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root/freemol/trunk/src/mengine/src/type_mmx.c

#	Line 37 | Line 37
37		int nnit,nnh,nc,no,nox,nitatom;
38		int ktype,jtype, jjik;
39		int  adjn, nplus, adjn1, noxide, icurr;
40	<	int mmxtype,mm3type,mmfftype,ambertype,oplstype, ia, ib, ia1, ib1;
40	>	int mmxtype,mm3type,mmfftype, ia, ib, ia1, ib1;
41		int ndouble, ntriple;
42		int icycl3, icycl4, icycl5, icycl6;
43		int full_ring, non_pi;
#	Line 70 | Line 70
70		mmxtype = atom[i].mmx_type;
71		mm3type = atom[i].mm3_type;
72		mmfftype = atom[i].mmff_type;
73	–	ambertype = atom[i].amber_type;
74	–	oplstype = atom[i].opls_type;
73		if (atom[i].atomnum != 0 && !(atom[i].flags & type_mask) )
74		{
75		if (mmxtype == 100 || mmxtype == 101 || mmxtype == 102 || mmxtype == 103 ) // user defined type
#	Line 86 | Line 84
84		mmxtype = 60;
85		mm3type = 200;
86		mmfftype = 5;
89	–	ambertype = 33;
90	–	oplstype = 29;
87		goto L_10;
88		}
89		if (atom[i].mmx_type == 45)  // TS H
#	Line 95 | Line 91
91		mmxtype = 45;
92		mm3type = 0;
93		mmfftype = 0;
98	–	ambertype = 33;
94		goto L_10;
95		}
96		if (atom[i].mmx_type == 36) // Deuterium
#	Line 103 | Line 98
98		mmxtype = 36;
99		mm3type = 36;
100		mmfftype = 5;
106	–	ambertype = 33;
101		goto L_10;
102		}
103		jji = 0;
#	Line 122 | Line 116
116		mmxtype = 5;
117		mm3type = 5;
118		mmfftype = 5;
125	–	ambertype = 34;
126	–	oplstype = 29;
119		jatm = atom[i].iat[0];
120		for (j=0; j < 3; j++)   // Acetylene
121		{
122		if (atom[jatm].bo[j] == 3)
123		{
124		mm3type = 124;
133	–	oplstype = 33;
125		goto L_10;
126		}
127		}
137	–	for (j=0; j < MAXIAT; j++)  // ammonium
138	–	{
139	–	if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].atomnum == 7)
140	–	{
141	–	jjik = 0;
142	–	katm = atom[jatm].iat[j];
143	–	for (k=0; k < MAXIAT; k++)
144	–	{
145	–	if (atom[katm].iat[j] != 0)
146	–	jjik++;
147	–	}
148	–	if (jjik == 4) // H-C-N+
149	–	{
150	–	ambertype = 38;
151	–	goto L_10;
152	–	}
153	–	}
154	–	}
155	–	for (j=0; j < MAXIAT; j++)
156	–	{
157	–	if (atom[jatm].bo[j] == 2 && !(atom[jatm].flags && aromatic_mask) )
158	–	{
159	–	if (atom[atom[jatm].iat[j]].atomnum == 6)
160	–	oplstype = 30;
161	–	else if (atom[atom[jatm].iat[j]].atomnum == 7)
162	–	oplstype = 31;
163	–	goto L_10;
164	–	}
165	–	if (atom[jatm].bo[j] == 2 && atom[atom[jatm].iat[j]].atomnum == 8 )
166	–	{
167	–	oplstype = 32;
168	–	goto L_10;
169	–	}
170	–	}
171	–	jji = 0;
172	–	nnit = 0;
173	–	nitatom = 0;
174	–	for (j=0; j < MAXIAT; j++)
175	–	{
176	–	if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20)
177	–	jji++;
178	–	if (atom[atom[jatm].iat[j]].atomnum == 7 || atom[atom[jatm].iat[j]].atomnum == 8 ||
179	–	atom[atom[jatm].iat[j]].atomnum == 16)
180	–	{
181	–	nnit++;
182	–	nitatom = atom[jatm].iat[j];
183	–	}
184	–	}
185	–	if ( jji == 3 && nnit == 2)
186	–	{
187	–	ambertype = 40; // H5
188	–	oplstype = 43;
189	–	} else if ( jji == 4 && nnit == 2)
190	–	{
191	–	ambertype = 36; // H2
192	–	oplstype = 29;
193	–	} else if ( jji == 3 && nnit == 1)
194	–	{
195	–	ambertype = 39; // H4
196	–	oplstype = 42;
197	–	jjk = 0;
198	–	for (j=0; j < MAXIAT; j++)
199	–	{
200	–	if (atom[nitatom].iat[j] != 0 && atom[atom[nitatom].iat[j]].mmx_type != 20)
201	–	jjk++;
202	–	}
203	–	if (jjk == 2)
204	–	oplstype = 34;
205	–	}else if ( jji == 4 && nnit == 1)
206	–	{
207	–	ambertype = 35; // H1
208	–	oplstype = 29;
209	–	}else if ( jji == 3 && nnit == 0)
210	–	{
211	–	ambertype = 33; // HA
212	–	oplstype = 34;
213	–	}else if ( jji == 4 && nnit == 0)
214	–	{
215	–	ambertype = 34; // HC
216	–	oplstype = 29;
217	–	}else if ( jji == 4 && nnit == 3)
218	–	{
219	–	ambertype = 37; // H3
220	–	oplstype = 29;
221	–	}
128		goto L_10;
129		} else if (atom[atom[i].iat[0]].atomnum == 7)  // nitrogen
130		{
#	Line 230 | Line 136
136		mmxtype = 23;
137		mm3type = 23;
138		mmfftype = 23;
233	–	ambertype = 29;
234	–	oplstype = 38;
139		for (j=0; j < MAXIAT; j++)
140		{
141		if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].mmx_type != 20 )
#	Line 263 | Line 167
167		mm3type = 23;
168		}
169		mmfftype = 36;
266	–	oplstype = 40;
170		if (noxide == TRUE)
171		mmfftype = 23;
172		goto L_10;
#	Line 273 | Line 176
176		mmxtype = 23;
177		mm3type = 23;
178		mmfftype = 23;
276	–	oplstype = 38;
179		if (is_cyclo5(jatm,array) )
180		{
181		jjk = 0;
#	Line 365 | Line 267
267		mmxtype = 23;
268		mm3type = 28;
269		mmfftype = 28;
368	–	oplstype = 39;
270		goto L_10;
271		} else if (atom[atom[katm].iat[k]].atomnum == 6 || atom[atom[katm].iat[k]].atomnum == 7)
272		{
#	Line 394 | Line 295
295		mmxtype = 21;
296		mm3type = 21;
297		mmfftype = 21;
397	–	ambertype = 31;
398	–	oplstype = 36;
298		jatm = atom[i].iat[0];
299		if (atom[jatm].iat[0] != i)
300		katm = atom[jatm].iat[0];
#	Line 412 | Line 311
311		mmxtype = 21;
312		mm3type = 21;
313		mmfftype = 31;
415	–	ambertype = 30;
416	–	oplstype = 41;
314		goto L_10;
315		} else if (atom[katm].atomnum == 1 && jji == 3) // h3o+
316		{
317		mmxtype = 24;
318		mm3type = 21;
319		mmfftype = 50;
423	–	ambertype = 31;
424	–	oplstype = 36;
320		goto L_10;
321		}
322		if (atom[katm].atomnum == 15) // h-o-p
#	Line 429 | Line 324
324		mmxtype = 24;
325		mm3type = 24;
326		mmfftype = 24;
432	–	ambertype = 31;
433	–	oplstype = 36;
327		goto L_10;
328		}
329		if (atom[katm].atomnum == 16) // h-o-s
#	Line 438 | Line 331
331		mmxtype = 24;
332		mm3type = 24;
333		mmfftype = 33;
441	–	ambertype = 31;
442	–	oplstype = 36;
334		goto L_10;
335		}
336		jji = 0;
#	Line 453 | Line 344
344		mmxtype = 24;
345		mm3type = 21;
346		mmfftype = 50;
456	–	ambertype = 31;
347		goto L_10;
348		}
349		for (j=0; j < MAXIAT; j++)
#	Line 465 | Line 355
355		mmxtype = 24;
356		mm3type = 24;
357		mmfftype = 24;
468	–	ambertype = 31;
358		goto L_10;
359		}
360		}
#	Line 477 | Line 366
366		mmxtype = 28;
367		mm3type = 73;
368		mmfftype = 29;
480	–	ambertype = 31;
369		goto L_10;
370		}
371		}
#	Line 504 | Line 392
392		mmxtype = 23;
393		mm3type = 5;
394		mmfftype = 71;
507	–	ambertype = 32;
508	–	oplstype = 37;
395		goto L_10;
396		} else if (atom[atom[i].iat[0]].atomnum == 9 || atom[atom[i].iat[0]].atomnum == 17 ||
397		atom[atom[i].iat[0]].atomnum == 35 || atom[atom[i].iat[0]].atomnum == 53) // halogens
#	Line 513 | Line 399
399		mmxtype = 21;
400		mm3type = 5;
401		mmfftype = 71;
516	–	ambertype = 32;
517	–	oplstype = 37;
402		goto L_10;
403		} else if (atom[atom[i].iat[0]].atomnum == 16) // sulfur
404		{
405		mmxtype = 21;
406		mm3type = 5;
407		mmfftype = 71;
524	–	ambertype = 32;
525	–	oplstype = 37;
408		goto L_10;
409		} else if (atom[atom[i].iat[0]].atomnum == 15) // phosphorous
410		{
411		mmxtype = 23;
412		mm3type = 5;
413		mmfftype = 71;
532	–	ambertype = 0;
533	–	oplstype = 36;
414		goto L_10;
415		} else  //  bridging hydrogens
416		{
#	Line 546 | Line 426
426		mmxtype = 5;
427		mm3type = 5;
428		mmfftype = 5;
549	–	ambertype = 31;
429		}
430		goto L_10;
431		}
#	Line 613 | Line 492
492		mmxtype = 29;
493		mm3type = 29;
494		mmfftype = 0;
616	–	ambertype = 0;
617	–	oplstype = 0;
495		goto L_10;
496		} else if (mmxtype == 30) // C cation
497		{
498		mmxtype = 30;
499		mm3type = 30;
500		mmfftype = 0;
624	–	ambertype = 0;
625	–	oplstype = 0;
501		goto L_10;
502		} else if (mmxtype == 48) // C anion
503		{
504		mmxtype = 48;
505		mm3type = 0;
506		mmfftype = 0;
632	–	ambertype = 0;
633	–	oplstype = 0;
507		goto L_10;
508		} else if (mmxtype == 40) // aromatic carbon
509		{
510		mmxtype = 40;
511		mm3type = 50;
512		mmfftype = 37;
640	–	ambertype = 3;
641	–	oplstype = 7;
513		goto L_10;
514		} else if (mmxtype == 49 || mmxtype == 50 || mmxtype == 51 || mmxtype == 52)  // TS atoms
515		{
516		mm3type = 0;
517		mmfftype = 0;
647	–	ambertype = 0;
648	–	oplstype = 0;
518		goto L_10;
519		}
520		//   check rings
#	Line 676 | Line 545
545		mmxtype = 2;
546		mm3type = 2;
547		mmfftype = 78;
679	–	ambertype  = 11;
680	–	oplstype = 11;
548		goto L_10;
549		}
550		//
#	Line 705 | Line 572
572		mm3type = 2;
573		for (ij=0; ij < icycl5; ij++)
574		{
708	–	// do ambertypes first
709	–	nh = 0;
710	–	nnit = 0;
711	–	nnh = 0;
712	–	for (j=0; j < MAXIAT; j++)
713	–	{
714	–	if (atom[atom[i].iat[j]].atomnum == 1)
715	–	nh++;
716	–	else if (atom[atom[i].iat[j]].atomnum == 7)
717	–	{
718	–	nnit++;
719	–	for(k=0; k < MAXIAT; k++)
720	–	{
721	–	if (atom[atom[atom[i].iat[j]].iat[k]].atomnum == 1)
722	–	nnh++;
723	–	}
724	–	}
725	–	}
726	–	if (nh ==1 && nnit == 2 && nnh == 1)
727	–	{
728	–	ambertype = 8;
729	–	oplstype = 15;
730	–	}else if (nh == 1 && nnh == 1)
731	–	{
732	–	ambertype = 7;
733	–	oplstype = 12;
734	–	}else if (nh == 1 && nnit == 1)
735	–	{
736	–	ambertype = 6;
737	–	oplstype = 13;
738	–	}else if (nh == 1 && nnit == 2 && nnh == 0)
739	–	{
740	–	ambertype = 12;
741	–	oplstype = 18;
742	–	} else if (nh == 0 && nnit == 1)
743	–	{
744	–	ambertype = 5;
745	–	oplstype = 12;
746	–	} else if (nh == 0 && nnit == 0)
747	–	{
748	–	ambertype = 10;
749	–	oplstype = 17;
750	–	}
575		// do mmff types
576		get_rsize(i,5,ij,array);
577		if (aromatic_5(ij,array))
#	Line 824 | Line 648
648		}
649		}
650		}
827	–	if (atom[array[ia]].atomnum == 7 && atom[array[ib]].atomnum == 6)  // n=c-c
828	–	{
829	–	oplstype = 23;
830	–	//                              goto L_10;
831	–	} else if (atom[array[ia]].atomnum == 6 && atom[array[ib]].atomnum == 7)  // n=c-c
832	–	{
833	–	oplstype = 23;
834	–	//                             goto L_10;
835	–	}
651		if (nplus == TRUE) // found N+ in ring
652		{
653		noxide = FALSE;
#	Line 958 | Line 773
773		atom[array[ia]].atomnum == 16 || atom[array[ib]].atomnum == 16 )
774		{
775		mmfftype = 63;
961	–	oplstype = 14;
776		goto L_10;
777		}
778		// check beta
#	Line 998 | Line 812
812		atom[array[ia]].atomnum == 16 || atom[array[ib]].atomnum == 16 )
813		{
814		mmfftype = 64;
1001	–	oplstype = 22;
1002	–	nnit = 0;
1003	–	for (j=0; j < 5; j++)
1004	–	{
1005	–	if (atom[array[j]].atomnum != 6)
1006	–	nnit++;
1007	–	}
1008	–	if (nnit > 1)
1009	–	oplstype = 7;
815		goto L_10;
816		}
817		}
#	Line 1036 | Line 841
841		}
842		if (full_ring == FALSE) mmfftype = 2;
843		//
1039	–	ambertype = 3;
1040	–	oplstype = 7;
1041	–	nh = 0;
1042	–	nnit = 0;
1043	–	no = 0;
1044	–	for (j=0; j < MAXIAT; j++)
1045	–	{
1046	–	if (atom[atom[i].iat[j]].atomnum == 1)
1047	–	nh++;
1048	–	else if (atom[atom[i].iat[j]].atomnum == 7)
1049	–	nnit++;
1050	–	else if (atom[atom[i].iat[j]].atomnum == 8)
1051	–	no++;
1052	–	}
1053	–	if (nh ==1 && nnit == 2)
1054	–	{
1055	–	ambertype = 13;
1056	–	oplstype = 19;
1057	–	goto L_10;
1058	–	}
1059	–	if (no == 1)
1060	–	{
1061	–	ambertype = 2; // tyrosine ring
1062	–	oplstype =  7;
1063	–	goto L_10;
1064	–	}
1065	–	if (jji == 3) // aromatic carbon from pdb file
1066	–	{
1067	–	ambertype = 3;
1068	–	oplstype =  7;
1069	–	goto L_10;
1070	–	}
844		}
845		if (icycl3 >= 1 )
846		{
#	Line 1098 | Line 871
871		mmxtype = 4;
872		mm3type = 4;
873		mmfftype = 4;
1101	–	ambertype = 0;
1102	–	oplstype =  24;
874		if (jji == 1 && atom[atom[i].iat[0]].atomnum == 7)
875		{
876		mmfftype = 60;  // isonitrile carbon
1106	–	oplstype =  0;
877		}
878		if ( (atom[atom[i].iat[0]].mmx_type >= 300) &&
879		atom[atom[i].iat[1]].mmx_type == 46)
#	Line 1125 | Line 895
895		goto L_10;
896		}
897		}
1128	–	if (atom[atom[i].iat[0]].atomnum == 1 || atom[atom[i].iat[1]].atomnum == 1)
1129	–	oplstype = 24;
898		goto L_10;
899		}
900		if (ndouble == 2)   // allenes and ketenes
#	Line 1134 | Line 902
902		mmxtype = 4;
903		mm3type = 68;
904		mmfftype = 4;
1137	–	ambertype = 0;
905		for (j=0; j < MAXIAT; j++)  // metal carbene
906		{
907		if ( atom[atom[i].iat[j]].mmx_type >= 300)
#	Line 1160 | Line 927
927		mmxtype = 2;
928		mm3type = 2;
929		mmfftype = 3;
1163	–	oplstype = 10;
930		goto L_10;
931		}
932		if (atom[jatm].atomnum == 16) // c=s
#	Line 1168 | Line 934
934		mmxtype = 2;
935		mm3type = 2;
936		mmfftype = 3;
1171	–	ambertype = 3;
1172	–	oplstype = 10;
937		for (k=0; k < MAXIAT; k++)
938		{
939		if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9)
#	Line 1198 | Line 962
962		mmxtype = 3;
963		mm3type = 3;
964		mmfftype = 3;
1201	–	ambertype = 2;
1202	–	oplstype = 5;
965		if (is_cyclo3(i,array))          // cyclopropanone
966		mm3type = 67;
967		else if (is_cyclo4(i,array))   // cyclobutanone
#	Line 1222 | Line 984
984		if (jjk == 1)
985		{
986		mmfftype = 41;
1225	–	oplstype = 5;
987		break;
988		}
989		}
#	Line 1235 | Line 996
996		mmxtype = 2;
997		mm3type = 2;
998		mmfftype = 3;
1238	–	ambertype = 3;
1239	–	oplstype = 10;
999		if (jji == 3)
1000		{
1001		if (atom[i].iat[0] == jatm)
#	Line 1258 | Line 1017
1017		kbo = 0;
1018		lbo = 0;
1019		adjn = FALSE;
1261	–	oplstype = 8;
1020		for (j=0; j < MAXIAT; j++)
1021		{
1022		if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20)
#	Line 1279 | Line 1037
1037		if (jbo == 4 && kbo == 3 && lbo == 3 && adjn == FALSE)
1038		{
1039		mmfftype = 57;
1282	–	oplstype = 8;
1040		goto L_10;
1041		}
1042		}
#	Line 1302 | Line 1059
1059		if (jbo == 4 && kbo == 3 && adjn == FALSE)
1060		{
1061		mmfftype = 57;
1305	–	oplstype = 8;
1062		goto L_10;
1063		}
1308	–	if (jbo == 3 && kbo == 3 && adjn == FALSE) // cytosine c4
1309	–	{
1310	–	if (atom[latm].atomnum != 7)
1311	–	{
1312	–	oplstype = 9;
1313	–	goto L_10;
1314	–	}
1315	–	}
1064		}
1065		if (atom[jatm].atomnum == 7 && atom[latm].atomnum == 7)
1066		{
#	Line 1333 | Line 1081
1081		if (jbo == 4 && lbo == 3 && adjn == FALSE)
1082		{
1083		mmfftype = 57;
1336	–	oplstype = 8;
1084		goto L_10;
1085		}
1339	–	if (jbo == 3 && lbo == 3 && adjn == FALSE) // cytosine c4
1340	–	{
1341	–	if (atom[katm].atomnum != 7)
1342	–	{
1343	–	oplstype = 9;
1344	–	goto L_10;
1345	–	}
1346	–	}
1086		}
1087		}
1088		goto L_10;
#	Line 1352 | Line 1091
1091		mmxtype = 2;
1092		mm3type = 2;
1093		mmfftype = 2;
1355	–	ambertype = 4;
1356	–	oplstype = 10;
1094		if (is_cyclo3(i,array))    // cyclopropene
1095		{
1096		mm3type = 38;
#	Line 1373 | Line 1110
1110		mmxtype = 2;
1111		mm3type = 2;
1112		mmfftype = 2;
1376	–	ambertype = 4;
1377	–	oplstype = 10;
1113		goto L_10;
1114		}
1115		goto L_10;
#	Line 1383 | Line 1118
1118		mmxtype = 1;
1119		mm3type = 1;
1120		mmfftype = 1;
1386	–	ambertype = 1;
1387	–	oplstype = 1;
1121		if (is_cyclo3(i,array))
1122		{
1123		mmxtype = 22;
1124		mm3type = 22;
1125		mmfftype = 22;
1393	–	oplstype = 28;
1126		goto L_10;
1127		} else if (is_cyclo4(i,array))
1128		{
#	Line 1398 | Line 1130
1130		mm3type = 56;
1131		mmfftype = 20;
1132		goto L_10;
1133	<	} else  // look for adjacent triple bonds for opls
1402	<	{
1403	<	for (j=0; j < MAXIAT; j++)
1404	<	{
1405	<	if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].atomnum == 6)
1406	<	{
1407	<	jatm = atom[i].iat[j];
1408	<	for (k=0; k < MAXIAT; k++)
1409	<	{
1410	<	if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] == 3)
1411	<	{
1412	<	oplstype = 25;
1413	<	nh = 0;
1414	<	for (l = 0; l < MAXIAT; l++)
1415	<	{
1416	<	if (atom[i].iat[l] != 0 && atom[atom[i].iat[l]].atomnum == 1)
1417	<	nh++;
1418	<	}
1419	<	if (nh == 0) oplstype = 27;
1420	<	if (nh == 1) oplstype = 26;
1421	<	if (nh == 2) oplstype = 25;
1422	<	goto L_10;
1423	<	}
1424	<	}
1425	<	}
1426	<	}
1427	<	}
1428	<	// acetal type
1429	<	nh = 0;
1430	<	for (j=0; j < MAXIAT; j++)
1431	<	{
1432	<	if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].atomnum == 8 && atom[i].bo[j] != 2)
1433	<	nh++;
1434	<	}
1435	<	if (nh == 2 || nh == 3)
1436	<	oplstype = 21;
1133	>	}
1134		goto L_10;
1135		} else if (atom[i].atomnum == 7) // nitrogen
1136		{
#	Line 1456 | Line 1153
1153		}
1154		icycl5 = find_rsize(5,i);
1155		icycl6 = find_rsize(6,i);
1459	–	// amber types
1460	–	if (icycl5 >= 1 && nh == 0 && (nc == 2 || nc == 1))
1461	–	{
1462	–	ambertype = 16; // NB
1463	–	oplstype = 59;
1464	–	goto L_1001;
1465	–	}else if (icycl5 >=1 && nh <= 1 && (nc == 2 || nc == 1))
1466	–	{
1467	–	// need to check for proline
1468	–	for (j=0; j < MAXIAT; j++)
1469	–	{
1470	–	if (atom[atom[i].iat[j]].atomnum == 6)
1471	–	{
1472	–	jatm = atom[i].iat[j];
1473	–	for (k=0; k < MAXIAT; k++)
1474	–	{
1475	–	if (atom[atom[jatm].iat[k]].atomnum == 6)
1476	–	{
1477	–	katm = atom[jatm].iat[k];
1478	–	for (l=0; l < MAXIAT; l++)
1479	–	{
1480	–	if (atom[katm].iat[l] != 0 && atom[katm].bo[l] == 2 && atom[atom[katm].iat[l]].atomnum == 8)
1481	–	{
1482	–	ambertype = 14;
1483	–	oplstype = 53;
1484	–	goto L_1001;
1485	–	}
1486	–	}
1487	–	}
1488	–	}
1489	–	}
1490	–	}
1491	–	ambertype = 15; // NA
1492	–	oplstype = 58;
1493	–	goto L_1001;
1494	–	} else if (icycl5 >= 1 && nh == 0 && nc == 3)
1495	–	{
1496	–	for (j=0; j < MAXIAT; j++)
1497	–	{
1498	–	if (atom[atom[i].iat[j]].atomnum == 6)
1499	–	{
1500	–	jatm = atom[i].iat[j];
1501	–	for (k=0; k < MAXIAT; k++)
1502	–	{
1503	–	if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].bo[k] == 2)
1504	–	{
1505	–	ambertype = 14;
1506	–	oplstype = 55;
1507	–	goto L_1001;
1508	–	}
1509	–	}
1510	–	}
1511	–	}
1512	–	ambertype = 18; // N*
1513	–	oplstype = 61;
1514	–	goto L_1001;
1515	–	}
1516	–	if (icycl6 >= 1)
1517	–	{
1518	–	if (nh == 1)
1519	–	{
1520	–	ambertype = 15; // NA
1521	–	oplstype = 58;
1522	–	} else if (nh == 0 && nc == 3)
1523	–	{
1524	–	ambertype = 18; // N*;
1525	–	oplstype = 61;
1526	–	}else if (nh == 0 && nc == 2)
1527	–	{
1528	–	ambertype = 17; // NC
1529	–	oplstype = 60;
1530	–	}
1531	–	goto L_1001;
1532	–	}
1533	–	if (jji == 4)
1534	–	{
1535	–	ambertype = 20; // N3
1536	–	oplstype = 56;
1537	–	goto L_1001;
1538	–	}
1539	–	// only amides and guanadinium ions left
1540	–	for (j=0; j< MAXIAT; j++)
1541	–	{
1542	–	if (atom[atom[i].iat[j]].atomnum == 6)
1543	–	{
1544	–	jatm = atom[i].iat[j];
1545	–	for (k=0; k < MAXIAT; k++)
1546	–	{
1547	–	if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].bo[k] == 2)
1548	–	{
1549	–	ambertype = 14; // N amide
1550	–	oplstype = 55;
1551	–	goto L_1001;
1552	–	}
1553	–	if (atom[atom[jatm].iat[k]].atomnum == 7 && atom[jatm].bo[k] == 2)
1554	–	{
1555	–	ambertype = 19; // guanadinium
1556	–	oplstype = 57;
1557	–	goto L_1001;
1558	–	}
1559	–	if (atom[atom[jatm].iat[k]].atomnum == 6 && atom[jatm].bo[k] == 2)
1560	–	{
1561	–	ambertype = 19; // guanadinium
1562	–	oplstype = 54;
1563	–	goto L_1001;
1564	–	}
1565	–	}
1566	–	}
1567	–	}
1568	–	ambertype = 20; // N2
1569	–	oplstype = 53;
1570	–	L_1001:
1156		//
1157		if (icycl5 >= 1 && atom[i].flags & aromatic_mask)
1158		{
#	Line 2238 | Line 1823
1823		mmxtype = 41;
1824		mm3type = 39;
1825		mmfftype = 34;
2241	–	oplstype = 56;
1826		for (j=0; j < MAXIAT; j++)
1827		{
1828		if (atom[i].iat[j] != 0 && (atom[atom[i].iat[j]].mmx_type >= 300))
#	Line 2589 | Line 2173
2173		atom[atom[jatm].iat[1]].atomnum == 7 && atom[atom[jatm].iat[2]].atomnum == 7) )
2174		{
2175		mmfftype = 56;
2592	–	oplstype = 57;
2176		goto L_10;
2177		}
2178		}
#	Line 2620 | Line 2203
2203		mmxtype = 53;
2204		mm3type = 0;
2205		mmfftype = 0;
2623	–	ambertype = 0;
2206		goto L_10;
2207		}
2208		jjbo = 0;
#	Line 2634 | Line 2216
2216		{
2217		mmxtype = 46;
2218		mmfftype = 49;
2637	–	ambertype = 0;
2219		mm3type = 0;
2639	–	oplstype = 0;
2220		for (j=0; j < MAXIAT; j++)
2221		{
2222		if (atom[i].iat[j] != 0 && atom[i].bo[j] == 2)
#	Line 2652 | Line 2232
2232		{
2233		mm3type = 47;
2234		mmfftype = 32;
2655	–	ambertype = 25;
2656	–	oplstype = 50;
2235		}
2236		if (mmxtype == 6 || mmxtype == 7 || mmxtype == 66)
2237		{
#	Line 2664 | Line 2242
2242		mmxtype = 7;
2243		mm3type = 7;
2244		mmfftype = 7;
2667	–	ambertype = 25;
2668	–	oplstype = 49;
2245		jatm = atom[i].iat[j];
2246		if (atom[jatm].atomnum == 15)   // p=o
2247		{
#	Line 2688 | Line 2264
2264		}
2265		}
2266		mmfftype = 32;
2691	–	oplstype = 50;
2267		goto L_10;
2268		}
2269		if (atom[jatm].atomnum == 16)   // s=o
#	Line 2711 | Line 2286
2286		if (jjk == 1 && jj_bo == 1 && atom[katm].mmx_type == 42)
2287		{
2288		mmxtype = 66;
2289	<	mm3type = 47;
2289	>	mm3type = 47;
2290		mmfftype = 32;
2716	–	oplstype = 50;
2291		goto L_10;
2292		}
2293		}
#	Line 2738 | Line 2312
2312		if (jjk == 1)   // carboxylate
2313		{
2314		mmxtype = 66;
2315	<	mm3type = 47;
2315	>	mm3type = 47;
2316		mmfftype = 32;
2743	–	ambertype = 25;
2744	–	oplstype = 50;
2317		goto L_10;
2318		}
2319		if (jjk == 2)  // ester and acids
#	Line 2749 | Line 2321
2321		if ( atom[atom[katm].iat[0]].atomnum != 1 && atom[atom[katm].iat[1]].atomnum != 1) // ester
2322		{
2323		mm3type = 78;
2752	–	ambertype = 25;
2753	–	oplstype = 49;
2324		goto L_10;
2325		} else if ( atom[atom[katm].iat[0]].atomnum == 1 || atom[atom[katm].iat[1]].atomnum == 1) // acid
2326		{
2327		mm3type = 77;
2758	–	ambertype = 24;
2759	–	oplstype = 49;
2328		goto L_10;
2329		}
2330		}
#	Line 2769 | Line 2337
2337		{
2338		if (atom[atom[jatm].iat[k]].atomnum == 7)  // amide
2339		{
2772	–	ambertype = 24;
2773	–	oplstype = 49;
2340		mm3type = 7;  // should be 79 but database only has 58-79
2341		goto L_10;
2342		}
#	Line 2812 | Line 2378
2378		mmxtype = 66;
2379		mm3type =  47;
2380		mmfftype = 32;
2815	–	ambertype = 24;
2816	–	oplstype = 50;
2381		goto L_10;
2382		}
2383		} else if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].iat[k] != i && atom[jatm].bo[k] == 2)
2384		{
2385		mmfftype = 32;
2822	–	oplstype = 50;
2386		goto L_10;
2387		} else if (atom[atom[jatm].iat[k]].atomnum == 16 && atom[jatm].iat[k] != i && atom[jatm].bo[k] == 2)
2388		{
#	Line 2834 | Line 2397
2397		{
2398		mmxtype = 66;
2399		mm3type = 47;
2837	–	oplstype = 50;
2400		}
2401		mmfftype = 32;
2402		goto L_10;
#	Line 2864 | Line 2426
2426		}
2427		if (jji == 1) // only one bond
2428		{
2867	–	oplstype = 52;
2429		if (atom[atom[i].iat[0]].atomnum == 6)
2430		{
2431		jatm = atom[i].iat[0];
#	Line 2873 | Line 2434
2434		if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2)
2435		{
2436
2876	–	if (atom[atom[jatm].iat[j]].atomnum == 8) // c=c
2877	–	{
2878	–	oplstype = 50;
2879	–	goto L_10;
2880	–	}
2437		if (atom[atom[jatm].iat[j]].atomnum == 6) // c=c
2438		{
2439		mmfftype = 35;
#	Line 2891 | Line 2447
2447		mmxtype = 66;
2448		mm3type = 69;
2449		mmfftype = 32;
2894	–	oplstype = 50;
2450		goto L_10;
2451		}
2452		if (atom[atom[i].iat[0]].atomnum == 15 || atom[atom[i].iat[0]].atomnum == 16)  //  p-o
#	Line 2899 | Line 2454
2454		mmxtype = 66;
2455		mm3type = 7;
2456		mmfftype = 32;
2902	–	oplstype = 50;
2457		goto L_10;
2458		}
2459
#	Line 2917 | Line 2471
2471		{
2472		mmfftype = 59;
2473		mm3type = 41;
2920	–	ambertype = 23;
2921	–	oplstype = 47;
2474		goto L_10;
2475		}
2476		}
#	Line 2927 | Line 2479
2479		if (nh == 2) // mmff water
2480		{
2481		mmfftype = 70;
2930	–	ambertype = 21;
2931	–	oplstype = 51;
2482		goto L_10;
2483		} else if (nh == 1) // ROH and RCOOH
2484		{
2485		mm3type = 6;
2486		mmfftype = 6;
2937	–	ambertype = 22;
2938	–	oplstype = 44;
2487		jatm = atom[i].iat[0];
2488		for (j=0; j < MAXIAT; j++)
2489		{
#	Line 2944 | Line 2492
2492		if (atom[atom[jatm].iat[j]].atomnum == 8)
2493		{
2494		mm3type = 75;
2947	–	oplstype = 46;
2495		break;
2496		}
2497		}
#	Line 2953 | Line 2500
2500		} else
2501		{
2502		mmfftype = 6;
2503	<	ambertype = 23;   // ether
2957	<	oplstype = 47;
2958	<	jatm = atom[i].iat[0];  // acetal
2959	<	katm = atom[i].iat[1];
2960	<	nox = 0;
2961	<	for (j=0; j < MAXIAT; j++)
2962	<	{
2963	<	if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].atomnum == 8 && atom[jatm].bo[j] != 2)
2964	<	nox++;
2965	<	}
2966	<	if (nox == 2 || nox == 3)
2967	<	oplstype = 48;
2968	<	nox = 0;
2969	<	for (j=0; j < MAXIAT; j++)
2970	<	{
2971	<	if (atom[katm].iat[j] != 0 && atom[atom[katm].iat[j]].atomnum == 8 && atom[katm].bo[j] != 2)
2972	<	nox++;
2973	<	}
2974	<	if (nox == 2 || nox == 3)
2975	<	oplstype = 48;
2976	<
2503	>	goto L_10;
2504		}
2505		jatm = atom[i].iat[0];
2506		jtype = 0;
#	Line 3026 | Line 2553
2553		mmxtype = 6;
2554		mm3type = 6;
2555		mmfftype = 6;
3029	–	ambertype = 22;
3030	–	oplstype = 47;
2556		}
2557		goto L_10;
2558		} else if (mmxtype == 42)
2559		{
2560		mmfftype = 32;
3036	–	ambertype = 25;
3037	–	oplstype = 52;
2561		for (j=0; j < MAXIAT; j++)
2562		{
2563		if (atom[atom[i].iat[j]].atomnum == 16 || atom[atom[i].iat[j]].atomnum == 15)
#	Line 3042 | Line 2565
2565		mmxtype = 66;
2566		mm3type = 47;
2567		mmfftype = 32;
3045	–	oplstype = 50;
2568		goto L_10;
2569		}
2570		if (atom[atom[i].iat[j]].atomnum == 7)
#	Line 3060 | Line 2582
2582		mmxtype = 66;
2583		mm3type = 69;
2584		mmfftype = 32;
3063	–	oplstype = 50;
2585		} else
2586		mmfftype = 35;
2587		goto L_10;
#	Line 3076 | Line 2597
2597		mmxtype = 66;
2598		mm3type = 47;
2599		mmfftype = 32;
3079	–	oplstype = 50;
2600		goto L_10;
2601		}
2602		}
#	Line 3101 | Line 2621
2621		mmxtype = 25;
2622		mm3type = 25;
2623		mmfftype = 25;
3104	–	ambertype = 28;
3105	–	oplstype = 66;
2624		jji = 0;
2625		for (j=0; j < MAXIAT; j++)
2626		{
#	Line 3112 | Line 2630
2630		{
2631		mmxtype = 67;
2632		mmfftype = 75;
3115	–	oplstype = 67;
2633		goto L_10;
2634		}
2635		if (atom[atom[i].iat[j]].atomnum == 8 && atom[i].bo[j] == 2)
#	Line 3122 | Line 2639
2639		{
2640		mmxtype = 47;
2641		mm3type = 60;
3125	–	oplstype = 67;
2642		}else if (jji == 3)
2643		{
2644		mmxtype = 25;
#	Line 3134 | Line 2650
2650		mmxtype = 15;
2651		mm3type = 15;
2652		mmfftype = 15;
3137	–	ambertype = 26;
3138	–	oplstype = 69;
3139	–	if (atom[atom[i].iat[0]].atomnum == 1 || atom[atom[i].iat[1]].atomnum == 1)
3140	–	{
3141	–	ambertype = 27;
3142	–	oplstype = 68;
3143	–	}
2653		jji = 0;
2654		ndouble = 0;
2655		for (j=0; j < MAXIAT; j++)
#	Line 3252 | Line 2761
2761		mm3type = 12;
2762		mmxtype = 12;
2763		mmfftype = 12;
3255	–	oplstype = 63;
2764		jji = 0;
2765		for (j=0; j < MAXIAT; j++)
2766		if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9)
#	Line 3277 | Line 2785
2785		mmxtype = 11;
2786		mm3type = 11;
2787		mmfftype = 11;
3280	–	oplstype = 62;
2788		goto L_10;
2789		} else if (atom[i].atomnum == 35)   // Bromine
2790		{
2791		mmxtype = 13;
2792		mm3type = 13;
2793		mmfftype = 13;
3287	–	oplstype = 64;
2794		goto L_10;
2795		} else if (atom[i].atomnum == 53)    // Iodine
2796		{
#	Line 3298 | Line 2804
2804		mmxtype = 14;
2805		mm3type = 14;
2806		mmfftype = 14;
3301	–	oplstype = 65;
2807		goto L_10;
2808		} else if (atom[i].atomnum == 14 )  // Silicon
2809		{
#	Line 3315 | Line 2820
2820		} else if (mmxtype >= 300) // metal atom - try to assign MMFF type
2821		{
2822		mm3type = mmxtype;
3318	–	ambertype = mmxtype;
2823		if (mmfftype == 0)
2824		mmfftype = mmxtype;
3321	–	oplstype = mmxtype;
2825		}
2826		L_10:
2827	<	set_atomtype(i,mmxtype,mm3type,mmfftype,ambertype,oplstype);
2827	>	set_atomtype(i,mmxtype,mm3type,mmfftype,0,0);
2828		L_20:
2829		continue;  // do nothing
2830		}

Diff Legend

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