1 |
/********************************************************************** |
2 |
chains.h - Parse for macromolecule chains and residues |
3 |
|
4 |
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
5 |
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
6 |
|
7 |
This file is part of the Open Babel project. |
8 |
For more information, see <http://openbabel.sourceforge.net/> |
9 |
|
10 |
This program is free software; you can redistribute it and/or modify |
11 |
it under the terms of the GNU General Public License as published by |
12 |
the Free Software Foundation version 2 of the License. |
13 |
|
14 |
This program is distributed in the hope that it will be useful, |
15 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
16 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
17 |
GNU General Public License for more details. |
18 |
***********************************************************************/ |
19 |
|
20 |
#ifndef OB_CHAINS_H |
21 |
#define OB_CHAINS_H |
22 |
|
23 |
#define MaxMonoAtom 20 |
24 |
#define MaxMonoBond 20 |
25 |
|
26 |
namespace OpenBabel |
27 |
{ |
28 |
|
29 |
class OBAtom; |
30 |
class OBMol; |
31 |
|
32 |
//! Structure for atomic patterns (templates) in residues for OBChainsParser |
33 |
typedef struct |
34 |
{ |
35 |
int flag; |
36 |
short elem, count; |
37 |
int n1, n2, n3, n4; |
38 |
} |
39 |
Template; |
40 |
|
41 |
//! \brief Perceives peptide or nucleotide chains and residues in an OBMol |
42 |
class OBAPI OBChainsParser |
43 |
{ |
44 |
public: |
45 |
|
46 |
OBChainsParser(void); |
47 |
~OBChainsParser(void); |
48 |
|
49 |
bool PerceiveChains(OBMol &, bool nukeSingleResidue = false); |
50 |
|
51 |
private: // methods |
52 |
|
53 |
bool DetermineHetAtoms(OBMol &); |
54 |
bool DetermineConnectedChains(OBMol &); |
55 |
bool DeterminePeptideBackbone(OBMol &); |
56 |
bool DeterminePeptideSidechains(OBMol &); |
57 |
bool DetermineNucleicBackbone(OBMol &); |
58 |
bool DetermineNucleicSidechains(OBMol &); |
59 |
bool DetermineHydrogens(OBMol &); |
60 |
|
61 |
void SetupMol(OBMol &); |
62 |
void SetResidueInformation(OBMol &, bool nukeSingleResidue); |
63 |
void ClearResidueInformation(OBMol &); |
64 |
void CleanupMol(void); |
65 |
|
66 |
void AssignResidue(OBMol &, int, int, int); |
67 |
int IdentifyResidue(void *, OBMol &, int, int); // ByteCode * |
68 |
|
69 |
void DefineMonomer(void **, int, char *); // ByteCode ** |
70 |
int IdentifyElement(char *); |
71 |
|
72 |
bool MatchConstraint(OBAtom *, int); |
73 |
bool Match2Constraints(Template *, OBAtom *, OBAtom *); |
74 |
bool Match3Constraints(Template *, OBAtom *, OBAtom *, OBAtom *); |
75 |
bool Match4Constraints(Template *, OBAtom *, OBAtom *, OBAtom *, OBAtom *); |
76 |
|
77 |
void ConstrainBackbone(OBMol &, Template *, int); |
78 |
|
79 |
int RecurseChain(OBMol &, int, int); |
80 |
void TraceNucleicChain(OBMol &, int, int); |
81 |
void TracePeptideChain(OBMol &, int, int); |
82 |
|
83 |
char *ParseSmiles(char *, int); |
84 |
|
85 |
private: // members |
86 |
|
87 |
void *PDecisionTree; // ByteCode * |
88 |
void *NDecisionTree; // ByteCode * |
89 |
|
90 |
int ResMonoAtom[MaxMonoAtom]; |
91 |
int ResMonoBond[MaxMonoBond]; |
92 |
|
93 |
unsigned short *bitmasks; |
94 |
unsigned char *resids; |
95 |
unsigned char *flags; |
96 |
bool *hetflags; |
97 |
short *atomids; |
98 |
short *resnos; |
99 |
short *sernos; |
100 |
char *hcounts; |
101 |
char *chains; |
102 |
}; |
103 |
|
104 |
} |
105 |
#endif // OB_CHAINS_H |
106 |
|
107 |
//! \file chains.h |
108 |
//! \brief Parse for macromolecule chains and residues. |