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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; |
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|
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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; |
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} |
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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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--------------------------------------------------------------------------------- |
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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; |
| 354 |
#else |
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strstream errorMsg; |
| 356 |
#endif |
| 357 |
|
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// Setup strings and string buffers |
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buffer[70] = '\0'; |
| 360 |
if (strlen(buffer) < 70) |
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{ |
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errorMsg << "WARNING: Problems reading a PDB file\n" |
| 363 |
<< " 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 |
| 371 |
// connect record, to which the other atoms connect to. |
| 372 |
long int startAtomSerialNumber; |
| 373 |
if (readIntegerFromRecord(buffer, 7, &startAtomSerialNumber) == false) |
| 374 |
{ |
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errorMsg << "WARNING: Problems reading a PDB file\n" |
| 376 |
<< " Problems reading a CONECT record.\n" |
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<< " According to the PDB specification,\n" |
| 378 |
<< " 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); |
| 381 |
return(false); |
| 382 |
} |
| 383 |
|
| 384 |
// Find a pointer to the first atom. |
| 385 |
OBAtom *firstAtom = 0L; |
| 386 |
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 |
{ |
| 391 |
firstAtom = a1; |
| 392 |
break; |
| 393 |
} |
| 394 |
if (firstAtom == 0L) |
| 395 |
{ |
| 396 |
errorMsg << "WARNING: Problems reading a PDB file:\n" |
| 397 |
<< " 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."; |
| 402 |
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 |
