000 0.061 X94\n"
"0 5 1 6 37 0.000 0.000 0.106 C94\n"
"0 5 1 6 45 0.000 0.000 -0.174 X94\n"
"0 6 1 6 1 0.229 -0.710 0.722 C94\n"
"5 6 1 6 1 0.000 0.000 0.040 C94\n"
"0 6 1 6 21 1.488 -3.401 -0.320 C94\n"
"0 37 1 6 21 0.712 1.320 -0.507 C94\n"
"0 0 1 8 0 0.000 -0.300 0.500 C94 "
"0:*-1-8-* Def\n"
"5 0 1 8 0 0.000 0.000 0.297 E94 "
"5:*1-8-* Def\n"
"0 1 1 8 1 -0.439 0.786 0.272 C94\n"
"5 1 1 8 1 0.115 -0.390 0.658 C94\n"
"0 1 1 8 6 -0.608 0.339 1.496 C94\n"
"0 1 1 8 23 -0.428 0.323 0.280 C94\n"
"0 2 1 8 23 0.594 -0.409 0.155 C94\n"
"0 5 1 8 1 0.393 -0.385 0.562 C94\n"
"0 5 1 8 6 0.598 -0.158 0.399 C94\n"
"0 5 1 8 23 -0.152 -0.440 0.357 C94\n"
"0 0 1 9 0 0.000 0.000 0.000 C94 "
"0:*-1-9-* Def\n"
"5 0 1 9 0 0.000 0.000 0.000 E94 "
"5:*1-9-* Def\n"
"0 5 1 9 3 0.204 -0.335 -0.352 C94\n"
"0 5 1 9 53 0.000 0.000 0.097 X94\n"
"0 0 1 10 0 0.000 0.000 0.300 C94 "
"0:*-1-10-* Def\n"
"5 0 1 10 0 0.000 0.000 0.000 E94 "
"5:*1-10-* Def\n"
"0 0 1 10 3 0.000 0.000 1.000 C94 "
"0:*-1-10-3 Def\n"
"0 1 1 10 3 -1.027 0.694 0.948 C94\n"
"0 1 1 10 6 0.159 -0.552 0.198 C94\n"
"0 1 1 10 28 0.552 -0.380 0.326 C94\n"
"0 3 1 10 3 3.100 -2.529 1.494 C94\n"
"0 3 1 10 28 0.079 0.280 0.402 C94\n"
"0 5 1 10 1 0.000 0.000 0.779 C94\n"
"0 5 1 10 3 -2.099 1.363 0.021 C94\n"
"0 5 1 10 6 -0.162 0.832 0.552 C94\n"
"0 5 1 10 28 -0.616 0.000 0.274 C94\n"
"0 0 1 15 0 0.000 0.000 0.400 C94 "
"0:*-1-15-* Def\n"
"5 0 1 15 0 0.000 0.000 0.336 E94 "
"5:*1-15-* Def\n"
"0 1 1 15 1 -1.047 0.170 0.398 C94\n"
"0 1 1 15 15 -1.438 0.263 0.501 C94\n"
"0 1 1 15 71 -0.376 -0.133 0.288 C94\n"
"0 5 1 15 1 1.143 -0.231 0.447 C94\n"
"0 5 1 15 15 1.555 -0.323 0.456 C94\n"
"0 5 1 15 37 0.000 0.000 0.459 C94\n"
"0 5 1 15 71 0.229 0.203 0.440 C94\n"
"0 0 1 17 0 0.000 0.000 0.350 C94 "
"0:*-1-17-* Def\n"
"5 0 1 17 0 0.000 0.000 0.000 E94 "
"5:*1-17-* Def\n"
"0 5 1 17 1 0.000 0.000 0.536 X94\n"
"0 5 1 17 7 0.000 0.000 0.212 X94\n"
"0 0 1 18 0 0.000 0.000 0.100 C94 "
"0:*-1-18-* Def\n"
"5 0 1 18 0 0.000 0.000 0.112 E94 "
"5:*1-18-* Def\n"
"0 5 1 18 1 0.000 0.000 0.000 X94\n"
"0 5 1 18 6 0.000 0.000 0.099 X94\n"
"0 5 1 18 32 0.000 0.585 0.388 X94\n"
"0 5 1 18 43 0.000 -0.412 0.121 X94\n"
"0 5 1 18 48 0.000 0.000 0.195 X94\n"
"0 5 1 18 62 0.000 0.000 -0.088 X94\n"
"0 0 1 19 0 0.000 0.000 0.150 C94 "
"0:*-1-19-* Def\n"
"5 0 1 19 0 0.000 0.000 0.179 E94 "
"5:*1-19-* Def\n"
"0 5 1 19 5 0.000 0.000 0.196 X94\n"
"0 5 1 19 6 0.000 0.000 0.176 X94\n"
"0 5 1 19 12 0.000 0.000 0.152 X94\n"
"0 0 1 20 0 0.000 0.000 0.350 C94 "
"0:*-1-20-* Def\n"
"5 0 1 20 0 0.000 0.000 0.350 C94 "
"5:*-1-20-* Def\n"
"0 5 1 20 5 0.000 0.000 0.344 C94\n"
"0 5 1 20 20 0.000 0.000 0.361 C94\n"
"0 0 1 22 0 0.000 0.000 0.236 E94 "
"0:*1-22-* Def\n"
"5 0 1 22 0 0.000 0.000 0.236 E94 "
"5:*1-22-* Def\n"
"0 0 1 25 0 0.000 0.000 0.300 C94 "
"0:*-1-25-* Def\n"
"5 0 1 25 0 0.000 0.000 0.251 E94 "
"5:*1-25-* Def\n"
"0 1 1 25 1 0.000 -0.207 0.232 X94\n"
"0 1 1 25 32 0.000 0.288 0.218 X94\n"
"0 5 1 25 1 0.000 0.152 0.235 X94\n"
"0 5 1 25 6 0.000 0.000 0.495 X94\n"
"0 5 1 25 32 0.000 -0.130 0.214 X94\n"
"0 5 1 25 43 0.000 0.000 0.466 X94\n"
"0 5 1 25 72 0.000 0.000 0.243 X94\n"
"0 0 1 26 0 0.000 0.000 0.450 C94 "
"0:*-1-26-* Def\n"
"5 0 1 26 0 0.000 0.000 0.376 E94 "
"5:*1-26-* Def\n"
"0 5 1 26 12 0.000 0.000 0.439 X94\n"
"0 5 1 26 71 0.000 0.000 0.472 X94\n"
"0 0 1 34 0 0.000 0.000 0.250 C94 "
"0:*-1-34-* Def\n"
"5 0 1 34 0 0.000 0.000 0.198 E94 "
"5:*1-34-* Def\n"
"0 1 1 34 36 0.000 0.000 0.187 C94\n"
"0 5 1 34 1 0.000 0.000 0.247 C94\n"
"0 5 1 34 36 0.000 0.000 0.259 C94\n"
"0 0 1 37 0 0.000 0.000 0.200 C94 "
"0:*-1-37-* Def\n"
"5 0 1 37 0 0.000 0.000 0.000 E94 "
"5:*1-37-* Def\n"
"0 1 1 37 37 0.000 0.449 0.000 C94\n"
"0 5 1 37 37 0.000 -0.420 0.391 C94\n"
"0 6 1 37 37 0.000 0.000 0.150 C94\n"
"0 0 1 39 0 0.000 0.000 0.000 C94 "
"0:*-1-39-* Def\n"
"5 0 1 39 0 0.000 0.000 0.000 E94 "
"5:*1-39-* Def\n"
"0 1 1 39 63 0.000 -0.080 -0.056 C94\n"
"0 5 1 39 63 0.000 0.000 -0.113 C94\n"
"0 0 1 40 0 0.000 0.000 0.250 C94 "
"0:*-1-40-* Def\n"
"5 0 1 40 0 0.000 0.000 0.297 E94 "
"5:*1-40-* Def\n"
"0 5 1 40 28 0.000 -0.097 0.203 C94\n"
"0 5 1 40 37 0.000 0.000 0.329 C94\n"
"0 0 1 41 0 0.000 0.600 0.000 C94 "
"0:*-1-41-* Def\n"
"0 1 1 41 32 0.000 1.263 0.000 C94\n"
"0 5 1 41 32 0.000 0.000 -0.106 C94\n"
"0 5 1 41 72 0.000 0.632 0.000 X94\n"
"0 0 1 43 0 0.000 0.000 0.150 C94 "
"0:*-1-43-* Def\n"
"5 0 1 43 0 0.000 0.000 0.297 E94 "
"5:*1-43-* Def\n"
"0 5 1 43 18 0.357 -0.918 0.000 X94\n"
"0 5 1 43 25 0.000 0.000 0.061 X94\n"
"0 5 1 43 28 -0.249 0.382 0.343 X94\n"
"0 0 1 45 0 0.000 0.000 0.100 C94 "
"0:*-1-45-* Def\n"
"0 5 1 45 32 0.000 0.000 0.125 X94\n"
"0 0 1 46 0 0.000 0.000 -0.500 C94 "
"0:*-1-46-* Def\n"
"0 5 1 46 7 0.000 0.000 -0.540 X94\n"
"0 0 1 54 0 0.000 0.000 0.000 C94 "
"0:*-1-54-* Def\n"
"2 0 1 54 0 0.000 0.000 0.000 E94 "
"2:*1-54-* Def\n"
"5 0 1 54 0 0.000 0.000 0.000 E94 "
"5:*1-54-* Def\n"
"0 5 1 54 3 0.000 0.000 -0.315 C94\n"
"0 5 1 54 36 0.000 0.000 0.315 C94\n"
"0 0 1 55 0 0.000 0.000 0.000 C94 "
"0:*-1-55-* Def\n"
"5 0 1 55 0 0.000 0.000 0.000 E94 "
"5:*1-55-* Def\n"
"0 5 1 55 36 0.000 -0.058 0.084 C94\n"
"0 5 1 55 57 0.000 -0.058 -0.092 C94\n"
"0 0 1 56 0 0.000 0.000 -0.300 C94 "
"0:*-1-56-* Def\n"
"0 1 1 56 36 0.875 0.668 -0.015 C94\n"
"0 1 1 56 57 -0.870 0.775 -0.406 C94\n"
"0 5 1 56 36 -0.958 -0.629 -0.372 C94\n"
"0 5 1 56 57 0.952 -0.715 -0.483 C94\n"
"0 0 1 57 0 0.000 0.000 0.000 E94 "
"0:*1-57-* Def\n"
"5 0 1 57 0 0.000 0.000 0.000 E94 "
"5:*1-57-* Def\n"
"0 0 1 58 0 0.000 0.000 0.000 E94 "
"0:*1-58-* Def\n"
"0 0 1 62 0 0.000 0.000 0.250 C94 "
"0:*-1-62-* Def\n"
"0 5 1 62 18 0.000 0.000 0.270 X94\n"
"0 0 1 63 0 0.000 0.000 0.000 E94 "
"0:*1-63-* Def\n"
"5 0 1 63 0 0.000 0.000 0.000 E94 "
"5:*1-63-* Def\n"
"0 0 1 64 0 0.000 0.000 0.000 E94 "
"0:*1-64-* Def\n"
"5 0 1 64 0 0.000 0.000 0.000 E94 "
"5:*1-64-* Def\n"
"0 0 1 67 0 0.000 0.000 0.000 E94 "
"0:*1-67-* Def\n"
"5 0 1 67 0 0.000 0.000 0.000 E94 "
"5:*1-67-* Def\n"
"0 0 1 68 0 0.000 0.000 0.400 C94 "
"0:*-1-68-* Def\n"
"0 1 1 68 1 -0.117 0.090 0.751 C94\n"
"0 1 1 68 23 0.373 0.153 0.635 C94\n"
"0 1 1 68 32 -0.090 -0.169 0.075 C94\n"
"0 5 1 68 1 0.134 -0.112 0.329 C94\n"
"0 5 1 68 23 -0.361 -0.202 0.560 C94\n"
"0 5 1 68 32 0.072 0.218 0.093 C94\n"
"0 0 1 73 0 0.000 0.000 0.500 C94 "
"0:*-1-73-* Def\n"
"0 5 1 73 32 0.000 0.000 0.509 X94\n"
"0 5 1 73 72 0.000 0.000 0.443 X94\n"
"0 0 1 75 0 0.000 0.000 0.000 E94 "
"0:*1-75-* Def\n"
"0 0 1 78 0 0.000 0.000 0.000 E94 "
"0:*1-78-* Def\n"
"0 0 1 80 0 0.000 0.000 0.000 E94 "
"0:*1-80-* Def\n"
"0 0 1 81 0 0.000 0.000 0.000 E94 "
"0:*1-81-* Def\n"
"0 0 2 2 0 0.000 12.000 0.000 C94 "
"0:*-2=2-* Def\n"
"1 0 2 2 0 0.000 1.800 0.000 C94 "
"1:*=2-2=* Def\n"
"5 0 2 2 0 0.000 12.000 0.000 C94 "
"5:*-2=2-* Def\n"
"0 1 2 2 1 -0.403 12.000 0.000 C94\n"
"0 1 2 2 2 0.000 12.000 0.000 C94\n"
"1 1 2 2 2 -0.418 2.089 -0.310 C94\n"
"0 1 2 2 5 0.000 12.000 0.000 C94\n"
"1 1 2 2 5 0.412 2.120 0.269 C94\n"
"1 2 2 2 2 0.094 1.621 0.877 C94\n"
"0 2 2 2 5 0.000 12.000 0.000 C94\n"
"1 2 2 2 5 0.317 1.421 -0.870 C94\n"
"0 3 2 2 5 0.000 12.000 0.000 C94\n"
"0 5 2 2 5 0.000 12.000 0.000 C94\n"
"1 5 2 2 5 -0.406 1.767 0.000 C94\n"
"0 5 2 2 6 0.000 12.000 0.000 C94\n"
"0 5 2 2 37 0.000 12.000 0.000 C94\n"
"0 5 2 2 40 0.000 12.000 0.000 C94\n"
"0 5 2 2 41 0.000 12.000 0.000 C94\n"
"0 5 2 2 45 0.000 12.000 0.000 X94\n"
"0 5 2 2 62 0.000 12.000 0.000 X94\n"
"1 0 2 3 0 0.000 2.500 0.000 #E94 "
"0:*-2-3-* Def\n"
"1 1 2 3 1 0.136 1.798 0.630 C94\n"
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"0 0 37 69 0 0.000 7.000 0.000 C94 "
"0:*-37-69-* Def\n"
"0 0 37 78 0 0.000 6.000 0.000 E94 "
"0:*-37-78-* Def\n"
"0 0 37 81 0 0.000 6.000 0.000 E94 "
"0:*-37-81-* Def\n"
"1 0 37 81 0 0.000 4.800 0.000 E94 "
"1:*-37-81-* Def\n"
"0 0 38 38 0 0.000 7.000 0.000 C94 "
"0:*-38-38-* Def\n"
"0 0 38 58 0 0.000 7.000 0.000 C94 "
"0:*-38-58-* Def\n"
"0 0 38 63 0 0.000 7.000 0.000 C94 "
"0:*-38-63-* Def\n"
"0 0 38 64 0 0.000 7.000 0.000 C94 "
"0:*-38-64-* Def\n"
"0 0 38 69 0 0.000 6.000 0.000 E94 "
"0:*-38-69-* Def\n"
"0 0 38 78 0 0.000 6.000 0.000 E94 "
"0:*-38-78-* Def\n"
"0 0 39 40 0 0.000 0.000 0.000 E94 "
"0:*-39-40-* Def\n"
"0 0 39 45 0 0.000 6.000 0.000 E94 "
"0:*-39-45-* Def\n"
"0 0 39 63 0 0.000 4.000 0.000 C94 "
"0:*-39-63-* Def\n"
"1 0 39 63 0 0.000 6.000 0.000 E94 "
"1:*-39-63-* Def\n"
"5 0 39 63 0 0.000 3.600 0.000 E94 "
"5:*-39-63-* Def\n"
"0 1 39 63 5 0.000 4.000 0.000 C94\n"
"0 1 39 63 64 0.000 4.000 0.000 C94\n"
"0 18 39 63 5 0.000 4.000 0.000 X94\n"
"0 18 39 63 64 0.000 4.000 0.000 X94\n"
"0 63 39 63 5 0.000 4.000 0.000 C94\n"
"0 63 39 63 64 0.000 4.000 0.000 C94\n"
"0 0 39 64 0 0.000 3.600 0.000 E94 "
"0:*-39-64-* Def\n"
"1 0 39 64 0 0.000 6.000 0.000 E94 "
"1:*-39-64-* Def\n"
"0 0 39 65 0 0.000 4.000 0.000 C94 "
"0:*-39-65-* Def\n"
"0 0 39 78 0 0.000 3.600 0.000 E94 "
"0:*-39-78-* Def\n"
"0 0 40 40 0 0.000 0.000 0.375 E94 "
"0:*-40-40-* Def\n"
"0 0 40 45 0 0.000 3.600 0.000 E94 "
"0:*-40-45-* Def\n"
"0 0 40 46 0 0.000 3.600 0.000 E94 "
"0:*-40-46-* Def\n"
"0 0 40 54 0 0.000 3.600 0.000 E94 "
"0:*-40-54-* Def\n"
"2 0 40 54 0 0.000 3.600 0.000 E94 "
"2:*-40-54-* Def\n"
"0 0 40 63 0 0.000 3.600 0.000 E94 "
"0:*-40-63-* Def\n"
"0 0 40 64 0 0.000 3.600 0.000 E94 "
"0:*-40-64-* Def\n"
"0 0 40 78 0 0.000 3.600 0.000 E94 "
"0:*-40-78-* Def\n"
"0 0 41 41 0 0.000 1.800 0.000 E94 "
"0:*-41-41-* Def\n"
"0 0 41 55 0 0.000 4.800 0.000 E94 "
"0:*-41-55-* Def\n"
"0 0 41 62 0 0.000 3.600 0.000 E94 "
"0:*-41-62-* Def\n"
"0 0 41 80 0 0.000 1.800 0.000 E94 "
"0:*-41-80-* Def\n"
"0 0 43 43 0 0.000 0.000 0.375 E94 "
"0:*-43-43-* Def\n"
"0 0 43 45 0 0.000 3.600 0.000 E94 "
"0:*-43-45-* Def\n"
"0 0 43 64 0 0.000 3.600 0.000 E94 "
"0:*-43-64-* Def\n"
"0 0 44 57 0 0.000 7.000 0.000 C94 "
"0:*-44-57-* Def\n"
"0 0 44 63 0 0.000 7.000 0.000 C94 "
"0:*-44-63-* Def\n"
"0 0 44 65 0 0.000 7.000 0.000 C94 "
"0:*-44-65-* Def\n"
"0 0 44 78 0 0.000 2.846 0.000 E94 "
"0:*-44-78-* Def\n"
"0 0 44 80 0 0.000 2.846 0.000 E94 "
"0:*-44-80-* Def\n"
"0 0 45 63 0 0.000 1.800 0.000 E94 "
"0:*-45-63-* Def\n"
"0 0 45 64 0 0.000 1.800 0.000 E94 "
"0:*-45-64-* Def\n"
"0 0 45 78 0 0.000 1.800 0.000 E94 "
"0:*-45-78-* Def\n"
"0 0 55 57 0 0.000 10.000 0.000 C94 "
"0:*-55-57-* Def\n"
"2 0 55 57 0 0.000 4.800 0.000 E94 "
"2:*-55-57-* Def\n"
"5 0 55 57 0 0.000 4.800 0.000 E94 "
"5:*-55-57-* Def\n"
"0 1 55 57 5 0.423 12.064 0.090 C94\n"
"0 1 55 57 55 -0.428 12.044 0.000 C94\n"
"0 36 55 57 5 -0.268 8.077 -0.806 C94\n"
"0 36 55 57 55 0.273 8.025 0.692 C94\n"
"0 0 55 62 0 0.000 3.600 0.000 E94 "
"0:*-55-62-* Def\n"
"0 0 55 64 0 0.000 4.800 0.000 E94 "
"0:*-55-64-* Def\n"
"0 0 55 80 0 0.000 4.800 0.000 E94 "
"0:*-55-80-* Def\n"
"0 0 56 57 0 0.000 6.000 0.000 C94 "
"0:*-56-57-* Def\n"
"0 1 56 57 56 0.000 6.886 -0.161 C94\n"
"0 36 56 57 56 0.000 4.688 0.107 C94\n"
"0 0 56 63 0 0.000 4.800 0.000 E94 "
"0:*-56-63-* Def\n"
"0 0 56 80 0 0.000 4.800 0.000 E94 "
"0:*-56-80-* Def\n"
"1 0 57 63 0 0.000 1.800 0.000 E94 "
"1:*-57-63-* Def\n"
"1 0 57 64 0 0.000 1.800 0.000 E94 "
"1:*-57-64-* Def\n"
"0 0 58 63 0 0.000 6.000 0.000 E94 "
"0:*-58-63-* Def\n"
"0 0 58 64 0 0.000 6.000 0.000 E94 "
"0:*-58-64-* Def\n"
"0 0 59 63 0 0.000 7.000 0.000 C94 "
"0:*-59-63-* Def\n"
"0 0 59 65 0 0.000 7.000 0.000 C94 "
"0:*-59-65-* Def\n"
"0 0 59 78 0 0.000 3.600 0.000 E94 "
"0:*-59-78-* Def\n"
"0 0 59 80 0 0.000 3.600 0.000 E94 "
"0:*-59-80-* Def\n"
"0 0 59 82 0 0.000 3.600 0.000 E94 "
"0:*-59-82-* Def\n"
"0 0 62 63 0 0.000 3.600 0.000 E94 "
"0:*-62-63-* Def\n"
"0 0 62 64 0 0.000 3.600 0.000 E94 "
"0:*-62-64-* Def\n"
"1 0 63 63 0 0.000 1.800 0.000 E94 "
"1:*-63-63-* Def\n"
"0 0 63 64 0 0.000 7.000 0.000 C94 "
"0:*-63-64-* Def\n"
"0 5 63 64 5 0.000 7.000 0.000 C94\n"
"0 5 63 64 64 0.000 7.000 0.000 C94\n"
"0 39 63 64 5 0.000 7.000 0.000 C94\n"
"0 39 63 64 64 0.000 7.000 0.000 C94\n"
"0 0 63 66 0 0.000 7.000 0.000 C94 "
"0:*-63-66-* Def\n"
"0 0 63 78 0 0.000 6.000 0.000 E94 "
"0:*-63-78-* Def\n"
"0 0 63 81 0 0.000 6.000 0.000 E94 "
"0:*-63-81-* Def\n"
"0 0 64 64 0 0.000 7.000 0.000 C94 "
"0:*-64-64-* Def\n"
"1 0 64 64 0 0.000 1.800 0.000 E94 "
"1:*-64-64-* Def\n"
"0 5 64 64 5 0.000 7.000 0.000 C94\n"
"0 5 64 64 63 0.000 7.000 0.000 C94\n"
"0 63 64 64 63 0.000 7.000 0.000 C94\n"
"0 0 64 65 0 0.000 7.000 0.000 C94 "
"0:*-64-65-* Def\n"
"0 0 64 66 0 0.000 7.000 0.000 C94 "
"0:*-64-66-* Def\n"
"0 0 64 78 0 0.000 6.000 0.000 E94 "
"0:*-64-78-* Def\n"
"0 0 64 81 0 0.000 6.000 0.000 E94 "
"0:*-64-81-* Def\n"
"5 0 64 81 0 0.000 6.000 0.000 E94 "
"5:*-64-81-* Def\n"
"0 0 64 82 0 0.000 6.000 0.000 E94 "
"0:*-64-82-* Def\n"
"0 0 65 66 0 0.000 7.000 0.000 C94 "
"0:*-65-66-* Def\n"
"0 0 65 78 0 0.000 6.000 0.000 E94 "
"0:*-65-78-* Def\n"
"0 0 65 81 0 0.000 6.000 0.000 E94 "
"0:*-65-81-* Def\n"
"0 0 65 82 0 0.000 6.000 0.000 E94 "
"0:*-65-82-* Def\n"
"0 0 66 66 0 0.000 7.000 0.000 C94 "
"0:*-66-66-* Def\n"
"0 0 66 78 0 0.000 6.000 0.000 E94 "
"0:*-66-78-* Def\n"
"0 0 66 81 0 0.000 6.000 0.000 E94 "
"0:*-66-81-* Def\n"
"0 0 67 67 0 0.000 12.000 0.000 E94 "
"0:*-67-67-* Def\n"
"5 0 67 67 0 0.000 12.000 0.000 E94 "
"5:*-67-67-* Def\n"
"0 0 76 76 0 0.000 3.600 0.000 E94 "
"0:*-76-76-* Def\n"
"0 0 76 78 0 0.000 3.600 0.000 E94 "
"0:*-76-78-* Def\n"
"0 0 78 78 0 0.000 7.000 0.000 C94 "
"0:*-78-78-* Def\n"
"0 0 78 79 0 0.000 6.000 0.000 E94 "
"0:*-78-79-* Def\n"
"0 0 78 81 0 0.000 4.000 0.000 C94 "
"0:*-78-81-* Def\n"
"0 0 79 79 0 0.000 6.000 0.000 E94 "
"0:*-79-79-* Def\n"
"0 0 79 81 0 0.000 6.000 0.000 E94 "
"0:*-79-81-* Def\n"
"0 0 80 81 0 0.000 4.000 0.000 C94 "
"0:*-80-81-* Def\n";
const std::string defaultMMFFsTor =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999\n"
"* All Rights Reserved\n"
"*\n"
"* MMFF94s TORSION PARAMETERS\n"
"* C94 - CORE MMFF94 parameter - from fits to conformational energies\n"
"* C94S - CORE MMFF94s parameter - from fits to conformational energies\n"
"* X94 - EXTD MMFF94 parameter - also from fits to conformational E's\n"
"* E94 - EXTD MMFF94 parameter - from empirical rule\n"
"* #E94 - Adjusted from empirical rule value\n"
"*\n"
"* atom types V1 V2 V3 Source\n"
"0 0 1 1 0 0.000 0.000 0.300 C94 "
"0:*-1-1-* Def\n"
"5 0 1 1 0 0.200 -0.800 1.500 C94 "
"5:*-1-1-* Def\n"
"0 1 1 1 1 0.103 0.681 0.332 C94\n"
"5 1 1 1 1 0.144 -0.547 1.126 C94\n"
"0 1 1 1 2 -0.295 0.438 0.584 C94\n"
"0 1 1 1 3 0.066 -0.156 0.143 C94\n"
"0 1 1 1 5 0.639 -0.630 0.264 C94\n"
"0 1 1 1 6 -0.688 1.757 0.477 C94\n"
"5 1 1 1 6 0.000 0.000 0.054 C94\n"
"0 1 1 1 8 -1.420 -0.092 1.101 C94\n"
"5 1 1 1 8 0.000 -0.158 0.323 C94\n"
"0 1 1 1 11 0.593 0.662 1.120 C94\n"
"0 1 1 1 12 -0.678 0.417 0.624 C94\n"
"0 1 1 1 15 -0.714 0.698 0.000 C94\n"
"0 1 1 1 34 -0.647 0.550 0.590 C94\n"
"0 2 1 1 5 0.321 -0.411 0.144 C94\n"
"0 3 1 1 3 0.443 0.000 -1.140 C94\n"
"0 3 1 1 5 -0.256 0.058 0.000 C94\n"
"0 3 1 1 6 -0.679 -0.029 0.000 C94\n"
"0 5 1 1 5 0.284 -1.386 0.314 C94\n"
"0 5 1 1 6 -0.654 1.072 0.279 C94\n"
"0 5 1 1 8 -0.744 -1.235 0.337 C94\n"
"0 5 1 1 10 0.000 0.000 0.418 C94S\n"
"0 5 1 1 11 0.000 0.516 0.291 C94\n"
"0 5 1 1 12 0.678 -0.602 0.398 C94\n"
"0 5 1 1 15 1.142 -0.644 0.367 C94\n"
"0 5 1 1 25 0.000 0.000 0.295 X94\n"
"0 5 1 1 34 0.692 -0.530 0.278 C94\n"
"0 5 1 1 37 0.000 0.000 0.389 C94\n"
"0 5 1 1 39 0.000 0.000 0.278 C94\n"
"0 5 1 1 41 0.000 0.000 -0.141 C94\n"
"0 5 1 1 56 0.000 0.000 0.324 C94\n"
"0 5 1 1 68 0.000 0.000 0.136 C94\n"
"0 6 1 1 6 0.408 1.397 0.961 C94\n"
"5 6 1 1 6 0.313 -1.035 1.631 C94\n"
"0 8 1 1 8 1.055 0.834 0.000 C94\n"
"0 11 1 1 11 -0.387 -0.543 1.405 C94\n"
"0 12 1 1 12 0.000 0.000 0.893 C94\n"
"0 15 1 1 15 -0.177 0.000 0.049 C94\n"
"0 0 1 2 0 0.000 0.000 0.000 C94 "
"0:*-1-2-* Def\n"
"2 0 1 2 0 0.000 0.000 0.000 E94 "
"2:*1-2-* Def\n"
"5 0 1 2 0 0.000 0.000 0.000 C94 "
"5:*-1-2-* Def\n"
"0 0 1 2 2 0.000 0.000 -0.650 C94 "
"0:*-1-2=2 Def\n"
"5 0 1 2 2 0.000 0.000 -0.650 C94 "
"5:*-1-2=2 Def\n"
"0 1 1 2 1 0.419 0.296 0.282 C94\n"
"0 1 1 2 2 -0.494 0.274 -0.630 C94\n"
"0 1 1 2 5 0.075 0.000 0.358 C94\n"
"0 2 1 2 2 -0.293 0.115 -0.508 C94\n"
"0 2 1 2 5 0.301 0.104 0.507 C94\n"
"0 3 1 2 1 0.565 -0.554 0.234 C94\n"
"0 3 1 2 2 -0.577 -0.482 -0.427 C94\n"
"0 3 1 2 5 0.082 0.000 0.123 C94\n"
"0 5 1 2 1 0.000 -0.184 0.220 C94\n"
"0 5 1 2 2 0.501 -0.410 -0.535 C94\n"
"2 5 1 2 2 0.000 0.000 0.055 C94\n"
"2 5 1 2 3 0.000 0.000 -0.108 C94\n"
"0 5 1 2 5 -0.523 -0.228 0.208 C94\n"
"2 5 1 2 37 0.000 0.000 0.000 C94\n"
"0 6 1 2 1 -0.467 0.000 0.490 C94\n"
"0 6 1 2 2 0.425 0.168 -0.875 C94\n"
"0 6 1 2 5 0.000 0.136 0.396 C94\n"
"0 8 1 2 1 -0.504 0.371 0.557 C94\n"
"0 8 1 2 2 0.541 0.539 -1.009 C94\n"
"0 8 1 2 5 0.000 0.204 0.464 C94\n"
"0 0 1 3 0 0.000 0.400 0.300 C94 "
"0:*-1-3-* Def\n"
"2 0 1 3 0 0.000 0.500 0.350 C94 "
"2:*-1-3-* Def\n"
"5 0 1 3 0 0.000 0.000 0.000 E94 "
"5:*1-3-* Def\n"
"0 0 1 3 1 0.000 0.000 0.550 C94 "
"0:*-1-3-1 Def\n"
"0 0 1 3 5 0.000 0.200 0.700 C94 "
"0:*-1-3-5 Def\n"
"0 0 1 3 7 0.000 0.400 0.400 C94 "
"0:*-1-3-7 Def\n"
"0 1 1 3 1 0.103 0.177 0.545 C94\n"
"0 1 1 3 5 -0.072 0.316 0.674 C94\n"
"0 1 1 3 6 -0.117 -0.333 0.202 C94\n"
"0 1 1 3 7 0.825 0.139 0.325 C94\n"
"0 1 1 3 10 -0.763 1.244 0.986 C94S\n"
"0 2 1 3 5 0.663 -0.167 0.426 C94\n"
"0 2 1 3 7 -0.758 0.112 0.563 C94\n"
"0 5 1 3 1 -0.073 0.085 0.531 C94\n"
"2 5 1 3 2 0.000 0.000 0.115 C94\n"
"2 5 1 3 3 0.000 0.000 0.446 C94\n"
"0 5 1 3 5 -0.822 0.501 1.008 C94\n"
"0 5 1 3 6 0.000 -0.624 0.330 C94\n"
"0 5 1 3 7 0.659 -1.407 0.308 C94\n"
"0 5 1 3 10 -0.687 1.244 0.136 C94S\n"
"2 5 1 3 37 0.000 0.000 0.056 C94\n"
"0 5 1 3 43 0.000 1.027 0.360 X94\n"
"0 5 1 3 51 0.000 1.543 0.350 X94\n"
"0 5 1 3 53 0.000 0.501 0.000 X94\n"
"0 5 1 3 74 0.000 0.513 -0.344 X94\n"
"0 5 1 3 75 0.000 0.511 -0.186 X94\n"
"0 6 1 3 6 0.447 0.652 0.318 C94\n"
"0 6 1 3 7 -0.395 0.730 -0.139 C94\n"
"0 10 1 3 7 0.530 2.905 2.756 C94S\n"
"0 10 1 3 10 0.465 -0.241 1.850 C94S\n"
"0 0 1 4 0 0.000 0.000 0.000 C94 "
"0:*-1-4-* Def\n"
"0 0 1 6 0 0.000 0.000 0.200 C94 "
"0:*-1-6-* Def\n"
"5 0 1 6 0 0.000 -0.200 0.400 C94 "
"5:*-1-6-* Def\n"
"0 1 1 6 1 -0.681 0.755 0.755 C94\n"
"5 1 1 6 1 0.000 0.243 -0.596 C94\n"
"0 1 1 6 3 -0.547 0.000 0.320 C94\n"
"0 1 1 6 21 0.000 0.270 0.237 C94\n"
"0 2 1 6 21 0.102 0.460 -0.128 C94\n"
"0 3 1 6 21 -1.652 -1.660 0.283 C94\n"
"0 5 1 6 1 0.571 0.319 0.570 C94\n"
"0 5 1 6 2 0.000 0.000 0.306 C94\n"
"0 5 1 6 3 0.572 0.000 -0.304 C94\n"
"0 5 1 6 21 0.596 -0.276 0.346 C94\n"
"0 5 1 6 25 0.000 0.000 0.061 X94\n"
"0 5 1 6 37 0.000 0.000 0.106 C94\n"
"0 5 1 6 45 0.000 0.000 -0.174 X94\n"
"0 6 1 6 1 0.229 -0.710 0.722 C94\n"
"5 6 1 6 1 0.000 0.000 0.040 C94\n"
"0 6 1 6 21 1.488 -3.401 -0.320 C94\n"
"0 37 1 6 21 0.712 1.320 -0.507 C94\n"
"0 0 1 8 0 0.000 -0.300 0.500 C94 "
"0:*-1-8-* Def\n"
"5 0 1 8 0 0.000 0.000 0.297 E94 "
"5:*1-8-* Def\n"
"0 1 1 8 1 -0.439 0.786 0.272 C94\n"
"5 1 1 8 1 0.115 -0.390 0.658 C94\n"
"0 1 1 8 6 -0.608 0.339 1.496 C94\n"
"0 1 1 8 23 -0.428 0.323 0.280 C94\n"
"0 2 1 8 23 0.594 -0.409 0.155 C94\n"
"0 5 1 8 1 0.393 -0.385 0.562 C94\n"
"0 5 1 8 6 0.598 -0.158 0.399 C94\n"
"0 5 1 8 23 -0.152 -0.440 0.357 C94\n"
"0 0 1 9 0 0.000 0.000 0.000 C94 "
"0:*-1-9-* Def\n"
"5 0 1 9 0 0.000 0.000 0.000 E94 "
"5:*1-9-* Def\n"
"0 5 1 9 3 0.204 -0.335 -0.352 C94\n"
"0 5 1 9 53 0.000 0.000 0.097 X94\n"
"0 0 1 10 0 0.000 0.000 0.300 C94 "
"0:*-1-10-* Def\n"
"5 0 1 10 0 0.000 0.000 0.000 E94 "
"5:*1-10-* Def\n"
"0 0 1 10 3 0.000 0.000 1.000 C94 "
"0:*-1-10-3 Def\n"
"0 1 1 10 3 -0.884 0.578 0.818 C94S\n"
"0 1 1 10 6 0.000 -0.379 0.565 C94S\n"
"0 1 1 10 28 0.750 -0.404 0.369 C94S\n"
"0 3 1 10 3 3.219 -2.699 1.875 C94S\n"
"0 3 1 10 28 0.207 0.461 0.324 C94S\n"
"0 5 1 10 1 0.000 0.000 0.706 C94S\n"
"0 5 1 10 3 -2.334 1.517 -0.065 C94S\n"
"0 5 1 10 6 0.000 0.688 0.665 C94S\n"
"0 5 1 10 28 -0.982 -0.207 0.166 C94S\n"
"0 0 1 15 0 0.000 0.000 0.400 C94 "
"0:*-1-15-* Def\n"
"5 0 1 15 0 0.000 0.000 0.336 E94 "
"5:*1-15-* Def\n"
"0 1 1 15 1 -1.047 0.170 0.398 C94\n"
"0 1 1 15 15 -1.438 0.263 0.501 C94\n"
"0 1 1 15 71 -0.376 -0.133 0.288 C94\n"
"0 5 1 15 1 1.143 -0.231 0.447 C94\n"
"0 5 1 15 15 1.555 -0.323 0.456 C94\n"
"0 5 1 15 37 0.000 0.000 0.459 C94\n"
"0 5 1 15 71 0.229 0.203 0.440 C94\n"
"0 0 1 17 0 0.000 0.000 0.350 C94 "
"0:*-1-17-* Def\n"
"5 0 1 17 0 0.000 0.000 0.000 E94 "
"5:*1-17-* Def\n"
"0 5 1 17 1 0.000 0.000 0.536 X94\n"
"0 5 1 17 7 0.000 0.000 0.212 X94\n"
"0 0 1 18 0 0.000 0.000 0.100 C94 "
"0:*-1-18-* Def\n"
"5 0 1 18 0 0.000 0.000 0.112 E94 "
"5:*1-18-* Def\n"
"0 5 1 18 1 0.000 0.000 0.000 X94\n"
"0 5 1 18 6 0.000 0.000 0.099 X94\n"
"0 5 1 18 32 0.000 0.585 0.388 X94\n"
"0 5 1 18 43 0.000 -0.412 0.121 X94\n"
"0 5 1 18 48 0.000 0.000 0.195 X94\n"
"0 5 1 18 62 0.000 0.000 -0.088 X94\n"
"0 0 1 19 0 0.000 0.000 0.150 C94 "
"0:*-1-19-* Def\n"
"5 0 1 19 0 0.000 0.000 0.179 E94 "
"5:*1-19-* Def\n"
"0 5 1 19 5 0.000 0.000 0.196 X94\n"
"0 5 1 19 6 0.000 0.000 0.176 X94\n"
"0 5 1 19 12 0.000 0.000 0.152 X94\n"
"0 0 1 20 0 0.000 0.000 0.350 C94 "
"0:*-1-20-* Def\n"
"5 0 1 20 0 0.000 0.000 0.350 C94 "
"5:*-1-20-* Def\n"
"0 5 1 20 5 0.000 0.000 0.344 C94\n"
"0 5 1 20 20 0.000 0.000 0.361 C94\n"
"0 0 1 22 0 0.000 0.000 0.236 E94 "
"0:*1-22-* Def\n"
"5 0 1 22 0 0.000 0.000 0.236 E94 "
"5:*1-22-* Def\n"
"0 0 1 25 0 0.000 0.000 0.300 C94 "
"0:*-1-25-* Def\n"
"5 0 1 25 0 0.000 0.000 0.251 E94 "
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"0:*-20-40-* Def\n"
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"0:*-22-22-* Def\n"
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"4:*-22-22-* Def\n"
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"5:*-22-22-* Def\n"
"0 0 22 30 0 0.000 0.000 0.000 E94 "
"0:*-22-30-* Def\n"
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"4:*-22-30-* Def\n"
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"0:*-25-43-* Def\n"
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"0 32 25 43 1 2.108 1.896 0.965 X94\n"
"0 32 25 43 28 2.977 0.732 -0.502 X94\n"
"0 0 25 57 0 0.000 0.000 0.000 E94 "
"0:*-25-57-* Def\n"
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"0:*-25-63-* Def\n"
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"0:*-26-26-* Def\n"
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"5:*-26-26-* Def\n"
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"0:*-26-34-* Def\n"
"5 0 26 34 0 0.000 0.000 0.316 E94 "
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"0:*-26-37-* Def\n"
"0 0 26 40 0 0.000 0.000 0.474 E94 "
"0:*-26-40-* Def\n"
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"5:*-37-37-* Def\n"
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"0 3 37 37 37 0.000 7.000 0.000 C94\n"
"0 5 37 37 5 0.000 7.000 0.000 C94\n"
"0 5 37 37 6 0.000 7.000 0.000 C94\n"
"0 5 37 37 15 0.000 7.000 0.000 C94\n"
"0 5 37 37 18 0.000 7.000 0.000 X94\n"
"0 5 37 37 37 0.000 7.000 0.000 C94\n"
"0 5 37 37 40 0.000 7.000 0.000 C94\n"
"0 5 37 37 43 0.000 7.000 0.000 X94\n"
"0 6 37 37 37 0.000 7.000 0.000 C94\n"
"0 15 37 37 37 0.000 7.000 0.000 C94\n"
"0 18 37 37 37 0.000 7.000 0.000 X94\n"
"0 37 37 37 37 0.000 7.000 0.000 C94\n"
"0 37 37 37 40 0.000 7.000 0.000 C94\n"
"0 37 37 37 43 0.000 7.000 0.000 X94\n"
"0 0 37 38 0 0.000 7.000 0.000 C94 "
"0:*-37-38-* Def\n"
"0 0 37 39 0 0.000 3.600 0.000 E94 "
"0:*-37-39-* Def\n"
"1 0 37 39 0 0.000 6.000 0.000 E94 "
"1:*-37-39-* Def\n"
"0 0 37 40 0 0.000 4.000 0.000 C94 "
"0:*-37-40-* Def\n"
"5 0 37 40 0 0.000 3.600 0.000 E94 "
"5:*-37-40-* Def\n"
"0 37 37 40 1 0.000 4.095 0.382 C94S\n"
"0 37 37 40 28 0.698 2.542 3.072 C94S\n"
"0 0 37 41 0 0.000 1.800 0.000 E94 "
"0:*-37-41-* Def\n"
"0 0 37 43 0 0.000 2.000 1.800 C94 "
"0:*-37-43-* Def\n"
"5 0 37 43 0 0.000 3.600 0.000 E94 "
"5:*-37-43-* Def\n"
"0 37 37 43 18 0.372 2.284 2.034 X94\n"
"0 37 37 43 28 0.000 1.694 1.508 X94\n"
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"0:*-37-45-* Def\n"
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"0:*-37-55-* Def\n"
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"0:*-37-58-* Def\n"
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"1:*-37-58-* Def\n"
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"0:*-37-62-* Def\n"
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"0:*-37-63-* Def\n"
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"1:*-37-63-* Def\n"
"0 0 37 64 0 0.000 7.000 0.000 C94 "
"0:*-37-64-* Def\n"
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"5:*-39-63-* Def\n"
"0 1 39 63 5 0.000 4.000 0.000 C94\n"
"0 1 39 63 64 0.000 4.000 0.000 C94\n"
"0 18 39 63 5 0.000 4.000 0.000 X94\n"
"0 18 39 63 64 0.000 4.000 0.000 X94\n"
"0 63 39 63 5 0.000 4.000 0.000 C94\n"
"0 63 39 63 64 0.000 4.000 0.000 C94\n"
"0 0 39 64 0 0.000 3.600 0.000 E94 "
"0:*-39-64-* Def\n"
"1 0 39 64 0 0.000 6.000 0.000 E94 "
"1:*-39-64-* Def\n"
"0 0 39 65 0 0.000 4.000 0.000 C94 "
"0:*-39-65-* Def\n"
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"0:*-39-78-* Def\n"
"0 0 40 40 0 0.000 0.000 0.375 E94 "
"0:*-40-40-* Def\n"
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"2:*-40-54-* Def\n"
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"0:*-44-80-* Def\n"
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"0:*-45-63-* Def\n"
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"0:*-45-64-* Def\n"
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"0:*-45-78-* Def\n"
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"0:*-55-57-* Def\n"
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"2:*-55-57-* Def\n"
"5 0 55 57 0 0.000 4.800 0.000 E94 "
"5:*-55-57-* Def\n"
"0 1 55 57 5 0.423 12.064 0.090 C94\n"
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"0 36 55 57 5 -0.268 8.077 -0.806 C94\n"
"0 36 55 57 55 0.273 8.025 0.692 C94\n"
"0 0 55 62 0 0.000 3.600 0.000 E94 "
"0:*-55-62-* Def\n"
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"0:*-55-64-* Def\n"
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"0:*-55-80-* Def\n"
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"0:*-56-57-* Def\n"
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"0:*-56-63-* Def\n"
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"0:*-56-80-* Def\n"
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"0:*-58-63-* Def\n"
"0 0 58 64 0 0.000 6.000 0.000 E94 "
"0:*-58-64-* Def\n"
"0 0 59 63 0 0.000 7.000 0.000 C94 "
"0:*-59-63-* Def\n"
"0 0 59 65 0 0.000 7.000 0.000 C94 "
"0:*-59-65-* Def\n"
"0 0 59 78 0 0.000 3.600 0.000 E94 "
"0:*-59-78-* Def\n"
"0 0 59 80 0 0.000 3.600 0.000 E94 "
"0:*-59-80-* Def\n"
"0 0 59 82 0 0.000 3.600 0.000 E94 "
"0:*-59-82-* Def\n"
"0 0 62 63 0 0.000 3.600 0.000 E94 "
"0:*-62-63-* Def\n"
"0 0 62 64 0 0.000 3.600 0.000 E94 "
"0:*-62-64-* Def\n"
"1 0 63 63 0 0.000 1.800 0.000 E94 "
"1:*-63-63-* Def\n"
"0 0 63 64 0 0.000 7.000 0.000 C94 "
"0:*-63-64-* Def\n"
"0 5 63 64 5 0.000 7.000 0.000 C94\n"
"0 5 63 64 64 0.000 7.000 0.000 C94\n"
"0 39 63 64 5 0.000 7.000 0.000 C94\n"
"0 39 63 64 64 0.000 7.000 0.000 C94\n"
"0 0 63 66 0 0.000 7.000 0.000 C94 "
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"0 0 63 78 0 0.000 6.000 0.000 E94 "
"0:*-63-78-* Def\n"
"0 0 63 81 0 0.000 6.000 0.000 E94 "
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"0 0 64 64 0 0.000 7.000 0.000 C94 "
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"1 0 64 64 0 0.000 1.800 0.000 E94 "
"1:*-64-64-* Def\n"
"0 5 64 64 5 0.000 7.000 0.000 C94\n"
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"0:*-64-81-* Def\n"
"5 0 64 81 0 0.000 6.000 0.000 E94 "
"5:*-64-81-* Def\n"
"0 0 64 82 0 0.000 6.000 0.000 E94 "
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"0:*-65-81-* Def\n"
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"0:*-67-67-* Def\n"
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"5:*-67-67-* Def\n"
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"0:*-76-76-* Def\n"
"0 0 76 78 0 0.000 3.600 0.000 E94 "
"0:*-76-78-* Def\n"
"0 0 78 78 0 0.000 7.000 0.000 C94 "
"0:*-78-78-* Def\n"
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"0:*-78-79-* Def\n"
"0 0 78 81 0 0.000 4.000 0.000 C94 "
"0:*-78-81-* Def\n"
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"0:*-79-79-* Def\n"
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"0:*-79-81-* Def\n"
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"0:*-80-81-* Def\n";
class MMFFVdWCollection *MMFFVdWCollection::ds_instance = NULL;
extern const std::string defaultMMFFVdW;
MMFFVdWCollection *MMFFVdWCollection::getMMFFVdW(const std::string &mmffVdW) {
if (!ds_instance) {
ds_instance = new MMFFVdWCollection(mmffVdW);
} else if (mmffVdW != "") {
delete ds_instance;
ds_instance = new MMFFVdWCollection(mmffVdW);
}
return ds_instance;
}
MMFFVdWCollection::MMFFVdWCollection(std::string mmffVdW) {
if (mmffVdW == "") {
mmffVdW = defaultMMFFVdW;
}
std::istringstream inStream(mmffVdW);
bool firstLine = true;
std::string inLine = RDKit::getLine(inStream);
while (!(inStream.eof())) {
if (inLine[0] != '*') {
boost::char_separator<char> tabSep("\t");
tokenizer tokens(inLine, tabSep);
tokenizer::iterator token = tokens.begin();
if (firstLine) {
firstLine = false;
this->power = boost::lexical_cast<double>(*token);
++token;
this->B = boost::lexical_cast<double>(*token);
++token;
this->Beta = boost::lexical_cast<double>(*token);
++token;
this->DARAD = boost::lexical_cast<double>(*token);
++token;
this->DAEPS = boost::lexical_cast<double>(*token);
++token;
} else {
MMFFVdW mmffVdWObj;
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
unsigned int atomType = boost::lexical_cast<unsigned int>(*token);
#else
d_atomType.push_back(
(boost::uint8_t)(boost::lexical_cast<unsigned int>(*token)));
#endif
++token;
mmffVdWObj.alpha_i = boost::lexical_cast<double>(*token);
++token;
mmffVdWObj.N_i = boost::lexical_cast<double>(*token);
++token;
mmffVdWObj.A_i = boost::lexical_cast<double>(*token);
++token;
mmffVdWObj.G_i = boost::lexical_cast<double>(*token);
++token;
mmffVdWObj.DA = (boost::lexical_cast<std::string>(*token)).at(0);
++token;
mmffVdWObj.R_star =
mmffVdWObj.A_i * pow(mmffVdWObj.alpha_i, this->power);
#ifdef RDKIT_MMFF_PARAMS_USE_STD_MAP
d_params[atomType] = mmffVdWObj;
#else
d_params.push_back(mmffVdWObj);
#endif
}
}
inLine = RDKit::getLine(inStream);
}
}
const std::string defaultMMFFVdW =
"*\n"
"* Copyright (c) Merck and Co., Inc., 1994, 1995, 1996\n"
"* All Rights Reserved\n"
"*\n"
"* E94 - From empirical rule (JACS 1992, 114, 7827) \n"
"* C94 - Adjusted in fit to HF/6-31G* dimer energies and geometries\n"
"* X94 - Chosen in the extension of the paratererization for MMFF \n"
"* by analogy to other, similar atom types or, for ions, by\n"
"* fitting to atomic radii (and sometimes to association energies\n"
"* for hydrates)\n"
"*\n"
"* power B Beta DARAD DAEPS\n"
"0.25 0.2 12. 0.8 0.5\n"
"*\n"
"* type alpha-i N-i A-i G-i DA Symb Origin\n"
"*------------------------------------------------------------\n"
"1 1.050 2.490 3.890 1.282 - CR E94\n"
"2 1.350 2.490 3.890 1.282 - C=C E94\n"
"3 1.100 2.490 3.890 1.282 - C=O E94\n"
"4 1.300 2.490 3.890 1.282 - CSP E94\n"
"5 0.250 0.800 4.200 1.209 - HC C94\n"
"6 0.70 3.150 3.890 1.282 A OR C94\n"
"7 0.65 3.150 3.890 1.282 A O=C C94\n"
"8 1.15 2.820 3.890 1.282 A NR C94\n"
"9 0.90 2.820 3.890 1.282 A N=C C94\n"
"10 1.000 2.820 3.890 1.282 A NC=O E94\n"
"11 0.35 3.480 3.890 1.282 A F C94\n"
"12 2.300 5.100 3.320 1.345 A CL E94\n"
"13 3.400 6.000 3.190 1.359 A BR E94\n"
"14 5.500 6.950 3.080 1.404 A I E94\n"
"15 3.00 4.800 3.320 1.345 A S C94\n"
"16 3.900 4.800 3.320 1.345 A S=C E94\n"
"17 2.700 4.800 3.320 1.345 - SO E94\n"
"18 2.100 4.800 3.320 1.345 - SO2 E94\n"
"19 4.500 4.200 3.320 1.345 - SI E94\n"
"20 1.050 2.490 3.890 1.282 - CR3R E94\n"
"21 0.150 0.800 4.200 1.209 D HOR C94\n"
"22 1.100 2.490 3.890 1.282 - CR3R E94\n"
"23 0.150 0.800 4.200 1.209 D HNR C94\n"
"24 0.150 0.800 4.200 1.209 D HOCO C94\n"
"25 1.600 4.500 3.320 1.345 - PO4 E94\n"
"26 3.600 4.500 3.320 1.345 A P E94\n"
"27 0.150 0.800 4.200 1.209 D HN=C C94\n"
"28 0.150 0.800 4.200 1.209 D HNCO C94\n"
"29 0.150 0.800 4.200 1.209 D HOCC C94\n"
"30 1.350 2.490 3.890 1.282 - CE4R E94\n"
"31 0.150 0.800 4.200 1.209 D HOH C94\n"
"32 0.75 3.150 3.890 1.282 A O2CM C94\n"
"33 0.150 0.800 4.200 1.209 D HOS C94\n"
"34 1.00 2.820 3.890 1.282 - NR+ C94\n"
"35 1.50 3.150 3.890 1.282 A OM X94\n"
"36 0.150 0.800 4.200 1.209 D HNR+ C94\n"
"37 1.350 2.490 3.890 1.282 - CB E94\n"
"38 0.85 2.820 3.890 1.282 A NPYD C94\n"
"39 1.10 2.820 3.890 1.282 - NPYL C94\n"
"40 1.00 2.820 3.890 1.282 A NC=C E94\n"
"41 1.100 2.490 3.890 1.282 - CO2M C94\n"
"42 1.000 2.820 3.890 1.282 A NSP E94\n"
"43 1.000 2.820 3.890 1.282 A NSO2 E94\n"
"44 3.00 4.800 3.320 1.345 A STHI C94\n"
"45 1.150 2.820 3.890 1.282 - NO2 E94\n"
"46 1.300 2.820 3.890 1.282 - N=O E94\n"
"47 1.000 2.820 3.890 1.282 A NAZT X94\n"
"48 1.200 2.820 3.890 1.282 A NSO X94\n"
"49 1.00 3.150 3.890 1.282 - O+ X94\n"
"50 0.150 0.800 4.200 1.209 D HO+ C94\n"
"51 0.400 3.150 3.890 1.282 - O=+ E94\n"
"52 0.150 0.800 4.200 1.209 D HO=+ C94\n"
"53 1.000 2.820 3.890 1.282 - =N= X94\n"
"54 1.30 2.820 3.890 1.282 - N+=C C94\n"
"55 0.80 2.820 3.890 1.282 - NCN+ E94\n"
"56 0.80 2.820 3.890 1.282 - NGD+ E94\n"
"57 1.000 2.490 3.890 1.282 - CNN+ E94\n"
"58 0.80 2.820 3.890 1.282 - NPD+ E94\n"
"59 0.65 3.150 3.890 1.282 A OFUR C94\n"
"60 1.800 2.490 3.890 1.282 A C%- E94\n"
"61 0.800 2.820 3.890 1.282 A NR% E94\n"
"62 1.300 2.820 3.890 1.282 A NM X94\n"
"63 1.350 2.490 3.890 1.282 - C5A E94\n"
"64 1.350 2.490 3.890 1.282 - C5B E94\n"
"65 1.000 2.820 3.890 1.282 A N5A E94\n"
"66 0.75 2.820 3.890 1.282 A N5B C94\n"
"67 0.950 2.82 3.890 1.282 A N2OX X94\n"
"68 0.90 2.82 3.890 1.282 A N3OX C94\n"
"69 0.950 2.82 3.890 1.282 A NPOX C94\n"
"70 0.87 3.150 3.890 1.282 A OH2 C94\n"
"71 0.150 0.800 4.200 1.209 D HS C94\n"
"72 4.000 4.800 3.320 1.345 A SM X94\n"
"73 3.000 4.800 3.320 1.345 - SMO2 X94\n"
"74 3.000 4.800 3.320 1.345 - =S=O X94\n"
"75 4.000 4.500 3.320 1.345 A -P=C X94\n"
"76 1.200 2.820 3.890 1.282 A N5M X94\n"
"77 1.500 5.100 3.320 1.345 A CLO4 X94\n"
"78 1.350 2.490 3.890 1.282 - C5 X94\n"
"79 1.000 2.820 3.890 1.282 A N5 X94\n"
"80 1.000 2.490 3.890 1.282 - CIM+ C94\n"
"81 0.80 2.820 3.890 1.282 - NIM+ C94\n"
"82 0.950 2.82 3.890 1.282 A N5OX X94\n"
"87 0.45 6.0 4.0 1.4 - FE+2 X94\n"
"88 0.55 6.0 4.0 1.4 - FE+3 X94\n"
"89 1.4 3.48 3.890 1.282 A F- X94\n"
"90 4.5 5.100 3.320 1.345 A CL- X94\n"
"91 6.0 6.000 3.190 1.359 A BR- X94\n"
"92 0.15 2.0 4.0 1.3 - LI+ X94\n"
"93 0.4 3.5 4.0 1.3 - NA+ X94\n"
"94 1.0 5.0 4.0 1.3 - K+ X94\n"
"95 0.43 6.0 4.0 1.4 - ZN+2 X94\n"
"96 0.9 5.0 4.0 1.4 - CA+2 X94\n"
"97 0.35 6.0 4.0 1.4 - CU+1 X94\n"
"98 0.40 6.0 4.0 1.4 - CU+2 X94\n"
"99 0.35 3.5 4.0 1.3 - MG+2 X94\n";
} // end of namespace MMFF
} // end of namespace ForceFields
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