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/********************************************************************** |
| 2 |
residue.cpp - Handle macromolecule residues. |
| 3 |
|
| 4 |
Copyright (C) 2001, 2002 OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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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/> |
| 9 |
|
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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 |
| 12 |
the Free Software Foundation version 2 of the License. |
| 13 |
|
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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. |
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***********************************************************************/ |
| 19 |
|
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/********************************************************************** |
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Global arrays Residue, ElemDesc and function GetResidueNumber were |
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obtained in part or whole from RasMol2 by Roger Sayle. |
| 23 |
***********************************************************************/ |
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|
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/////////////////////////////////////////////////////////////////////////////// |
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// File Includes |
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/////////////////////////////////////////////////////////////////////////////// |
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|
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#include "babelconfig.hpp" |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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|
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#if HAVE_FSTREAM |
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#include <fstream> |
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#elif HAVE_FSTREAM_H |
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#include <fstream.h> |
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#endif |
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|
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#include "mol.hpp" |
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#include "bitvec.hpp" |
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|
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using namespace std; |
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|
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namespace OpenBabel |
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{ |
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/** \class OBResidue |
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\brief Residue information |
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|
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The residue information is drawn from PDB or MOL2 files (or similar), which |
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track biomolecule information, |
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and are stored in the OBResidue class. OBResidues are stored inside the |
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OBAtom class and OBMol classes. |
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The residue information for an atom can be requested in |
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the following way: |
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\code |
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OBAtom *atom; |
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OBResidue *r; |
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atom = mol.GetAtom(1); |
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r = atom->GetResidue(); |
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\endcode |
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The residue information for a molecule can be manipulated too: |
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\code |
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cout << "This molecule has " << mol.NumResidues() << " residues." << endl; |
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OBResidue *r; |
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r = mol.GetResidue(1); |
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\endcode |
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*/ |
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|
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/////////////////////////////////////////////////////////////////////////////// |
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// Global Definitions |
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/////////////////////////////////////////////////////////////////////////////// |
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|
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#define MAXSETNO 40 |
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#define MAXELEM 1024 |
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#define MINELEM 29 |
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#define MAXRES 100 |
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#define MINRES 54 |
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|
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/////////////////////////////////////////////////////////////////////////////// |
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// Amino Acid Definitions |
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/////////////////////////////////////////////////////////////////////////////// |
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|
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#define AA_ALA (1<<1) |
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#define AA_GLY (1<<2) |
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#define AA_LEU (1<<3) |
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#define AA_SER (1<<4) |
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#define AA_VAL (1<<5) |
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#define AA_THR (1<<6) |
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#define AA_LYS (1<<7) |
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#define AA_ASP (1<<8) |
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#define AA_ILE (1<<9) |
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#define AA_ASN (1<<10) |
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#define AA_GLU (1<<11) |
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#define AA_PRO (1<<12) |
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#define AA_ARG (1<<13) |
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#define AA_PHE (1<<14) |
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#define AA_GLN (1<<15) |
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#define AA_TYR (1<<16) |
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#define AA_HIS (1<<17) |
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#define AA_CYS (1<<18) |
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#define AA_MET (1<<19) |
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#define AA_TRP (1<<20) |
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|
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//! Residue property definitions |
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namespace OBAminoAcidProperty |
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{ |
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static const unsigned int ACIDIC = 0; |
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static const unsigned int ACYCLIC = 1; |
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static const unsigned int ALIPHATIC = 2; |
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static const unsigned int AROMATIC = 3; |
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static const unsigned int BASIC = 4; |
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static const unsigned int BURIED = 5; |
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static const unsigned int CHARGED = 6; |
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static const unsigned int CYCLIC = 7; |
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static const unsigned int HYDROPHOBIC = 8; |
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static const unsigned int LARGE = 9; |
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static const unsigned int MEDIUM = 10; |
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static const unsigned int NEGATIVE = 11; |
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static const unsigned int NEUTRAL = 12; |
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static const unsigned int POLAR = 13; |
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static const unsigned int POSITIVE = 14; |
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static const unsigned int SMALL = 15; |
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static const unsigned int SURFACE = 16; |
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} |
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|
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//! Residue atom properties |
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namespace OBResidueAtomProperty |
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{ |
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static const unsigned int ALPHA_CARBON = 0; |
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static const unsigned int AMINO_BACKBONE = 1; |
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static const unsigned int BACKBONE = 2; |
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static const unsigned int CYSTEINE_SULPHUR = 3; |
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static const unsigned int LIGAND = 4; |
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static const unsigned int NUCLEIC_BACKBONE = 5; |
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static const unsigned int SHAPELY_BACKBONE = 6; |
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static const unsigned int SHAPELY_SPECIAL = 7; |
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static const unsigned int SIDECHAIN = 8; |
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static const unsigned int SUGAR_PHOSPHATE = 9; |
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} |
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/// Residue names |
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namespace OBResidueIndex |
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{ |
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static const unsigned int ALA = 0; |
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static const unsigned int GLY = 1; |
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static const unsigned int LEU = 2; |
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static const unsigned int SER = 3; |
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static const unsigned int VAL = 4; |
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static const unsigned int THR = 5; |
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static const unsigned int LYS = 6; |
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static const unsigned int ASP = 7; |
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static const unsigned int ILE = 8; |
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static const unsigned int ASN = 9; |
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static const unsigned int GLU = 10; |
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static const unsigned int PRO = 11; |
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static const unsigned int ARG = 12; |
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static const unsigned int PHE = 13; |
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static const unsigned int GLN = 14; |
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static const unsigned int TYR = 15; |
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static const unsigned int HIS = 16; |
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static const unsigned int CYS = 17; |
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static const unsigned int MET = 18; |
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static const unsigned int TRP = 19; |
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static const unsigned int ASX = 20; |
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static const unsigned int GLX = 21; |
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static const unsigned int PCA = 22; |
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static const unsigned int HYP = 23; |
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static const unsigned int A = 24; |
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static const unsigned int C = 25; |
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static const unsigned int G = 26; |
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static const unsigned int T = 27; |
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static const unsigned int U = 28; |
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static const unsigned int UPLUS = 29; |
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static const unsigned int I = 30; |
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//static const unsigned int _1MA = 31; |
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//static const unsigned int _5MC = 32; |
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static const unsigned int OMC = 33; |
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//static const unsigned int _1MG = 34; |
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//static const unsigned int _2MG = 35; |
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static const unsigned int M2G = 36; |
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//static const unsigned int _7MG = 37; |
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static const unsigned int OMG = 38; |
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static const unsigned int YG = 39; |
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static const unsigned int H2U = 40; |
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//static const unsigned int _5MU = 41; |
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static const unsigned int PSU = 42; |
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static const unsigned int UNK = 43; |
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static const unsigned int ACE = 44; |
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static const unsigned int FOR = 45; |
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static const unsigned int HOH = 46; |
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static const unsigned int DOD = 47; |
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static const unsigned int SO4 = 48; |
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static const unsigned int PO4 = 49; |
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static const unsigned int NAD = 50; |
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static const unsigned int COA = 51; |
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static const unsigned int NAP = 52; |
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static const unsigned int NDP = 53; |
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} |
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/// Residue types. |
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namespace OBResidueProperty |
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{ |
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static const unsigned int AMINO = 0; |
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static const unsigned int AMINO_NUCLEO = 1; |
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static const unsigned int COENZYME = 2; |
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static const unsigned int ION = 3; |
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static const unsigned int NUCLEO = 4; |
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static const unsigned int PROTEIN = 5; |
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static const unsigned int PURINE = 6; |
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static const unsigned int PYRIMIDINE = 7; |
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static const unsigned int SOLVENT = 8; |
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static const unsigned int WATER = 9; |
| 215 |
} |
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|
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/////////////////////////////////////////////////////////////////////////////// |
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// Amino Acid Property Definitions |
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/////////////////////////////////////////////////////////////////////////////// |
| 220 |
|
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#define IS_ACIDIC(x) ((x) & ((AA_ASP)|(AA_GLU))) |
| 222 |
#define IS_ACYCLIC(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)| \ |
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(AA_VAL)|(AA_THR)|(AA_LYS)|(AA_ASP)| \ |
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(AA_ILE)|(AA_ASN)|(AA_GLU)|(AA_GLN)| \ |
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(AA_CYS)|(AA_MET))) |
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#define IS_ALIPHATIC(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_ILE)|(AA_LEU)| \ |
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(AA_VAL))) |
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#define IS_AROMATIC(x) ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR))) |
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#define IS_BASIC(x) ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS))) |
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#define IS_BURIED(x) ((x) & ((AA_ALA)|(AA_CYS)|(AA_ILE)|(AA_LEU)| \ |
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(AA_MET)|(AA_PHE)|(AA_TRP)|(AA_VAL))) |
| 232 |
#define IS_CHARGED(x) ((x) & ((AA_ASP)|(AA_GLU)|(AA_ARG)|(AA_HIS)| \ |
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(AA_LYS))) |
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#define IS_CYCLIC(x) ((x) & ((AA_HIS)|(AA_PHE)|(AA_PRO)|(AA_TRP)| \ |
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(AA_TYR))) |
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#define IS_HYDROPHOBIC(x) ((x) & ((AA_ALA)|(AA_LEU)|(AA_VAL)|(AA_ILE)| \ |
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(AA_PRO)|(AA_PHE)|(AA_MET)|(AA_TRP))) |
| 238 |
#define IS_LARGE(x) ((x) & ((AA_ARG)|(AA_PHE)|(AA_GLN)|(AA_TYR)| \ |
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(AA_HIS)|(AA_LEU)|(AA_LYS)|(AA_ILE)| \ |
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(AA_GLU)|(AA_MET)|(AA_TRP))) |
| 241 |
#define IS_MEDIUM(x) ((x) & ((AA_VAL)|(AA_THR)|(AA_ASP)|(AA_ASN)| \ |
| 242 |
(AA_PRO)|(AA_CYS))) |
| 243 |
#define IS_NEGATIVE(x) ((x) & ((AA_ASP)|(AA_GLU))) |
| 244 |
#define IS_NEUTRAL(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)| \ |
| 245 |
(AA_VAL)|(AA_THR)|(AA_PHE)|(AA_GLN)| \ |
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(AA_TYR)|(AA_HIS)|(AA_CYS)|(AA_MET)| \ |
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(AA_TRP)|(AA_ILE)|(AA_ASN)|(AA_PRO))) |
| 248 |
#define IS_POLAR(x) ((x) & ((AA_ASP)|(AA_ILE)|(AA_ASN)|(AA_GLU)| \ |
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(AA_SER)|(AA_THR)|(AA_ARG)|(AA_GLN)| \ |
| 250 |
(AA_CYS)|(AA_HIS))) |
| 251 |
#define IS_POSITIVE(x) ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS))) |
| 252 |
#define IS_SMALL(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER))) |
| 253 |
#define IS_SURFACE(x) ((x) & ((AA_THR)|(AA_LYS)|(AA_ASP)|(AA_ILE)| \ |
| 254 |
(AA_ASN)|(AA_GLU)|(AA_PRO)|(AA_ARG)| \ |
| 255 |
(AA_GLY)|(AA_SER)|(AA_GLN)|(AA_TYR)| \ |
| 256 |
(AA_HIS))) |
| 257 |
|
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//////////////////////////////////////////////////////////////////////////////// |
| 259 |
// Global Variables |
| 260 |
//////////////////////////////////////////////////////////////////////////////// |
| 261 |
|
| 262 |
static char Residue[MAXRES][4] = { |
| 263 |
/*===============*/ |
| 264 |
/* Amino Acids */ |
| 265 |
/*===============*/ |
| 266 |
|
| 267 |
/* Ordered by Cumulative Frequency in Brookhaven * |
| 268 |
* Protein Databank, December 1991 */ |
| 269 |
|
| 270 |
"ALA", /* 8.4% */ "GLY", /* 8.3% */ |
| 271 |
"LEU", /* 8.0% */ "SER", /* 7.5% */ |
| 272 |
"VAL", /* 7.1% */ "THR", /* 6.4% */ |
| 273 |
"LYS", /* 5.8% */ "ASP", /* 5.5% */ |
| 274 |
"ILE", /* 5.2% */ "ASN", /* 4.9% */ |
| 275 |
"GLU", /* 4.9% */ "PRO", /* 4.4% */ |
| 276 |
"ARG", /* 3.8% */ "PHE", /* 3.7% */ |
| 277 |
"GLN", /* 3.5% */ "TYR", /* 3.5% */ |
| 278 |
"HIS", /* 2.3% */ "CYS", /* 2.0% */ |
| 279 |
"MET", /* 1.8% */ "TRP", /* 1.4% */ |
| 280 |
|
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"ASX", "GLX", "PCA", "HYP", |
| 282 |
|
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/*===================*/ |
| 284 |
/* DNA Nucleotides */ |
| 285 |
/*===================*/ |
| 286 |
" A", " C", " G", " T", |
| 287 |
|
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/*===================*/ |
| 289 |
/* RNA Nucleotides */ |
| 290 |
/*===================*/ |
| 291 |
" U", " +U", " I", "1MA", |
| 292 |
"5MC", "OMC", "1MG", "2MG", |
| 293 |
"M2G", "7MG", "OMG", " YG", |
| 294 |
"H2U", "5MU", "PSU", |
| 295 |
|
| 296 |
/*=================*/ |
| 297 |
/* Miscellaneous */ |
| 298 |
/*=================*/ |
| 299 |
"UNK", "ACE", "FOR", "HOH", |
| 300 |
"DOD", "SO4", "PO4", "NAD", |
| 301 |
"COA", "NAP", "NDP" |
| 302 |
}; |
| 303 |
|
| 304 |
/* Avoid SGI Compiler Warnings! */ |
| 305 |
static char ElemDesc[MAXELEM][4] = { |
| 306 |
{ ' ', 'N', ' ', ' ' }, /* 0*/ |
| 307 |
{ ' ', 'C', 'A', ' ' }, /* 1*/ |
| 308 |
{ ' ', 'C', ' ', ' ' }, /* 2*/ |
| 309 |
{ ' ', 'O', ' ', ' ' }, /* 3*/ /* 0-3 Amino Acid Backbone */ |
| 310 |
{ ' ', 'C', '\'', ' ' }, /* 4*/ |
| 311 |
{ ' ', 'O', 'T', ' ' }, /* 5*/ |
| 312 |
{ ' ', 'S', ' ', ' ' }, /* 6*/ |
| 313 |
{ ' ', 'P', ' ', ' ' }, /* 7*/ /* 4-7 Shapely Amino Backbone */ |
| 314 |
{ ' ', 'O', '1', 'P' }, /* 8*/ |
| 315 |
{ ' ', 'O', '2', 'P' }, /* 9*/ |
| 316 |
{ ' ', 'O', '5', '*' }, /*10*/ |
| 317 |
{ ' ', 'C', '5', '*' }, /*11*/ |
| 318 |
{ ' ', 'C', '4', '*' }, /*12*/ |
| 319 |
{ ' ', 'O', '4', '*' }, /*13*/ |
| 320 |
{ ' ', 'C', '3', '*' }, /*14*/ |
| 321 |
{ ' ', 'O', '3', '*' }, /*15*/ |
| 322 |
{ ' ', 'C', '2', '*' }, /*16*/ |
| 323 |
{ ' ', 'O', '2', '*' }, /*17*/ |
| 324 |
{ ' ', 'C', '1', '*' }, /*18*/ /* 7-18 Nucleic Acid Backbone */ |
| 325 |
{ ' ', 'C', 'A', '2' }, /*19*/ /* 19 Shapely Special */ |
| 326 |
{ ' ', 'S', 'G', ' ' }, /*20*/ /* 20 Cysteine Sulphur */ |
| 327 |
{ ' ', 'N', '1', ' ' }, /*21*/ |
| 328 |
{ ' ', 'N', '2', ' ' }, /*22*/ |
| 329 |
{ ' ', 'N', '3', ' ' }, /*23*/ |
| 330 |
{ ' ', 'N', '4', ' ' }, /*24*/ |
| 331 |
{ ' ', 'N', '6', ' ' }, /*25*/ |
| 332 |
{ ' ', 'O', '2', ' ' }, /*26*/ |
| 333 |
{ ' ', 'O', '4', ' ' }, /*27*/ |
| 334 |
{ ' ', 'O', '6', ' ' } /*28*/ /* 21-28 Nucleic Acid H-Bonding */ |
| 335 |
}; |
| 336 |
|
| 337 |
static unsigned int ResNo = MINRES; |
| 338 |
static unsigned int ElemNo = MINELEM; |
| 339 |
|
| 340 |
/////////////////////////////////////////////////////////////////////////////// |
| 341 |
// Residue Functions |
| 342 |
/////////////////////////////////////////////////////////////////////////////// |
| 343 |
|
| 344 |
static unsigned int GetAtomIDNumber(const char *atomid) |
| 345 |
{ |
| 346 |
if (atomid != NULL) |
| 347 |
{ |
| 348 |
int ch1 = toupper(atomid[0]); |
| 349 |
int ch2 = toupper(atomid[1]); |
| 350 |
int ch3 = toupper(atomid[2]); |
| 351 |
int ch4 = toupper(atomid[3]); |
| 352 |
|
| 353 |
if (ch1 == ' ') |
| 354 |
{ |
| 355 |
switch(ch2) |
| 356 |
{ |
| 357 |
case 'C': |
| 358 |
|
| 359 |
switch(ch3) |
| 360 |
{ |
| 361 |
case 'A': |
| 362 |
|
| 363 |
if (ch4 == ' ') |
| 364 |
return 1; |
| 365 |
else if (ch4 == '2') |
| 366 |
return 19; |
| 367 |
|
| 368 |
break; |
| 369 |
|
| 370 |
case ' ': |
| 371 |
if (ch4 == ' ') |
| 372 |
return 2; |
| 373 |
break; |
| 374 |
|
| 375 |
case '\'': |
| 376 |
if (ch4 == ' ') |
| 377 |
return 4; |
| 378 |
break; |
| 379 |
|
| 380 |
case '1': |
| 381 |
if (ch4 == '*') |
| 382 |
return 18; |
| 383 |
break; |
| 384 |
|
| 385 |
case '2': |
| 386 |
if (ch4 == '*') |
| 387 |
return 16; |
| 388 |
break; |
| 389 |
|
| 390 |
case '3': |
| 391 |
if (ch4 == '*') |
| 392 |
return 14; |
| 393 |
break; |
| 394 |
|
| 395 |
case '4': |
| 396 |
if (ch4 == '*') |
| 397 |
return 12; |
| 398 |
break; |
| 399 |
|
| 400 |
case '5': |
| 401 |
if (ch4 == '*') |
| 402 |
return 11; |
| 403 |
break; |
| 404 |
|
| 405 |
} |
| 406 |
|
| 407 |
break; |
| 408 |
|
| 409 |
case 'N': |
| 410 |
|
| 411 |
if (ch4 == ' ') |
| 412 |
{ |
| 413 |
switch (ch3) |
| 414 |
{ |
| 415 |
case ' ': |
| 416 |
return 0; |
| 417 |
case '1': |
| 418 |
return 21; |
| 419 |
case '2': |
| 420 |
return 22; |
| 421 |
case '3': |
| 422 |
return 23; |
| 423 |
case '4': |
| 424 |
return 24; |
| 425 |
case '6': |
| 426 |
return 25; |
| 427 |
} |
| 428 |
} |
| 429 |
|
| 430 |
break; |
| 431 |
|
| 432 |
case 'O': |
| 433 |
|
| 434 |
switch(ch3) |
| 435 |
{ |
| 436 |
case ' ': |
| 437 |
|
| 438 |
if (ch4 == ' ') |
| 439 |
return 3; |
| 440 |
|
| 441 |
break; |
| 442 |
|
| 443 |
case 'T': |
| 444 |
|
| 445 |
if (ch4 == ' ') |
| 446 |
return 5; |
| 447 |
|
| 448 |
break; |
| 449 |
|
| 450 |
case '1': |
| 451 |
|
| 452 |
if (ch4 == 'P') |
| 453 |
return 8; |
| 454 |
|
| 455 |
break; |
| 456 |
|
| 457 |
case '2': |
| 458 |
|
| 459 |
if (ch4 == 'P') |
| 460 |
return 9; |
| 461 |
else if (ch4 == '*') |
| 462 |
return 17; |
| 463 |
else if (ch4 == ' ') |
| 464 |
return 26; |
| 465 |
|
| 466 |
break; |
| 467 |
|
| 468 |
case '3': |
| 469 |
|
| 470 |
if (ch4 == '*') |
| 471 |
return 15; |
| 472 |
|
| 473 |
break; |
| 474 |
|
| 475 |
case '4': |
| 476 |
|
| 477 |
if (ch4 == '*') |
| 478 |
return 13; |
| 479 |
else if (ch4 == ' ') |
| 480 |
return 27; |
| 481 |
|
| 482 |
break; |
| 483 |
|
| 484 |
case '5': |
| 485 |
|
| 486 |
if (ch4 == '*') |
| 487 |
return 10; |
| 488 |
|
| 489 |
break; |
| 490 |
|
| 491 |
case '6': |
| 492 |
|
| 493 |
if (ch4 == ' ') |
| 494 |
return 28; |
| 495 |
|
| 496 |
break; |
| 497 |
} |
| 498 |
|
| 499 |
break; |
| 500 |
|
| 501 |
case 'P': |
| 502 |
|
| 503 |
if ((ch3 == ' ') && (ch4 == ' ')) |
| 504 |
return 7; |
| 505 |
|
| 506 |
break; |
| 507 |
|
| 508 |
case 'S': |
| 509 |
|
| 510 |
if (ch4 == ' ') |
| 511 |
{ |
| 512 |
if (ch3 == ' ') |
| 513 |
return 6; |
| 514 |
else if (ch3 == 'G') |
| 515 |
return 20; |
| 516 |
} |
| 517 |
|
| 518 |
break; |
| 519 |
} |
| 520 |
} |
| 521 |
|
| 522 |
unsigned int refno; |
| 523 |
for( refno = MINELEM ; refno < ElemNo ; refno++ ) |
| 524 |
if( !strncmp(ElemDesc[refno], atomid, 4) ) |
| 525 |
return refno; |
| 526 |
|
| 527 |
if ( ElemNo < MAXELEM - 1 ) |
| 528 |
{ |
| 529 |
ElemNo++; |
| 530 |
ElemDesc[refno][0] = (char) ch1; |
| 531 |
ElemDesc[refno][1] = (char) ch2; |
| 532 |
ElemDesc[refno][2] = (char) ch3; |
| 533 |
ElemDesc[refno][3] = (char) ch4; |
| 534 |
return refno; |
| 535 |
} |
| 536 |
else |
| 537 |
{ |
| 538 |
obErrorLog.ThrowError(__FUNCTION__, "Maximum number of atom ids exceeded", obWarning); |
| 539 |
return 0; |
| 540 |
} |
| 541 |
} |
| 542 |
else |
| 543 |
{ |
| 544 |
obErrorLog.ThrowError(__FUNCTION__, "NULL Atom IDs specified", obWarning); |
| 545 |
return 0; |
| 546 |
} |
| 547 |
} |
| 548 |
|
| 549 |
static unsigned int GetResidueNumber(const char *res) |
| 550 |
{ |
| 551 |
if (res != NULL) |
| 552 |
{ |
| 553 |
int ch1 = toupper(res[0]); |
| 554 |
int ch2 = toupper(res[1]); |
| 555 |
int ch3 = toupper(res[2]); |
| 556 |
|
| 557 |
switch( ch1 ) |
| 558 |
{ |
| 559 |
case(' '): |
| 560 |
|
| 561 |
if( ch2 == ' ' ) |
| 562 |
{ |
| 563 |
switch( ch3 ) |
| 564 |
{ |
| 565 |
case('A'): return( 24 ); |
| 566 |
case('C'): return( 25 ); |
| 567 |
case('G'): return( 26 ); |
| 568 |
case('T'): return( 27 ); |
| 569 |
case('U'): return( 28 ); |
| 570 |
case('I'): return( 30 ); |
| 571 |
} |
| 572 |
} |
| 573 |
else if( ch2 == '+' ) |
| 574 |
{ |
| 575 |
if( ch3 == 'U' ) |
| 576 |
return( 29 ); |
| 577 |
} |
| 578 |
else if( ch2 == 'Y' ) |
| 579 |
{ |
| 580 |
if( ch3 == 'G' ) |
| 581 |
return( 39 ); |
| 582 |
} |
| 583 |
|
| 584 |
break; |
| 585 |
|
| 586 |
case('0'): |
| 587 |
|
| 588 |
if( ch2 == 'M' ) |
| 589 |
{ |
| 590 |
if( ch3 == 'C' ) |
| 591 |
return( 33 ); |
| 592 |
else if( ch3 == 'G' ) |
| 593 |
return( 38 ); |
| 594 |
} |
| 595 |
|
| 596 |
break; |
| 597 |
|
| 598 |
case('1'): |
| 599 |
|
| 600 |
if( ch2 == 'M' ) |
| 601 |
{ |
| 602 |
if( ch3 == 'A' ) |
| 603 |
return( 31 ); |
| 604 |
else if( ch3 == 'G' ) |
| 605 |
return( 34 ); |
| 606 |
} |
| 607 |
|
| 608 |
break; |
| 609 |
|
| 610 |
case('2'): |
| 611 |
|
| 612 |
if( ch2 == 'M' ) |
| 613 |
if( ch3 == 'G' ) |
| 614 |
return( 35 ); |
| 615 |
|
| 616 |
break; |
| 617 |
|
| 618 |
case('5'): |
| 619 |
|
| 620 |
if( ch2 == 'M' ) |
| 621 |
{ |
| 622 |
if( ch3 == 'C' ) |
| 623 |
return( 32 ); |
| 624 |
else if( ch3 == 'U' ) |
| 625 |
return( 41 ); |
| 626 |
} |
| 627 |
|
| 628 |
break; |
| 629 |
|
| 630 |
case('7'): |
| 631 |
|
| 632 |
if( ch2 == 'M' ) |
| 633 |
if( ch3 == 'G' ) |
| 634 |
return( 37 ); |
| 635 |
|
| 636 |
break; |
| 637 |
|
| 638 |
case('A'): |
| 639 |
|
| 640 |
if( ch2 == 'L' ) |
| 641 |
{ |
| 642 |
if( ch3 == 'A' ) |
| 643 |
return( 0 ); |
| 644 |
} |
| 645 |
else if( ch2 == 'S' ) |
| 646 |
{ |
| 647 |
if( ch3 == 'P' ) |
| 648 |
return( 7 ); |
| 649 |
else if( ch3 == 'N' ) |
| 650 |
return( 9 ); |
| 651 |
else if( ch3 == 'X' ) |
| 652 |
return( 20 ); |
| 653 |
} |
| 654 |
else if( ch2 == 'R' ) |
| 655 |
{ |
| 656 |
if( ch3 == 'G' ) |
| 657 |
return( 12 ); |
| 658 |
} |
| 659 |
else if( ch2 == 'C' ) |
| 660 |
{ |
| 661 |
if( ch3 == 'E' ) |
| 662 |
return( 44 ); |
| 663 |
} |
| 664 |
else if( ch2 == 'D' ) |
| 665 |
{ |
| 666 |
if( ch3 == 'E' ) |
| 667 |
return( 24 ); /* "ADE" -> " A" */ |
| 668 |
} |
| 669 |
|
| 670 |
break; |
| 671 |
|
| 672 |
case('C'): |
| 673 |
|
| 674 |
if( ch2 == 'Y' ) |
| 675 |
{ |
| 676 |
if( ch3 == 'S' ) |
| 677 |
return( 17 ); |
| 678 |
else if( ch3 == 'H' ) |
| 679 |
return( 17 ); /* "CYH" -> "CYS" */ |
| 680 |
else if( ch3 == 'T' ) |
| 681 |
return( 25 ); /* "CYT" -> " C" */ |
| 682 |
} |
| 683 |
else if( ch2 == 'O' ) |
| 684 |
{ |
| 685 |
if( ch3 == 'A' ) |
| 686 |
return( 51 ); |
| 687 |
} |
| 688 |
else if( ch2 == 'P' ) |
| 689 |
{ |
| 690 |
if( ch3 == 'R' ) |
| 691 |
return( 11 ); /* "CPR" -> "PRO" */ |
| 692 |
} |
| 693 |
else if( ch2 == 'S' ) |
| 694 |
{ |
| 695 |
if( ch3 == 'H' ) |
| 696 |
return( 17 ); /* "CSH" -> "CYS" */ |
| 697 |
else if( ch3 == 'M' ) |
| 698 |
return( 17 ); /* "CSM" -> "CYS" */ |
| 699 |
} |
| 700 |
|
| 701 |
break; |
| 702 |
|
| 703 |
case('D'): |
| 704 |
|
| 705 |
if( ch2 == 'O' ) |
| 706 |
{ |
| 707 |
if( ch3 == 'D' ) |
| 708 |
return( 47 ); |
| 709 |
} |
| 710 |
else if( ch2 == '2' ) |
| 711 |
{ |
| 712 |
if( ch3 == 'O' ) |
| 713 |
return( 47 ); /* "D2O" -> "DOD" */ |
| 714 |
} |
| 715 |
|
| 716 |
break; |
| 717 |
|
| 718 |
case('F'): |
| 719 |
|
| 720 |
if( ch2 == 'O' ) |
| 721 |
if( ch3 == 'R' ) |
| 722 |
return( 45 ); |
| 723 |
|
| 724 |
break; |
| 725 |
|
| 726 |
case('G'): |
| 727 |
|
| 728 |
if( ch2 == 'L' ) |
| 729 |
{ |
| 730 |
if( ch3 == 'Y' ) |
| 731 |
return( 1 ); |
| 732 |
else if( ch3 == 'U' ) |
| 733 |
return( 10 ); |
| 734 |
else if( ch3 == 'N' ) |
| 735 |
return( 14 ); |
| 736 |
else if( ch3 == 'X' ) |
| 737 |
return( 21 ); |
| 738 |
} |
| 739 |
else if( ch2 == 'U' ) |
| 740 |
{ |
| 741 |
if( ch3 == 'A' ) |
| 742 |
return( 26 ); /* "GUA" -> " G" */ |
| 743 |
} |
| 744 |
|
| 745 |
break; |
| 746 |
|
| 747 |
case('H'): |
| 748 |
|
| 749 |
if( ch2 == 'I' ) |
| 750 |
{ |
| 751 |
if( ch3 == 'S' ) |
| 752 |
return( 16 ); |
| 753 |
} |
| 754 |
else if( ch2 == 'O' ) |
| 755 |
{ |
| 756 |
if( ch3 == 'H' ) |
| 757 |
return( 46 ); |
| 758 |
} |
| 759 |
else if( ch2 == 'Y' ) |
| 760 |
{ |
| 761 |
if( ch3 == 'P' ) |
| 762 |
return( 23 ); |
| 763 |
} |
| 764 |
else if( ch2 == '2' ) |
| 765 |
{ |
| 766 |
if( ch3 == 'O' ) |
| 767 |
return( 46 ); /* "H20" -> "HOH" */ |
| 768 |
else if( ch3 == 'U' ) |
| 769 |
return( 40 ); |
| 770 |
} |
| 771 |
|
| 772 |
break; |
| 773 |
|
| 774 |
case('I'): |
| 775 |
|
| 776 |
if( ch2 == 'L' ) |
| 777 |
if( ch3 == 'E' ) |
| 778 |
return( 8 ); |
| 779 |
|
| 780 |
break; |
| 781 |
|
| 782 |
case('L'): |
| 783 |
|
| 784 |
if( ch2 == 'E' ) |
| 785 |
{ |
| 786 |
if( ch3 == 'U' ) |
| 787 |
return( 2 ); |
| 788 |
} |
| 789 |
else if( ch2 == 'Y' ) |
| 790 |
{ |
| 791 |
if( ch3 == 'S' ) |
| 792 |
return( 6 ); |
| 793 |
} |
| 794 |
|
| 795 |
break; |
| 796 |
|
| 797 |
case('M'): |
| 798 |
|
| 799 |
if( ch2 == 'E' ) |
| 800 |
{ |
| 801 |
if( ch3 == 'T' ) |
| 802 |
return( 18 ); |
| 803 |
} |
| 804 |
else if( ch2 == '2' ) |
| 805 |
{ |
| 806 |
if( ch3 == 'G' ) |
| 807 |
return( 36 ); |
| 808 |
} |
| 809 |
|
| 810 |
break; |
| 811 |
|
| 812 |
case('N'): |
| 813 |
|
| 814 |
if( ch2 == 'A' ) |
| 815 |
{ |
| 816 |
if( ch3 == 'D' ) |
| 817 |
return( 50 ); |
| 818 |
else if( ch3 == 'P' ) |
| 819 |
return( 52 ); |
| 820 |
} |
| 821 |
else if( ch2 == 'D' ) |
| 822 |
{ |
| 823 |
if( ch3 == 'P' ) |
| 824 |
return( 53 ); |
| 825 |
} |
| 826 |
|
| 827 |
break; |
| 828 |
|
| 829 |
case('P'): |
| 830 |
|
| 831 |
if( ch2 == 'R' ) |
| 832 |
{ |
| 833 |
if( ch3 == 'O' ) |
| 834 |
return( 11 ); |
| 835 |
} |
| 836 |
else if( ch2 == 'H' ) |
| 837 |
{ |
| 838 |
if( ch3 == 'E' ) |
| 839 |
return( 13 ); |
| 840 |
} |
| 841 |
else if( ch2 == 'C' ) |
| 842 |
{ |
| 843 |
if( ch3 == 'A' ) |
| 844 |
return( 22 ); |
| 845 |
} |
| 846 |
else if( ch2 == 'O' ) |
| 847 |
{ |
| 848 |
if( ch3 == '4' ) |
| 849 |
return( 49 ); |
| 850 |
} |
| 851 |
else if( ch2 == 'S' ) |
| 852 |
{ |
| 853 |
if( ch3 == 'U' ) |
| 854 |
return( 42 ); |
| 855 |
} |
| 856 |
|
| 857 |
break; |
| 858 |
|
| 859 |
case('S'): |
| 860 |
|
| 861 |
if( ch2 == 'E' ) |
| 862 |
{ |
| 863 |
if( ch3 == 'R' ) |
| 864 |
return( 3 ); |
| 865 |
} |
| 866 |
else if( ch2 == 'O' ) |
| 867 |
{ |
| 868 |
if( ch3 == '4' ) |
| 869 |
return( 48 ); |
| 870 |
else if( ch3 == 'L' ) |
| 871 |
return( 46 ); /* "SOL" -> "HOH" */ |
| 872 |
} |
| 873 |
else if( ch2 == 'U' ) |
| 874 |
{ |
| 875 |
if( ch3 == 'L' ) |
| 876 |
return( 48 ); /* "SUL" -> "SO4" */ |
| 877 |
} |
| 878 |
|
| 879 |
break; |
| 880 |
|
| 881 |
case('T'): |
| 882 |
|
| 883 |
if( ch2 == 'H' ) |
| 884 |
{ |
| 885 |
if( ch3 == 'R' ) |
| 886 |
return( 5 ); |
| 887 |
else if( ch3 == 'Y' ) |
| 888 |
return( 27 ); /* "THY" -> " T" */ |
| 889 |
} |
| 890 |
else if( ch2 == 'Y' ) |
| 891 |
{ |
| 892 |
if( ch3 == 'R' ) |
| 893 |
return( 15 ); |
| 894 |
} |
| 895 |
else if( ch2 == 'R' ) |
| 896 |
{ |
| 897 |
if( ch3 == 'P' ) |
| 898 |
return( 19 ); |
| 899 |
else if( ch3 == 'Y' ) |
| 900 |
return( 19 ); /* "TRY" -> "TRP" */ |
| 901 |
} |
| 902 |
else if( ch2 == 'I' ) |
| 903 |
{ |
| 904 |
if( ch3 == 'P' ) |
| 905 |
return( 46 ); /* "TIP" -> "HOH" */ |
| 906 |
} |
| 907 |
|
| 908 |
break; |
| 909 |
|
| 910 |
case('U'): |
| 911 |
|
| 912 |
if( ch2 == 'N' ) |
| 913 |
{ |
| 914 |
if( ch3 == 'K' ) |
| 915 |
return( 43 ); |
| 916 |
} |
| 917 |
else if( ch2 == 'R' ) |
| 918 |
{ |
| 919 |
if( ch3 == 'A' ) |
| 920 |
return( 28 ); /* "URA" -> " U" */ |
| 921 |
else if( ch3 == 'I' ) |
| 922 |
return( 28 ); /* "URI" -> " U" */ |
| 923 |
} |
| 924 |
|
| 925 |
break; |
| 926 |
|
| 927 |
case('V'): |
| 928 |
|
| 929 |
if( ch2 == 'A' ) |
| 930 |
if( ch3 == 'L' ) |
| 931 |
return( 4 ); |
| 932 |
|
| 933 |
break; |
| 934 |
|
| 935 |
case('W'): |
| 936 |
|
| 937 |
if( ch2 == 'A' ) |
| 938 |
if( ch3 == 'T' ) |
| 939 |
return( 46 ); /* "WAT" -> "HOH" */ |
| 940 |
|
| 941 |
break; |
| 942 |
} |
| 943 |
|
| 944 |
unsigned int refno; |
| 945 |
for( refno = MINRES; refno < ResNo ; refno++ ) |
| 946 |
if( !strncmp(Residue[refno],res,3) ) |
| 947 |
return refno; |
| 948 |
|
| 949 |
if ( ResNo < MAXRES - 1 ) |
| 950 |
{ |
| 951 |
ResNo++; |
| 952 |
Residue[refno][0] = (char) ch1; |
| 953 |
Residue[refno][1] = (char) ch2; |
| 954 |
Residue[refno][2] = (char) ch3; |
| 955 |
return refno; |
| 956 |
} |
| 957 |
} |
| 958 |
|
| 959 |
return OBResidueIndex::UNK; |
| 960 |
} |
| 961 |
|
| 962 |
static void SetResidueKeys(const char *residue, |
| 963 |
unsigned int &reskey, |
| 964 |
unsigned int &aakey) |
| 965 |
{ |
| 966 |
reskey = GetResidueNumber(residue); |
| 967 |
switch(reskey) |
| 968 |
{ |
| 969 |
case OBResidueIndex::ALA: |
| 970 |
aakey = AA_ALA; |
| 971 |
break; |
| 972 |
case OBResidueIndex::GLY: |
| 973 |
aakey = AA_GLY; |
| 974 |
break; |
| 975 |
case OBResidueIndex::LEU: |
| 976 |
aakey = AA_LEU; |
| 977 |
break; |
| 978 |
case OBResidueIndex::SER: |
| 979 |
aakey = AA_SER; |
| 980 |
break; |
| 981 |
case OBResidueIndex::VAL: |
| 982 |
aakey = AA_VAL; |
| 983 |
break; |
| 984 |
case OBResidueIndex::THR: |
| 985 |
aakey = AA_THR; |
| 986 |
break; |
| 987 |
case OBResidueIndex::LYS: |
| 988 |
aakey = AA_LYS; |
| 989 |
break; |
| 990 |
case OBResidueIndex::ASP: |
| 991 |
aakey = AA_ASP; |
| 992 |
break; |
| 993 |
case OBResidueIndex::ILE: |
| 994 |
aakey = AA_ILE; |
| 995 |
break; |
| 996 |
case OBResidueIndex::ASN: |
| 997 |
aakey = AA_ASN; |
| 998 |
break; |
| 999 |
case OBResidueIndex::GLU: |
| 1000 |
aakey = AA_GLU; |
| 1001 |
break; |
| 1002 |
case OBResidueIndex::PRO: |
| 1003 |
aakey = AA_PRO; |
| 1004 |
break; |
| 1005 |
case OBResidueIndex::ARG: |
| 1006 |
aakey = AA_ARG; |
| 1007 |
break; |
| 1008 |
case OBResidueIndex::PHE: |
| 1009 |
aakey = AA_PHE; |
| 1010 |
break; |
| 1011 |
case OBResidueIndex::GLN: |
| 1012 |
aakey = AA_GLN; |
| 1013 |
break; |
| 1014 |
case OBResidueIndex::TYR: |
| 1015 |
aakey = AA_TYR; |
| 1016 |
break; |
| 1017 |
case OBResidueIndex::HIS: |
| 1018 |
aakey = AA_HIS; |
| 1019 |
break; |
| 1020 |
case OBResidueIndex::CYS: |
| 1021 |
aakey = AA_CYS; |
| 1022 |
break; |
| 1023 |
case OBResidueIndex::MET: |
| 1024 |
aakey = AA_MET; |
| 1025 |
break; |
| 1026 |
case OBResidueIndex::TRP: |
| 1027 |
aakey = AA_TRP; |
| 1028 |
break; |
| 1029 |
default: |
| 1030 |
aakey = 0; |
| 1031 |
break; |
| 1032 |
} |
| 1033 |
} |
| 1034 |
|
| 1035 |
/////////////////////////////////////////////////////////////////////////////// |
| 1036 |
// OBResidue: Constructors / Destructor |
| 1037 |
/////////////////////////////////////////////////////////////////////////////// |
| 1038 |
|
| 1039 |
OBResidue::OBResidue() |
| 1040 |
{ |
| 1041 |
_chain = 'A'; |
| 1042 |
_idx = 0; |
| 1043 |
_aakey = 0; |
| 1044 |
_reskey = OBResidueIndex::UNK; |
| 1045 |
_resnum = 0; |
| 1046 |
_resname = ""; |
| 1047 |
_vdata.clear(); |
| 1048 |
} |
| 1049 |
|
| 1050 |
OBResidue::OBResidue(const OBResidue &src) |
| 1051 |
// Currently does not copy vdata information |
| 1052 |
{ |
| 1053 |
_chain = src._chain; |
| 1054 |
_aakey = src._aakey; |
| 1055 |
_reskey = src._reskey; |
| 1056 |
_resnum = src._resnum; |
| 1057 |
_resname = src._resname; |
| 1058 |
_atomid = src._atomid; |
| 1059 |
_hetatm = src._hetatm; |
| 1060 |
_sernum = src._sernum; |
| 1061 |
} |
| 1062 |
|
| 1063 |
OBResidue::~OBResidue() |
| 1064 |
{ |
| 1065 |
vector<OBAtom*>::iterator a; |
| 1066 |
for ( a = _atoms.begin() ; a != _atoms.end() ; a++ ) |
| 1067 |
(*a)->SetResidue(NULL); |
| 1068 |
_atoms.clear(); |
| 1069 |
if (!_vdata.empty()) |
| 1070 |
{ |
| 1071 |
vector<OBGenericData*>::iterator m; |
| 1072 |
for (m = _vdata.begin();m != _vdata.end();m++) |
| 1073 |
delete *m; |
| 1074 |
_vdata.clear(); |
| 1075 |
} |
| 1076 |
} |
| 1077 |
|
| 1078 |
/////////////////////////////////////////////////////////////////////////////// |
| 1079 |
// OBResidue: Operator Overloads |
| 1080 |
/////////////////////////////////////////////////////////////////////////////// |
| 1081 |
|
| 1082 |
OBResidue &OBResidue::operator = (const OBResidue &src) |
| 1083 |
//copy residue information |
| 1084 |
// Currently does not copy vdata informtion |
| 1085 |
{ |
| 1086 |
if (this != &src) |
| 1087 |
{ |
| 1088 |
_chain = src._chain; |
| 1089 |
_aakey = src._aakey; |
| 1090 |
_reskey = src._reskey; |
| 1091 |
_resnum = src._resnum; |
| 1092 |
_resname = src._resname; |
| 1093 |
_atomid = src._atomid; |
| 1094 |
_hetatm = src._hetatm; |
| 1095 |
_sernum = src._sernum; |
| 1096 |
} |
| 1097 |
|
| 1098 |
return(*this); |
| 1099 |
} |
| 1100 |
|
| 1101 |
/////////////////////////////////////////////////////////////////////////////// |
| 1102 |
// OBResidue: Data Access / Manipulation |
| 1103 |
/////////////////////////////////////////////////////////////////////////////// |
| 1104 |
|
| 1105 |
void OBResidue::AddAtom(OBAtom *atom) |
| 1106 |
{ |
| 1107 |
if (atom != NULL) |
| 1108 |
{ |
| 1109 |
atom->SetResidue(this); |
| 1110 |
|
| 1111 |
_atoms.push_back(atom); |
| 1112 |
_atomid.push_back(""); |
| 1113 |
_hetatm.push_back(false); |
| 1114 |
_sernum.push_back(0); |
| 1115 |
} |
| 1116 |
} |
| 1117 |
|
| 1118 |
void OBResidue::InsertAtom(OBAtom *atom) |
| 1119 |
{ |
| 1120 |
if (atom != NULL) |
| 1121 |
{ |
| 1122 |
atom->SetResidue(this); |
| 1123 |
|
| 1124 |
_atoms.push_back(atom); |
| 1125 |
_atomid.push_back(""); |
| 1126 |
_hetatm.push_back(false); |
| 1127 |
_sernum.push_back(0); |
| 1128 |
} |
| 1129 |
} |
| 1130 |
|
| 1131 |
void OBResidue::RemoveAtom(OBAtom *atom) |
| 1132 |
{ |
| 1133 |
if (atom != NULL) |
| 1134 |
{ |
| 1135 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1136 |
{ |
| 1137 |
if (_atoms[i] == atom) |
| 1138 |
{ |
| 1139 |
atom->SetResidue(NULL); |
| 1140 |
_atoms.erase(_atoms.begin() + i); |
| 1141 |
_atomid.erase(_atomid.begin() + i); |
| 1142 |
_hetatm.erase(_hetatm.begin() + i); |
| 1143 |
_sernum.erase(_sernum.begin() + i); |
| 1144 |
} |
| 1145 |
} |
| 1146 |
} |
| 1147 |
} |
| 1148 |
|
| 1149 |
void OBResidue::Clear(void) |
| 1150 |
{ |
| 1151 |
for (unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1152 |
_atoms[i]->SetResidue(NULL); |
| 1153 |
|
| 1154 |
_chain = 'A'; |
| 1155 |
_idx = 0; |
| 1156 |
_aakey = 0; |
| 1157 |
_reskey = OBResidueIndex::UNK; |
| 1158 |
_resnum = 0; |
| 1159 |
_resname = ""; |
| 1160 |
|
| 1161 |
_atoms.clear(); |
| 1162 |
_atomid.clear(); |
| 1163 |
_hetatm.clear(); |
| 1164 |
_sernum.clear(); |
| 1165 |
} |
| 1166 |
|
| 1167 |
void OBResidue::SetChain(char chain) |
| 1168 |
{ |
| 1169 |
_chain = chain; |
| 1170 |
} |
| 1171 |
|
| 1172 |
void OBResidue::SetChainNum(unsigned int chainnum) |
| 1173 |
{ |
| 1174 |
_chain = (char) ('A' + chainnum - 1); |
| 1175 |
} |
| 1176 |
|
| 1177 |
void OBResidue::SetIdx(unsigned int idx) |
| 1178 |
{ |
| 1179 |
_idx = idx; |
| 1180 |
} |
| 1181 |
|
| 1182 |
void OBResidue::SetName(const string &name) |
| 1183 |
{ |
| 1184 |
_resname = name; |
| 1185 |
SetResidueKeys(_resname.c_str(), _reskey, _aakey); |
| 1186 |
} |
| 1187 |
|
| 1188 |
void OBResidue::SetNum(unsigned int resnum) |
| 1189 |
{ |
| 1190 |
_resnum = resnum; |
| 1191 |
} |
| 1192 |
|
| 1193 |
void OBResidue::SetAtomID(OBAtom *atom, const string &id) |
| 1194 |
{ |
| 1195 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1196 |
if (_atoms[i] == atom) |
| 1197 |
_atomid[i] = id; |
| 1198 |
} |
| 1199 |
|
| 1200 |
void OBResidue::SetHetAtom(OBAtom *atom, bool hetatm) |
| 1201 |
{ |
| 1202 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1203 |
if (_atoms[i] == atom) |
| 1204 |
_hetatm[i] = hetatm; |
| 1205 |
} |
| 1206 |
|
| 1207 |
void OBResidue::SetSerialNum(OBAtom *atom, unsigned int sernum) |
| 1208 |
{ |
| 1209 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1210 |
if (_atoms[i] == atom) |
| 1211 |
_sernum[i] = sernum; |
| 1212 |
} |
| 1213 |
|
| 1214 |
vector<OBAtom*> OBResidue::GetAtoms(void) const |
| 1215 |
{ |
| 1216 |
return _atoms; |
| 1217 |
} |
| 1218 |
|
| 1219 |
vector<OBBond*> OBResidue::GetBonds(bool exterior) const |
| 1220 |
{ |
| 1221 |
OBAtom *atom; |
| 1222 |
vector<OBBond*> bonds; |
| 1223 |
OBBitVec idxs; |
| 1224 |
unsigned int sz; |
| 1225 |
|
| 1226 |
sz = (unsigned int) _atoms.size(); |
| 1227 |
for ( unsigned int i = 0 ; i < sz ; i++ ) |
| 1228 |
{ |
| 1229 |
atom = _atoms[i]; |
| 1230 |
OBBond *bond; |
| 1231 |
vector<OBEdgeBase*>::iterator b; |
| 1232 |
for (bond = atom->BeginBond(b) ; bond ; bond = atom->NextBond(b)) |
| 1233 |
{ |
| 1234 |
if (!idxs.BitIsOn(bond->GetIdx())) |
| 1235 |
{ |
| 1236 |
if (!exterior) |
| 1237 |
{ |
| 1238 |
if (bond->GetNbrAtom(atom)->GetResidue() == this) |
| 1239 |
bonds.push_back(&(*bond)); |
| 1240 |
} |
| 1241 |
else |
| 1242 |
bonds.push_back(&(*bond)); |
| 1243 |
|
| 1244 |
idxs.SetBitOn(bond->GetIdx()); |
| 1245 |
} |
| 1246 |
} |
| 1247 |
} |
| 1248 |
|
| 1249 |
return bonds; |
| 1250 |
} |
| 1251 |
|
| 1252 |
string OBResidue::GetName(void) const |
| 1253 |
{ |
| 1254 |
return _resname; |
| 1255 |
} |
| 1256 |
|
| 1257 |
unsigned int OBResidue::GetNum(void) const |
| 1258 |
{ |
| 1259 |
return _resnum; |
| 1260 |
} |
| 1261 |
|
| 1262 |
unsigned int OBResidue::GetNumAtoms(void) const |
| 1263 |
{ |
| 1264 |
return (unsigned int)_atoms.size(); |
| 1265 |
} |
| 1266 |
|
| 1267 |
char OBResidue::GetChain(void) const |
| 1268 |
{ |
| 1269 |
return _chain; |
| 1270 |
} |
| 1271 |
|
| 1272 |
unsigned int OBResidue::GetChainNum(void) const |
| 1273 |
{ |
| 1274 |
if (isdigit(_chain)) |
| 1275 |
return (_chain - '0'); |
| 1276 |
else |
| 1277 |
return (_chain - 'A' + 1); |
| 1278 |
} |
| 1279 |
|
| 1280 |
unsigned int OBResidue::GetIdx(void) const |
| 1281 |
{ |
| 1282 |
return(_idx); |
| 1283 |
} |
| 1284 |
|
| 1285 |
unsigned int OBResidue::GetResKey(void) const |
| 1286 |
{ |
| 1287 |
return(_reskey); |
| 1288 |
} |
| 1289 |
|
| 1290 |
string OBResidue::GetAtomID(OBAtom *atom) const |
| 1291 |
{ |
| 1292 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1293 |
if (_atoms[i] == atom) |
| 1294 |
return _atomid[i]; |
| 1295 |
return ""; |
| 1296 |
} |
| 1297 |
|
| 1298 |
unsigned int OBResidue::GetSerialNum(OBAtom *atom) const |
| 1299 |
{ |
| 1300 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1301 |
if (_atoms[i] == atom) |
| 1302 |
return _sernum[i]; |
| 1303 |
return 0; |
| 1304 |
} |
| 1305 |
|
| 1306 |
bool OBResidue::IsHetAtom(OBAtom *atom) const |
| 1307 |
{ |
| 1308 |
for ( unsigned int i = 0 ; i < _atoms.size() ; i++ ) |
| 1309 |
if (_atoms[i] == atom) |
| 1310 |
return _hetatm[i]; |
| 1311 |
return false; |
| 1312 |
} |
| 1313 |
|
| 1314 |
/////////////////////////////////////////////////////////////////////////////// |
| 1315 |
// OBResidue: Iteration Utilities |
| 1316 |
/////////////////////////////////////////////////////////////////////////////// |
| 1317 |
|
| 1318 |
OBAtom *OBResidue::BeginAtom(vector<OBAtom*>::iterator &i) |
| 1319 |
{ |
| 1320 |
i = _atoms.begin(); |
| 1321 |
return ((i == _atoms.end()) ? NULL : *i); |
| 1322 |
} |
| 1323 |
|
| 1324 |
OBAtom *OBResidue::NextAtom(vector<OBAtom*>::iterator &i) |
| 1325 |
{ |
| 1326 |
i++; |
| 1327 |
return ((i == _atoms.end()) ? NULL : *i); |
| 1328 |
} |
| 1329 |
|
| 1330 |
/////////////////////////////////////////////////////////////////////////////// |
| 1331 |
// OBResidue: Information Functions |
| 1332 |
/////////////////////////////////////////////////////////////////////////////// |
| 1333 |
|
| 1334 |
bool OBResidue::GetAminoAcidProperty(int property) const |
| 1335 |
{ |
| 1336 |
switch(property) |
| 1337 |
{ |
| 1338 |
case OBAminoAcidProperty::ACIDIC: |
| 1339 |
return IS_ACIDIC(_aakey) != 0; |
| 1340 |
case OBAminoAcidProperty::ACYCLIC: |
| 1341 |
return IS_ACYCLIC(_aakey) != 0; |
| 1342 |
case OBAminoAcidProperty::ALIPHATIC: |
| 1343 |
return IS_ALIPHATIC(_aakey) != 0; |
| 1344 |
case OBAminoAcidProperty::AROMATIC: |
| 1345 |
return IS_AROMATIC(_aakey) != 0; |
| 1346 |
case OBAminoAcidProperty::BASIC: |
| 1347 |
return IS_BASIC(_aakey) != 0; |
| 1348 |
case OBAminoAcidProperty::BURIED: |
| 1349 |
return IS_BURIED(_aakey) != 0; |
| 1350 |
case OBAminoAcidProperty::CHARGED: |
| 1351 |
return IS_CHARGED(_aakey) != 0; |
| 1352 |
case OBAminoAcidProperty::CYCLIC: |
| 1353 |
return IS_CYCLIC(_aakey) != 0; |
| 1354 |
case OBAminoAcidProperty::HYDROPHOBIC: |
| 1355 |
return IS_HYDROPHOBIC(_aakey) != 0; |
| 1356 |
case OBAminoAcidProperty::LARGE: |
| 1357 |
return IS_LARGE(_aakey) != 0; |
| 1358 |
case OBAminoAcidProperty::MEDIUM: |
| 1359 |
return IS_MEDIUM(_aakey) != 0; |
| 1360 |
case OBAminoAcidProperty::NEGATIVE: |
| 1361 |
return IS_NEGATIVE(_aakey) != 0; |
| 1362 |
case OBAminoAcidProperty::NEUTRAL: |
| 1363 |
return IS_NEUTRAL(_aakey) != 0; |
| 1364 |
case OBAminoAcidProperty::POLAR: |
| 1365 |
return IS_POLAR(_aakey) != 0; |
| 1366 |
case OBAminoAcidProperty::POSITIVE: |
| 1367 |
return IS_POSITIVE(_aakey) != 0; |
| 1368 |
case OBAminoAcidProperty::SMALL: |
| 1369 |
return IS_SMALL(_aakey) != 0; |
| 1370 |
case OBAminoAcidProperty::SURFACE: |
| 1371 |
return IS_SURFACE(_aakey) != 0; |
| 1372 |
default: |
| 1373 |
return false; |
| 1374 |
} |
| 1375 |
} |
| 1376 |
|
| 1377 |
bool OBResidue::GetAtomProperty(OBAtom *atom, int property) const |
| 1378 |
{ |
| 1379 |
if (atom != NULL) |
| 1380 |
{ |
| 1381 |
unsigned int atomid = GetAtomIDNumber(GetAtomID(atom).c_str()); |
| 1382 |
|
| 1383 |
switch(property) |
| 1384 |
{ |
| 1385 |
case OBResidueAtomProperty::ALPHA_CARBON: |
| 1386 |
return (atomid == 1); |
| 1387 |
|
| 1388 |
case OBResidueAtomProperty::AMINO_BACKBONE: |
| 1389 |
return (atomid <= 3); |
| 1390 |
|
| 1391 |
case OBResidueAtomProperty::BACKBONE: |
| 1392 |
return (atomid <= 18); |
| 1393 |
|
| 1394 |
case OBResidueAtomProperty::CYSTEINE_SULPHUR: |
| 1395 |
return (atomid == 20); |
| 1396 |
|
| 1397 |
case OBResidueAtomProperty::LIGAND: |
| 1398 |
return IsHetAtom(atom) && |
| 1399 |
!GetResidueProperty(OBResidueProperty::SOLVENT); |
| 1400 |
|
| 1401 |
case OBResidueAtomProperty::NUCLEIC_BACKBONE: |
| 1402 |
return ((atomid >= 7) && (atomid <= 18)); |
| 1403 |
|
| 1404 |
case OBResidueAtomProperty::SHAPELY_BACKBONE: |
| 1405 |
return (atomid <= 7); |
| 1406 |
|
| 1407 |
case OBResidueAtomProperty::SHAPELY_SPECIAL: |
| 1408 |
return (atomid == 19); |
| 1409 |
|
| 1410 |
case OBResidueAtomProperty::SIDECHAIN: |
| 1411 |
return GetResidueProperty(OBResidueProperty::AMINO_NUCLEO) && |
| 1412 |
(atomid > 18); |
| 1413 |
|
| 1414 |
case OBResidueAtomProperty::SUGAR_PHOSPHATE: |
| 1415 |
return (atomid == 7); |
| 1416 |
} |
| 1417 |
} |
| 1418 |
|
| 1419 |
return false; |
| 1420 |
} |
| 1421 |
|
| 1422 |
bool OBResidue::GetResidueProperty(int property) const |
| 1423 |
{ |
| 1424 |
switch(property) |
| 1425 |
{ |
| 1426 |
case OBResidueProperty::AMINO: |
| 1427 |
return (_reskey <= OBResidueIndex::HYP); |
| 1428 |
|
| 1429 |
case OBResidueProperty::AMINO_NUCLEO: |
| 1430 |
return (_reskey <= OBResidueIndex::PSU); |
| 1431 |
|
| 1432 |
case OBResidueProperty::COENZYME: |
| 1433 |
return (_reskey >= OBResidueIndex::NAD) && |
| 1434 |
(_reskey <= OBResidueIndex::NDP); |
| 1435 |
|
| 1436 |
case OBResidueProperty::ION: |
| 1437 |
return (_reskey == OBResidueIndex::SO4) || |
| 1438 |
(_reskey == OBResidueIndex::PO4); |
| 1439 |
|
| 1440 |
case OBResidueProperty::NUCLEO: |
| 1441 |
return (_reskey >= OBResidueIndex::A) && |
| 1442 |
(_reskey <= OBResidueIndex::PSU); |
| 1443 |
|
| 1444 |
case OBResidueProperty::PROTEIN: |
| 1445 |
return (_reskey <= OBResidueIndex::HYP) || |
| 1446 |
((_reskey >= OBResidueIndex::UNK) && |
| 1447 |
(_reskey <= OBResidueIndex::FOR)); |
| 1448 |
|
| 1449 |
case OBResidueProperty::PURINE: |
| 1450 |
return (_reskey == OBResidueIndex::A) || |
| 1451 |
(_reskey == OBResidueIndex::G); |
| 1452 |
|
| 1453 |
case OBResidueProperty::PYRIMIDINE: |
| 1454 |
return (_reskey == OBResidueIndex::C) || |
| 1455 |
(_reskey == OBResidueIndex::T); |
| 1456 |
|
| 1457 |
case OBResidueProperty::SOLVENT: |
| 1458 |
return (_reskey >= OBResidueIndex::HOH) && |
| 1459 |
(_reskey <= OBResidueIndex::PO4); |
| 1460 |
|
| 1461 |
case OBResidueProperty::WATER: |
| 1462 |
return (_reskey == OBResidueIndex::HOH) || |
| 1463 |
(_reskey == OBResidueIndex::DOD); |
| 1464 |
|
| 1465 |
default: |
| 1466 |
return false; |
| 1467 |
} |
| 1468 |
} |
| 1469 |
|
| 1470 |
bool OBResidue::IsResidueType(int restype) const |
| 1471 |
{ |
| 1472 |
return ((int)_reskey == restype); |
| 1473 |
} |
| 1474 |
|
| 1475 |
// OBGenericData methods |
| 1476 |
bool OBResidue::HasData(string &s) |
| 1477 |
//returns true if the generic attribute/value pair exists |
| 1478 |
{ |
| 1479 |
if (_vdata.empty()) |
| 1480 |
return(false); |
| 1481 |
|
| 1482 |
vector<OBGenericData*>::iterator i; |
| 1483 |
|
| 1484 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1485 |
if ((*i)->GetAttribute() == s) |
| 1486 |
return(true); |
| 1487 |
|
| 1488 |
return(false); |
| 1489 |
} |
| 1490 |
|
| 1491 |
bool OBResidue::HasData(const char *s) |
| 1492 |
//returns true if the generic attribute/value pair exists |
| 1493 |
{ |
| 1494 |
if (_vdata.empty()) |
| 1495 |
return(false); |
| 1496 |
|
| 1497 |
vector<OBGenericData*>::iterator i; |
| 1498 |
|
| 1499 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1500 |
if ((*i)->GetAttribute() == s) |
| 1501 |
return(true); |
| 1502 |
|
| 1503 |
return(false); |
| 1504 |
} |
| 1505 |
|
| 1506 |
bool OBResidue::HasData(unsigned int dt) |
| 1507 |
//returns true if the generic attribute/value pair exists |
| 1508 |
{ |
| 1509 |
if (_vdata.empty()) |
| 1510 |
return(false); |
| 1511 |
|
| 1512 |
vector<OBGenericData*>::iterator i; |
| 1513 |
|
| 1514 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1515 |
if ((*i)->GetDataType() == dt) |
| 1516 |
return(true); |
| 1517 |
|
| 1518 |
return(false); |
| 1519 |
} |
| 1520 |
|
| 1521 |
OBGenericData *OBResidue::GetData(string &s) |
| 1522 |
//returns the value given an attribute |
| 1523 |
{ |
| 1524 |
vector<OBGenericData*>::iterator i; |
| 1525 |
|
| 1526 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1527 |
if ((*i)->GetAttribute() == s) |
| 1528 |
return(*i); |
| 1529 |
|
| 1530 |
return(NULL); |
| 1531 |
} |
| 1532 |
|
| 1533 |
OBGenericData *OBResidue::GetData(const char *s) |
| 1534 |
//returns the value given an attribute |
| 1535 |
{ |
| 1536 |
vector<OBGenericData*>::iterator i; |
| 1537 |
|
| 1538 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1539 |
if ((*i)->GetAttribute() == s) |
| 1540 |
return(*i); |
| 1541 |
|
| 1542 |
return(NULL); |
| 1543 |
} |
| 1544 |
|
| 1545 |
OBGenericData *OBResidue::GetData(unsigned int dt) |
| 1546 |
{ |
| 1547 |
vector<OBGenericData*>::iterator i; |
| 1548 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1549 |
if ((*i)->GetDataType() == dt) |
| 1550 |
return(*i); |
| 1551 |
return(NULL); |
| 1552 |
} |
| 1553 |
|
| 1554 |
void OBResidue::DeleteData(unsigned int dt) |
| 1555 |
{ |
| 1556 |
vector<OBGenericData*> vdata; |
| 1557 |
vector<OBGenericData*>::iterator i; |
| 1558 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1559 |
if ((*i)->GetDataType() == dt) |
| 1560 |
delete *i; |
| 1561 |
else |
| 1562 |
vdata.push_back(*i); |
| 1563 |
_vdata = vdata; |
| 1564 |
} |
| 1565 |
|
| 1566 |
void OBResidue::DeleteData(vector<OBGenericData*> &vg) |
| 1567 |
{ |
| 1568 |
vector<OBGenericData*> vdata; |
| 1569 |
vector<OBGenericData*>::iterator i,j; |
| 1570 |
|
| 1571 |
bool del; |
| 1572 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1573 |
{ |
| 1574 |
del = false; |
| 1575 |
for (j = vg.begin();j != vg.end();j++) |
| 1576 |
if (*i == *j) |
| 1577 |
{ |
| 1578 |
del = true; |
| 1579 |
break; |
| 1580 |
} |
| 1581 |
if (del) |
| 1582 |
delete *i; |
| 1583 |
else |
| 1584 |
vdata.push_back(*i); |
| 1585 |
} |
| 1586 |
_vdata = vdata; |
| 1587 |
} |
| 1588 |
|
| 1589 |
void OBResidue::DeleteData(OBGenericData *gd) |
| 1590 |
{ |
| 1591 |
vector<OBGenericData*>::iterator i; |
| 1592 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 1593 |
if (*i == gd) |
| 1594 |
{ |
| 1595 |
delete *i; |
| 1596 |
_vdata.erase(i); |
| 1597 |
} |
| 1598 |
|
| 1599 |
} |
| 1600 |
|
| 1601 |
} // end namespace OpenBabel |
| 1602 |
|
| 1603 |
//! \file residue.cpp |
| 1604 |
//! \brief Handle macromolecule residues. |
