src/openbabel/pdbformat.cpp

/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2003-2005 Geoffrey R. Hutchison
Some portions Copyright (C) 2004 by Chris Morley
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#include "pdbformat.hpp"


#if !HAVE_SNPRINTF
extern "C" int snprintf( char *, size_t, const char *, /* args */ ...);
#endif

#include <vector>
#include <map>

#ifdef HAVE_SSTREAM
#include <sstream>
#else
#include <strstream>
#endif

using namespace std;
namespace OpenBabel
{

static bool ParseAtomRecord(char *, OBMol &,int);
static bool ParseConectRecord(char *,OBMol &);

//extern OBResidueData    resdat; now in mol.h

/////////////////////////////////////////////////////////////////
bool PDBFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{

    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
        return false;

    //Define some references so we can use the old parameter names
    istream &ifs = *pConv->GetInStream();
    OBMol &mol = *pmol;
    const char* title = pConv->GetTitle();

    int chainNum = 1;
    char buffer[BUFF_SIZE];
    OBBitVec bs;

    mol.SetTitle(title);

    mol.BeginModify();
    while (ifs.getline(buffer,BUFF_SIZE) && !EQn(buffer,"END",3))
    {
        if (EQn(buffer,"TER",3))
            chainNum++;
        if (EQn(buffer,"ATOM",4) || EQn(buffer,"HETATM",6))
        {
            ParseAtomRecord(buffer,mol,chainNum);
            if (EQn(buffer,"ATOM",4))
                bs.SetBitOn(mol.NumAtoms());
        }

        if (EQn(buffer,"CONECT",6))
            ParseConectRecord(buffer,mol);
    }

    resdat.AssignBonds(mol,bs);
    /*assign hetatm bonds based on distance*/

    if (!pConv->IsOption("b",OBConversion::INOPTIONS))
      mol.ConnectTheDots();

    if (mol.NumAtoms() < 250) // Minimize time required on real proteins
      if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
        mol.PerceiveBondOrders();

    // clean out remaining blank lines
    while(ifs.peek() != EOF && ifs.good() && 
          (ifs.peek() == '\n' || ifs.peek() == '\r'))
      ifs.getline(buffer,BUFF_SIZE);

    mol.EndModify();

    mol.SetAtomTypesPerceived();
    atomtyper.AssignImplicitValence(mol);

    if (!mol.NumAtoms())
        return(false);
    return(true);
}

////////////////////////////////////////////////////////////////
static bool ParseAtomRecord(char *buffer, OBMol &mol,int chainNum)
/* ATOMFORMAT "(i5,1x,a4,a1,a3,1x,a1,i4,a1,3x,3f8.3,2f6.2,1x,i3)" */
{
    string sbuf = &buffer[6];
    if (sbuf.size() < 48)
        return(false);

    bool hetatm = (EQn(buffer,"HETATM",6)) ? true : false;

    /* serial number */
    string serno = sbuf.substr(0,5);
    //SerialNum(the_atom) = atoi(tmp_str);

    /* atom name */
    string atmid = sbuf.substr(6,4);

    /* element */
    string element;
    if (sbuf.size() > 71)
        element = sbuf.substr(70,2);
    else
        element = "  ";

    //trim spaces on the right and left sides
    while (!atmid.empty() && atmid[0] == ' ')
        atmid = atmid.substr(1,atmid.size()-1);

    while (!atmid.empty() && atmid[atmid.size()-1] == ' ')
        atmid = atmid.substr(0,atmid.size()-1);

    /* residue name */

    string resname = sbuf.substr(11,3);
    if (resname == "   ")
        resname = "UNK";
    else
    {
        while (!resname.empty() && resname[0] == ' ')
            resname = resname.substr(1,resname.size()-1);

        while (!resname.empty() && resname[resname.size()-1] == ' ')
            resname = resname.substr(0,resname.size()-1);
    }

    /* residue sequence number */

    string resnum = sbuf.substr(16,4);

    /* X, Y, Z */
    string xstr = sbuf.substr(24,8);
    string ystr = sbuf.substr(32,8);
    string zstr = sbuf.substr(40,8);

    string type;

    if (EQn(buffer,"ATOM",4))
    {
        type = atmid.substr(0,2);
        if (isdigit(type[0]))
          type = atmid.substr(1,1);
        else if (sbuf[6] == ' ' &&
                 strncasecmp(type.c_str(), "Zn", 2) != 0 &&
                 strncasecmp(type.c_str(), "Fe", 2) != 0)
          type = atmid.substr(0,1);     // one-character element
        

        if (resname.substr(0,2) == "AS" || resname[0] == 'N')
        {
            if (atmid == "AD1")
                type = "O";
            if (atmid == "AD2")
                type = "N";
        }
        if (resname.substr(0,3) == "HIS" || resname[0] == 'H')
        {
            if (atmid == "AD1" || atmid == "AE2")
                type = "N";
            if (atmid == "AE1" || atmid == "AD2")
                type = "C";
        }
        if (resname.substr(0,2) == "GL" || resname[0] == 'Q')
        {
            if (atmid == "AE1")
                type = "O";
            if (atmid == "AE2")
                type = "N";
        }
    }
    else //must be hetatm record
    {
        if (isalpha(element[1]) && (isalpha(element[0]) || (element[0] == ' ')))
        {
            if (isalpha(element[0]))
                type = element.substr(0,2);
            else
                type = element.substr(1,1);
            if (type.size() == 2)
                type[1] = tolower(type[1]);
        }
        else
          {
            if (isalpha(atmid[0]))
              type = atmid.substr(0,2);
            else if (atmid[0] == ' ')
              type = atmid.substr(1,1); // one char element
            else
              type = atmid.substr(1,2);

            if (atmid == resname)
              {
                type = atmid;
                if (type.size() == 2)
                  type[1] = tolower(type[1]);
              }
            else
              if (resname == "ADR" || resname == "COA" || resname == "FAD" ||
                  resname == "GPG" || resname == "NAD" || resname == "NAL" ||
                  resname == "NDP")
                {
                  if (type.size() > 1)
                    type = type.substr(0,1);
                  //type.erase(1,type.size()-1);
                }
              else
                if (isdigit(type[0]))
                  {
                    type = type.substr(1,1);
                    //type.erase(0,1);
                    //if (type.size() > 1) type.erase(1,type.size()-1);
                  }
                else
                  if (type.size() > 1 && isdigit(type[1]))
                    type = type.substr(0,1);
            //type.erase(1,1);
                  else
                    if (type.size() > 1 && isalpha(type[1]) && isupper(type[1]))
                      type[1] = tolower(type[1]);
          }
        
    }

    OBAtom atom;
    vector3 v(atof(xstr.c_str()),atof(ystr.c_str()),atof(zstr.c_str()));
    atom.SetVector(v);

    atom.SetAtomicNum(etab.GetAtomicNum(type.c_str()));
    atom.SetType(type);

    int        rnum = atoi(resnum.c_str());
    OBResidue *res  = (mol.NumResidues() > 0) ? mol.GetResidue(mol.NumResidues()-1) : NULL;
    if (res == NULL || res->GetName() != resname || static_cast<int>(res->GetNum())
            != rnum)
    {
        vector<OBResidue*>::iterator ri;
        for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri))
            if (res->GetName() == resname && static_cast<int>(res->GetNum())
                    == rnum)
                break;

        if (res == NULL)
        {
            res = mol.NewResidue()
                  ;
            res->SetChainNum(chainNum);
            res->SetName(resname);
            res->SetNum(rnum);
        }
    }

    if (!mol.AddAtom(atom)
       )
        return(false);
    else
    {
        OBAtom *atom = mol.GetAtom(mol.NumAtoms());

        res->AddAtom(atom);
        res->SetSerialNum(atom, atoi(serno.c_str()));
        res->SetAtomID(atom, atmid);
        res->SetHetAtom(atom, hetatm);

        return(true);
    }
}

/////////////////////////////////////////////////////////////////////////
//! Utility function to read a 5-digit integer starting from a specified column
/*! This function reads a 5-digit integer, starting from column
  columnAsSpecifiedInPDB from the buffer, converts it to a long
  integer, and returns either false or true, if the conversion was
  successful or not. If the conversion was not successful, the target
  is set to a random value.
 
  For instance, the PDB Format Description for a CONECT record specifies
 
  COLUMNS        DATA TYPE        FIELD           DEFINITION
  ---------------------------------------------------------------------------------
  1 -  6         Record name      "CONECT"
  7 - 11         Integer          serial          Atom serial number
  ...
 
  To read the Atom serial number, you would call
 
  long int target;
  if ( readIntegerFromRecord(buffer, 7, &target) == false ) {
    cerr << "Could not parse" << endl;
  }
  
  This function does not check the length of the buffer, or
  strlen(buffer). If the buffer is not long enough => SEGFAULT. 
 */
static bool readIntegerFromRecord(char *buffer, unsigned int columnAsSpecifiedInPDB, long int *target)
{
    char integerBuffer[6];
    integerBuffer[5] = 0;

    strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5);

    char *errorCheckingEndPtr;
    *target = strtol(integerBuffer, &errorCheckingEndPtr, 10);
    if (integerBuffer == errorCheckingEndPtr)
        return(false);
    return(true);
}

//! Read a CONECT record
/*! This function reads a CONECT record, as specified
  http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html,
  in short:
 
  COLUMNS         DATA TYPE        FIELD           DEFINITION
  ---------------------------------------------------------------------------------
   1 -  6         Record name      "CONECT"
   7 - 11         Integer          serial          Atom serial number
  12 - 16         Integer          serial          Serial number of bonded atom
  17 - 21         Integer          serial          Serial number of bonded atom
  22 - 26         Integer          serial          Serial number of bonded atom
  27 - 31         Integer          serial          Serial number of bonded atom
  32 - 36         Integer          serial          Serial number of hydrogen bonded atom
  37 - 41         Integer          serial          Serial number of hydrogen bonded atom
  42 - 46         Integer          serial          Serial number of salt bridged atom
  47 - 51         Integer          serial          Serial number of hydrogen bonded atom
  52 - 56         Integer          serial          Serial number of hydrogen bonded atom
  57 - 61         Integer          serial          Serial number of salt bridged atom
 
  Hydrogen bonds and salt bridges are ignored. --Stefan Kebekus.
*/

static bool ParseConectRecord(char *buffer,OBMol &mol)
{
#ifdef HAVE_SSTREAM
    stringstream errorMsg;
#else
    strstream errorMsg;
#endif

    // Setup strings and string buffers
    buffer[70] = '\0';
    if (strlen(buffer) < 70)
    {
        errorMsg << "WARNING: Problems reading a PDB file\n"
                 << "  Problems reading a CONECT record.\n"
                 << "  According to the PDB specification,\n"
                 << "  the record should have 70 columns, but OpenBabel found "
                 << strlen(buffer) << " columns.";
        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obInfo);
    }

    // Serial number of the first atom, read from column 7-11 of the
    // connect record, to which the other atoms connect to.
    long int startAtomSerialNumber;
    if (readIntegerFromRecord(buffer, 7, &startAtomSerialNumber) == false)
    {
      errorMsg << "WARNING: Problems reading a PDB file\n"
               << "  Problems reading a CONECT record.\n"
               << "  According to the PDB specification,\n"
               << "  columns 7-11 should contain the serial number of an atom.\n"
               << "  THIS CONECT RECORD WILL BE IGNORED.";
        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning);
        return(false);
    }

    // Find a pointer to the first atom.
    OBAtom *firstAtom = 0L;
    vector<OBNodeBase*>::iterator i;
    for (OBAtom *a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i))
        if (static_cast<long int>(a1->GetResidue()->
                                  GetSerialNum(a1)) == startAtomSerialNumber)
        {
            firstAtom = a1;
            break;
        }
    if (firstAtom == 0L)
    {
        errorMsg << "WARNING: Problems reading a PDB file:\n"
                 << "  Problems reading a CONECT record.\n"
                 << "  According to the PDB specification,\n"
                 << "  columns 7-11 should contain the serial number of an atom.\n"
                 << "  No atom was found with this serial number.\n"
                 << "  THIS CONECT RECORD WILL BE IGNORED.";
        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning);
        return(false);
    }

    // Serial numbers of the atoms which bind to firstAtom, read from
    // columns 12-16, 17-21, 22-27 and 27-31 of the connect record. Note
    // that we reserve space for 5 integers, but read only four of
    // them. This is to simplify the determination of the bond order;
    // see below.
    long int boundedAtomsSerialNumbers[5]  = {0,0,0,0,0};
    // Bools which tell us which of the serial numbers in
    // boundedAtomsSerialNumbers are read from the file, and which are
    // invalid
    bool boundedAtomsSerialNumbersValid[5] = {false, false, false, false, false};

    // Now read the serial numbers. If the first serial number is not
    // present, this connect record probably contains only hydrogen
    // bonds and salt bridges, which we ignore. In that case, we just
    // exit gracefully.
    boundedAtomsSerialNumbersValid[0] = readIntegerFromRecord(buffer, 12, boundedAtomsSerialNumbers+0);
    if (boundedAtomsSerialNumbersValid[0] == false)
        return(true);
    boundedAtomsSerialNumbersValid[1] = readIntegerFromRecord(buffer, 17, boundedAtomsSerialNumbers+1);
    boundedAtomsSerialNumbersValid[2] = readIntegerFromRecord(buffer, 22, boundedAtomsSerialNumbers+2);
    boundedAtomsSerialNumbersValid[3] = readIntegerFromRecord(buffer, 27, boundedAtomsSerialNumbers+3);

    // Now iterate over the VALID boundedAtomsSerialNumbers and connect
    // the atoms.
    for(unsigned int k=0; boundedAtomsSerialNumbersValid[k]; k++)
    {
        // Find atom that is connected to, write an error message
        OBAtom *connectedAtom = 0L;
        for (OBAtom *a1 = mol.BeginAtom(i);a1;a1 = mol.NextAtom(i))
            if (static_cast<long int>(a1->GetResidue()->
                                      GetSerialNum(a1)) == boundedAtomsSerialNumbers[k])
            {
                connectedAtom = a1;
                break;
            }
        if (connectedAtom == 0L)
        {
            errorMsg << "WARNING: Problems reading a PDB file:\n"
                     << "  Problems reading a CONECT record.\n"
                     << "  According to the PDB specification,\n"
                     << "  Atoms with serial #" << startAtomSerialNumber 
                     << " and #" << boundedAtomsSerialNumbers[k]
                     << " should be connected\n"
                     << "  However, an atom with serial #" << boundedAtomsSerialNumbers[k] << " was not found.\n"
                     << "  THIS CONECT RECORD WILL BE IGNORED.";
            obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning);
            break;
        }

        // Figure the bond order
        unsigned char order = 0;
        while(boundedAtomsSerialNumbersValid[k+order+1] && (boundedAtomsSerialNumbers[k+order]
                == boundedAtomsSerialNumbers[k+order+1]))
            order++;
        k += order;

        // Generate the bond
        mol.AddBond(firstAtom->GetIdx(), connectedAtom->GetIdx(), order+1);
    }
    return(true);
}

//////////////////////////////////////////////////////////////////////////////
bool PDBFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
        return false;

    //Define some references so we can use the old parameter names
    ostream &ofs = *pConv->GetOutStream();
    OBMol &mol = *pmol;

    unsigned int i;
    char buffer[BUFF_SIZE];
    char type_name[10], padded_name[10];
    char the_res[10];
    char *element_name;
    int res_num;
    bool het=true;

    //  sprintf(buffer,"HEADER    PROTEIN");
    //  ofs << buffer << endl;

    if (strlen(mol.GetTitle()) > 0)
        sprintf(buffer,"COMPND    %s ",mol.GetTitle());
    else
        sprintf(buffer,"COMPND    UNNAMED");
    ofs << buffer << endl;

    sprintf(buffer,"AUTHOR    GENERATED BY OPEN BABEL %s",BABEL_VERSION);
    ofs << buffer << endl;

    OBAtom *atom;
    OBResidue *res;
    for (i = 1; i <= mol.NumAtoms(); i++)
    {
        atom = mol.GetAtom(i);
        strcpy(type_name,etab.GetSymbol(atom->GetAtomicNum()));

        //two char. elements are on position 13 and 14 one char. start at 14
        if (strlen(type_name) > 1)
            type_name[1] = toupper(type_name[1]);
        else
        {
            char tmp[10];
            strcpy(tmp, type_name);
            sprintf(type_name, " %-3s", tmp);
        }

        if ( (res = atom->GetResidue()) )
        {
            het = res->IsHetAtom(atom);
            snprintf(the_res,4,"%s",(char*)res->GetName().c_str());
            snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str());

            //two char. elements are on position 13 and 14 one char. start at 14
            if (strlen(etab.GetSymbol(atom->GetAtomicNum())) == 1)
            {
                if (strlen(type_name) < 4)
                {
                    char tmp[10];
                    strcpy(tmp, type_name);
                    sprintf(padded_name," %-3s", tmp);
                    strncpy(type_name,padded_name,4);
                    type_name[4] = '\0';
                }
                else
                {
                    type_name[4] = type_name[3];
                    type_name[3] = type_name[2];
                    type_name[2] = type_name[1];
                    type_name[1] = type_name[0];
                    type_name[0] = type_name[4];
                    type_name[4] = '\0';
                }
            }
            res_num = res->GetNum();
        }
        else
        {
            strcpy(the_res,"UNK");
            sprintf(padded_name,"%s",type_name);
            strncpy(type_name,padded_name,4);
            type_name[4] = '\0';
            res_num = 1;
        }

        element_name = etab.GetSymbol(atom->GetAtomicNum());
        if (strlen(element_name) == 2)
            element_name[1] = toupper(element_name[1]);
        sprintf(buffer,"%s%5d %-4s %-3s  %4d    %8.3f%8.3f%8.3f  1.00  0.00          %2s  \n",
                het?"HETATM":"ATOM  ",
                i,
                type_name,
                the_res,
                res_num,
                atom->GetX(),
                atom->GetY(),
                atom->GetZ(),
                element_name);
        ofs << buffer;
    }

    OBAtom *nbr;
    int count;
    vector<OBEdgeBase*>::iterator k;
    for (i = 1; i <= mol.NumAtoms(); i ++)
    {
        atom = mol.GetAtom(i);
        if (atom->GetValence() <= 4)
        {
            sprintf(buffer,"CONECT%5d", i);
            ofs << buffer;
            for (nbr = atom->BeginNbrAtom(k);nbr;nbr = atom->NextNbrAtom(k))
            {
                sprintf(buffer,"%5d", nbr->GetIdx());
                ofs << buffer;
            }
            for (count = 0; count < (4 - (int)atom->GetValence()); count++)
            {
                sprintf(buffer, "     ");
                ofs << buffer;
            }
            ofs << "                                       " << endl;
        }
    }
    sprintf(buffer,"MASTER        0    0    0    0    0    0    0    0 ");
    ofs << buffer;
    sprintf(buffer,"%4d    0 %4d    0",mol.NumAtoms(),mol.NumAtoms());
    ofs << buffer << endl;
    sprintf(buffer,"END");
    ofs << buffer << endl;
    return(true);
}


} //namespace OpenBabel
Revision:	746
Committed:	Wed Nov 16 21:22:51 2005 UTC (19 years, 5 months ago) by tim
File size:	19897 byte(s)
Log Message:	adding more readers/writers
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
3			Some portions Copyright (C) 2003-2005 Geoffrey R. Hutchison
4			Some portions Copyright (C) 2004 by Chris Morley
5
6			This program is free software; you can redistribute it and/or modify
7			it under the terms of the GNU General Public License as published by
8			the Free Software Foundation version 2 of the License.
9
10			This program is distributed in the hope that it will be useful,
11			but WITHOUT ANY WARRANTY; without even the implied warranty of
12			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13			GNU General Public License for more details.
14			***********************************************************************/
15
16	tim	746	#include "pdbformat.hpp"
17	tim	741
18	tim	746
19	tim	741	#if !HAVE_SNPRINTF
20			extern "C" int snprintf( char , size_t, const char , /* args */ ...);
21			#endif
22
23			#include <vector>
24			#include <map>
25
26			#ifdef HAVE_SSTREAM
27			#include <sstream>
28			#else
29			#include <strstream>
30			#endif
31
32			using namespace std;
33			namespace OpenBabel
34			{
35
36			static bool ParseAtomRecord(char *, OBMol &,int);
37			static bool ParseConectRecord(char *,OBMol &);
38
39			//extern OBResidueData resdat; now in mol.h
40
41			/////////////////////////////////////////////////////////////////
42			bool PDBFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
43			{
44
45			OBMol* pmol = dynamic_cast<OBMol*>(pOb);
46			if(pmol==NULL)
47			return false;
48
49			//Define some references so we can use the old parameter names
50			istream &ifs = *pConv->GetInStream();
51			OBMol &mol = *pmol;
52			const char* title = pConv->GetTitle();
53
54			int chainNum = 1;
55			char buffer[BUFF_SIZE];
56			OBBitVec bs;
57
58			mol.SetTitle(title);
59
60			mol.BeginModify();
61			while (ifs.getline(buffer,BUFF_SIZE) && !EQn(buffer,"END",3))
62			{
63			if (EQn(buffer,"TER",3))
64			chainNum++;
65			if (EQn(buffer,"ATOM",4) \|\| EQn(buffer,"HETATM",6))
66			{
67			ParseAtomRecord(buffer,mol,chainNum);
68			if (EQn(buffer,"ATOM",4))
69			bs.SetBitOn(mol.NumAtoms());
70			}
71
72			if (EQn(buffer,"CONECT",6))
73			ParseConectRecord(buffer,mol);
74			}
75
76			resdat.AssignBonds(mol,bs);
77			/assign hetatm bonds based on distance/
78
79			if (!pConv->IsOption("b",OBConversion::INOPTIONS))
80			mol.ConnectTheDots();
81
82			if (mol.NumAtoms() < 250) // Minimize time required on real proteins
83			if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
84			mol.PerceiveBondOrders();
85
86			// clean out remaining blank lines
87			while(ifs.peek() != EOF && ifs.good() &&
88			(ifs.peek() == '\n' \|\| ifs.peek() == '\r'))
89			ifs.getline(buffer,BUFF_SIZE);
90
91			mol.EndModify();
92
93			mol.SetAtomTypesPerceived();
94			atomtyper.AssignImplicitValence(mol);
95
96			if (!mol.NumAtoms())
97			return(false);
98			return(true);
99			}
100
101			////////////////////////////////////////////////////////////////
102			static bool ParseAtomRecord(char *buffer, OBMol &mol,int chainNum)
103			/* ATOMFORMAT "(i5,1x,a4,a1,a3,1x,a1,i4,a1,3x,3f8.3,2f6.2,1x,i3)" */
104			{
105			string sbuf = &buffer[6];
106			if (sbuf.size() < 48)
107			return(false);
108
109			bool hetatm = (EQn(buffer,"HETATM",6)) ? true : false;
110
111			/* serial number */
112			string serno = sbuf.substr(0,5);
113			//SerialNum(the_atom) = atoi(tmp_str);
114
115			/* atom name */
116			string atmid = sbuf.substr(6,4);
117
118			/* element */
119			string element;
120			if (sbuf.size() > 71)
121			element = sbuf.substr(70,2);
122			else
123			element = " ";
124
125			//trim spaces on the right and left sides
126			while (!atmid.empty() && atmid[0] == ' ')
127			atmid = atmid.substr(1,atmid.size()-1);
128
129			while (!atmid.empty() && atmid[atmid.size()-1] == ' ')
130			atmid = atmid.substr(0,atmid.size()-1);
131
132			/* residue name */
133
134			string resname = sbuf.substr(11,3);
135			if (resname == " ")
136			resname = "UNK";
137			else
138			{
139			while (!resname.empty() && resname[0] == ' ')
140			resname = resname.substr(1,resname.size()-1);
141
142			while (!resname.empty() && resname[resname.size()-1] == ' ')
143			resname = resname.substr(0,resname.size()-1);
144			}
145
146			/* residue sequence number */
147
148			string resnum = sbuf.substr(16,4);
149
150			/* X, Y, Z */
151			string xstr = sbuf.substr(24,8);
152			string ystr = sbuf.substr(32,8);
153			string zstr = sbuf.substr(40,8);
154
155			string type;
156
157			if (EQn(buffer,"ATOM",4))
158			{
159			type = atmid.substr(0,2);
160			if (isdigit(type[0]))
161			type = atmid.substr(1,1);
162			else if (sbuf[6] == ' ' &&
163			strncasecmp(type.c_str(), "Zn", 2) != 0 &&
164			strncasecmp(type.c_str(), "Fe", 2) != 0)
165			type = atmid.substr(0,1); // one-character element
166
167
168			if (resname.substr(0,2) == "AS" \|\| resname[0] == 'N')
169			{
170			if (atmid == "AD1")
171			type = "O";
172			if (atmid == "AD2")
173			type = "N";
174			}
175			if (resname.substr(0,3) == "HIS" \|\| resname[0] == 'H')
176			{
177			if (atmid == "AD1" \|\| atmid == "AE2")
178			type = "N";
179			if (atmid == "AE1" \|\| atmid == "AD2")
180			type = "C";
181			}
182			if (resname.substr(0,2) == "GL" \|\| resname[0] == 'Q')
183			{
184			if (atmid == "AE1")
185			type = "O";
186			if (atmid == "AE2")
187			type = "N";
188			}
189			}
190			else //must be hetatm record
191			{
192			if (isalpha(element[1]) && (isalpha(element[0]) \|\| (element[0] == ' ')))
193			{
194			if (isalpha(element[0]))
195			type = element.substr(0,2);
196			else
197			type = element.substr(1,1);
198			if (type.size() == 2)
199			type[1] = tolower(type[1]);
200			}
201			else
202			{
203			if (isalpha(atmid[0]))
204			type = atmid.substr(0,2);
205			else if (atmid[0] == ' ')
206			type = atmid.substr(1,1); // one char element
207			else
208			type = atmid.substr(1,2);
209
210			if (atmid == resname)
211			{
212			type = atmid;
213			if (type.size() == 2)
214			type[1] = tolower(type[1]);
215			}
216			else
217			if (resname == "ADR" \|\| resname == "COA" \|\| resname == "FAD" \|\|
218			resname == "GPG" \|\| resname == "NAD" \|\| resname == "NAL" \|\|
219			resname == "NDP")
220			{
221			if (type.size() > 1)
222			type = type.substr(0,1);
223			//type.erase(1,type.size()-1);
224			}
225			else
226			if (isdigit(type[0]))
227			{
228			type = type.substr(1,1);
229			//type.erase(0,1);
230			//if (type.size() > 1) type.erase(1,type.size()-1);
231			}
232			else
233			if (type.size() > 1 && isdigit(type[1]))
234			type = type.substr(0,1);
235			//type.erase(1,1);
236			else
237			if (type.size() > 1 && isalpha(type[1]) && isupper(type[1]))
238			type[1] = tolower(type[1]);
239			}
240
241			}
242
243			OBAtom atom;
244			vector3 v(atof(xstr.c_str()),atof(ystr.c_str()),atof(zstr.c_str()));
245			atom.SetVector(v);
246
247			atom.SetAtomicNum(etab.GetAtomicNum(type.c_str()));
248			atom.SetType(type);
249
250			int rnum = atoi(resnum.c_str());
251			OBResidue *res = (mol.NumResidues() > 0) ? mol.GetResidue(mol.NumResidues()-1) : NULL;
252			if (res == NULL \|\| res->GetName() != resname \|\| static_cast<int>(res->GetNum())
253			!= rnum)
254			{
255			vector<OBResidue*>::iterator ri;
256			for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri))
257			if (res->GetName() == resname && static_cast<int>(res->GetNum())
258			== rnum)
259			break;
260
261			if (res == NULL)
262			{
263			res = mol.NewResidue()
264			;
265			res->SetChainNum(chainNum);
266			res->SetName(resname);
267			res->SetNum(rnum);
268			}
269			}
270
271			if (!mol.AddAtom(atom)
272			)
273			return(false);
274			else
275			{
276			OBAtom *atom = mol.GetAtom(mol.NumAtoms());
277
278			res->AddAtom(atom);
279			res->SetSerialNum(atom, atoi(serno.c_str()));
280			res->SetAtomID(atom, atmid);
281			res->SetHetAtom(atom, hetatm);
282
283			return(true);
284			}
285			}
286
287			/////////////////////////////////////////////////////////////////////////
288			//! Utility function to read a 5-digit integer starting from a specified column
289			/*! This function reads a 5-digit integer, starting from column
290			columnAsSpecifiedInPDB from the buffer, converts it to a long
291			integer, and returns either false or true, if the conversion was
292			successful or not. If the conversion was not successful, the target
293			is set to a random value.
294
295			For instance, the PDB Format Description for a CONECT record specifies
296
297			COLUMNS DATA TYPE FIELD DEFINITION
298			---------------------------------------------------------------------------------
299			1 - 6 Record name "CONECT"
300			7 - 11 Integer serial Atom serial number
301			...
302
303			To read the Atom serial number, you would call
304
305			long int target;
306			if ( readIntegerFromRecord(buffer, 7, &target) == false ) {
307			cerr << "Could not parse" << endl;
308			}
309
310			This function does not check the length of the buffer, or
311			strlen(buffer). If the buffer is not long enough => SEGFAULT.
312			*/
313			static bool readIntegerFromRecord(char buffer, unsigned int columnAsSpecifiedInPDB, long int target)
314			{
315			char integerBuffer[6];
316			integerBuffer[5] = 0;
317
318			strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5);
319
320			char *errorCheckingEndPtr;
321			*target = strtol(integerBuffer, &errorCheckingEndPtr, 10);
322			if (integerBuffer == errorCheckingEndPtr)
323			return(false);
324			return(true);
325			}
326
327			//! Read a CONECT record
328			/*! This function reads a CONECT record, as specified
329			http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html,
330			in short:
331
332			COLUMNS DATA TYPE FIELD DEFINITION
333			---------------------------------------------------------------------------------
334			1 - 6 Record name "CONECT"
335			7 - 11 Integer serial Atom serial number
336			12 - 16 Integer serial Serial number of bonded atom
337			17 - 21 Integer serial Serial number of bonded atom
338			22 - 26 Integer serial Serial number of bonded atom
339			27 - 31 Integer serial Serial number of bonded atom
340			32 - 36 Integer serial Serial number of hydrogen bonded atom
341			37 - 41 Integer serial Serial number of hydrogen bonded atom
342			42 - 46 Integer serial Serial number of salt bridged atom
343			47 - 51 Integer serial Serial number of hydrogen bonded atom
344			52 - 56 Integer serial Serial number of hydrogen bonded atom
345			57 - 61 Integer serial Serial number of salt bridged atom
346
347			Hydrogen bonds and salt bridges are ignored. --Stefan Kebekus.
348			*/
349
350			static bool ParseConectRecord(char *buffer,OBMol &mol)
351			{
352			#ifdef HAVE_SSTREAM
353			stringstream errorMsg;
354			#else
355			strstream errorMsg;
356			#endif
357
358			// Setup strings and string buffers
359			buffer[70] = '\0';
360			if (strlen(buffer) < 70)
361			{
362			errorMsg << "WARNING: Problems reading a PDB file\n"
363			<< " Problems reading a CONECT record.\n"
364			<< " According to the PDB specification,\n"
365			<< " the record should have 70 columns, but OpenBabel found "
366			<< strlen(buffer) << " columns.";
367			obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obInfo);
368			}
369
370			// 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			{
375			errorMsg << "WARNING: Problems reading a PDB file\n"
376			<< " Problems reading a CONECT record.\n"
377			<< " According to the PDB specification,\n"
378			<< " columns 7-11 should contain the serial number of an atom.\n"
379			<< " THIS CONECT RECORD WILL BE IGNORED.";
380			obErrorLog.ThrowError(__FUNCTION__, 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(__FUNCTION__, 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(__FUNCTION__, 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