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/********************************************************************** |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2003-2005 Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004 by Chris Morley |
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|
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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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|
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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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#include "pdbformat.hpp" |
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|
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|
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#if !HAVE_SNPRINTF |
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extern "C" int snprintf( char *, size_t, const char *, /* args */ ...); |
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#endif |
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|
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#include <vector> |
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#include <map> |
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|
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#ifdef HAVE_SSTREAM |
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#include <sstream> |
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#else |
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#include <strstream> |
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#endif |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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|
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static bool ParseAtomRecord(char *, OBMol &,int); |
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static bool ParseConectRecord(char *,OBMol &); |
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|
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//extern OBResidueData resdat; now in mol.h |
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|
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///////////////////////////////////////////////////////////////// |
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bool PDBFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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|
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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if(pmol==NULL) |
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return false; |
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|
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//Define some references so we can use the old parameter names |
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istream &ifs = *pConv->GetInStream(); |
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OBMol &mol = *pmol; |
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const char* title = pConv->GetTitle(); |
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|
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int chainNum = 1; |
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char buffer[BUFF_SIZE]; |
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OBBitVec bs; |
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|
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mol.SetTitle(title); |
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|
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mol.BeginModify(); |
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while (ifs.getline(buffer,BUFF_SIZE) && !EQn(buffer,"END",3)) |
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{ |
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if (EQn(buffer,"TER",3)) |
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chainNum++; |
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if (EQn(buffer,"ATOM",4) || EQn(buffer,"HETATM",6)) |
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{ |
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ParseAtomRecord(buffer,mol,chainNum); |
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if (EQn(buffer,"ATOM",4)) |
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bs.SetBitOn(mol.NumAtoms()); |
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} |
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|
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if (EQn(buffer,"CONECT",6)) |
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ParseConectRecord(buffer,mol); |
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} |
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|
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resdat.AssignBonds(mol,bs); |
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/*assign hetatm bonds based on distance*/ |
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|
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if (!pConv->IsOption("b",OBConversion::INOPTIONS)) |
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mol.ConnectTheDots(); |
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|
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if (mol.NumAtoms() < 250) // Minimize time required on real proteins |
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if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS)) |
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mol.PerceiveBondOrders(); |
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|
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// clean out remaining blank lines |
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while(ifs.peek() != EOF && ifs.good() && |
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(ifs.peek() == '\n' || ifs.peek() == '\r')) |
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ifs.getline(buffer,BUFF_SIZE); |
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|
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mol.EndModify(); |
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|
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mol.SetAtomTypesPerceived(); |
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atomtyper.AssignImplicitValence(mol); |
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|
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if (!mol.NumAtoms()) |
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return(false); |
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return(true); |
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} |
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|
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//////////////////////////////////////////////////////////////// |
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static bool ParseAtomRecord(char *buffer, OBMol &mol,int chainNum) |
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/* ATOMFORMAT "(i5,1x,a4,a1,a3,1x,a1,i4,a1,3x,3f8.3,2f6.2,1x,i3)" */ |
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{ |
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string sbuf = &buffer[6]; |
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if (sbuf.size() < 48) |
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return(false); |
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|
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bool hetatm = (EQn(buffer,"HETATM",6)) ? true : false; |
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|
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/* serial number */ |
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string serno = sbuf.substr(0,5); |
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//SerialNum(the_atom) = atoi(tmp_str); |
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|
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/* atom name */ |
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string atmid = sbuf.substr(6,4); |
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|
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/* element */ |
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string element; |
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if (sbuf.size() > 71) |
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element = sbuf.substr(70,2); |
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else |
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element = " "; |
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|
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//trim spaces on the right and left sides |
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while (!atmid.empty() && atmid[0] == ' ') |
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atmid = atmid.substr(1,atmid.size()-1); |
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|
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while (!atmid.empty() && atmid[atmid.size()-1] == ' ') |
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atmid = atmid.substr(0,atmid.size()-1); |
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|
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/* residue name */ |
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|
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string resname = sbuf.substr(11,3); |
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if (resname == " ") |
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resname = "UNK"; |
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else |
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{ |
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while (!resname.empty() && resname[0] == ' ') |
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resname = resname.substr(1,resname.size()-1); |
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|
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while (!resname.empty() && resname[resname.size()-1] == ' ') |
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resname = resname.substr(0,resname.size()-1); |
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} |
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|
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/* residue sequence number */ |
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|
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string resnum = sbuf.substr(16,4); |
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|
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/* X, Y, Z */ |
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string xstr = sbuf.substr(24,8); |
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string ystr = sbuf.substr(32,8); |
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string zstr = sbuf.substr(40,8); |
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|
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string type; |
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|
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if (EQn(buffer,"ATOM",4)) |
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{ |
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type = atmid.substr(0,2); |
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if (isdigit(type[0])) |
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type = atmid.substr(1,1); |
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else if (sbuf[6] == ' ' && |
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strncasecmp(type.c_str(), "Zn", 2) != 0 && |
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strncasecmp(type.c_str(), "Fe", 2) != 0) |
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type = atmid.substr(0,1); // one-character element |
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|
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|
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if (resname.substr(0,2) == "AS" || resname[0] == 'N') |
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{ |
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if (atmid == "AD1") |
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type = "O"; |
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if (atmid == "AD2") |
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type = "N"; |
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} |
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if (resname.substr(0,3) == "HIS" || resname[0] == 'H') |
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{ |
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if (atmid == "AD1" || atmid == "AE2") |
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type = "N"; |
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if (atmid == "AE1" || atmid == "AD2") |
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type = "C"; |
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} |
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if (resname.substr(0,2) == "GL" || resname[0] == 'Q') |
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{ |
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if (atmid == "AE1") |
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type = "O"; |
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if (atmid == "AE2") |
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type = "N"; |
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} |
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} |
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else //must be hetatm record |
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{ |
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if (isalpha(element[1]) && (isalpha(element[0]) || (element[0] == ' '))) |
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{ |
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if (isalpha(element[0])) |
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type = element.substr(0,2); |
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else |
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type = element.substr(1,1); |
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if (type.size() == 2) |
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type[1] = tolower(type[1]); |
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} |
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else |
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{ |
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if (isalpha(atmid[0])) |
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type = atmid.substr(0,2); |
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else if (atmid[0] == ' ') |
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type = atmid.substr(1,1); // one char element |
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else |
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type = atmid.substr(1,2); |
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|
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if (atmid == resname) |
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{ |
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type = atmid; |
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if (type.size() == 2) |
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type[1] = tolower(type[1]); |
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} |
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else |
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if (resname == "ADR" || resname == "COA" || resname == "FAD" || |
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resname == "GPG" || resname == "NAD" || resname == "NAL" || |
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resname == "NDP") |
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{ |
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if (type.size() > 1) |
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type = type.substr(0,1); |
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//type.erase(1,type.size()-1); |
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} |
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else |
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if (isdigit(type[0])) |
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{ |
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type = type.substr(1,1); |
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//type.erase(0,1); |
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//if (type.size() > 1) type.erase(1,type.size()-1); |
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} |
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else |
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if (type.size() > 1 && isdigit(type[1])) |
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type = type.substr(0,1); |
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//type.erase(1,1); |
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else |
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if (type.size() > 1 && isalpha(type[1]) && isupper(type[1])) |
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type[1] = tolower(type[1]); |
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} |
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|
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} |
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|
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OBAtom atom; |
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vector3 v(atof(xstr.c_str()),atof(ystr.c_str()),atof(zstr.c_str())); |
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atom.SetVector(v); |
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|
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atom.SetAtomicNum(etab.GetAtomicNum(type.c_str())); |
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atom.SetType(type); |
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|
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int rnum = atoi(resnum.c_str()); |
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OBResidue *res = (mol.NumResidues() > 0) ? mol.GetResidue(mol.NumResidues()-1) : NULL; |
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if (res == NULL || res->GetName() != resname || static_cast<int>(res->GetNum()) |
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!= rnum) |
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{ |
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vector<OBResidue*>::iterator ri; |
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for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri)) |
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if (res->GetName() == resname && static_cast<int>(res->GetNum()) |
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== rnum) |
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break; |
260 |
|
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if (res == NULL) |
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{ |
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res = mol.NewResidue() |
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; |
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res->SetChainNum(chainNum); |
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res->SetName(resname); |
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res->SetNum(rnum); |
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} |
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} |
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|
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if (!mol.AddAtom(atom) |
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) |
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return(false); |
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else |
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{ |
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OBAtom *atom = mol.GetAtom(mol.NumAtoms()); |
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|
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res->AddAtom(atom); |
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res->SetSerialNum(atom, atoi(serno.c_str())); |
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res->SetAtomID(atom, atmid); |
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res->SetHetAtom(atom, hetatm); |
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|
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return(true); |
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} |
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} |
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|
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///////////////////////////////////////////////////////////////////////// |
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//! Utility function to read a 5-digit integer starting from a specified column |
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/*! This function reads a 5-digit integer, starting from column |
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columnAsSpecifiedInPDB from the buffer, converts it to a long |
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integer, and returns either false or true, if the conversion was |
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successful or not. If the conversion was not successful, the target |
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is set to a random value. |
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|
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For instance, the PDB Format Description for a CONECT record specifies |
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|
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COLUMNS DATA TYPE FIELD DEFINITION |
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--------------------------------------------------------------------------------- |
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1 - 6 Record name "CONECT" |
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7 - 11 Integer serial Atom serial number |
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... |
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|
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To read the Atom serial number, you would call |
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|
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long int target; |
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if ( readIntegerFromRecord(buffer, 7, &target) == false ) { |
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cerr << "Could not parse" << endl; |
308 |
} |
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|
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This function does not check the length of the buffer, or |
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strlen(buffer). If the buffer is not long enough => SEGFAULT. |
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*/ |
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static bool readIntegerFromRecord(char *buffer, unsigned int columnAsSpecifiedInPDB, long int *target) |
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{ |
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char integerBuffer[6]; |
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integerBuffer[5] = 0; |
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|
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strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); |
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|
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char *errorCheckingEndPtr; |
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*target = strtol(integerBuffer, &errorCheckingEndPtr, 10); |
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if (integerBuffer == errorCheckingEndPtr) |
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return(false); |
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return(true); |
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} |
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|
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//! Read a CONECT record |
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/*! This function reads a CONECT record, as specified |
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http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html, |
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in short: |
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|
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COLUMNS DATA TYPE FIELD DEFINITION |
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--------------------------------------------------------------------------------- |
334 |
1 - 6 Record name "CONECT" |
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7 - 11 Integer serial Atom serial number |
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12 - 16 Integer serial Serial number of bonded atom |
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17 - 21 Integer serial Serial number of bonded atom |
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22 - 26 Integer serial Serial number of bonded atom |
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27 - 31 Integer serial Serial number of bonded atom |
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32 - 36 Integer serial Serial number of hydrogen bonded atom |
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37 - 41 Integer serial Serial number of hydrogen bonded atom |
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42 - 46 Integer serial Serial number of salt bridged atom |
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47 - 51 Integer serial Serial number of hydrogen bonded atom |
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52 - 56 Integer serial Serial number of hydrogen bonded atom |
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57 - 61 Integer serial Serial number of salt bridged atom |
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|
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Hydrogen bonds and salt bridges are ignored. --Stefan Kebekus. |
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*/ |
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|
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static bool ParseConectRecord(char *buffer,OBMol &mol) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
357 |
|
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// Setup strings and string buffers |
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buffer[70] = '\0'; |
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if (strlen(buffer) < 70) |
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{ |
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errorMsg << "WARNING: Problems reading a PDB file\n" |
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<< " Problems reading a CONECT record.\n" |
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<< " According to the PDB specification,\n" |
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<< " the record should have 70 columns, but OpenBabel found " |
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<< strlen(buffer) << " columns."; |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obInfo); |
368 |
} |
369 |
|
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// Serial number of the first atom, read from column 7-11 of the |
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// connect record, to which the other atoms connect to. |
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long int startAtomSerialNumber; |
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if (readIntegerFromRecord(buffer, 7, &startAtomSerialNumber) == false) |
374 |
{ |
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errorMsg << "WARNING: Problems reading a PDB file\n" |
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<< " Problems reading a CONECT record.\n" |
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<< " According to the PDB specification,\n" |
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<< " columns 7-11 should contain the serial number of an atom.\n" |
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<< " THIS CONECT RECORD WILL BE IGNORED."; |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
382 |
} |
383 |
|
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// Find a pointer to the first atom. |
385 |
OBAtom *firstAtom = 0L; |
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vector<OBNodeBase*>::iterator i; |
387 |
for (OBAtom *a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i)) |
388 |
if (static_cast<long int>(a1->GetResidue()-> |
389 |
GetSerialNum(a1)) == startAtomSerialNumber) |
390 |
{ |
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firstAtom = a1; |
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break; |
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} |
394 |
if (firstAtom == 0L) |
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{ |
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errorMsg << "WARNING: Problems reading a PDB file:\n" |
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<< " Problems reading a CONECT record.\n" |
398 |
<< " According to the PDB specification,\n" |
399 |
<< " columns 7-11 should contain the serial number of an atom.\n" |
400 |
<< " No atom was found with this serial number.\n" |
401 |
<< " THIS CONECT RECORD WILL BE IGNORED."; |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
403 |
return(false); |
404 |
} |
405 |
|
406 |
// Serial numbers of the atoms which bind to firstAtom, read from |
407 |
// columns 12-16, 17-21, 22-27 and 27-31 of the connect record. Note |
408 |
// that we reserve space for 5 integers, but read only four of |
409 |
// them. This is to simplify the determination of the bond order; |
410 |
// see below. |
411 |
long int boundedAtomsSerialNumbers[5] = {0,0,0,0,0}; |
412 |
// Bools which tell us which of the serial numbers in |
413 |
// boundedAtomsSerialNumbers are read from the file, and which are |
414 |
// invalid |
415 |
bool boundedAtomsSerialNumbersValid[5] = {false, false, false, false, false}; |
416 |
|
417 |
// Now read the serial numbers. If the first serial number is not |
418 |
// present, this connect record probably contains only hydrogen |
419 |
// bonds and salt bridges, which we ignore. In that case, we just |
420 |
// exit gracefully. |
421 |
boundedAtomsSerialNumbersValid[0] = readIntegerFromRecord(buffer, 12, boundedAtomsSerialNumbers+0); |
422 |
if (boundedAtomsSerialNumbersValid[0] == false) |
423 |
return(true); |
424 |
boundedAtomsSerialNumbersValid[1] = readIntegerFromRecord(buffer, 17, boundedAtomsSerialNumbers+1); |
425 |
boundedAtomsSerialNumbersValid[2] = readIntegerFromRecord(buffer, 22, boundedAtomsSerialNumbers+2); |
426 |
boundedAtomsSerialNumbersValid[3] = readIntegerFromRecord(buffer, 27, boundedAtomsSerialNumbers+3); |
427 |
|
428 |
// Now iterate over the VALID boundedAtomsSerialNumbers and connect |
429 |
// the atoms. |
430 |
for(unsigned int k=0; boundedAtomsSerialNumbersValid[k]; k++) |
431 |
{ |
432 |
// Find atom that is connected to, write an error message |
433 |
OBAtom *connectedAtom = 0L; |
434 |
for (OBAtom *a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i)) |
435 |
if (static_cast<long int>(a1->GetResidue()-> |
436 |
GetSerialNum(a1)) == boundedAtomsSerialNumbers[k]) |
437 |
{ |
438 |
connectedAtom = a1; |
439 |
break; |
440 |
} |
441 |
if (connectedAtom == 0L) |
442 |
{ |
443 |
errorMsg << "WARNING: Problems reading a PDB file:\n" |
444 |
<< " Problems reading a CONECT record.\n" |
445 |
<< " According to the PDB specification,\n" |
446 |
<< " Atoms with serial #" << startAtomSerialNumber |
447 |
<< " and #" << boundedAtomsSerialNumbers[k] |
448 |
<< " should be connected\n" |
449 |
<< " However, an atom with serial #" << boundedAtomsSerialNumbers[k] << " was not found.\n" |
450 |
<< " THIS CONECT RECORD WILL BE IGNORED."; |
451 |
obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
452 |
break; |
453 |
} |
454 |
|
455 |
// Figure the bond order |
456 |
unsigned char order = 0; |
457 |
while(boundedAtomsSerialNumbersValid[k+order+1] && (boundedAtomsSerialNumbers[k+order] |
458 |
== boundedAtomsSerialNumbers[k+order+1])) |
459 |
order++; |
460 |
k += order; |
461 |
|
462 |
// Generate the bond |
463 |
mol.AddBond(firstAtom->GetIdx(), connectedAtom->GetIdx(), order+1); |
464 |
} |
465 |
return(true); |
466 |
} |
467 |
|
468 |
////////////////////////////////////////////////////////////////////////////// |
469 |
bool PDBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
470 |
{ |
471 |
OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
472 |
if(pmol==NULL) |
473 |
return false; |
474 |
|
475 |
//Define some references so we can use the old parameter names |
476 |
ostream &ofs = *pConv->GetOutStream(); |
477 |
OBMol &mol = *pmol; |
478 |
|
479 |
unsigned int i; |
480 |
char buffer[BUFF_SIZE]; |
481 |
char type_name[10], padded_name[10]; |
482 |
char the_res[10]; |
483 |
char *element_name; |
484 |
int res_num; |
485 |
bool het=true; |
486 |
|
487 |
// sprintf(buffer,"HEADER PROTEIN"); |
488 |
// ofs << buffer << endl; |
489 |
|
490 |
if (strlen(mol.GetTitle()) > 0) |
491 |
sprintf(buffer,"COMPND %s ",mol.GetTitle()); |
492 |
else |
493 |
sprintf(buffer,"COMPND UNNAMED"); |
494 |
ofs << buffer << endl; |
495 |
|
496 |
sprintf(buffer,"AUTHOR GENERATED BY OPEN BABEL %s",BABEL_VERSION); |
497 |
ofs << buffer << endl; |
498 |
|
499 |
OBAtom *atom; |
500 |
OBResidue *res; |
501 |
for (i = 1; i <= mol.NumAtoms(); i++) |
502 |
{ |
503 |
atom = mol.GetAtom(i); |
504 |
strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum())); |
505 |
|
506 |
//two char. elements are on position 13 and 14 one char. start at 14 |
507 |
if (strlen(type_name) > 1) |
508 |
type_name[1] = toupper(type_name[1]); |
509 |
else |
510 |
{ |
511 |
char tmp[10]; |
512 |
strcpy(tmp, type_name); |
513 |
sprintf(type_name, " %-3s", tmp); |
514 |
} |
515 |
|
516 |
if ( (res = atom->GetResidue()) ) |
517 |
{ |
518 |
het = res->IsHetAtom(atom); |
519 |
snprintf(the_res,4,"%s",(char*)res->GetName().c_str()); |
520 |
snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str()); |
521 |
|
522 |
//two char. elements are on position 13 and 14 one char. start at 14 |
523 |
if (strlen(etab.GetSymbol(atom->GetAtomicNum())) == 1) |
524 |
{ |
525 |
if (strlen(type_name) < 4) |
526 |
{ |
527 |
char tmp[10]; |
528 |
strcpy(tmp, type_name); |
529 |
sprintf(padded_name," %-3s", tmp); |
530 |
strncpy(type_name,padded_name,4); |
531 |
type_name[4] = '\0'; |
532 |
} |
533 |
else |
534 |
{ |
535 |
type_name[4] = type_name[3]; |
536 |
type_name[3] = type_name[2]; |
537 |
type_name[2] = type_name[1]; |
538 |
type_name[1] = type_name[0]; |
539 |
type_name[0] = type_name[4]; |
540 |
type_name[4] = '\0'; |
541 |
} |
542 |
} |
543 |
res_num = res->GetNum(); |
544 |
} |
545 |
else |
546 |
{ |
547 |
strcpy(the_res,"UNK"); |
548 |
sprintf(padded_name,"%s",type_name); |
549 |
strncpy(type_name,padded_name,4); |
550 |
type_name[4] = '\0'; |
551 |
res_num = 1; |
552 |
} |
553 |
|
554 |
element_name = etab.GetSymbol(atom->GetAtomicNum()); |
555 |
if (strlen(element_name) == 2) |
556 |
element_name[1] = toupper(element_name[1]); |
557 |
sprintf(buffer,"%s%5d %-4s %-3s %4d %8.3f%8.3f%8.3f 1.00 0.00 %2s \n", |
558 |
het?"HETATM":"ATOM ", |
559 |
i, |
560 |
type_name, |
561 |
the_res, |
562 |
res_num, |
563 |
atom->GetX(), |
564 |
atom->GetY(), |
565 |
atom->GetZ(), |
566 |
element_name); |
567 |
ofs << buffer; |
568 |
} |
569 |
|
570 |
OBAtom *nbr; |
571 |
int count; |
572 |
vector<OBEdgeBase*>::iterator k; |
573 |
for (i = 1; i <= mol.NumAtoms(); i ++) |
574 |
{ |
575 |
atom = mol.GetAtom(i); |
576 |
if (atom->GetValence() <= 4) |
577 |
{ |
578 |
sprintf(buffer,"CONECT%5d", i); |
579 |
ofs << buffer; |
580 |
for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k)) |
581 |
{ |
582 |
sprintf(buffer,"%5d", nbr->GetIdx()); |
583 |
ofs << buffer; |
584 |
} |
585 |
for (count = 0; count < (4 - (int)atom->GetValence()); count++) |
586 |
{ |
587 |
sprintf(buffer, " "); |
588 |
ofs << buffer; |
589 |
} |
590 |
ofs << " " << endl; |
591 |
} |
592 |
} |
593 |
sprintf(buffer,"MASTER 0 0 0 0 0 0 0 0 "); |
594 |
ofs << buffer; |
595 |
sprintf(buffer,"%4d 0 %4d 0",mol.NumAtoms(),mol.NumAtoms()); |
596 |
ofs << buffer << endl; |
597 |
sprintf(buffer,"END"); |
598 |
ofs << buffer << endl; |
599 |
return(true); |
600 |
} |
601 |
|
602 |
|
603 |
} //namespace OpenBabel |