1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
|
/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (c) 2001-2002 by Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#ifndef OB_CHAINS_H
#define OB_CHAINS_H
#define MaxMonoAtom 20
#define MaxMonoBond 20
namespace OpenBabel {
class OBAtom;
class OBMol;
typedef struct
{
int flag;
short elem, count;
int n1, n2, n3, n4;
} Template;
class OBChainsParser
{
public:
OBChainsParser(void);
~OBChainsParser(void);
bool PerceiveChains(OBMol &);
private: // methods
bool DetermineHetAtoms(OBMol &);
bool DetermineConnectedChains(OBMol &);
bool DeterminePeptideBackbone(OBMol &);
bool DeterminePeptideSidechains(OBMol &);
bool DetermineNucleicBackbone(OBMol &);
bool DetermineNucleicSidechains(OBMol &);
bool DetermineHydrogens(OBMol &);
void SetupMol(OBMol &);
void SetResidueInformation(OBMol &);
void ClearResidueInformation(OBMol &);
void CleanupMol(void);
void AssignResidue(OBMol &, int, int, int);
int IdentifyResidue(void *, OBMol &, int, int); // ByteCode *
void DefineMonomer(void **, int, char *); // ByteCode **
int IdentifyElement(char *);
bool MatchConstraint(OBAtom *, int);
bool Match2Constraints(Template *, OBAtom *, OBAtom *);
bool Match3Constraints(Template *, OBAtom *, OBAtom *, OBAtom *);
bool Match4Constraints(Template *, OBAtom *, OBAtom *, OBAtom *, OBAtom *);
void ConstrainBackbone(OBMol &, Template *, int);
int RecurseChain(OBMol &, int, int);
void TraceNucleicChain(OBMol &, int, int);
void TracePeptideChain(OBMol &, int, int);
char *ParseSmiles(char *, int);
private: // members
void *PDecisionTree; // ByteCode *
void *NDecisionTree; // ByteCode *
int ResMonoAtom[MaxMonoAtom];
int ResMonoBond[MaxMonoBond];
unsigned short *bitmasks;
unsigned char *resids;
unsigned char *flags;
bool *hetflags;
short *atomids;
short *resnos;
short *sernos;
char *hcounts;
char *chains;
};
}
#endif // OB_CHAINS_H
|
