1 |
tim |
77 |
/********************************************************************** |
2 |
|
|
* Copyright (C) 2002-2003 by Gezelter's Group
|
3 |
|
|
*This program is free software; you can redistribute it and/or modify
|
4 |
|
|
*it under the terms of the GNU General Public License as published by
|
5 |
|
|
*the Free Software Foundation version 2 of the License.
|
6 |
|
|
*
|
7 |
|
|
*This program is distributed in the hope that it will be useful,
|
8 |
|
|
*but WITHOUT ANY WARRANTY; without even the implied warranty of
|
9 |
|
|
*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
10 |
|
|
*GNU General Public License for more details.
|
11 |
|
|
*
|
12 |
|
|
************************************************************************ |
13 |
|
|
*Author: Teng Lin Email: tlin@nd.edu |
14 |
|
|
*Date: 08/13/2002 Version: 1.0 |
15 |
|
|
* |
16 |
|
|
************************************************************************ |
17 |
|
|
*Description: |
18 |
|
|
* |
19 |
|
|
***********************************************************************/ |
20 |
tim |
66 |
#include <iostream> |
21 |
|
|
#include <vector> |
22 |
|
|
#include "fasatom.h" |
23 |
|
|
|
24 |
|
|
using namespace std; |
25 |
|
|
|
26 |
|
|
void TFASAtom::Clear() |
27 |
|
|
{ |
28 |
|
|
_index = 0; |
29 |
|
|
_atomicNum = 0; |
30 |
|
|
_nameIndex = 0; |
31 |
|
|
_typeIndex = 0; |
32 |
|
|
_resid = 0; |
33 |
|
|
_residIndex = 0; |
34 |
|
|
_resnameIndex = 0; |
35 |
|
|
_chainIndex = 0; |
36 |
|
|
_segnameIndex = 0; |
37 |
|
|
_atomProp = TAtomProp::apNormal; |
38 |
|
|
_mass = 0; |
39 |
|
|
_charge = 0; |
40 |
|
|
_covRadius = 0; |
41 |
|
|
_vdwRadius = 0; |
42 |
|
|
_maxBonds = 0; |
43 |
|
|
_pcharge = 0; |
44 |
|
|
_hyb = 0; |
45 |
|
|
_impval = 0; |
46 |
|
|
_pseudo = false; |
47 |
|
|
_residue = NULL; |
48 |
|
|
_mol = NULL; |
49 |
|
|
_model = NULL; |
50 |
|
|
_bondList.clear(); |
51 |
|
|
|
52 |
|
|
} |
53 |
|
|
|
54 |
|
|
TFASAtom::TFASAtom(int index) |
55 |
|
|
{ |
56 |
|
|
Clear(); |
57 |
|
|
_index = index; |
58 |
|
|
} |
59 |
|
|
|
60 |
|
|
TFASAtom::~TFASAtom() |
61 |
|
|
{ |
62 |
|
|
|
63 |
|
|
} |
64 |
|
|
|
65 |
|
|
unsigned int TFASAtom::GetHvyValence() |
66 |
|
|
{ |
67 |
|
|
unsigned int count; |
68 |
|
|
vector<TFASBond *>::iterator i; |
69 |
|
|
TFASAtom *atom; |
70 |
|
|
count=0; |
71 |
|
|
|
72 |
|
|
for(atom = BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i)) |
73 |
|
|
if(!atom->IsHydrogen()) count++; |
74 |
|
|
|
75 |
|
|
return count; |
76 |
|
|
} |
77 |
|
|
|
78 |
|
|
void TFASAtom::AddBond(TFASBond * bond) |
79 |
|
|
{ |
80 |
|
|
if (bond==NULL) |
81 |
|
|
{ |
82 |
|
|
|
83 |
|
|
} |
84 |
|
|
else |
85 |
|
|
{ |
86 |
|
|
_bondList.push_back(bond); |
87 |
|
|
} |
88 |
|
|
} |
89 |
|
|
|
90 |
|
|
void TFASAtom::DeleteBond(TFASBond *bond) |
91 |
|
|
{ |
92 |
|
|
vector<TFASBond *>::iterator i; |
93 |
|
|
i = find(_bondList.begin(), _bondList.end(), bond); |
94 |
|
|
if (i != _bondList.end()) |
95 |
|
|
{ |
96 |
|
|
_bondList.erase(i); |
97 |
|
|
} |
98 |
|
|
else |
99 |
|
|
{ |
100 |
|
|
|
101 |
|
|
} |
102 |
|
|
} |
103 |
|
|
|
104 |
|
|
TFASBond * TFASAtom::GetBond(TFASAtom *nbrAtom) |
105 |
|
|
{ |
106 |
|
|
TFASBond *bond; |
107 |
|
|
vector<TFASBond *>::iterator i; |
108 |
|
|
if(nbrAtom == NULL) |
109 |
|
|
{ |
110 |
|
|
|
111 |
|
|
} |
112 |
|
|
else |
113 |
|
|
{ |
114 |
|
|
|
115 |
|
|
for(bond = BeginBond(i); bond != NULL; bond = NextBond(i)) |
116 |
|
|
{ |
117 |
|
|
if (bond->GetNbrAtom(this) == nbrAtom) return bond; |
118 |
|
|
} |
119 |
|
|
return NULL; |
120 |
|
|
} |
121 |
|
|
} |
122 |
|
|
|
123 |
|
|
TFASBond * TFASAtom::BeginBond(vector<TFASBond *>::iterator &i) |
124 |
|
|
{ |
125 |
|
|
i = _bondList.begin(); |
126 |
|
|
return (i == _bondList.end()) ? NULL : *i; |
127 |
|
|
} |
128 |
|
|
|
129 |
|
|
TFASBond * TFASAtom::NextBond(vector<TFASBond *>::iterator &i) |
130 |
|
|
{ |
131 |
|
|
i++; |
132 |
|
|
return (i == _bondList.end()) ? NULL : *i; |
133 |
|
|
} |
134 |
|
|
|
135 |
|
|
TFASAtom * TFASAtom::BeginNbrAtom(vector<TFASBond *>::iterator &i) |
136 |
|
|
{ |
137 |
|
|
TFASBond * bond = BeginBond(i); |
138 |
|
|
|
139 |
|
|
if(bond != NULL) |
140 |
|
|
{ |
141 |
|
|
return bond->GetNbrAtom(this); |
142 |
|
|
} |
143 |
|
|
else |
144 |
|
|
{ |
145 |
|
|
|
146 |
|
|
} |
147 |
|
|
} |
148 |
|
|
|
149 |
|
|
TFASAtom * TFASAtom::NextNbrAtom(vector<TFASBond *>::iterator &i) |
150 |
|
|
{ |
151 |
|
|
TFASBond * bond = NextBond(i); |
152 |
|
|
|
153 |
|
|
if(bond != NULL) |
154 |
|
|
{ |
155 |
|
|
return bond->GetNbrAtom(this); |
156 |
|
|
} |
157 |
|
|
else |
158 |
|
|
{ |
159 |
|
|
|
160 |
|
|
} |
161 |
|
|
} |
162 |
|
|
|
163 |
|
|
bool TFASAtom::IsConnected(TFASAtom *atom) |
164 |
|
|
{ |
165 |
|
|
vector<TFASBond *>::iterator i; |
166 |
|
|
TFASAtom *nbrAtom; |
167 |
|
|
|
168 |
|
|
for(nbrAtom = BeginNbrAtom(i); nbrAtom != NULL; nbrAtom = NextNbrAtom(i)) |
169 |
|
|
{ |
170 |
|
|
if (atom == nbrAtom) |
171 |
|
|
{ |
172 |
|
|
return true; |
173 |
|
|
} |
174 |
|
|
} |
175 |
|
|
|
176 |
|
|
return false; |
177 |
|
|
} |
178 |
|
|
|
179 |
|
|
bool TFASAtom::IsOneThree(TFASAtom *atom) |
180 |
|
|
{ |
181 |
|
|
TFASAtom *thisNbr; |
182 |
|
|
TFASAtom *atomNbr; |
183 |
|
|
vector<TFASBond *>::iterator i; |
184 |
|
|
vector<TFASBond *>::iterator j; |
185 |
|
|
|
186 |
|
|
for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i)) |
187 |
|
|
for(atomNbr = atom->BeginNbrAtom(j); thisNbr != NULL; atomNbr = atom->NextNbrAtom(j)) |
188 |
|
|
if (atomNbr == thisNbr) return true; |
189 |
|
|
|
190 |
|
|
return false; |
191 |
|
|
|
192 |
|
|
} |
193 |
|
|
|
194 |
|
|
bool TFASAtom::IsOneFour(TFASAtom *atom) |
195 |
|
|
{ |
196 |
|
|
TFASAtom *thisNbr; |
197 |
|
|
TFASAtom *atomNbr; |
198 |
|
|
vector<TFASBond *>::iterator i; |
199 |
|
|
vector<TFASBond *>::iterator j; |
200 |
|
|
|
201 |
|
|
for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i)) |
202 |
|
|
for(atomNbr = atom->BeginNbrAtom(j); atomNbr != NULL; atomNbr = atom->NextNbrAtom(j)) |
203 |
|
|
if (thisNbr->IsConnected(atomNbr)) return true; |
204 |
|
|
|
205 |
|
|
return false; |
206 |
|
|
|
207 |
|
|
} |
208 |
|
|
|
209 |
|
|
bool TFASAtom::IsCarboxylOxygen() |
210 |
|
|
{ |
211 |
|
|
if (!IsOxygen()) return false; |
212 |
|
|
if (GetHvyValence() != 1) return false; |
213 |
|
|
|
214 |
|
|
TFASAtom *atom; |
215 |
|
|
vector<TFASBond *>::iterator i; |
216 |
|
|
|
217 |
|
|
for(atom=BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i)) |
218 |
|
|
if (atom->IsCarbon()) break; |
219 |
|
|
|
220 |
|
|
if (atom == NULL) return false; |
221 |
|
|
|
222 |
|
|
|
223 |
|
|
} |
224 |
|
|
|
225 |
|
|
bool TFASAtom::IsPhosphateOxygen() |
226 |
|
|
{ |
227 |
|
|
|
228 |
|
|
} |
229 |
|
|
|
230 |
|
|
bool TFASAtom::IsSulfateOxygen() |
231 |
|
|
{ |
232 |
|
|
|
233 |
|
|
} |
234 |
|
|
|
235 |
|
|
bool TFASAtom::IsNitroOxygen() |
236 |
|
|
{ |
237 |
|
|
|
238 |
|
|
} |
239 |
|
|
|
240 |
|
|
bool TFASAtom::IsAmideNitrogen() |
241 |
|
|
{ |
242 |
|
|
|
243 |
|
|
} |
244 |
|
|
|
245 |
|
|
bool TFASAtom::IsPolarHydrogen() |
246 |
|
|
{ |
247 |
|
|
|
248 |
|
|
} |
249 |
|
|
|
250 |
|
|
bool TFASAtom::IsNonPolarHydrogen() |
251 |
|
|
{ |
252 |
|
|
|
253 |
|
|
} |
254 |
|
|
|
255 |
|
|
bool TFASAtom::IsInRing() |
256 |
|
|
{ |
257 |
|
|
|
258 |
|
|
} |
259 |
|
|
|
260 |
|
|
bool TFASAtom::IsInRingSize(int ringSize) |
261 |
|
|
{ |
262 |
|
|
|
263 |
|
|
} |
264 |
|
|
|
265 |
|
|
bool TFASAtom::IsAromatic() |
266 |
|
|
{ |
267 |
|
|
|
268 |
|
|
} |
269 |
|
|
|
270 |
|
|
bool TFASAtom::IsAromaticNOxide() |
271 |
|
|
{ |
272 |
|
|
|
273 |
|
|
} |
274 |
|
|
|
275 |
|
|
bool TFASAtom::IsChiral() |
276 |
|
|
{ |
277 |
|
|
|
278 |
|
|
} |
279 |
|
|
|
280 |
|
|
bool TFASAtom::IsAxial() |
281 |
|
|
{ |
282 |
|
|
|
283 |
|
|
} |
284 |
|
|
|
285 |
tim |
77 |
bool TFASAtom::HasAlphaBetaUnsat(bool includePandS) |
286 |
tim |
66 |
{ |
287 |
|
|
|
288 |
|
|
} |
289 |
|
|
|
290 |
|
|
bool TFASAtom::HasBondOfOrder(int order) |
291 |
|
|
{ |
292 |
|
|
|
293 |
|
|
} |
294 |
|
|
|
295 |
|
|
int TFASAtom::CountBondsOfOrder(int order) |
296 |
|
|
{ |
297 |
|
|
|
298 |
|
|
} |
299 |
|
|
|