| 1 |
gezelter |
1711 |
#include "UseTheForce/ForceField.hpp" |
| 2 |
|
|
|
| 3 |
|
|
AtomType* ForceField::getMatchingAtomType(const string &at) { |
| 4 |
|
|
|
| 5 |
|
|
map<string, AtomType*>::iterator iter; |
| 6 |
|
|
|
| 7 |
|
|
iter = atomTypeMap.find(at); |
| 8 |
|
|
if (iter != atomTypeMap.end()) { |
| 9 |
|
|
return iter->second; |
| 10 |
|
|
} else { |
| 11 |
|
|
return NULL; |
| 12 |
|
|
} |
| 13 |
|
|
} |
| 14 |
|
|
|
| 15 |
|
|
BondType* ForceField::getMatchingBondType(const string &at1, |
| 16 |
|
|
const string &at2) { |
| 17 |
|
|
|
| 18 |
|
|
map<pair<string,string>, BondType*>::iterator iter; |
| 19 |
|
|
vector<BondType*> foundTypes; |
| 20 |
|
|
|
| 21 |
|
|
iter = bondTypeMap.find(pair<at1, at2>); |
| 22 |
|
|
if (iter != bondTypeMap.end()) { |
| 23 |
|
|
// exact match, so just return it |
| 24 |
|
|
return iter->second; |
| 25 |
|
|
} |
| 26 |
|
|
|
| 27 |
|
|
iter = bondTypeMap.find(pair<at2, at1>); |
| 28 |
|
|
if (iter != bondTypeMap.end()) { |
| 29 |
|
|
// exact match in reverse order, so just return it |
| 30 |
|
|
return iter->second; |
| 31 |
|
|
} |
| 32 |
|
|
|
| 33 |
|
|
iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>); |
| 34 |
|
|
if (iter != bondTypeMap.end()) { |
| 35 |
|
|
foundTypes.push_back(iter->second); |
| 36 |
|
|
} |
| 37 |
|
|
|
| 38 |
|
|
iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>); |
| 39 |
|
|
if (iter != bondTypeMap.end()) { |
| 40 |
|
|
foundTypes.push_back(iter->second); |
| 41 |
|
|
} |
| 42 |
|
|
|
| 43 |
|
|
iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>); |
| 44 |
|
|
if (iter != bondTypeMap.end()) { |
| 45 |
|
|
foundTypes.push_back(iter->second); |
| 46 |
|
|
} |
| 47 |
|
|
|
| 48 |
|
|
iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>); |
| 49 |
|
|
if (iter != bondTypeMap.end()) { |
| 50 |
|
|
foundTypes.push_back(iter->second); |
| 51 |
|
|
} |
| 52 |
|
|
|
| 53 |
|
|
if (foundTypes.empty()) { |
| 54 |
|
|
return NULL; |
| 55 |
|
|
} else { |
| 56 |
|
|
|
| 57 |
|
|
|
| 58 |
|
|
|
| 59 |
|
|
|
| 60 |
|
|
|
| 61 |
|
|
|
| 62 |
|
|
|
| 63 |
|
|
|
| 64 |
|
|
|
| 65 |
|
|
BendType* ForceField::getMatchingBendType(const string &at1, const string &at2, |
| 66 |
|
|
const string &at3); |
| 67 |
|
|
TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2, |
| 68 |
|
|
const string &at3, const string &at4); |
| 69 |
|
|
|
| 70 |
|
|
double ForceField::getRcutForAtomType(AtomType* at); |
| 71 |
|
|
|
| 72 |
|
|
|
| 73 |
|
|
vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) { |
| 74 |
|
|
|
| 75 |
|
|
vector<vector<string> > results; |
| 76 |
|
|
|
| 77 |
|
|
|
| 78 |
|
|
|
| 79 |
|
|
|
| 80 |
|
|
vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) { |
| 81 |
|
|
|
| 82 |
|
|
int nStrings; |
| 83 |
|
|
vector<string> oneResult; |
| 84 |
|
|
vector<vector<string> > allResults; |
| 85 |
|
|
|
| 86 |
|
|
nStrings = myAts.size(); |
| 87 |
|
|
|
| 88 |
|
|
if (nStrings == 1) { |
| 89 |
|
|
oneResult.push_back(wildcardCharacter); |
| 90 |
|
|
allResults.push_back(oneResult); |
| 91 |
|
|
return allResults; |
| 92 |
|
|
} else { |
| 93 |
|
|
|
| 94 |
|
|
for (i=0; i < nStrings; i++) { |
| 95 |
|
|
oneResult = myAts; |
| 96 |
|
|
replace(oneResult.begin(), oneResult.end(), |
