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tim |
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/********************************************************************** |
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chains.cpp - Parse for macromolecule chains and residues. |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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(original author, Roger Sayle, version 1.6, March 1998) |
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(modified by Joe Corkery, OpenEye Scientific Software, March 2001) |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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////////////////////////////////////////////////////////////////////////////// |
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// File Includes |
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////////////////////////////////////////////////////////////////////////////// |
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#include <stdlib.h> |
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#include <string.h> |
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#include <stdio.h> |
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#include <ctype.h> |
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#include <map> |
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#include "mol.hpp" |
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#include "chains.hpp" |
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using namespace std; |
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////////////////////////////////////////////////////////////////////////////// |
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// Preprocessor Definitions |
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////////////////////////////////////////////////////////////////////////////// |
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#define RESIDMIN 3 |
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#define RESIDMAX 32 |
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#define ATOMMAX 68 |
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#define ATOMMINAMINO 4 |
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#define ATOMMINNUCLEIC 50 |
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#define ELEMMAX 104 |
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#define MAXPEPTIDE 11 |
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#define MAXNUCLEIC 15 |
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#define AMINOMAX 21 |
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#define NUCLEOMAX 6 |
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#define STACKSIZE 20 |
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#define BUFMAX 8192 |
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#define MAXCOVAL 2.0 |
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#define SLOPFACTOR 0.56 |
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#define THRESHOLD 12 |
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#define AI_N 0 |
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#define AI_CA 1 |
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#define AI_C 2 |
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#define AI_O 3 |
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#define AI_OXT 37 |
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#define AI_P 38 |
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#define AI_O1P 39 |
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#define AI_O2P 40 |
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#define AI_O5 41 |
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#define AI_C5 42 |
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#define AI_C4 43 |
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#define AI_O4 44 |
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#define AI_C3 45 |
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#define AI_O3 46 |
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#define AI_C2 47 |
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#define AI_O2 48 |
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#define AI_C1 49 |
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#define BitN 0x0001 |
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#define BitNTer 0x0002 |
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#define BitNPro 0x0004 |
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#define BitNPT 0x0008 |
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#define BitCA 0x0010 |
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#define BitCAGly 0x0020 |
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#define BitC 0x0100 |
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#define BitCTer 0x0200 |
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#define BitCOXT 0x0400 |
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#define BitO 0x1000 |
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#define BitOXT 0x2000 |
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#define BitNAll 0x000F |
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#define BitCAAll 0x0030 |
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#define BitCAll 0x0700 |
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#define BitOAll 0x3000 |
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#define BitP 0x0001 |
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#define BitPTer 0x0002 |
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#define BitOP 0x0004 |
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#define BitO5 0x0008 |
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#define BitO5Ter 0x0010 |
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#define BitC5 0x0020 |
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#define BitC4 0x0040 |
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#define BitO4 0x0080 |
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#define BitC3 0x0100 |
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#define BitO3 0x0200 |
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#define BitO3Ter 0x0400 |
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#define BitC2RNA 0x0800 |
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#define BitC2DNA 0x1000 |
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#define BitO2 0x2000 |
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#define BitC1 0x4000 |
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#define BitPAll 0x0003 |
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#define Bit05All 0x0018 |
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#define BitO3All 0x0600 |
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#define BitC2All 0x1800 |
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#define BC_ASSIGN 0x01 |
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#define BC_COUNT 0x02 |
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#define BC_ELEM 0x03 |
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#define BC_EVAL 0x04 |
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#define BC_IDENT 0x05 |
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#define BC_LOCAL 0x06 |
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#define BF_SINGLE 0x01 |
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#define BF_DOUBLE 0x02 |
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#define BF_TRIPLE 0x04 |
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#define BF_AROMATIC 0x08 |
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namespace OpenBabel |
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{ |
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OBChainsParser chainsparser; |
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////////////////////////////////////////////////////////////////////////////// |
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// Structure / Type Definitions |
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////////////////////////////////////////////////////////////////////////////// |
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typedef struct |
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{ |
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char *name; |
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char *data; |
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} |
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ResidType; |
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typedef struct |
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{ |
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int atomid,elem; |
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int bcount; |
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int index; |
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} |
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MonoAtomType; |
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typedef struct |
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{ |
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int src,dst; |
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int index; |
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int flag; |
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} |
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MonoBondType; |
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typedef struct |
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{ |
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int type; |
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union _ByteCode *next; |
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} |
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MonOpStruct; |
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typedef struct |
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{ |
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int type; |
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int value; |
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union _ByteCode *tcond; |
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union _ByteCode *fcond; |
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} |
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BinOpStruct; |
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typedef struct |
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{ |
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int type; |
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int resid; |
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int *atomid; |
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int *bflags; |
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} |
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AssignStruct; |
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typedef union _ByteCode |
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{ |
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int type; |
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MonOpStruct eval; /* BC_EVAL */ |
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BinOpStruct count; /* BC_COUNT */ |
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BinOpStruct elem; /* BC_ELEM */ |
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BinOpStruct ident; /* BC_IDENT */ |
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BinOpStruct local; /* BC_LOCAL */ |
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AssignStruct assign; /* BC_ASSIGN */ |
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} ByteCode; |
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typedef struct |
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{ |
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int atom,bond; |
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int prev; |
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} |
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StackType; |
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////////////////////////////////////////////////////////////////////////////// |
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// Global Variables / Tables |
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////////////////////////////////////////////////////////////////////////////// |
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static char ChainsAtomName[ATOMMAX][4] = { |
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/* 0 */ { ' ', 'N', ' ', ' ' }, |
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/* 1 */ { ' ', 'C', 'A', ' ' }, |
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/* 2 */ { ' ', 'C', ' ', ' ' }, |
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/* 3 */ { ' ', 'O', ' ', ' ' }, |
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/* 4 */ { ' ', 'C', 'B', ' ' }, |
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/* 5 */ { ' ', 'S', 'G', ' ' }, |
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/* 6 */ { ' ', 'O', 'G', ' ' }, |
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/* 7 */ { ' ', 'C', 'G', ' ' }, |
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/* 8 */ { ' ', 'O', 'G', '1' }, |
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/* 9 */ { ' ', 'C', 'G', '1' }, |
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/* 10 */ { ' ', 'C', 'G', '2' }, |
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/* 11 */ { ' ', 'C', 'D', ' ' }, |
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/* 12 */ { ' ', 'O', 'D', ' ' }, |
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/* 13 */ { ' ', 'S', 'D', ' ' }, |
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/* 14 */ { ' ', 'C', 'D', '1' }, |
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/* 15 */ { ' ', 'O', 'D', '1' }, |
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/* 16 */ { ' ', 'N', 'D', '1' }, |
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/* 17 */ { ' ', 'C', 'D', '2' }, |
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/* 18 */ { ' ', 'O', 'D', '2' }, |
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/* 19 */ { ' ', 'N', 'D', '2' }, |
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/* 20 */ { ' ', 'C', 'E', ' ' }, |
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/* 21 */ { ' ', 'N', 'E', ' ' }, |
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/* 22 */ { ' ', 'C', 'E', '1' }, |
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/* 23 */ { ' ', 'O', 'E', '1' }, |
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/* 24 */ { ' ', 'N', 'E', '1' }, |
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/* 25 */ { ' ', 'C', 'E', '2' }, |
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/* 26 */ { ' ', 'O', 'E', '2' }, |
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/* 27 */ { ' ', 'N', 'E', '2' }, |
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/* 28 */ { ' ', 'C', 'E', '3' }, |
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/* 29 */ { ' ', 'C', 'Z', ' ' }, |
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/* 30 */ { ' ', 'N', 'Z', ' ' }, |
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/* 31 */ { ' ', 'C', 'Z', '2' }, |
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/* 32 */ { ' ', 'C', 'Z', '3' }, |
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/* 33 */ { ' ', 'O', 'H', ' ' }, |
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/* 34 */ { ' ', 'N', 'H', '1' }, |
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/* 35 */ { ' ', 'N', 'H', '2' }, |
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/* 36 */ { ' ', 'C', 'H', '2' }, |
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/* 37 */ { ' ', 'O', 'X', 'T' }, |
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/* 38 */ { ' ', 'P', ' ', ' ' }, |
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/* 39 */ { ' ', 'O', '1', 'P' }, |
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/* 40 */ { ' ', 'O', '2', 'P' }, |
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/* 41 */ { ' ', 'O', '5', '*' }, |
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/* 42 */ { ' ', 'C', '5', '*' }, |
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/* 43 */ { ' ', 'C', '4', '*' }, |
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/* 44 */ { ' ', 'O', '4', '*' }, |
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/* 45 */ { ' ', 'C', '3', '*' }, |
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/* 46 */ { ' ', 'O', '3', '*' }, |
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/* 47 */ { ' ', 'C', '2', '*' }, |
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/* 48 */ { ' ', 'O', '2', '*' }, |
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/* 49 */ { ' ', 'C', '1', '*' }, |
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/* 50 */ { ' ', 'N', '9', ' ' }, |
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/* 51 */ { ' ', 'C', '8', ' ' }, |
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/* 52 */ { ' ', 'N', '7', ' ' }, |
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/* 53 */ { ' ', 'C', '5', ' ' }, |
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/* 54 */ { ' ', 'C', '6', ' ' }, |
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/* 55 */ { ' ', 'O', '6', ' ' }, |
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/* 56 */ { ' ', 'N', '6', ' ' }, |
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/* 57 */ { ' ', 'N', '1', ' ' }, |
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/* 58 */ { ' ', 'C', '2', ' ' }, |
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/* 59 */ { ' ', 'O', '2', ' ' }, |
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/* 60 */ { ' ', 'N', '2', ' ' }, |
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/* 61 */ { ' ', 'N', '3', ' ' }, |
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/* 62 */ { ' ', 'C', '4', ' ' }, |
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/* 63 */ { ' ', 'O', '4', ' ' }, |
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/* 64 */ { ' ', 'N', '4', ' ' }, |
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/* 65 */ { ' ', 'C', '5', ' ' }, |
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/* 66 */ { ' ', 'C', '5', 'M' }, |
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/* 67 */ { ' ', 'C', '6', ' ' } |
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}; |
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static Template Peptide[MAXPEPTIDE] = { |
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/* N */ { 0x0001, 7, 2, 0x0030, 0x0100, 0, 0 }, |
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/* NTer */ { 0x0002, 7, 1, 0x0030, 0, 0, 0 }, |
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/* NPro */ { 0x0004, 7, 3, 0x0030, 0x0100, -6, 0 }, |
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/* NPT */ { 0x0008, 7, 2, 0x0030, -6, 0, 0 }, |
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/* CA */ { 0x0010, 6, 3, 0x000F, 0x0700, -6, 0 }, |
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/* CAGly */ { 0x0020, 6, 2, 0x0003, 0x0700, 0, 0 }, |
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/* C */ { 0x0100, 6, 3, 0x0030, 0x1000, 0x0005, 0 }, |
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/* CTer */ { 0x0200, 6, 2, 0x0030, 0x1000, 0, 0 }, |
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/* COXT */ { 0x0400, 6, 3, 0x0030, 0x1000, 0x2000, 0 }, |
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/* O */ { 0x1000, 8, 1, 0x0700, 0, 0, 0 }, |
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/* OXT */ { 0x2000, 8, 1, 0x0400, 0, 0, 0 } |
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}; |
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static Template Nucleotide[MAXNUCLEIC] = { |
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/* P */ { 0x0001, 15, 4, 0x0004, 0x0004, 0x0008, 0x0200 }, |
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/* PTer */ { 0x0002, 15, 3, 0x0004, 0x0004, 0x0008, 0 }, |
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/* OP */ { 0x0004, 8, 1, 0x0003, 0, 0, 0 }, |
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/* O5 */ { 0x0008, 8, 2, 0x0020, 0x0003, 0, 0 }, |
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/* O5Ter */ { 0x0010, 8, 1, 0x0020, 0, 0, 0 }, |
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/* C5 */ { 0x0020, 6, 2, 0x0018, 0x0040, 0, 0 }, |
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/* C4 */ { 0x0040, 6, 3, 0x0020, 0x0080, 0x0100, 0 }, |
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/* O4 */ { 0x0080, 8, 2, 0x0040, 0x4000, 0, 0 }, |
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/* C3 */ { 0x0100, 6, 3, 0x0040, 0x0600, 0x1800, 0 }, |
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/* O3 */ { 0x0200, 8, 2, 0x0100, 0x0001, 0, 0 }, |
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/* O3Ter */ { 0x0400, 8, 1, 0x0100, 0, 0, 0 }, |
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/* C2RNA */ { 0x0800, 6, 3, 0x0100, 0x4000, 0x2000, 0 }, |
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/* C2DNA */ { 0x1000, 6, 2, 0x0100, 0x4000, 0, 0 }, |
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/* O2 */ { 0x2000, 8, 1, 0x0800, 0, 0, 0 }, |
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/* C1 */ { 0x4000, 6, 3, 0x0080, 0x1800, -7, 0 } |
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}; |
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static char ChainsResName[RESIDMAX][4] = { |
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/*0*/ "UNK", /*1*/ "HOH", /*2*/ "LIG" |
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}; |
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static ResidType AminoAcids[AMINOMAX] = { |
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{ "ILE", "1-4(-9-14)-10" }, |
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{ "VAL", "1-4(-9)-10" }, |
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{ "ALA", "1-4" }, |
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{ "ASN", "1-4-7(=15)-19" }, |
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{ "ASP", "1-4-7(=15)-18" }, |
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{ "ARG", "1-4-7-11-21-29(=34)-35" }, |
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{ "CYS", "1-4-5" }, |
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{ "GLN", "1-4-7-11(=23)-27" }, |
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{ "GLU", "1-4-7-11(=23)-26" }, |
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{ "GLY", "1" }, |
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{ "HIS", "1-4-7^16~22^27^17~7" }, |
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{ "HYP", "1-4-7(-12)-11-0" }, /* ??? */ |
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{ "LEU", "1-4-7(-14)-17" }, |
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{ "LYS", "1-4-7-11-20-30" }, |
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{ "MET", "1-4-7-13-20" }, |
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{ "PHE", "1-4-7~14^22~29^25~17^7" }, |
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{ "PRO", "1-4-7-11-0" }, |
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{ "SER", "1-4-6" }, |
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{ "THR", "1-4(-8)-10" }, |
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{ "TRP", "1-4-7~14^24^25~17(^7)^28~32^36~31^25" }, |
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{ "TYR", "1-4-7~14^22~29(-33)^25~17^7" } |
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}; |
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/* Pyroglutamate (PCA): 1-4-7-11(=" OE ")-0 PDB Example: 1CEL */ |
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/* Amino-N-Butyric Acid (ABA): 1-4-7 PDB Example: 1BBO */ |
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/* Selenic Acid (SEC): 1-4-"SEG "(-15)-18 PDB Example: 1GP1 */ |
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|
|
static ResidType Nucleotides[NUCLEOMAX] = { |
| 343 |
|
|
{ " A", "49-50-51-52-53-54(-56)-57-58-61-62(-53)-50" }, |
| 344 |
|
|
{ " C", "49-57-58(-59)-61-62(-64)-65-67-57" }, |
| 345 |
|
|
{ " G", "49-50-51-52-53-54(-55)-57-58(-60)-61-62(-53)-50" }, |
| 346 |
|
|
{ " T", "49-57-58(-59)-61-62(-63)-65(-66)-67-57" }, |
| 347 |
|
|
{ " U", "49-57-58(-59)-61-62(-63)-65-67-57" }, |
| 348 |
|
|
{ " I", "49-50-51-52-53-54(-55)-57-58-61-62(-53)-50" } |
| 349 |
|
|
}; |
| 350 |
|
|
|
| 351 |
|
|
static MonoAtomType MonoAtom[MaxMonoAtom]; |
| 352 |
|
|
static MonoBondType MonoBond[MaxMonoBond]; |
| 353 |
|
|
static int MonoAtomCount; |
| 354 |
|
|
static int MonoBondCount; |
| 355 |
|
|
|
| 356 |
|
|
static StackType Stack[STACKSIZE]; |
| 357 |
|
|
static int StackPtr; |
| 358 |
|
|
|
| 359 |
|
|
static int AtomIndex; |
| 360 |
|
|
static int BondIndex; |
| 361 |
|
|
static bool StrictFlag = false; |
| 362 |
|
|
|
| 363 |
|
|
////////////////////////////////////////////////////////////////////////////// |
| 364 |
|
|
// Static Functions |
| 365 |
|
|
////////////////////////////////////////////////////////////////////////////// |
| 366 |
|
|
|
| 367 |
|
|
static ByteCode *AllocateByteCode(int type) |
| 368 |
|
|
{ |
| 369 |
|
|
ByteCode *result; |
| 370 |
|
|
|
| 371 |
|
|
result = (ByteCode*)malloc(sizeof(ByteCode)); |
| 372 |
|
|
if( !result ) |
| 373 |
|
|
{ |
| 374 |
|
|
obErrorLog.ThrowError(__FUNCTION__, "Unable to allocate byte codes for biomolecule residue perception.", obError); |
| 375 |
|
|
// exit(1); |
| 376 |
|
|
} |
| 377 |
|
|
result->type = type; |
| 378 |
|
|
result->eval.next = NULL; |
| 379 |
|
|
result->count.tcond = NULL; |
| 380 |
|
|
result->count.fcond = NULL; |
| 381 |
|
|
result->elem.tcond = NULL; |
| 382 |
|
|
result->elem.fcond = NULL; |
| 383 |
|
|
result->ident.tcond = NULL; |
| 384 |
|
|
result->ident.fcond = NULL; |
| 385 |
|
|
result->local.tcond = NULL; |
| 386 |
|
|
result->local.fcond = NULL; |
| 387 |
|
|
result->assign.atomid = NULL; |
| 388 |
|
|
result->assign.bflags = NULL; |
| 389 |
|
|
|
| 390 |
|
|
return (result); |
| 391 |
|
|
} |
| 392 |
|
|
|
| 393 |
|
|
static void DeleteByteCode(ByteCode *node) |
| 394 |
|
|
{ |
| 395 |
|
|
if (node == NULL) |
| 396 |
|
|
return; |
| 397 |
|
|
else |
| 398 |
|
|
{ |
| 399 |
|
|
switch (node->type) |
| 400 |
|
|
{ |
| 401 |
|
|
case BC_ASSIGN: |
| 402 |
|
|
|
| 403 |
|
|
if (node->assign.atomid != NULL) |
| 404 |
|
|
free(node->assign.atomid); |
| 405 |
|
|
if (node->assign.bflags != NULL) |
| 406 |
|
|
free(node->assign.bflags); |
| 407 |
|
|
|
| 408 |
|
|
break; |
| 409 |
|
|
|
| 410 |
|
|
case BC_COUNT: |
| 411 |
|
|
|
| 412 |
|
|
DeleteByteCode(node->count.tcond); |
| 413 |
|
|
DeleteByteCode(node->count.fcond); |
| 414 |
|
|
break; |
| 415 |
|
|
case BC_ELEM: |
| 416 |
|
|
|
| 417 |
|
|
DeleteByteCode(node->elem.tcond); |
| 418 |
|
|
DeleteByteCode(node->elem.fcond); |
| 419 |
|
|
break; |
| 420 |
|
|
|
| 421 |
|
|
case BC_EVAL: |
| 422 |
|
|
|
| 423 |
|
|
DeleteByteCode(node->eval.next); |
| 424 |
|
|
break; |
| 425 |
|
|
|
| 426 |
|
|
case BC_IDENT: |
| 427 |
|
|
|
| 428 |
|
|
DeleteByteCode(node->ident.tcond); |
| 429 |
|
|
DeleteByteCode(node->ident.fcond); |
| 430 |
|
|
break; |
| 431 |
|
|
|
| 432 |
|
|
case BC_LOCAL: |
| 433 |
|
|
|
| 434 |
|
|
DeleteByteCode(node->local.tcond); |
| 435 |
|
|
DeleteByteCode(node->local.fcond); |
| 436 |
|
|
break; |
| 437 |
|
|
} |
| 438 |
|
|
|
| 439 |
|
|
free(node); |
| 440 |
|
|
} |
| 441 |
|
|
} |
| 442 |
|
|
|
| 443 |
|
|
static void FatalMemoryError(void) |
| 444 |
|
|
{ |
| 445 |
|
|
obErrorLog.ThrowError(__FUNCTION__, "Unable to allocate memory for biomolecule residue / chain perception.", obError); |
| 446 |
|
|
// exit(1); |
| 447 |
|
|
} |
| 448 |
|
|
|
| 449 |
|
|
void GenerateByteCodes(ByteCode **node, int resid, int curr, int prev, int bond) |
| 450 |
|
|
{ |
| 451 |
|
|
StackType neighbour[4]; |
| 452 |
|
|
StackType original; |
| 453 |
|
|
int count,i,j; |
| 454 |
|
|
ByteCode *ptr; |
| 455 |
|
|
bool done,found; |
| 456 |
|
|
|
| 457 |
|
|
if( curr != prev ) |
| 458 |
|
|
{ |
| 459 |
|
|
if( MonoAtom[curr].atomid < ATOMMINAMINO ) |
| 460 |
|
|
{ |
| 461 |
|
|
found = false; |
| 462 |
|
|
while( *node && ((*node)->type==BC_IDENT) ) |
| 463 |
|
|
{ |
| 464 |
|
|
if( (*node)->ident.value == MonoAtom[curr].atomid ) |
| 465 |
|
|
{ |
| 466 |
|
|
node = (ByteCode**)&(*node)->ident.tcond; |
| 467 |
|
|
found = true; |
| 468 |
|
|
break; |
| 469 |
|
|
} |
| 470 |
|
|
else |
| 471 |
|
|
node = (ByteCode**)&(*node)->ident.fcond; |
| 472 |
|
|
} |
| 473 |
|
|
|
| 474 |
|
|
if (!found) |
| 475 |
|
|
{ |
| 476 |
|
|
ptr = AllocateByteCode(BC_IDENT); |
| 477 |
|
|
ptr->ident.tcond = (ByteCode*)0; |
| 478 |
|
|
ptr->ident.fcond = *node; |
| 479 |
|
|
*node = ptr; |
| 480 |
|
|
node = (ByteCode**)&ptr->ident.tcond; |
| 481 |
|
|
ptr->ident.value = MonoAtom[curr].atomid; |
| 482 |
|
|
} |
| 483 |
|
|
MonoBond[bond].index = BondIndex++; |
| 484 |
|
|
done = true; |
| 485 |
|
|
} |
| 486 |
|
|
else if( MonoAtom[curr].index != -1 ) |
| 487 |
|
|
{ |
| 488 |
|
|
while( *node && ((*node)->type==BC_IDENT) ) |
| 489 |
|
|
node = (ByteCode**)&(*node)->ident.fcond; |
| 490 |
|
|
|
| 491 |
|
|
found = false; |
| 492 |
|
|
while( *node && ((*node)->type==BC_LOCAL) ) |
| 493 |
|
|
{ |
| 494 |
|
|
if( (*node)->local.value == MonoAtom[curr].index ) |
| 495 |
|
|
{ |
| 496 |
|
|
node = (ByteCode**)&(*node)->local.tcond; |
| 497 |
|
|
found = true; |
| 498 |
|
|
break; |
| 499 |
|
|
} |
| 500 |
|
|
else |
| 501 |
|
|
node = (ByteCode**)&(*node)->local.fcond; |
| 502 |
|
|
} |
| 503 |
|
|
|
| 504 |
|
|
if (!found) |
| 505 |
|
|
{ |
| 506 |
|
|
ptr = AllocateByteCode(BC_LOCAL); |
| 507 |
|
|
ptr->local.tcond = (ByteCode*)0; |
| 508 |
|
|
ptr->local.fcond = *node; |
| 509 |
|
|
*node = ptr; |
| 510 |
|
|
node = (ByteCode**)&ptr->local.tcond; |
| 511 |
|
|
ptr->local.value = MonoAtom[curr].index; |
| 512 |
|
|
} |
| 513 |
|
|
|
| 514 |
|
|
MonoBond[bond].index = BondIndex++; |
| 515 |
|
|
done = true; |
| 516 |
|
|
} |
| 517 |
|
|
else |
| 518 |
|
|
{ |
| 519 |
|
|
while( *node && ((*node)->type==BC_IDENT) ) |
| 520 |
|
|
node = (ByteCode**)&(*node)->ident.fcond; |
| 521 |
|
|
while( *node && ((*node)->type==BC_LOCAL) ) |
| 522 |
|
|
node = (ByteCode**)&(*node)->local.fcond; |
| 523 |
|
|
|
| 524 |
|
|
found = false; |
| 525 |
|
|
while( *node && ((*node)->type==BC_ELEM) ) |
| 526 |
|
|
{ |
| 527 |
|
|
if( (*node)->elem.value == MonoAtom[curr].elem ) |
| 528 |
|
|
{ |
| 529 |
|
|
node = (ByteCode**)&(*node)->elem.tcond; |
| 530 |
|
|
found = true; |
| 531 |
|
|
break; |
| 532 |
|
|
} |
| 533 |
|
|
else |
| 534 |
|
|
node = (ByteCode**)&(*node)->elem.fcond; |
| 535 |
|
|
} |
| 536 |
|
|
|
| 537 |
|
|
if( !found ) |
| 538 |
|
|
{ |
| 539 |
|
|
ptr = AllocateByteCode(BC_ELEM); |
| 540 |
|
|
ptr->elem.tcond = (ByteCode*)0; |
| 541 |
|
|
ptr->elem.fcond = *node; |
| 542 |
|
|
*node = ptr; |
| 543 |
|
|
node = (ByteCode**)&ptr->elem.tcond; |
| 544 |
|
|
ptr->elem.value = MonoAtom[curr].elem; |
| 545 |
|
|
} |
| 546 |
|
|
|
| 547 |
|
|
MonoAtom[curr].index = AtomIndex++; |
| 548 |
|
|
MonoBond[bond].index = BondIndex++; |
| 549 |
|
|
done = false; |
| 550 |
|
|
} |
| 551 |
|
|
} |
| 552 |
|
|
else |
| 553 |
|
|
{ |
| 554 |
|
|
MonoAtom[curr].index = AtomIndex++; |
| 555 |
|
|
done = false; |
| 556 |
|
|
} |
| 557 |
|
|
|
| 558 |
|
|
count = 0; |
| 559 |
|
|
if (!done) |
| 560 |
|
|
{ |
| 561 |
|
|
for( i=0; i<MonoBondCount; i++ ) |
| 562 |
|
|
{ |
| 563 |
|
|
if( MonoBond[i].src == curr ) |
| 564 |
|
|
{ |
| 565 |
|
|
if( MonoBond[i].dst != prev ) |
| 566 |
|
|
{ |
| 567 |
|
|
neighbour[count].atom = MonoBond[i].dst; |
| 568 |
|
|
neighbour[count].bond = i; |
| 569 |
|
|
count++; |
| 570 |
|
|
} |
| 571 |
|
|
} |
| 572 |
|
|
else if( MonoBond[i].dst == curr ) |
| 573 |
|
|
{ |
| 574 |
|
|
if( MonoBond[i].src != prev ) |
| 575 |
|
|
{ |
| 576 |
|
|
neighbour[count].atom = MonoBond[i].src; |
| 577 |
|
|
neighbour[count].bond = i; |
| 578 |
|
|
count++; |
| 579 |
|
|
} |
| 580 |
|
|
} |
| 581 |
|
|
} |
| 582 |
|
|
|
| 583 |
|
|
if ( *node && ((*node)->type==BC_EVAL) ) |
| 584 |
|
|
{ |
| 585 |
|
|
found = false; |
| 586 |
|
|
node = (ByteCode**)&(*node)->eval.next; |
| 587 |
|
|
while( *node && ((*node)->type==BC_COUNT) ) |
| 588 |
|
|
{ |
| 589 |
|
|
if( (*node)->count.value == count ) |
| 590 |
|
|
{ |
| 591 |
|
|
node = (ByteCode**)&(*node)->count.tcond; |
| 592 |
|
|
found = true; |
| 593 |
|
|
break; |
| 594 |
|
|
} |
| 595 |
|
|
else |
| 596 |
|
|
node = (ByteCode**)&(*node)->count.fcond; |
| 597 |
|
|
} |
| 598 |
|
|
|
| 599 |
|
|
if( !found ) |
| 600 |
|
|
{ |
| 601 |
|
|
ptr = AllocateByteCode(BC_COUNT); |
| 602 |
|
|
ptr->count.tcond = (ByteCode*)0; |
| 603 |
|
|
ptr->count.fcond = *node; |
| 604 |
|
|
*node = ptr; |
| 605 |
|
|
node = (ByteCode**)&ptr->count.tcond; |
| 606 |
|
|
ptr->count.value = count; |
| 607 |
|
|
} |
| 608 |
|
|
} |
| 609 |
|
|
else if( count || StrictFlag || StackPtr ) |
| 610 |
|
|
{ |
| 611 |
|
|
ptr = AllocateByteCode(BC_EVAL); |
| 612 |
|
|
ptr->eval.next = *node; |
| 613 |
|
|
*node = ptr; |
| 614 |
|
|
node = (ByteCode**)&ptr->eval.next; |
| 615 |
|
|
|
| 616 |
|
|
ptr = AllocateByteCode(BC_COUNT); |
| 617 |
|
|
ptr->count.tcond = (ByteCode*)0; |
| 618 |
|
|
ptr->count.fcond = *node; |
| 619 |
|
|
*node = ptr; |
| 620 |
|
|
node = (ByteCode**)&ptr->count.tcond; |
| 621 |
|
|
ptr->count.value = count; |
| 622 |
|
|
} |
| 623 |
|
|
} |
| 624 |
|
|
|
| 625 |
|
|
if( count == 1 ) |
| 626 |
|
|
{ |
| 627 |
|
|
GenerateByteCodes(node,resid,neighbour[0].atom, curr,neighbour[0].bond); |
| 628 |
|
|
} |
| 629 |
|
|
else if( count == 2 ) |
| 630 |
|
|
{ |
| 631 |
|
|
original = Stack[StackPtr++]; |
| 632 |
|
|
Stack[StackPtr-1] = neighbour[0]; |
| 633 |
|
|
Stack[StackPtr-1].prev = curr; |
| 634 |
|
|
GenerateByteCodes(node,resid,neighbour[1].atom, |
| 635 |
|
|
curr,neighbour[1].bond); |
| 636 |
|
|
Stack[StackPtr-1] = neighbour[1]; |
| 637 |
|
|
Stack[StackPtr-1].prev = curr; |
| 638 |
|
|
GenerateByteCodes(node,resid,neighbour[0].atom, |
| 639 |
|
|
curr,neighbour[0].bond); |
| 640 |
|
|
Stack[--StackPtr] = original; |
| 641 |
|
|
} |
| 642 |
|
|
else if( count ) |
| 643 |
|
|
{ |
| 644 |
|
|
#ifdef HAVE_SSTREAM |
| 645 |
|
|
stringstream errorMsg; |
| 646 |
|
|
#else |
| 647 |
|
|
strstream errorMsg; |
| 648 |
|
|
#endif |
| 649 |
|
|
errorMsg << "Maximum Monomer Fanout Exceeded!" << endl; |
| 650 |
|
|
errorMsg << "Residue " << ChainsResName[resid] << " atom " |
| 651 |
|
|
<< curr << endl; |
| 652 |
|
|
errorMsg << "Previous = " << prev << " Fanout = " << count << endl; |
| 653 |
|
|
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning); |
| 654 |
|
|
// exit(1); |
| 655 |
|
|
} |
| 656 |
|
|
else if( StackPtr ) |
| 657 |
|
|
{ |
| 658 |
|
|
StackPtr--; |
| 659 |
|
|
GenerateByteCodes(node,resid,Stack[StackPtr].atom, |
| 660 |
|
|
Stack[StackPtr].prev,Stack[StackPtr].bond); |
| 661 |
|
|
StackPtr++; |
| 662 |
|
|
} |
| 663 |
|
|
else if( !(*node) ) |
| 664 |
|
|
{ |
| 665 |
|
|
ptr = AllocateByteCode(BC_ASSIGN); |
| 666 |
|
|
ptr->assign.resid = resid; |
| 667 |
|
|
ptr->assign.atomid = (int*)malloc(AtomIndex*sizeof(int)); |
| 668 |
|
|
if( !ptr->assign.atomid ) |
| 669 |
|
|
FatalMemoryError(); |
| 670 |
|
|
for( i=0; i<MonoAtomCount; i++ ) |
| 671 |
|
|
if( (j=MonoAtom[i].index) != -1 ) |
| 672 |
|
|
ptr->assign.atomid[j] = MonoAtom[i].atomid; |
| 673 |
|
|
if( BondIndex ) |
| 674 |
|
|
{ |
| 675 |
|
|
ptr->assign.bflags = (int*)malloc(BondIndex*sizeof(int)); |
| 676 |
|
|
for( i=0; i<MonoBondCount; i++ ) |
| 677 |
|
|
if( (j=MonoBond[i].index) != -1 ) |
| 678 |
|
|
ptr->assign.bflags[j] = MonoBond[i].flag; |
| 679 |
|
|
} |
| 680 |
|
|
*node = ptr; |
| 681 |
|
|
} |
| 682 |
|
|
else if( (*node)->type == BC_ASSIGN ) |
| 683 |
|
|
{ |
| 684 |
|
|
if( (*node)->assign.resid != resid ) |
| 685 |
|
|
{ |
| 686 |
|
|
fputs("Error: Duplicated Monomer Specification!\n",stderr); |
| 687 |
|
|
fprintf(stderr,"Residue %s matches resid",ChainsResName[resid]); |
| 688 |
|
|
fprintf(stderr,"ue %s!\n",ChainsResName[(*node)->assign.resid]); |
| 689 |
|
|
} |
| 690 |
|
|
} |
| 691 |
|
|
|
| 692 |
|
|
/* Restore State! */ |
| 693 |
|
|
if( curr != prev ) |
| 694 |
|
|
{ |
| 695 |
|
|
if( !done ) |
| 696 |
|
|
{ |
| 697 |
|
|
MonoAtom[curr].index = -1; |
| 698 |
|
|
AtomIndex--; |
| 699 |
|
|
} |
| 700 |
|
|
MonoBond[bond].index = -1; |
| 701 |
|
|
BondIndex--; |
| 702 |
|
|
} |
| 703 |
|
|
} |
| 704 |
|
|
|
| 705 |
|
|
////////////////////////////////////////////////////////////////////////////// |
| 706 |
|
|
// Constructors / Destructors |
| 707 |
|
|
////////////////////////////////////////////////////////////////////////////// |
| 708 |
|
|
|
| 709 |
|
|
// validated |
| 710 |
|
|
OBChainsParser::OBChainsParser(void) |
| 711 |
|
|
{ |
| 712 |
|
|
int i, res = RESIDMIN; |
| 713 |
|
|
|
| 714 |
|
|
PDecisionTree = (ByteCode*)0; |
| 715 |
|
|
for( i=0 ; i < AMINOMAX ; i++ ) |
| 716 |
|
|
{ |
| 717 |
|
|
strcpy(ChainsResName[res],AminoAcids[i].name); |
| 718 |
|
|
DefineMonomer(&PDecisionTree,res,AminoAcids[i].data); |
| 719 |
|
|
res++; |
| 720 |
|
|
} |
| 721 |
|
|
|
| 722 |
|
|
NDecisionTree = (ByteCode*)0; |
| 723 |
|
|
for( i=0 ; i< NUCLEOMAX ; i++ ) |
| 724 |
|
|
{ |
| 725 |
|
|
strcpy(ChainsResName[res],Nucleotides[i].name); |
| 726 |
|
|
DefineMonomer(&NDecisionTree,res,Nucleotides[i].data); |
| 727 |
|
|
res++; |
| 728 |
|
|
} |
| 729 |
|
|
|
| 730 |
|
|
bitmasks = NULL; |
| 731 |
|
|
hetflags = NULL; |
| 732 |
|
|
atomids = NULL; |
| 733 |
|
|
resids = NULL; |
| 734 |
|
|
resnos = NULL; |
| 735 |
|
|
sernos = NULL; |
| 736 |
|
|
hcounts = NULL; |
| 737 |
|
|
chains = NULL; |
| 738 |
|
|
flags = NULL; |
| 739 |
|
|
} |
| 740 |
|
|
|
| 741 |
|
|
OBChainsParser::~OBChainsParser(void) |
| 742 |
|
|
{ |
| 743 |
|
|
DeleteByteCode((ByteCode*)PDecisionTree); |
| 744 |
|
|
DeleteByteCode((ByteCode*)NDecisionTree); |
| 745 |
|
|
} |
| 746 |
|
|
|
| 747 |
|
|
////////////////////////////////////////////////////////////////////////////// |
| 748 |
|
|
// Setup / Cleanup Functions |
| 749 |
|
|
////////////////////////////////////////////////////////////////////////////// |
| 750 |
|
|
|
| 751 |
|
|
void OBChainsParser::SetupMol(OBMol &mol) |
| 752 |
|
|
{ |
| 753 |
|
|
CleanupMol(); |
| 754 |
|
|
|
| 755 |
|
|
int i; |
| 756 |
|
|
int asize = mol.NumAtoms(); |
| 757 |
|
|
int bsize = mol.NumBonds(); |
| 758 |
|
|
|
| 759 |
|
|
bitmasks = new unsigned short[asize]; |
| 760 |
|
|
resids = new unsigned char[asize]; |
| 761 |
|
|
flags = new unsigned char[bsize]; |
| 762 |
|
|
hetflags = new bool[asize]; |
| 763 |
|
|
atomids = new short[asize]; |
| 764 |
|
|
resnos = new short[asize]; |
| 765 |
|
|
sernos = new short[asize]; |
| 766 |
|
|
hcounts = new char[asize]; |
| 767 |
|
|
chains = new char[asize]; |
| 768 |
|
|
|
| 769 |
|
|
memset(bitmasks, 0, sizeof(unsigned short) * asize); |
| 770 |
|
|
memset(resids, 0, sizeof(unsigned char) * asize); |
| 771 |
|
|
memset(hetflags, 0, sizeof(bool) * asize); |
| 772 |
|
|
memset(resnos, 0, sizeof(short) * asize); |
| 773 |
|
|
memset(sernos, 0, sizeof(short) * asize); |
| 774 |
|
|
memset(hcounts, 0, sizeof(char) * asize); |
| 775 |
|
|
memset(chains, ' ', sizeof(char) * asize); |
| 776 |
|
|
|
| 777 |
|
|
memset(flags, 0, sizeof(unsigned char) * bsize); |
| 778 |
|
|
|
| 779 |
|
|
for ( i = 0 ; i < asize ; i++ ) |
| 780 |
|
|
{ |
| 781 |
|
|
atomids[i] = -1; |
| 782 |
|
|
} |
| 783 |
|
|
} |
| 784 |
|
|
|
| 785 |
|
|
void OBChainsParser::CleanupMol(void) |
| 786 |
|
|
{ |
| 787 |
|
|
if (bitmasks != NULL) |
| 788 |
|
|
{ |
| 789 |
|
|
delete bitmasks; |
| 790 |
|
|
bitmasks = NULL; |
| 791 |
|
|
} |
| 792 |
|
|
if (hetflags != NULL) |
| 793 |
|
|
{ |
| 794 |
|
|
delete hetflags; |
| 795 |
|
|
hetflags = NULL; |
| 796 |
|
|
} |
| 797 |
|
|
if (atomids != NULL) |
| 798 |
|
|
{ |
| 799 |
|
|
delete atomids; |
| 800 |
|
|
atomids = NULL; |
| 801 |
|
|
} |
| 802 |
|
|
if (resids != NULL) |
| 803 |
|
|
{ |
| 804 |
|
|
delete resids; |
| 805 |
|
|
resids = NULL; |
| 806 |
|
|
} |
| 807 |
|
|
if (resnos != NULL) |
| 808 |
|
|
{ |
| 809 |
|
|
delete resnos; |
| 810 |
|
|
resnos = NULL; |
| 811 |
|
|
} |
| 812 |
|
|
if (sernos != NULL) |
| 813 |
|
|
{ |
| 814 |
|
|
delete sernos; |
| 815 |
|
|
sernos = NULL; |
| 816 |
|
|
} |
| 817 |
|
|
if (hcounts != NULL) |
| 818 |
|
|
{ |
| 819 |
|
|
delete hcounts; |
| 820 |
|
|
hcounts = NULL; |
| 821 |
|
|
} |
| 822 |
|
|
if (chains != NULL) |
| 823 |
|
|
{ |
| 824 |
|
|
delete chains; |
| 825 |
|
|
chains = NULL; |
| 826 |
|
|
} |
| 827 |
|
|
if (flags != NULL) |
| 828 |
|
|
{ |
| 829 |
|
|
delete flags; |
| 830 |
|
|
flags = NULL; |
| 831 |
|
|
} |
| 832 |
|
|
} |
| 833 |
|
|
|
| 834 |
|
|
void OBChainsParser::ClearResidueInformation(OBMol &mol) |
| 835 |
|
|
{ |
| 836 |
|
|
OBResidue *residue; |
| 837 |
|
|
vector<OBResidue*> residues; |
| 838 |
|
|
vector<OBResidue*>::iterator r; |
| 839 |
|
|
|
| 840 |
|
|
for (residue = mol.BeginResidue(r) ; residue ; residue = mol.NextResidue(r)) |
| 841 |
|
|
residues.push_back(residue); |
| 842 |
|
|
|
| 843 |
|
|
for ( unsigned int i = 0 ; i < residues.size() ; i++ ) |
| 844 |
|
|
mol.DeleteResidue(residues[i]); |
| 845 |
|
|
|
| 846 |
|
|
residues.clear(); |
| 847 |
|
|
} |
| 848 |
|
|
|
| 849 |
|
|
void OBChainsParser::SetResidueInformation(OBMol &mol, bool nukeSingleResidue) |
| 850 |
|
|
{ |
| 851 |
|
|
char buffer[256]; |
| 852 |
|
|
char *symbol; |
| 853 |
|
|
string atomid, name; |
| 854 |
|
|
|
| 855 |
|
|
OBAtom *atom; |
| 856 |
|
|
OBResidue *residue; |
| 857 |
|
|
map<short, OBResidue *> resmap; |
| 858 |
|
|
|
| 859 |
|
|
int size = mol.NumAtoms(); |
| 860 |
|
|
for ( int i = 0 ; i < size ; i++ ) |
| 861 |
|
|
{ |
| 862 |
|
|
atom = mol.GetAtom(i+1); // WARNING: ATOM INDEX ISSUE |
| 863 |
|
|
|
| 864 |
|
|
if (atomids[i] == -1) |
| 865 |
|
|
{ |
| 866 |
|
|
symbol = etab.GetSymbol(atom->GetAtomicNum()); |
| 867 |
|
|
if( symbol[1] ) |
| 868 |
|
|
{ |
| 869 |
|
|
buffer[0] = symbol[0]; |
| 870 |
|
|
buffer[1] = (char) toupper(symbol[1]); |
| 871 |
|
|
} |
| 872 |
|
|
else |
| 873 |
|
|
{ |
| 874 |
|
|
buffer[0] = ' '; |
| 875 |
|
|
buffer[1] = symbol[0]; |
| 876 |
|
|
} |
| 877 |
|
|
buffer[2] = ' '; |
| 878 |
|
|
buffer[3] = ' '; |
| 879 |
|
|
buffer[4] = '\0'; |
| 880 |
|
|
} |
| 881 |
|
|
else if (atom->IsHydrogen()) |
| 882 |
|
|
{ |
| 883 |
|
|
if (hcounts[i]) |
| 884 |
|
|
sprintf(buffer, "%cH%.2s", hcounts[i]+'0', ChainsAtomName[atomids[i]]+2); |
| 885 |
|
|
else |
| 886 |
|
|
sprintf(buffer, "H%.2s", ChainsAtomName[atomids[i]]+2); |
| 887 |
|
|
} |
| 888 |
|
|
else |
| 889 |
|
|
sprintf(buffer, "%.4s", ChainsAtomName[atomids[i]]); |
| 890 |
|
|
|
| 891 |
|
|
if (buffer[3] == ' ') |
| 892 |
|
|
buffer[3] = '\0'; |
| 893 |
|
|
|
| 894 |
|
|
atomid = (buffer[0] == ' ') ? buffer + 1 : buffer; |
| 895 |
|
|
|
| 896 |
|
|
if (resmap.find(resnos[i]) != resmap.end()) |
| 897 |
|
|
{ |
| 898 |
|
|
residue = resmap[resnos[i]]; |
| 899 |
|
|
residue->AddAtom(atom); |
| 900 |
|
|
residue->SetAtomID(atom, atomid); |
| 901 |
|
|
residue->SetHetAtom(atom, hetflags[i]); |
| 902 |
|
|
residue->SetSerialNum(atom, sernos[i]); |
| 903 |
|
|
} |
| 904 |
|
|
else |
| 905 |
|
|
{ |
| 906 |
|
|
name = ChainsResName[resids[i]]; |
| 907 |
|
|
residue = mol.NewResidue(); |
| 908 |
|
|
|
| 909 |
|
|
residue->SetName(name); |
| 910 |
|
|
residue->SetNum(resnos[i]); |
| 911 |
|
|
residue->SetChain(chains[i]); |
| 912 |
|
|
residue->SetChainNum((chains[i] > 'A') ? (int)(chains[i] - 'A') : 1); |
| 913 |
|
|
|
| 914 |
|
|
residue->AddAtom(atom); |
| 915 |
|
|
residue->SetAtomID(atom, atomid); |
| 916 |
|
|
residue->SetHetAtom(atom, hetflags[i]); |
| 917 |
|
|
residue->SetSerialNum(atom, sernos[i]); |
| 918 |
|
|
|
| 919 |
|
|
resmap[resnos[i]] = residue; |
| 920 |
|
|
} |
| 921 |
|
|
} |
| 922 |
|
|
|
| 923 |
|
|
if (mol.NumResidues() == 1 && nukeSingleResidue) |
| 924 |
|
|
mol.DeleteResidue(mol.GetResidue(0)); |
| 925 |
|
|
} |
| 926 |
|
|
|
| 927 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 928 |
|
|
// Perception Functions |
| 929 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 930 |
|
|
|
| 931 |
|
|
bool OBChainsParser::PerceiveChains(OBMol &mol, bool nukeSingleResidue) |
| 932 |
|
|
{ |
| 933 |
|
|
bool result = true; |
| 934 |
|
|
|
| 935 |
|
|
SetupMol(mol); |
| 936 |
|
|
ClearResidueInformation(mol); |
| 937 |
|
|
|
| 938 |
|
|
result = DetermineHetAtoms(mol) && result; |
| 939 |
|
|
result = DetermineConnectedChains(mol) && result; |
| 940 |
|
|
result = DeterminePeptideBackbone(mol) && result; |
| 941 |
|
|
result = DeterminePeptideSidechains(mol) && result; |
| 942 |
|
|
result = DetermineNucleicBackbone(mol) && result; |
| 943 |
|
|
result = DetermineNucleicSidechains(mol) && result; |
| 944 |
|
|
result = DetermineHydrogens(mol) && result; |
| 945 |
|
|
|
| 946 |
|
|
SetResidueInformation(mol, nukeSingleResidue); |
| 947 |
|
|
CleanupMol(); |
| 948 |
|
|
|
| 949 |
|
|
obErrorLog.ThrowError(__FUNCTION__, |
| 950 |
|
|
"Ran OpenBabel::PerceiveChains", obAuditMsg); |
| 951 |
|
|
|
| 952 |
|
|
return result; |
| 953 |
|
|
} |
| 954 |
|
|
|
| 955 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 956 |
|
|
// Hetero Atom Perception |
| 957 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 958 |
|
|
|
| 959 |
|
|
bool OBChainsParser::DetermineHetAtoms(OBMol &mol) |
| 960 |
|
|
{ |
| 961 |
|
|
OBAtom *atom; |
| 962 |
|
|
vector<OBNodeBase *>::iterator a; |
| 963 |
|
|
for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a)) |
| 964 |
|
|
if (!atom->IsHydrogen() && atom->GetValence() == 0) |
| 965 |
|
|
{ |
| 966 |
|
|
resids[atom->GetIdx()-1] = (atom->IsOxygen()) ? 1 : 2; |
| 967 |
|
|
hetflags[atom->GetIdx()-1] = true; |
| 968 |
|
|
} |
| 969 |
|
|
return true; |
| 970 |
|
|
} |
| 971 |
|
|
|
| 972 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 973 |
|
|
// Connected Chain Perception |
| 974 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 975 |
|
|
|
| 976 |
|
|
bool OBChainsParser::DetermineConnectedChains(OBMol &mol) |
| 977 |
|
|
{ |
| 978 |
|
|
int resid; |
| 979 |
|
|
int resno; |
| 980 |
|
|
int count; |
| 981 |
|
|
int size; |
| 982 |
|
|
int i,idx; |
| 983 |
|
|
int numAtoms; |
| 984 |
|
|
|
| 985 |
|
|
resno = 1; |
| 986 |
|
|
count = 0; |
| 987 |
|
|
numAtoms = mol.NumAtoms(); |
| 988 |
|
|
|
| 989 |
|
|
OBAtom *atom; |
| 990 |
|
|
vector<OBNodeBase *>::iterator a; |
| 991 |
|
|
for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a)) |
| 992 |
|
|
{ |
| 993 |
|
|
idx = atom->GetIdx() - 1; |
| 994 |
|
|
if (!hetflags[idx] && chains[idx] == ' ' && !atom->IsHydrogen()) |
| 995 |
|
|
{ |
| 996 |
|
|
size = RecurseChain(mol, idx, 'A' + count); |
| 997 |
|
|
if (size < 10) |
| 998 |
|
|
{ |
| 999 |
|
|
if (size == 1 && atom->IsOxygen()) |
| 1000 |
|
|
resid = 1; /* HOH */ |
| 1001 |
|
|
else |
| 1002 |
|
|
resid = 2; |
| 1003 |
|
|
|
| 1004 |
|
|
for (i = 0 ; i < numAtoms ; i++) |
| 1005 |
|
|
{ |
| 1006 |
|
|
if (chains[i] == ('A' + count)) |
| 1007 |
|
|
{ |
| 1008 |
|
|
hetflags[i] = true; |
| 1009 |
|
|
resids[i] = resid; |
| 1010 |
|
|
resnos[i] = resno; |
| 1011 |
|
|
chains[i] = ' '; |
| 1012 |
|
|
} |
| 1013 |
|
|
} |
| 1014 |
|
|
resno++; |
| 1015 |
|
|
} |
| 1016 |
|
|
else |
| 1017 |
|
|
count++; |
| 1018 |
|
|
} |
| 1019 |
|
|
} |
| 1020 |
|
|
|
| 1021 |
|
|
if( count == 1 ) |
| 1022 |
|
|
for ( i = 0 ; i < numAtoms ; i++ ) |
| 1023 |
|
|
chains[i] = ' '; |
| 1024 |
|
|
|
| 1025 |
|
|
return true; |
| 1026 |
|
|
} |
| 1027 |
|
|
|
| 1028 |
|
|
int OBChainsParser::RecurseChain(OBMol &mol, int i, int c) |
| 1029 |
|
|
{ |
| 1030 |
|
|
OBAtom *atom, *nbr; |
| 1031 |
|
|
vector<OBEdgeBase *>::iterator b; |
| 1032 |
|
|
int result, index; |
| 1033 |
|
|
|
| 1034 |
|
|
atom = mol.GetAtom(i+1); |
| 1035 |
|
|
if (atom->IsHydrogen() ) |
| 1036 |
|
|
return 0; |
| 1037 |
|
|
|
| 1038 |
|
|
result = 1; |
| 1039 |
|
|
chains[i] = c; |
| 1040 |
|
|
|
| 1041 |
|
|
for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b)) |
| 1042 |
|
|
{ |
| 1043 |
|
|
index = nbr->GetIdx() - 1; |
| 1044 |
|
|
if (chains[index] == ' ') |
| 1045 |
|
|
result += RecurseChain(mol, index,c); |
| 1046 |
|
|
} |
| 1047 |
|
|
|
| 1048 |
|
|
return (result); |
| 1049 |
|
|
} |
| 1050 |
|
|
|
| 1051 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1052 |
|
|
// Peptide Backbone Perception |
| 1053 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1054 |
|
|
|
| 1055 |
|
|
bool OBChainsParser::DeterminePeptideBackbone(OBMol &mol) |
| 1056 |
|
|
{ |
| 1057 |
|
|
ConstrainBackbone(mol, Peptide, MAXPEPTIDE); |
| 1058 |
|
|
|
| 1059 |
|
|
int i, max = mol.NumAtoms(); |
| 1060 |
|
|
|
| 1061 |
|
|
/* |
| 1062 |
|
|
int count = 0; |
| 1063 |
|
|
for ( i = 0 ; i < max ; i++ ) |
| 1064 |
|
|
if ( bitmasks[i]&BitCAAll ) |
| 1065 |
|
|
count++; |
| 1066 |
|
|
|
| 1067 |
|
|
fprintf(stderr,"%d alpha carbons\n",count); |
| 1068 |
|
|
*/ |
| 1069 |
|
|
|
| 1070 |
|
|
/* Order Peptide Backbone */ |
| 1071 |
|
|
|
| 1072 |
|
|
for ( i = 0 ; i < max ; i++ ) |
| 1073 |
|
|
if (atomids[i] == -1) |
| 1074 |
|
|
{ |
| 1075 |
|
|
if( bitmasks[i] & BitNTer ) |
| 1076 |
|
|
{ |
| 1077 |
|
|
atomids[i] = AI_N; |
| 1078 |
|
|
TracePeptideChain(mol,i,1); |
| 1079 |
|
|
} |
| 1080 |
|
|
else if( (bitmasks[i]&BitNPT) && !(bitmasks[i]&BitN) ) |
| 1081 |
|
|
{ |
| 1082 |
|
|
atomids[i] = AI_N; |
| 1083 |
|
|
TracePeptideChain(mol,i,1); |
| 1084 |
|
|
} |
| 1085 |
|
|
} |
| 1086 |
|
|
|
| 1087 |
|
|
/* Carbonyl Double Bond */ |
| 1088 |
|
|
|
| 1089 |
|
|
OBBond *bond; |
| 1090 |
|
|
vector<OBEdgeBase*>::iterator b; |
| 1091 |
|
|
for (bond = mol.BeginBond(b) ; bond ; bond = mol.NextBond(b)) |
| 1092 |
|
|
{ |
| 1093 |
|
|
if ((atomids[bond->GetBeginAtomIdx()-1] == 2 && atomids[bond->GetEndAtomIdx()-1] == 3) || |
| 1094 |
|
|
(atomids[bond->GetBeginAtomIdx()-1] == 3 && atomids[bond->GetEndAtomIdx()-1] == 2)) |
| 1095 |
|
|
flags[bond->GetIdx()] |= BF_DOUBLE; |
| 1096 |
|
|
} |
| 1097 |
|
|
|
| 1098 |
|
|
return true; |
| 1099 |
|
|
} |
| 1100 |
|
|
|
| 1101 |
|
|
void OBChainsParser::ConstrainBackbone(OBMol &mol, Template *templ, int tmax) |
| 1102 |
|
|
{ |
| 1103 |
|
|
static OBAtom *neighbour[6]; |
| 1104 |
|
|
Template *pep; |
| 1105 |
|
|
OBAtom *na,*nb,*nc,*nd; |
| 1106 |
|
|
OBAtom *atom, *nbr; |
| 1107 |
|
|
bool change, result; |
| 1108 |
|
|
int count; |
| 1109 |
|
|
int i,idx; |
| 1110 |
|
|
|
| 1111 |
|
|
vector<OBNodeBase *>::iterator a; |
| 1112 |
|
|
vector<OBEdgeBase *>::iterator b; |
| 1113 |
|
|
|
| 1114 |
|
|
/* First Pass */ |
| 1115 |
|
|
|
| 1116 |
|
|
for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a)) |
| 1117 |
|
|
{ |
| 1118 |
|
|
idx = atom->GetIdx() - 1; |
| 1119 |
|
|
bitmasks[idx] = 0; |
| 1120 |
|
|
for ( i = 0 ; i < tmax ; i++ ) |
| 1121 |
|
|
if ( (static_cast<unsigned int>(templ[i].elem) == atom->GetAtomicNum()) |
| 1122 |
|
|
&& |
| 1123 |
|
|
(static_cast<unsigned int>(templ[i].count) == atom->GetValence())) |
| 1124 |
|
|
bitmasks[idx] |= templ[i].flag; |
| 1125 |
|
|
} |
| 1126 |
|
|
|
| 1127 |
|
|
/* Second Pass */ |
| 1128 |
|
|
|
| 1129 |
|
|
do |
| 1130 |
|
|
{ |
| 1131 |
|
|
change = false; |
| 1132 |
|
|
for (atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a)) |
| 1133 |
|
|
{ |
| 1134 |
|
|
idx = atom->GetIdx() - 1; |
| 1135 |
|
|
if (bitmasks[idx]) // Determine Neighbours |
| 1136 |
|
|
{ |
| 1137 |
|
|
count = 0; |
| 1138 |
|
|
for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b)) |
| 1139 |
|
|
if (!nbr->IsHydrogen()) |
| 1140 |
|
|
neighbour[count++] = nbr; |
| 1141 |
|
|
|
| 1142 |
|
|
na = neighbour[0]; |
| 1143 |
|
|
nb = neighbour[1]; |
| 1144 |
|
|
nc = neighbour[2]; |
| 1145 |
|
|
nd = neighbour[3]; |
| 1146 |
|
|
|
| 1147 |
|
|
for ( i = 0 ; i < tmax ; i++ ) |
| 1148 |
|
|
if ( templ[i].flag & bitmasks[idx] ) |
| 1149 |
|
|
{ |
| 1150 |
|
|
pep = &templ[i]; |
| 1151 |
|
|
result = true; |
| 1152 |
|
|
|
| 1153 |
|
|
if (count == 4) |
| 1154 |
|
|
result = Match4Constraints(pep,na,nb,nc,nd); |
| 1155 |
|
|
else if (count == 3) |
| 1156 |
|
|
result = Match3Constraints(pep,na,nb,nc); |
| 1157 |
|
|
else if (count == 2) |
| 1158 |
|
|
result = Match2Constraints(pep,na,nb); |
| 1159 |
|
|
else // count == 1 |
| 1160 |
|
|
result = MatchConstraint(na,pep->n1); |
| 1161 |
|
|
|
| 1162 |
|
|
if(result == false) |
| 1163 |
|
|
{ |
| 1164 |
|
|
bitmasks[idx] &= ~pep->flag; |
| 1165 |
|
|
change = true; |
| 1166 |
|
|
} |
| 1167 |
|
|
} |
| 1168 |
|
|
} |
| 1169 |
|
|
} |
| 1170 |
|
|
} |
| 1171 |
|
|
while( change ); |
| 1172 |
|
|
} |
| 1173 |
|
|
|
| 1174 |
|
|
bool OBChainsParser::MatchConstraint(OBAtom *atom, int mask) |
| 1175 |
|
|
{ |
| 1176 |
|
|
if (atom == NULL) |
| 1177 |
|
|
return (false); |
| 1178 |
|
|
|
| 1179 |
|
|
if( mask < 0 ) |
| 1180 |
|
|
return(atom->GetAtomicNum() == static_cast<unsigned int>(-mask)); |
| 1181 |
|
|
else |
| 1182 |
|
|
return(((bitmasks[atom->GetIdx()-1]&mask) == 0) ? false : true); |
| 1183 |
|
|
} |
| 1184 |
|
|
|
| 1185 |
|
|
bool OBChainsParser::Match2Constraints(Template *tmpl, OBAtom *na, OBAtom *nb) |
| 1186 |
|
|
{ |
| 1187 |
|
|
if (na == NULL || nb == NULL) |
| 1188 |
|
|
return (false); // don't even try to evaluate it |
| 1189 |
|
|
|
| 1190 |
|
|
if( MatchConstraint(na,tmpl->n2) ) |
| 1191 |
|
|
if( MatchConstraint(nb,tmpl->n1) ) |
| 1192 |
|
|
return( true ); |
| 1193 |
|
|
if( MatchConstraint(nb,tmpl->n2) ) |
| 1194 |
|
|
if( MatchConstraint(na,tmpl->n1) ) |
| 1195 |
|
|
return( true ); |
| 1196 |
|
|
return( false ); |
| 1197 |
|
|
} |
| 1198 |
|
|
|
| 1199 |
|
|
bool OBChainsParser::Match3Constraints(Template *tmpl, OBAtom *na, OBAtom *nb, OBAtom *nc) |
| 1200 |
|
|
{ |
| 1201 |
|
|
if (na == NULL || nb == NULL || nc == NULL) |
| 1202 |
|
|
return (false); // don't even try to evaluate it |
| 1203 |
|
|
|
| 1204 |
|
|
if( MatchConstraint(na,tmpl->n3) ) |
| 1205 |
|
|
if( Match2Constraints(tmpl,nb,nc) ) |
| 1206 |
|
|
return( true ); |
| 1207 |
|
|
if( MatchConstraint(nb,tmpl->n3) ) |
| 1208 |
|
|
if( Match2Constraints(tmpl,na,nc) ) |
| 1209 |
|
|
return( true ); |
| 1210 |
|
|
if( MatchConstraint(nc,tmpl->n3) ) |
| 1211 |
|
|
if( Match2Constraints(tmpl,na,nb) ) |
| 1212 |
|
|
return( true ); |
| 1213 |
|
|
return( false ); |
| 1214 |
|
|
} |
| 1215 |
|
|
|
| 1216 |
|
|
bool OBChainsParser::Match4Constraints(Template *tmpl, OBAtom *na, OBAtom *nb, OBAtom *nc, OBAtom *nd) |
| 1217 |
|
|
{ |
| 1218 |
|
|
if (na == NULL || nb == NULL || nc == NULL || nd == NULL) |
| 1219 |
|
|
return (false); // don't even try to evaluate it |
| 1220 |
|
|
|
| 1221 |
|
|
if( MatchConstraint(na,tmpl->n4) ) |
| 1222 |
|
|
if( Match3Constraints(tmpl,nb,nc,nd) ) |
| 1223 |
|
|
return( true ); |
| 1224 |
|
|
if( MatchConstraint(nb,tmpl->n4) ) |
| 1225 |
|
|
if( Match3Constraints(tmpl,na,nc,nd) ) |
| 1226 |
|
|
return( true ); |
| 1227 |
|
|
if( MatchConstraint(nc,tmpl->n4) ) |
| 1228 |
|
|
if( Match3Constraints(tmpl,na,nb,nd) ) |
| 1229 |
|
|
return( true ); |
| 1230 |
|
|
if( MatchConstraint(nd,tmpl->n4) ) |
| 1231 |
|
|
if( Match3Constraints(tmpl,na,nb,nc) ) |
| 1232 |
|
|
return( true ); |
| 1233 |
|
|
return( false ); |
| 1234 |
|
|
} |
| 1235 |
|
|
|
| 1236 |
|
|
void OBChainsParser::TracePeptideChain(OBMol &mol, int i, int r) |
| 1237 |
|
|
{ |
| 1238 |
|
|
int neighbour[4]; |
| 1239 |
|
|
int na,nb,nc; |
| 1240 |
|
|
OBAtom *atom, *nbr; |
| 1241 |
|
|
int count; |
| 1242 |
|
|
int j,k,idx; |
| 1243 |
|
|
|
| 1244 |
|
|
vector<OBEdgeBase *>::iterator b; |
| 1245 |
|
|
|
| 1246 |
|
|
/* Determine Neighbours */ |
| 1247 |
|
|
|
| 1248 |
|
|
atom = mol.GetAtom(i+1); |
| 1249 |
|
|
idx = atom->GetIdx() - 1; |
| 1250 |
|
|
|
| 1251 |
|
|
count = 0; |
| 1252 |
|
|
for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b)) |
| 1253 |
|
|
if (!nbr->IsHydrogen()) |
| 1254 |
|
|
neighbour[count++] = nbr->GetIdx()-1; |
| 1255 |
|
|
|
| 1256 |
|
|
resnos[idx] = r; |
| 1257 |
|
|
|
| 1258 |
|
|
na = neighbour[0]; |
| 1259 |
|
|
nb = neighbour[1]; |
| 1260 |
|
|
nc = neighbour[2]; |
| 1261 |
|
|
|
| 1262 |
|
|
switch( atomids[i] ) |
| 1263 |
|
|
{ |
| 1264 |
|
|
case(AI_N): |
| 1265 |
|
|
for( j=0; j<count; j++ ) |
| 1266 |
|
|
if( bitmasks[neighbour[j]] & BitCAAll ) |
| 1267 |
|
|
{ |
| 1268 |
|
|
atomids[neighbour[j]] = AI_CA; |
| 1269 |
|
|
TracePeptideChain(mol,neighbour[j],r); |
| 1270 |
|
|
} |
| 1271 |
|
|
break; |
| 1272 |
|
|
|
| 1273 |
|
|
case(AI_CA): |
| 1274 |
|
|
if( count == 3 ) |
| 1275 |
|
|
{ |
| 1276 |
|
|
if ( bitmasks[na] & BitNAll ) |
| 1277 |
|
|
na = nc; |
| 1278 |
|
|
else if ( bitmasks[nb] & BitNAll ) |
| 1279 |
|
|
nb = nc; |
| 1280 |
|
|
|
| 1281 |
|
|
if ( bitmasks[na] & BitC ) |
| 1282 |
|
|
{ |
| 1283 |
|
|
j = na; |
| 1284 |
|
|
k = nb; |
| 1285 |
|
|
} |
| 1286 |
|
|
else if ( bitmasks[nb] & BitC ) |
| 1287 |
|
|
{ |
| 1288 |
|
|
j = nb; |
| 1289 |
|
|
k = na; |
| 1290 |
|
|
} |
| 1291 |
|
|
else if( bitmasks[na] & BitCAll ) |
| 1292 |
|
|
{ |
| 1293 |
|
|
j = na; |
| 1294 |
|
|
k = nb; |
| 1295 |
|
|
} |
| 1296 |
|
|
else /* bitmasks[nb] & BitCAll */ |
| 1297 |
|
|
{ |
| 1298 |
|
|
j = nb; |
| 1299 |
|
|
k = na; |
| 1300 |
|
|
} |
| 1301 |
|
|
|
| 1302 |
|
|
atomids[j] = AI_C; |
| 1303 |
|
|
bitmasks[k] = 0; |
| 1304 |
|
|
|
| 1305 |
|
|
TracePeptideChain(mol,j,r); |
| 1306 |
|
|
} |
| 1307 |
|
|
else /* count == 2 */ |
| 1308 |
|
|
{ |
| 1309 |
|
|
if ( bitmasks[na] & BitCAll ) |
| 1310 |
|
|
{ |
| 1311 |
|
|
atomids[na] = AI_C; |
| 1312 |
|
|
TracePeptideChain(mol,na,r); |
| 1313 |
|
|
} |
| 1314 |
|
|
else |
| 1315 |
|
|
{ |
| 1316 |
|
|
atomids[nb] = AI_C; |
| 1317 |
|
|
TracePeptideChain(mol,nb,r); |
| 1318 |
|
|
} |
| 1319 |
|
|
} |
| 1320 |
|
|
break; |
| 1321 |
|
|
|
| 1322 |
|
|
case(AI_C): |
| 1323 |
|
|
k = AI_O; |
| 1324 |
|
|
for ( j = 0; j < count; j++ ) |
| 1325 |
|
|
{ |
| 1326 |
|
|
if ( bitmasks[neighbour[j]] & BitNAll ) |
| 1327 |
|
|
{ |
| 1328 |
|
|
atomids[neighbour[j]] = AI_N; |
| 1329 |
|
|
TracePeptideChain(mol,neighbour[j],r+1); |
| 1330 |
|
|
} |
| 1331 |
|
|
else if( bitmasks[neighbour[j]] & BitOAll ) |
| 1332 |
|
|
{ |
| 1333 |
|
|
atomids[neighbour[j]] = k; |
| 1334 |
|
|
resnos[neighbour[j]] = r; |
| 1335 |
|
|
k = AI_OXT; /* OXT */ |
| 1336 |
|
|
} |
| 1337 |
|
|
} |
| 1338 |
|
|
break; |
| 1339 |
|
|
} |
| 1340 |
|
|
} |
| 1341 |
|
|
|
| 1342 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1343 |
|
|
// Peptide Sidechains Perception |
| 1344 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1345 |
|
|
|
| 1346 |
|
|
bool OBChainsParser::DeterminePeptideSidechains(OBMol &mol) |
| 1347 |
|
|
{ |
| 1348 |
|
|
int resid; |
| 1349 |
|
|
int max = mol.NumAtoms(); |
| 1350 |
|
|
|
| 1351 |
|
|
for (int i = 0 ; i < max ; i++) |
| 1352 |
|
|
if (atomids[i] == 1) |
| 1353 |
|
|
{ |
| 1354 |
|
|
resid = IdentifyResidue(PDecisionTree, mol, i, resnos[i]); |
| 1355 |
|
|
AssignResidue(mol,resnos[i],chains[i],resid); |
| 1356 |
|
|
} |
| 1357 |
|
|
|
| 1358 |
|
|
return true; |
| 1359 |
|
|
} |
| 1360 |
|
|
|
| 1361 |
|
|
void OBChainsParser::AssignResidue(OBMol &mol, int r, int c, int i) |
| 1362 |
|
|
{ |
| 1363 |
|
|
int max = mol.NumAtoms(); |
| 1364 |
|
|
for (int j = 0 ; j < max ; j++) |
| 1365 |
|
|
if ((resnos[j] == r) && (chains[j] == c) && !hetflags[j]) |
| 1366 |
|
|
resids[j] = i; |
| 1367 |
|
|
} |
| 1368 |
|
|
|
| 1369 |
|
|
int OBChainsParser::IdentifyResidue(void *tree, OBMol &mol, int seed, int resno) |
| 1370 |
|
|
{ |
| 1371 |
|
|
ByteCode *ptr; |
| 1372 |
|
|
|
| 1373 |
|
|
int AtomCount, BondCount; |
| 1374 |
|
|
int curr,prev,bond; |
| 1375 |
|
|
int bcount; |
| 1376 |
|
|
int i,j; |
| 1377 |
|
|
|
| 1378 |
|
|
ptr = (ByteCode *) tree; |
| 1379 |
|
|
bcount = 0; |
| 1380 |
|
|
|
| 1381 |
|
|
Stack[0].atom = seed; |
| 1382 |
|
|
Stack[0].prev = seed; |
| 1383 |
|
|
StackPtr = 0; |
| 1384 |
|
|
|
| 1385 |
|
|
ResMonoAtom[0] = seed; |
| 1386 |
|
|
AtomCount = 1; |
| 1387 |
|
|
BondCount = 0; |
| 1388 |
|
|
|
| 1389 |
|
|
OBAtom *atom, *nbr; |
| 1390 |
|
|
vector<OBEdgeBase *>::iterator b; |
| 1391 |
|
|
|
| 1392 |
|
|
while( ptr ) |
| 1393 |
|
|
switch(ptr->type) |
| 1394 |
|
|
{ |
| 1395 |
|
|
case(BC_IDENT): curr = Stack[StackPtr-1].atom; |
| 1396 |
|
|
if( atomids[curr] == ptr->ident.value ) |
| 1397 |
|
|
{ |
| 1398 |
|
|
bond = Stack[StackPtr-1].bond; |
| 1399 |
|
|
ResMonoBond[BondCount++] = bond; |
| 1400 |
|
|
ptr = ptr->ident.tcond; |
| 1401 |
|
|
StackPtr--; |
| 1402 |
|
|
} |
| 1403 |
|
|
else |
| 1404 |
|
|
ptr = ptr->ident.fcond; |
| 1405 |
|
|
break; |
| 1406 |
|
|
|
| 1407 |
|
|
case(BC_LOCAL): curr = Stack[StackPtr-1].atom; |
| 1408 |
|
|
if( curr == ResMonoAtom[ptr->local.value] ) |
| 1409 |
|
|
{ |
| 1410 |
|
|
bond = Stack[StackPtr-1].bond; |
| 1411 |
|
|
ResMonoBond[BondCount++] = bond; |
| 1412 |
|
|
ptr = ptr->local.tcond; |
| 1413 |
|
|
StackPtr--; |
| 1414 |
|
|
} |
| 1415 |
|
|
else |
| 1416 |
|
|
ptr = ptr->local.fcond; |
| 1417 |
|
|
break; |
| 1418 |
|
|
|
| 1419 |
|
|
case(BC_ELEM): curr = Stack[StackPtr-1].atom; |
| 1420 |
|
|
if( mol.GetAtom(curr+1)->GetAtomicNum() == static_cast<unsigned int>(ptr->elem.value) |
| 1421 |
|
|
) |
| 1422 |
|
|
{ |
| 1423 |
|
|
bond = Stack[StackPtr-1].bond; |
| 1424 |
|
|
ResMonoAtom[AtomCount++] = curr; |
| 1425 |
|
|
ResMonoBond[BondCount++] = bond; |
| 1426 |
|
|
resnos[curr] = resno; |
| 1427 |
|
|
ptr = ptr->elem.tcond; |
| 1428 |
|
|
StackPtr--; |
| 1429 |
|
|
} |
| 1430 |
|
|
else |
| 1431 |
|
|
ptr = ptr->elem.fcond; |
| 1432 |
|
|
break; |
| 1433 |
|
|
|
| 1434 |
|
|
case(BC_EVAL): bcount = 0; |
| 1435 |
|
|
curr = Stack[StackPtr].atom; |
| 1436 |
|
|
prev = Stack[StackPtr].prev; |
| 1437 |
|
|
|
| 1438 |
|
|
atom = mol.GetAtom(curr+1); |
| 1439 |
|
|
for (nbr = atom->BeginNbrAtom(b); nbr; nbr = atom->NextNbrAtom(b)) |
| 1440 |
|
|
{ |
| 1441 |
|
|
j = nbr->GetIdx() - 1; |
| 1442 |
|
|
if (!((curr == prev) && bitmasks[j]) && (j != prev) && !(nbr->IsHydrogen())) |
| 1443 |
|
|
{ |
| 1444 |
|
|
Stack[StackPtr].prev = curr; |
| 1445 |
|
|
Stack[StackPtr].atom = j; |
| 1446 |
|
|
Stack[StackPtr].bond = (*b)->GetIdx(); |
| 1447 |
|
|
StackPtr++; |
| 1448 |
|
|
bcount++; |
| 1449 |
|
|
} |
| 1450 |
|
|
} |
| 1451 |
|
|
|
| 1452 |
|
|
ptr = ptr->eval.next; |
| 1453 |
|
|
break; |
| 1454 |
|
|
|
| 1455 |
|
|
case(BC_COUNT): |
| 1456 |
|
|
if( bcount == ptr->count.value ) |
| 1457 |
|
|
{ |
| 1458 |
|
|
ptr = ptr->count.tcond; |
| 1459 |
|
|
} |
| 1460 |
|
|
else |
| 1461 |
|
|
ptr = ptr->count.fcond; |
| 1462 |
|
|
break; |
| 1463 |
|
|
|
| 1464 |
|
|
case(BC_ASSIGN): |
| 1465 |
|
|
for( i=0; i<AtomCount; i++ ) |
| 1466 |
|
|
if( !bitmasks[ResMonoAtom[i]] ) |
| 1467 |
|
|
{ |
| 1468 |
|
|
j = ptr->assign.atomid[i]; |
| 1469 |
|
|
atomids[ResMonoAtom[i]] = j; |
| 1470 |
|
|
} |
| 1471 |
|
|
for( i=0; i<BondCount; i++ ) |
| 1472 |
|
|
{ |
| 1473 |
|
|
j = ptr->assign.bflags[i]; |
| 1474 |
|
|
flags[ResMonoBond[i]] = j; |
| 1475 |
|
|
} |
| 1476 |
|
|
return( ptr->assign.resid ); |
| 1477 |
|
|
break; |
| 1478 |
|
|
|
| 1479 |
|
|
default: /* Illegal Instruction! */ |
| 1480 |
|
|
return( 0 ); |
| 1481 |
|
|
} |
| 1482 |
|
|
return 0; |
| 1483 |
|
|
} |
| 1484 |
|
|
|
| 1485 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1486 |
|
|
// Nucleic Backbone Perception |
| 1487 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1488 |
|
|
|
| 1489 |
|
|
bool OBChainsParser::DetermineNucleicBackbone(OBMol &mol) |
| 1490 |
|
|
{ |
| 1491 |
|
|
ConstrainBackbone(mol, Nucleotide, MAXNUCLEIC); |
| 1492 |
|
|
|
| 1493 |
|
|
int i, max = mol.NumAtoms(); |
| 1494 |
|
|
|
| 1495 |
|
|
/* |
| 1496 |
|
|
int count = 0; |
| 1497 |
|
|
for ( i = 0 ; i < max ; i++ ) |
| 1498 |
|
|
if ( bitmasks[i] & BitC5 ) |
| 1499 |
|
|
count++; |
| 1500 |
|
|
|
| 1501 |
|
|
fprintf(stderr,"%d sugar phosphates\n",count); |
| 1502 |
|
|
*/ |
| 1503 |
|
|
|
| 1504 |
|
|
/* Order Nucleic Backbone */ |
| 1505 |
|
|
|
| 1506 |
|
|
for( i = 0 ; i < max ; i++ ) |
| 1507 |
|
|
if( atomids[i] == -1 ) |
| 1508 |
|
|
{ |
| 1509 |
|
|
if( bitmasks[i] & BitPTer ) |
| 1510 |
|
|
{ |
| 1511 |
|
|
atomids[i] = AI_P; |
| 1512 |
|
|
TraceNucleicChain(mol,i,1); |
| 1513 |
|
|
} |
| 1514 |
|
|
else if( bitmasks[i] & BitO5Ter ) |
| 1515 |
|
|
{ |
| 1516 |
|
|
atomids[i] = AI_O5; |
| 1517 |
|
|
TraceNucleicChain(mol,i,1); |
| 1518 |
|
|
} |
| 1519 |
|
|
} |
| 1520 |
|
|
|
| 1521 |
|
|
return true; |
| 1522 |
|
|
} |
| 1523 |
|
|
|
| 1524 |
|
|
void OBChainsParser::TraceNucleicChain(OBMol &mol, int i, int r) |
| 1525 |
|
|
{ |
| 1526 |
|
|
int neighbour[4]; |
| 1527 |
|
|
int na,nb,nc; |
| 1528 |
|
|
int count; |
| 1529 |
|
|
int j,k; |
| 1530 |
|
|
|
| 1531 |
|
|
OBAtom *atom, *nbr; |
| 1532 |
|
|
vector<OBEdgeBase *>::iterator b; |
| 1533 |
|
|
|
| 1534 |
|
|
count = 0; |
| 1535 |
|
|
atom = mol.GetAtom(i + 1); |
| 1536 |
|
|
for (nbr = atom->BeginNbrAtom(b) ; nbr ; nbr = atom->NextNbrAtom(b)) |
| 1537 |
|
|
if (!nbr->IsHydrogen()) |
| 1538 |
|
|
neighbour[count++] = nbr->GetIdx() - 1; |
| 1539 |
|
|
|
| 1540 |
|
|
resnos[i] = r; |
| 1541 |
|
|
|
| 1542 |
|
|
na = neighbour[0]; |
| 1543 |
|
|
nb = neighbour[1]; |
| 1544 |
|
|
nc = neighbour[2]; |
| 1545 |
|
|
|
| 1546 |
|
|
switch( atomids[i] ) |
| 1547 |
|
|
{ |
| 1548 |
|
|
case(AI_P): |
| 1549 |
|
|
k = AI_O1P; /* O1P */ |
| 1550 |
|
|
for( j=0; j<count; j++ ) |
| 1551 |
|
|
{ |
| 1552 |
|
|
if( bitmasks[neighbour[j]] & BitO5 ) |
| 1553 |
|
|
{ |
| 1554 |
|
|
atomids[neighbour[j]] = AI_O5; |
| 1555 |
|
|
TraceNucleicChain(mol,neighbour[j],r); |
| 1556 |
|
|
} |
| 1557 |
|
|
else if( bitmasks[neighbour[j]] & BitOP ) |
| 1558 |
|
|
{ |
| 1559 |
|
|
atomids[neighbour[j]] = k; |
| 1560 |
|
|
resnos[neighbour[j]] = r; |
| 1561 |
|
|
k = AI_O2P; /* O2P */ |
| 1562 |
|
|
} |
| 1563 |
|
|
} |
| 1564 |
|
|
|
| 1565 |
|
|
break; |
| 1566 |
|
|
|
| 1567 |
|
|
case(AI_O5): |
| 1568 |
|
|
for( j=0; j<count; j++ ) |
| 1569 |
|
|
if( bitmasks[neighbour[j]] & BitC5 ) |
| 1570 |
|
|
{ |
| 1571 |
|
|
atomids[neighbour[j]] = AI_C5; |
| 1572 |
|
|
TraceNucleicChain(mol,neighbour[j],r); |
| 1573 |
|
|
} |
| 1574 |
|
|
|
| 1575 |
|
|
break; |
| 1576 |
|
|
|
| 1577 |
|
|
case(AI_C5): |
| 1578 |
|
|
for( j=0 ; j<count; j++ ) |
| 1579 |
|
|
if( bitmasks[neighbour[j]] & BitC4 ) |
| 1580 |
|
|
{ |
| 1581 |
|
|
atomids[neighbour[j]] = AI_C4; |
| 1582 |
|
|
TraceNucleicChain(mol,neighbour[j],r); |
| 1583 |
|
|
} |
| 1584 |
|
|
|
| 1585 |
|
|
break; |
| 1586 |
|
|
|
| 1587 |
|
|
case(AI_C4): |
| 1588 |
|
|
for( j=0; j<count; j++ ) |
| 1589 |
|
|
{ |
| 1590 |
|
|
if( bitmasks[neighbour[j]] & BitC3 ) |
| 1591 |
|
|
{ |
| 1592 |
|
|
atomids[neighbour[j]] = AI_C3; |
| 1593 |
|
|
TraceNucleicChain(mol,neighbour[j],r); |
| 1594 |
|
|
} |
| 1595 |
|
|
else if( bitmasks[neighbour[j]] & BitO4 ) |
| 1596 |
|
|
{ |
| 1597 |
|
|
atomids[neighbour[j]] = AI_O4; |
| 1598 |
|
|
resnos[neighbour[j]] = r; |
| 1599 |
|
|
} |
| 1600 |
|
|
} |
| 1601 |
|
|
|
| 1602 |
|
|
break; |
| 1603 |
|
|
|
| 1604 |
|
|
case(AI_C3): |
| 1605 |
|
|
for( j=0; j<count; j++ ) |
| 1606 |
|
|
{ |
| 1607 |
|
|
if( bitmasks[neighbour[j]] & BitO3All ) |
| 1608 |
|
|
{ |
| 1609 |
|
|
atomids[neighbour[j]] = AI_O3; |
| 1610 |
|
|
TraceNucleicChain(mol,neighbour[j],r); |
| 1611 |
|
|
} |
| 1612 |
|
|
else if( bitmasks[neighbour[j]] & BitC2All ) |
| 1613 |
|
|
{ |
| 1614 |
|
|
atomids[neighbour[j]] = AI_C2; |
| 1615 |
|
|
TraceNucleicChain(mol,neighbour[j],r); |
| 1616 |
|
|
} |
| 1617 |
|
|
} |
| 1618 |
|
|
|
| 1619 |
|
|
break; |
| 1620 |
|
|
|
| 1621 |
|
|
case(AI_O3): |
| 1622 |
|
|
for( j=0; j<count; j++ ) |
| 1623 |
|
|
if( bitmasks[neighbour[j]] & BitP ) |
| 1624 |
|
|
{ |
| 1625 |
|
|
atomids[neighbour[j]] = AI_P; |
| 1626 |
|
|
TraceNucleicChain(mol,neighbour[j],r+1); |
| 1627 |
|
|
} |
| 1628 |
|
|
|
| 1629 |
|
|
break; |
| 1630 |
|
|
|
| 1631 |
|
|
case(AI_C2): |
| 1632 |
|
|
for( j=0; j<count; j++ ) |
| 1633 |
|
|
{ |
| 1634 |
|
|
if( bitmasks[neighbour[j]] & BitC1 ) |
| 1635 |
|
|
{ |
| 1636 |
|
|
atomids[neighbour[j]] = AI_C1; |
| 1637 |
|
|
resnos[neighbour[j]] = r; |
| 1638 |
|
|
} |
| 1639 |
|
|
else if( bitmasks[neighbour[j]] & BitO2 ) |
| 1640 |
|
|
{ |
| 1641 |
|
|
atomids[neighbour[j]] = AI_O2; |
| 1642 |
|
|
resnos[neighbour[j]] = r; |
| 1643 |
|
|
} |
| 1644 |
|
|
} |
| 1645 |
|
|
|
| 1646 |
|
|
break; |
| 1647 |
|
|
} |
| 1648 |
|
|
} |
| 1649 |
|
|
|
| 1650 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1651 |
|
|
// Nucleic Sidechains Perception |
| 1652 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1653 |
|
|
|
| 1654 |
|
|
bool OBChainsParser::DetermineNucleicSidechains(OBMol &mol) |
| 1655 |
|
|
{ |
| 1656 |
|
|
for( unsigned int i = 0 ; i < mol.NumAtoms() ; i++ ) |
| 1657 |
|
|
if( atomids[i] == 49 ) |
| 1658 |
|
|
{ |
| 1659 |
|
|
int resid = IdentifyResidue(NDecisionTree,mol,i,resnos[i]); |
| 1660 |
|
|
AssignResidue(mol,resnos[i],chains[i],resid); |
| 1661 |
|
|
} |
| 1662 |
|
|
|
| 1663 |
|
|
return true; |
| 1664 |
|
|
} |
| 1665 |
|
|
|
| 1666 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1667 |
|
|
// Hydrogens Perception |
| 1668 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1669 |
|
|
|
| 1670 |
|
|
bool OBChainsParser::DetermineHydrogens(OBMol &mol) |
| 1671 |
|
|
{ |
| 1672 |
|
|
OBAtom *atom, *nbr; |
| 1673 |
|
|
int idx,sidx; |
| 1674 |
|
|
|
| 1675 |
|
|
int max = mol.NumAtoms(); |
| 1676 |
|
|
for ( int i = 0 ; i < max ; i++ ) |
| 1677 |
|
|
hcounts[i] = 0; |
| 1678 |
|
|
|
| 1679 |
|
|
/* First Pass */ |
| 1680 |
|
|
|
| 1681 |
|
|
vector<OBNodeBase*>::iterator a; |
| 1682 |
|
|
vector<OBEdgeBase*>::iterator b; |
| 1683 |
|
|
|
| 1684 |
|
|
for(atom = mol.BeginAtom(a); atom ; atom = mol.NextAtom(a)) |
| 1685 |
|
|
if(atom->IsHydrogen()) |
| 1686 |
|
|
{ |
| 1687 |
|
|
nbr = atom->BeginNbrAtom(b); |
| 1688 |
|
|
if (nbr != NULL) |
| 1689 |
|
|
{ |
| 1690 |
|
|
idx = atom->GetIdx() - 1; |
| 1691 |
|
|
sidx = nbr->GetIdx() - 1; |
| 1692 |
|
|
|
| 1693 |
|
|
hcounts[idx] = ++hcounts[sidx]; |
| 1694 |
|
|
hetflags[idx] = hetflags[sidx]; |
| 1695 |
|
|
atomids[idx] = atomids[sidx]; |
| 1696 |
|
|
resids[idx] = resids[sidx]; |
| 1697 |
|
|
resnos[idx] = resnos[sidx]; |
| 1698 |
|
|
} |
| 1699 |
|
|
} |
| 1700 |
|
|
|
| 1701 |
|
|
/* Second Pass */ |
| 1702 |
|
|
|
| 1703 |
|
|
for(atom = mol.BeginAtom(a) ; atom ; atom = mol.NextAtom(a)) |
| 1704 |
|
|
if (atom->IsHydrogen()) |
| 1705 |
|
|
{ |
| 1706 |
|
|
nbr = atom->BeginNbrAtom(b); |
| 1707 |
|
|
if (nbr != NULL && hcounts[nbr->GetIdx()-1] == 1) |
| 1708 |
|
|
hcounts[atom->GetIdx()-1] = 0; |
| 1709 |
|
|
} |
| 1710 |
|
|
|
| 1711 |
|
|
return true; |
| 1712 |
|
|
} |
| 1713 |
|
|
|
| 1714 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1715 |
|
|
// Utility Functions |
| 1716 |
|
|
//////////////////////////////////////////////////////////////////////////////// |
| 1717 |
|
|
|
| 1718 |
|
|
// validated |
| 1719 |
|
|
void OBChainsParser::DefineMonomer(void **tree, int resid, char *smiles) |
| 1720 |
|
|
{ |
| 1721 |
|
|
int i; |
| 1722 |
|
|
|
| 1723 |
|
|
MonoAtomCount = 0; |
| 1724 |
|
|
MonoBondCount = 0; |
| 1725 |
|
|
|
| 1726 |
|
|
ParseSmiles(smiles,-1); |
| 1727 |
|
|
|
| 1728 |
|
|
for( i=0; i<MonoBondCount; i++ ) |
| 1729 |
|
|
MonoBond[i].index = -1; |
| 1730 |
|
|
for( i=0; i<MonoAtomCount; i++ ) |
| 1731 |
|
|
MonoAtom[i].index = -1; |
| 1732 |
|
|
AtomIndex = BondIndex = 0; |
| 1733 |
|
|
|
| 1734 |
|
|
StackPtr = 0; |
| 1735 |
|
|
GenerateByteCodes((ByteCode**)tree, resid, 0, 0, 0 ); |
| 1736 |
|
|
} |
| 1737 |
|
|
|
| 1738 |
|
|
int OBChainsParser::IdentifyElement(char *ptr) |
| 1739 |
|
|
{ |
| 1740 |
|
|
int ch; |
| 1741 |
|
|
|
| 1742 |
|
|
ch = toupper(ptr[1]); |
| 1743 |
|
|
switch( toupper(ptr[0]) ) |
| 1744 |
|
|
{ |
| 1745 |
|
|
case(' '): switch( ch ) |
| 1746 |
|
|
{ |
| 1747 |
|
|
case('B'): return( 5 ); |
| 1748 |
|
|
case('C'): return( 6 ); |
| 1749 |
|
|
case('D'): return( 1 ); |
| 1750 |
|
|
case('F'): return( 9 ); |
| 1751 |
|
|
case('H'): return( 1 ); |
| 1752 |
|
|
case('I'): return( 53 ); |
| 1753 |
|
|
case('K'): return( 19 ); |
| 1754 |
|
|
case('L'): return( 1 ); |
| 1755 |
|
|
case('N'): return( 7 ); |
| 1756 |
|
|
case('O'): return( 8 ); |
| 1757 |
|
|
case('P'): return( 15 ); |
| 1758 |
|
|
case('S'): return( 16 ); |
| 1759 |
|
|
case('U'): return( 92 ); |
| 1760 |
|
|
case('V'): return( 23 ); |
| 1761 |
|
|
case('W'): return( 74 ); |
| 1762 |
|
|
case('Y'): return( 39 ); |
| 1763 |
|
|
} |
| 1764 |
|
|
break; |
| 1765 |
|
|
|
| 1766 |
|
|
case('A'): switch( ch ) |
| 1767 |
|
|
{ |
| 1768 |
|
|
case('C'): return( 89 ); |
| 1769 |
|
|
case('G'): return( 47 ); |
| 1770 |
|
|
case('L'): return( 13 ); |
| 1771 |
|
|
case('M'): return( 95 ); |
| 1772 |
|
|
case('R'): return( 18 ); |
| 1773 |
|
|
case('S'): return( 33 ); |
| 1774 |
|
|
case('T'): return( 85 ); |
| 1775 |
|
|
case('U'): return( 79 ); |
| 1776 |
|
|
} |
| 1777 |
|
|
break; |
| 1778 |
|
|
|
| 1779 |
|
|
case('B'): switch( ch ) |
| 1780 |
|
|
{ |
| 1781 |
|
|
case('A'): return( 56 ); |
| 1782 |
|
|
case('E'): return( 4 ); |
| 1783 |
|
|
case('I'): return( 83 ); |
| 1784 |
|
|
case('K'): return( 97 ); |
| 1785 |
|
|
case('R'): return( 35 ); |
| 1786 |
|
|
case(' '): return( 5 ); |
| 1787 |
|
|
} |
| 1788 |
|
|
break; |
| 1789 |
|
|
|
| 1790 |
|
|
case('C'): switch( ch ) |
| 1791 |
|
|
{ |
| 1792 |
|
|
case('A'): return( 20 ); |
| 1793 |
|
|
case('D'): return( 48 ); |
| 1794 |
|
|
case('E'): return( 58 ); |
| 1795 |
|
|
case('F'): return( 98 ); |
| 1796 |
|
|
case('L'): return( 17 ); |
| 1797 |
|
|
case('M'): return( 96 ); |
| 1798 |
|
|
case('O'): return( 27 ); |
| 1799 |
|
|
case('R'): return( 24 ); |
| 1800 |
|
|
case('S'): return( 55 ); |
| 1801 |
|
|
case('U'): return( 29 ); |
| 1802 |
|
|
case(' '): return( 6 ); |
| 1803 |
|
|
} |
| 1804 |
|
|
break; |
| 1805 |
|
|
|
| 1806 |
|
|
case('D'): if( ch=='Y' ) |
| 1807 |
|
|
{ |
| 1808 |
|
|
return( 66 ); |
| 1809 |
|
|
} |
| 1810 |
|
|
else if( ch==' ' ) |
| 1811 |
|
|
return( 1 ); |
| 1812 |
|
|
break; |
| 1813 |
|
|
|
| 1814 |
|
|
case('E'): if( ch=='R' ) |
| 1815 |
|
|
{ |
| 1816 |
|
|
return( 68 ); |
| 1817 |
|
|
} |
| 1818 |
|
|
else if( ch=='S' ) |
| 1819 |
|
|
{ |
| 1820 |
|
|
return( 99 ); |
| 1821 |
|
|
} |
| 1822 |
|
|
else if( ch=='U' ) |
| 1823 |
|
|
return( 63 ); |
| 1824 |
|
|
break; |
| 1825 |
|
|
|
| 1826 |
|
|
case('F'): if( ch=='E' ) |
| 1827 |
|
|
{ |
| 1828 |
|
|
return( 26 ); |
| 1829 |
|
|
} |
| 1830 |
|
|
else if( ch=='M' ) |
| 1831 |
|
|
{ |
| 1832 |
|
|
return( 100 ); |
| 1833 |
|
|
} |
| 1834 |
|
|
else if( ch=='R' ) |
| 1835 |
|
|
{ |
| 1836 |
|
|
return( 87 ); |
| 1837 |
|
|
} |
| 1838 |
|
|
else if( ch=='F' ) |
| 1839 |
|
|
return( 9 ); |
| 1840 |
|
|
break; |
| 1841 |
|
|
|
| 1842 |
|
|
case('G'): if( ch=='A' ) |
| 1843 |
|
|
{ |
| 1844 |
|
|
return( 31 ); |
| 1845 |
|
|
} |
| 1846 |
|
|
else if( ch=='D' ) |
| 1847 |
|
|
{ |
| 1848 |
|
|
return( 64 ); |
| 1849 |
|
|
} |
| 1850 |
|
|
else if( ch=='E' ) |
| 1851 |
|
|
return( 32 ); |
| 1852 |
|
|
break; |
| 1853 |
|
|
|
| 1854 |
|
|
case('H'): if( ch=='E' ) |
| 1855 |
|
|
{ |
| 1856 |
|
|
return( 2 ); |
| 1857 |
|
|
} |
| 1858 |
|
|
else if( ch=='F' ) |
| 1859 |
|
|
{ |
| 1860 |
|
|
return( 72 ); |
| 1861 |
|
|
} |
| 1862 |
|
|
else if( ch=='G' ) |
| 1863 |
|
|
{ |
| 1864 |
|
|
return( 80 ); |
| 1865 |
|
|
} |
| 1866 |
|
|
else if( ch=='O' ) |
| 1867 |
|
|
{ |
| 1868 |
|
|
return( 67 ); |
| 1869 |
|
|
} |
| 1870 |
|
|
else if( ch==' ' ) |
| 1871 |
|
|
return( 1 ); |
| 1872 |
|
|
break; |
| 1873 |
|
|
|
| 1874 |
|
|
case('I'): if( ch=='N' ) |
| 1875 |
|
|
{ |
| 1876 |
|
|
return( 49 ); |
| 1877 |
|
|
} |
| 1878 |
|
|
else if( ch=='R' ) |
| 1879 |
|
|
{ |
| 1880 |
|
|
return( 77 ); |
| 1881 |
|
|
} |
| 1882 |
|
|
else if( ch==' ' ) |
| 1883 |
|
|
return( 53 ); |
| 1884 |
|
|
break; |
| 1885 |
|
|
|
| 1886 |
|
|
case('K'): if( ch=='R' ) |
| 1887 |
|
|
{ |
| 1888 |
|
|
return( 36 ); |
| 1889 |
|
|
} |
| 1890 |
|
|
else if( ch==' ' ) |
| 1891 |
|
|
return( 19 ); |
| 1892 |
|
|
break; |
| 1893 |
|
|
|
| 1894 |
|
|
case('L'): if( ch=='A' ) |
| 1895 |
|
|
{ |
| 1896 |
|
|
return( 57 ); |
| 1897 |
|
|
} |
| 1898 |
|
|
else if( ch=='I' ) |
| 1899 |
|
|
{ |
| 1900 |
|
|
return( 3 ); |
| 1901 |
|
|
} |
| 1902 |
|
|
else if( (ch=='R') || (ch=='W') ) |
| 1903 |
|
|
{ |
| 1904 |
|
|
return( 103 ); |
| 1905 |
|
|
} |
| 1906 |
|
|
else if( ch=='U' ) |
| 1907 |
|
|
{ |
| 1908 |
|
|
return( 71 ); |
| 1909 |
|
|
} |
| 1910 |
|
|
else if( ch==' ' ) |
| 1911 |
|
|
return( 1 ); |
| 1912 |
|
|
break; |
| 1913 |
|
|
|
| 1914 |
|
|
case('M'): if( ch=='D' ) |
| 1915 |
|
|
{ |
| 1916 |
|
|
return( 101 ); |
| 1917 |
|
|
} |
| 1918 |
|
|
else if( ch=='G' ) |
| 1919 |
|
|
{ |
| 1920 |
|
|
return( 12 ); |
| 1921 |
|
|
} |
| 1922 |
|
|
else if( ch=='N' ) |
| 1923 |
|
|
{ |
| 1924 |
|
|
return( 25 ); |
| 1925 |
|
|
} |
| 1926 |
|
|
else if( ch=='O' ) |
| 1927 |
|
|
return( 42 ); |
| 1928 |
|
|
break; |
| 1929 |
|
|
|
| 1930 |
|
|
case('N'): switch( ch ) |
| 1931 |
|
|
{ |
| 1932 |
|
|
case('A'): return( 11 ); |
| 1933 |
|
|
case('B'): return( 41 ); |
| 1934 |
|
|
case('D'): return( 60 ); |
| 1935 |
|
|
case('E'): return( 10 ); |
| 1936 |
|
|
case('I'): return( 28 ); |
| 1937 |
|
|
case('O'): return( 102 ); |
| 1938 |
|
|
case('P'): return( 93 ); |
| 1939 |
|
|
case(' '): return( 7 ); |
| 1940 |
|
|
} |
| 1941 |
|
|
break; |
| 1942 |
|
|
|
| 1943 |
|
|
case('O'): if( ch=='S' ) |
| 1944 |
|
|
{ |
| 1945 |
|
|
return( 76 ); |
| 1946 |
|
|
} |
| 1947 |
|
|
else if( ch==' ' ) |
| 1948 |
|
|
return( 8 ); |
| 1949 |
|
|
break; |
| 1950 |
|
|
|
| 1951 |
|
|
case('P'): switch( ch ) |
| 1952 |
|
|
{ |
| 1953 |
|
|
case('A'): return( 91 ); |
| 1954 |
|
|
case('B'): return( 82 ); |
| 1955 |
|
|
case('D'): return( 46 ); |
| 1956 |
|
|
case('M'): return( 61 ); |
| 1957 |
|
|
case('O'): return( 84 ); |
| 1958 |
|
|
case('R'): return( 59 ); |
| 1959 |
|
|
case('T'): return( 78 ); |
| 1960 |
|
|
case('U'): return( 94 ); |
| 1961 |
|
|
case(' '): return( 15 ); |
| 1962 |
|
|
} |
| 1963 |
|
|
break; |
| 1964 |
|
|
|
| 1965 |
|
|
case('R'): switch( ch ) |
| 1966 |
|
|
{ |
| 1967 |
|
|
case('A'): return( 88 ); |
| 1968 |
|
|
case('B'): return( 37 ); |
| 1969 |
|
|
case('E'): return( 75 ); |
| 1970 |
|
|
case('H'): return( 45 ); |
| 1971 |
|
|
case('N'): return( 86 ); |
| 1972 |
|
|
case('U'): return( 44 ); |
| 1973 |
|
|
} |
| 1974 |
|
|
break; |
| 1975 |
|
|
|
| 1976 |
|
|
case('S'): switch( ch ) |
| 1977 |
|
|
{ |
| 1978 |
|
|
case('B'): return( 51 ); |
| 1979 |
|
|
case('C'): return( 21 ); |
| 1980 |
|
|
case('E'): return( 34 ); |
| 1981 |
|
|
case('I'): return( 14 ); |
| 1982 |
|
|
case('M'): return( 62 ); |
| 1983 |
|
|
case('N'): return( 50 ); |
| 1984 |
|
|
case('R'): return( 38 ); |
| 1985 |
|
|
case(' '): return( 16 ); |
| 1986 |
|
|
} |
| 1987 |
|
|
break; |
| 1988 |
|
|
|
| 1989 |
|
|
case('T'): switch( ch ) |
| 1990 |
|
|
{ |
| 1991 |
|
|
case('A'): return( 73 ); |
| 1992 |
|
|
case('B'): return( 65 ); |
| 1993 |
|
|
case('C'): return( 43 ); |
| 1994 |
|
|
case('E'): return( 52 ); |
| 1995 |
|
|
case('H'): return( 90 ); |
| 1996 |
|
|
case('I'): return( 22 ); |
| 1997 |
|
|
case('L'): return( 81 ); |
| 1998 |
|
|
case('M'): return( 69 ); |
| 1999 |
|
|
} |
| 2000 |
|
|
break; |
| 2001 |
|
|
|
| 2002 |
|
|
case('U'): if( ch==' ' ) |
| 2003 |
|
|
return( 92 ); |
| 2004 |
|
|
break; |
| 2005 |
|
|
|
| 2006 |
|
|
case('V'): if( ch==' ' ) |
| 2007 |
|
|
return( 23 ); |
| 2008 |
|
|
break; |
| 2009 |
|
|
|
| 2010 |
|
|
case('W'): if( ch==' ' ) |
| 2011 |
|
|
return( 74 ); |
| 2012 |
|
|
break; |
| 2013 |
|
|
|
| 2014 |
|
|
case('X'): if( ch=='E' ) |
| 2015 |
|
|
return( 54 ); |
| 2016 |
|
|
break; |
| 2017 |
|
|
|
| 2018 |
|
|
case('Y'): if( ch=='B' ) |
| 2019 |
|
|
{ |
| 2020 |
|
|
return( 70 ); |
| 2021 |
|
|
} |
| 2022 |
|
|
else if( ch==' ' ) |
| 2023 |
|
|
return( 39 ); |
| 2024 |
|
|
break; |
| 2025 |
|
|
|
| 2026 |
|
|
case('Z'): if( ch=='N' ) |
| 2027 |
|
|
{ |
| 2028 |
|
|
return( 30 ); |
| 2029 |
|
|
} |
| 2030 |
|
|
else if( ch=='R' ) |
| 2031 |
|
|
return( 40 ); |
| 2032 |
|
|
break; |
| 2033 |
|
|
} |
| 2034 |
|
|
|
| 2035 |
|
|
if( (*ptr>='0') && (*ptr<='9') ) |
| 2036 |
|
|
if( (ch=='H') || (ch=='D') ) |
| 2037 |
|
|
return( 1 ); /* Hydrogen */ |
| 2038 |
|
|
|
| 2039 |
|
|
return( 0 ); |
| 2040 |
|
|
} |
| 2041 |
|
|
|
| 2042 |
|
|
char *OBChainsParser::ParseSmiles(char *ptr, int prev) |
| 2043 |
|
|
{ |
| 2044 |
|
|
char *name; |
| 2045 |
|
|
int atomid; |
| 2046 |
|
|
int next; |
| 2047 |
|
|
int type; |
| 2048 |
|
|
int ch; |
| 2049 |
|
|
|
| 2050 |
|
|
type = 0; |
| 2051 |
|
|
while( (ch = *ptr++) ) |
| 2052 |
|
|
{ |
| 2053 |
|
|
switch( ch ) |
| 2054 |
|
|
{ |
| 2055 |
|
|
case('-'): type = BF_SINGLE; |
| 2056 |
|
|
break; |
| 2057 |
|
|
case('='): type = BF_DOUBLE; |
| 2058 |
|
|
break; |
| 2059 |
|
|
case('#'): type = BF_TRIPLE; |
| 2060 |
|
|
break; |
| 2061 |
|
|
case('^'): type = BF_SINGLE|BF_AROMATIC; |
| 2062 |
|
|
break; |
| 2063 |
|
|
case('~'): type = BF_DOUBLE|BF_AROMATIC; |
| 2064 |
|
|
break; |
| 2065 |
|
|
|
| 2066 |
|
|
case(')'): return( ptr ); |
| 2067 |
|
|
case('.'): prev = -1; |
| 2068 |
|
|
break; |
| 2069 |
|
|
case('('): ptr = ParseSmiles(ptr,prev); |
| 2070 |
|
|
break; |
| 2071 |
|
|
|
| 2072 |
|
|
default: |
| 2073 |
|
|
atomid = ch-'0'; |
| 2074 |
|
|
while( isdigit(*ptr) ) |
| 2075 |
|
|
atomid = (atomid*10)+(*ptr++)-'0'; |
| 2076 |
|
|
|
| 2077 |
|
|
for( next=0; next<MonoAtomCount; next++ ) |
| 2078 |
|
|
if( MonoAtom[next].atomid == atomid ) |
| 2079 |
|
|
break; |
| 2080 |
|
|
|
| 2081 |
|
|
if( next == MonoAtomCount ) |
| 2082 |
|
|
{ |
| 2083 |
|
|
name = ChainsAtomName[atomid]; |
| 2084 |
|
|
MonoAtom[next].elem = IdentifyElement(name); |
| 2085 |
|
|
MonoAtom[next].atomid = atomid; |
| 2086 |
|
|
MonoAtom[next].bcount = 0; |
| 2087 |
|
|
MonoAtomCount++; |
| 2088 |
|
|
} |
| 2089 |
|
|
|
| 2090 |
|
|
if( prev != -1 ) |
| 2091 |
|
|
{ |
| 2092 |
|
|
MonoBond[MonoBondCount].flag = type; |
| 2093 |
|
|
MonoBond[MonoBondCount].src = prev; |
| 2094 |
|
|
MonoBond[MonoBondCount].dst = next; |
| 2095 |
|
|
MonoBondCount++; |
| 2096 |
|
|
|
| 2097 |
|
|
MonoAtom[prev].bcount++; |
| 2098 |
|
|
MonoAtom[next].bcount++; |
| 2099 |
|
|
} |
| 2100 |
|
|
prev = next; |
| 2101 |
|
|
} |
| 2102 |
|
|
} |
| 2103 |
|
|
return( ptr-1 ); |
| 2104 |
|
|
} |
| 2105 |
|
|
|
| 2106 |
|
|
#ifdef _I_WANT_TO_OUTPUT_PDB_ |
| 2107 |
|
|
|
| 2108 |
|
|
static ChainsAtom *PDBOrder[MaxChainsAtom]; |
| 2109 |
|
|
|
| 2110 |
|
|
int PDBSort(ChainsAtom **arg1, ChainsAtom **arg2) |
| 2111 |
|
|
{ |
| 2112 |
|
|
ChainsAtom *atom1; |
| 2113 |
|
|
ChainsAtom *atom2; |
| 2114 |
|
|
|
| 2115 |
|
|
atom1 = *arg1; |
| 2116 |
|
|
atom2 = *arg2; |
| 2117 |
|
|
|
| 2118 |
|
|
if( atom1->chain != atom2->chain ) |
| 2119 |
|
|
return( atom1->chain - atom2->chain ); |
| 2120 |
|
|
|
| 2121 |
|
|
if( atom1->hetflag != atom2->hetflag ) |
| 2122 |
|
|
return( atom1->hetflag? 1 : -1 ); |
| 2123 |
|
|
|
| 2124 |
|
|
if( atom1->resno != atom2->resno ) |
| 2125 |
|
|
return( atom1->resno - atom2->resno ); |
| 2126 |
|
|
|
| 2127 |
|
|
if( (atom1->elem==1) && (atom2->elem!=1) ) |
| 2128 |
|
|
return( 1 ); |
| 2129 |
|
|
if( (atom1->elem!=1) && (atom2->elem==1) ) |
| 2130 |
|
|
return( -1 ); |
| 2131 |
|
|
|
| 2132 |
|
|
if( atom1->atomid != atom2->atomid ) |
| 2133 |
|
|
return( atom1->atomid - atom2->atomid ); |
| 2134 |
|
|
|
| 2135 |
|
|
if( (atom1->elem==1) && (atom2->elem==1) ) |
| 2136 |
|
|
return( atom1->hcount - atom2->hcount ); |
| 2137 |
|
|
return( 0 ); |
| 2138 |
|
|
} |
| 2139 |
|
|
|
| 2140 |
|
|
static void OutputPDBFile(ChainsMolecule *mol, FILE *fp) |
| 2141 |
|
|
{ |
| 2142 |
|
|
int src,dst; |
| 2143 |
|
|
ChainsAtom *atom; |
| 2144 |
|
|
char *ptr; |
| 2145 |
|
|
int i; |
| 2146 |
|
|
|
| 2147 |
|
|
for( i=0; i<mol->acount; i++ ) |
| 2148 |
|
|
PDBOrder[i] = &mol->atom[i]; |
| 2149 |
|
|
|
| 2150 |
|
|
#ifdef __STDC__ |
| 2151 |
|
|
|
| 2152 |
|
|
qsort(PDBOrder,mol->acount,sizeof(ChainsAtom*), |
| 2153 |
|
|
(int(*)(const void*,const void*))PDBSort); |
| 2154 |
|
|
#else |
| 2155 |
|
|
|
| 2156 |
|
|
qsort(PDBOrder,mol->acount,sizeof(ChainsAtom*),PDBSort); |
| 2157 |
|
|
#endif |
| 2158 |
|
|
|
| 2159 |
|
|
ptr = mol->name; |
| 2160 |
|
|
while( *ptr == ' ' ) |
| 2161 |
|
|
ptr++; |
| 2162 |
|
|
|
| 2163 |
|
|
if( *ptr ) |
| 2164 |
|
|
{ |
| 2165 |
|
|
fputs("COMPND ",fp); |
| 2166 |
|
|
while( *ptr ) |
| 2167 |
|
|
fputc(*ptr++,fp); |
| 2168 |
|
|
fputc('\n',fp); |
| 2169 |
|
|
} |
| 2170 |
|
|
|
| 2171 |
|
|
for( i=0; i<mol->acount; i++ ) |
| 2172 |
|
|
{ |
| 2173 |
|
|
atom = PDBOrder[i]; |
| 2174 |
|
|
atom->serno = i+1; |
| 2175 |
|
|
|
| 2176 |
|
|
if( atom->hetflag ) |
| 2177 |
|
|
{ |
| 2178 |
|
|
fputs("HETATM ",fp); |
| 2179 |
|
|
} |
| 2180 |
|
|
else |
| 2181 |
|
|
fputs("ATOM ",fp); |
| 2182 |
|
|
|
| 2183 |
|
|
fprintf(fp,"%4d ",atom->serno); |
| 2184 |
|
|
|
| 2185 |
|
|
if( atom->atomid == -1 ) |
| 2186 |
|
|
{ |
| 2187 |
|
|
fprintf(fp,"%s ", etab.GetSymbol(atom->elem)); |
| 2188 |
|
|
} |
| 2189 |
|
|
else if( atom->elem == 1 ) |
| 2190 |
|
|
{ |
| 2191 |
|
|
if( atom->hcount ) |
| 2192 |
|
|
{ |
| 2193 |
|
|
fputc(atom->hcount+'0',fp); |
| 2194 |
|
|
} |
| 2195 |
|
|
else |
| 2196 |
|
|
fputc(' ',fp); |
| 2197 |
|
|
fprintf(fp,"H%.2s",ChainsAtomName[atom->atomid]+2); |
| 2198 |
|
|
} |
| 2199 |
|
|
else |
| 2200 |
|
|
fprintf(fp,"%.4s",ChainsAtomName[atom->atomid]); |
| 2201 |
|
|
|
| 2202 |
|
|
fprintf(fp," %s ",ChainsResName[atom->resid]); |
| 2203 |
|
|
fprintf(fp,"%c%4d",atom->chain,atom->resno); |
| 2204 |
|
|
fprintf(fp," %8.3lf%8.3lf%8.3lf",atom->x,atom->y,atom->z); |
| 2205 |
|
|
fputs(" 1.00 0.00\n",fp); |
| 2206 |
|
|
} |
| 2207 |
|
|
|
| 2208 |
|
|
for( i=0; i<mol->bcount; i++ ) |
| 2209 |
|
|
if( mol->bond[i].flag & BF_DOUBLE ) |
| 2210 |
|
|
{ |
| 2211 |
|
|
src = mol->atom[mol->bond[i].src].serno; |
| 2212 |
|
|
dst = mol->atom[mol->bond[i].dst].serno; |
| 2213 |
|
|
fprintf(fp,"CONECT%5d%5d%5d\n",src,dst,dst); |
| 2214 |
|
|
fprintf(fp,"CONECT%5d%5d%5d\n",dst,src,src); |
| 2215 |
|
|
} |
| 2216 |
|
|
fputs("END \n",fp); |
| 2217 |
|
|
} |
| 2218 |
|
|
|
| 2219 |
|
|
#endif |
| 2220 |
|
|
|
| 2221 |
|
|
} // end namespace OpenBabel |
| 2222 |
|
|
|
| 2223 |
|
|
//! \file chains.cpp |
| 2224 |
|
|
//! \brief Parse for macromolecule chains and residues. |
