bool MOL2Format::ReadMolecule(OBBase* pOb, OBConversion* pConv) { OBMol* pmol = pOb->CastAndClear<OBMol>(); if(pmol==NULL) return false; //Define some references so we can use the old parameter names istream &ifs = *pConv->GetInStream(); OBMol &mol = *pmol; //Old code follows... bool foundAtomLine = false; char buffer[BUFF_SIZE]; char *comment = NULL; string str,str1; vector<string> vstr; int len; mol.BeginModify(); for (;;) { if (!ifs.getline(buffer,BUFF_SIZE)) return(false); if (EQn(buffer,"@<TRIPOS>MOLECULE",17)) break; } int lcount; int natoms,nbonds; for (lcount=0;;lcount++) { if (!ifs.getline(buffer,BUFF_SIZE)) return(false); if (EQn(buffer,"@<TRIPOS>ATOM",13)) { foundAtomLine = true; break; } if (lcount == 0) { tokenize(vstr,buffer); if (!vstr.empty()) mol.SetTitle(buffer); } else if (lcount == 1) sscanf(buffer,"%d%d",&natoms,&nbonds); else if (lcount == 4) //energy { tokenize(vstr,buffer); if (!vstr.empty() && vstr.size() == 3) if (vstr[0] == "Energy") mol.SetEnergy(atof(vstr[2].c_str())); } else if (lcount == 5) //comment { if ( buffer[0] ) { len = (int) strlen(buffer)+1; // TODO allow better multi-line comments // which don't allow ill-formed data to consume memory // Thanks to Andrew Dalke for the pointer if (comment != NULL) delete [] comment; comment = new char [len]; memcpy(comment,buffer,len); } } } if (!foundAtomLine) { mol.EndModify(); mol.Clear(); obErrorLog.ThrowError(__FUNCTION__, "Unable to read Mol2 format file. No atoms found.", obWarning); return(false); } mol.ReserveAtoms(natoms); int i; vector3 v; OBAtom atom; bool hasPartialCharges=false; double x,y,z,pcharge; char temp_type[BUFF_SIZE], resname[BUFF_SIZE], atmid[BUFF_SIZE]; int elemno, resnum = -1; ttab.SetFromType("SYB"); for (i = 0;i < natoms;i++) { if (!ifs.getline(buffer,BUFF_SIZE)) return(false); sscanf(buffer," %*s %1024s %lf %lf %lf %1024s %d %1024s %lf", atmid, &x,&y,&z, temp_type, &resnum, resname, &pcharge); atom.SetVector(x, y, z); // Handle "CL" and "BR" and other mis-typed atoms str = temp_type; if (strncmp(temp_type, "CL", 2) == 0) { str = "Cl"; } else if (strncmp(temp_type,"BR",2) == 0) { str = "Br"; } else if (strncmp(temp_type,"S.o2", 4) == 02) { str = "S.O2"; } else if (strncmp(temp_type,"S.o", 3) == 0) { str = "S.O"; } else if (strncmp(temp_type,"SI", 2) == 0) { str = "Si"; // The following cases are entries which are not in openbabel/data/types.txt // and should probably be added there } else if (strncmp(temp_type,"S.1", 3) == 0) { str = "S.2"; // no idea what the best type might be here } else if (strncmp(temp_type,"P.", 2) == 0) { str = "P.3"; } else if (strncasecmp(temp_type,"Ti.", 3) == 0) { // e.g. Ti.th str = "Ti"; } else if (strncasecmp(temp_type,"Ru.", 3) == 0) { // e.g. Ru.oh str = "Ru"; } ttab.SetToType("ATN"); ttab.Translate(str1,str); elemno = atoi(str1.c_str()); ttab.SetToType("IDX"); // We might have missed some SI or FE type things above, so here's // another check if( !elemno && isupper(temp_type[1]) ) { temp_type[1] = (char)tolower(temp_type[1]); str = temp_type; ttab.Translate(str1,str); elemno = atoi(str1.c_str()); } // One last check if there isn't a period in the type, // it's a malformed atom type, but it may be the element symbol // GaussView does this (PR#1739905) if ( !elemno ) { obErrorLog.ThrowError(__FUNCTION__, "This Mol2 file is non-standard. Cannot interpret atom types correctly, instead attempting to interpret as elements instead.", obWarning); string::size_type dotPos = str.find('.'); if (dotPos == string::npos) { elemno = etab.GetAtomicNum(str.c_str()); } } atom.SetAtomicNum(elemno); ttab.SetToType("INT"); ttab.Translate(str1,str); atom.SetType(str1); atom.SetPartialCharge(pcharge); if (!mol.AddAtom(atom)) return(false); if (!IsNearZero(pcharge)) hasPartialCharges = true; // Add residue information if it exists if (resnum != -1 && resnum != 0 && strlen(resname) != 0 && strncmp(resname,"<1>", 3) != 0) { OBResidue *res = (mol.NumResidues() > 0) ? mol.GetResidue(mol.NumResidues()-1) : NULL; if (res == NULL || res->GetName() != resname || static_cast<int>(res->GetNum()) != resnum) { vector<OBResidue*>::iterator ri; for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri)) if (res->GetName() == resname && static_cast<int>(res->GetNum()) == resnum) break; if (res == NULL) { res = mol.NewResidue(); res->SetName(resname); res->SetNum(resnum); } } OBAtom *atomPtr = mol.GetAtom(mol.NumAtoms()); res->AddAtom(atomPtr); res->SetAtomID(atomPtr, atmid); } // end adding residue info } for (;;) { if (!ifs.getline(buffer,BUFF_SIZE)) return(false); str = buffer; if (!strncmp(buffer,"@<TRIPOS>BOND",13)) break; } int start,end,order; for (i = 0; i < nbonds; i++) { if (!ifs.getline(buffer,BUFF_SIZE)) return(false); sscanf(buffer,"%*d %d %d %1024s",&start,&end,temp_type); str = temp_type; order = 1; if (str == "ar" || str == "AR" || str == "Ar") order = 5; else if (str == "AM" || str == "am" || str == "Am") order = 1; else order = atoi(str.c_str()); mol.AddBond(start,end,order); } // update neighbour bonds information for each atom. vector<OBAtom*>::iterator apos; vector<OBBond*>::iterator bpos; OBAtom* patom; OBBond* pbond; for (patom = mol.BeginAtom(apos); patom; patom = mol.NextAtom(apos)) { patom->ClearBond(); for (pbond = mol.BeginBond(bpos); pbond; pbond = mol.NextBond(bpos)) { if (patom == pbond->GetBeginAtom() || patom == pbond->GetEndAtom()) { patom->AddBond(pbond); } } } // Suggestion by Liu Zhiguo 2008-01-26 // Mol2 files define atom types -- there is no need to re-perceive mol.SetAtomTypesPerceived(); mol.EndModify(); //must add generic data after end modify - otherwise it will be blown away if (comment) { OBCommentData *cd = new OBCommentData; cd->SetData(comment); cd->SetOrigin(fileformatInput); mol.SetData(cd); delete [] comment; comment = NULL; } if (hasPartialCharges) mol.SetPartialChargesPerceived(); // continue untill EOF or untill next molecule record streampos pos; for(;;) { pos = ifs.tellg(); if (!ifs.getline(buffer,BUFF_SIZE)) break; if (EQn(buffer,"@<TRIPOS>MOLECULE",17)) break; } ifs.seekg(pos); // go back to the end of the molecule 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,a2,a2)" */ { string sbuf = &buffer[6]; if (sbuf.size() < 48) return(false); bool hetatm = (EQn(buffer,"HETATM",6)) ? true : false; bool elementFound = false; // true if correct element found in col 77-78 /* serial number */ string serno = sbuf.substr(0,5); /* atom name */ string atmid = sbuf.substr(6,4); /* chain */ char chain = sbuf.substr(15,1)[0]; /* element */ string element = " "; if (sbuf.size() > 71) { element = sbuf.substr(70,2); if (isalpha(element[1])) { if (element[0] == ' ') { element.erase(0, 1); elementFound = true; } else if (isalpha(element[0])) { elementFound = true; } } } if (!elementFound) { stringstream errorMsg; errorMsg << "WARNING: Problems reading a PDB file\n" << " Problems reading a HETATM or ATOM record.\n" << " According to the PDB specification,\n" << " columns 77-78 should contain the element symbol of an atom.\n" << " but OpenBabel found '" << element << "' (atom " << mol.NumAtoms()+1 << ")"; obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning); } // charge - optional string scharge; if (sbuf.size() > 73) { scharge = sbuf.substr(72,2); } //trim spaces on the right and left sides while (!atmid.empty() && atmid[0] == ' ') atmid = atmid.erase(0, 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); } string type; if (!elementFound) { // OK, we have to fall back to determining the element from the atom type // This is unreliable, but there's no other choice if (EQn(buffer,"ATOM",4)) { type = atmid.substr(0,2); if (isdigit(type[0])) { // sometimes non-standard files have, e.g 11HH if (!isdigit(type[1])) type = atmid.substr(1,1); else type = atmid.substr(2,1); } else if ((sbuf[6] == ' ' && strncasecmp(type.c_str(), "Zn", 2) != 0 && strncasecmp(type.c_str(), "Fe", 2) != 0) || isdigit(type[1])) //type[1] is digit in Platon 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"; } // fix: #2002557 if (atmid[0] == 'H' && (atmid[1] == 'D' || atmid[1] == 'E' || atmid[1] == 'G' || atmid[1] == 'H')) // HD, HE, HG, HH, .. type = "H"; } 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 { // no element column to use if (isalpha(atmid[0])) { if (atmid.size() > 2 && (atmid[2] == '\0' || atmid[2] == ' ')) type = atmid.substr(0,2); else if (atmid[0] == 'A') // alpha prefix type = atmid.substr(1, atmid.size() - 1); else type = atmid.substr(0,1); } else if (atmid[0] == ' ') type = atmid.substr(1,1); // one char element else type = atmid.substr(1,2); // Some cleanup steps 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" || resname == "ABA") { if (type.size() > 1) type = type.substr(0,1); //type.erase(1,type.size()-1); } else // other residues if (isdigit(type[0])){ type = type.substr(1,1); } else if (type.size() > 1 && isdigit(type[1])) type = type.substr(0,1); else if (type.size() > 1 && isalpha(type[1])) { if (type[0] == 'O' && type[1] == 'H') type = type.substr(0,1); // no "Oh" element (e.g. 1MBN) else if(isupper(type[1])) { type[1] = tolower(type[1]); } } } } // HETATM records } // no element column to use OBAtom atom; /* X, Y, Z */ string xstr = sbuf.substr(24,8); string ystr = sbuf.substr(32,8); string zstr = sbuf.substr(40,8); vector3 v(atof(xstr.c_str()),atof(ystr.c_str()),atof(zstr.c_str())); atom.SetVector(v); atom.ForceImplH(); // useful for debugging unknown atom types (e.g., PR#1577238) // cout << mol.NumAtoms() + 1 << " : '" << element << "'" << " " << etab.GetAtomicNum(element.c_str()) << endl; if (elementFound) atom.SetAtomicNum(etab.GetAtomicNum(element.c_str())); else // use our old-style guess from athe atom type atom.SetAtomicNum(etab.GetAtomicNum(type.c_str())); if ( (! scharge.empty()) && " " != scharge ) { if ( isdigit(scharge[0]) && ('+' == scharge[1] || '-' == scharge[1]) ) { const char reorderCharge[3] = { scharge[1], scharge[0], '\0' }; const int charge = atoi(reorderCharge); atom.SetFormalCharge(charge); } else { stringstream errorMsg; errorMsg << "WARNING: Problems reading a PDB file\n" << " Problems reading a HETATM or ATOM record.\n" << " According to the PDB specification,\n" << " columns 79-80 should contain charge of the atom\n" << " but OpenBabel found '" << scharge << "' (atom " << mol.NumAtoms()+1 << ")."; obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning); } } else { atom.SetFormalCharge(0); } /* residue sequence number */ string resnum = sbuf.substr(16,4); OBResidue *res = (mol.NumResidues() > 0) ? mol.GetResidue(mol.NumResidues()-1) : NULL; if (res == NULL || res->GetName() != resname || res->GetNumString() != resnum || res->GetChain() != chain) { vector<OBResidue*>::iterator ri; for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri)) if (res->GetName() == resname && res->GetNumString() == resnum && static_cast<int>(res->GetChain()) == chain) break; if (res == NULL) { res = mol.NewResidue(); res->SetChain(chain); res->SetName(resname); res->SetNum(resnum); } } 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, sbuf.substr(6,4)); res->SetHetAtom(atom, hetatm); return(true); } } // end reading atom records