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basic_fun.h
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basic_fun.h
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/* File parsing and basic geometry operations */
#ifndef TMalign_basic_fun_h
#define TMalign_basic_fun_h 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <string.h>
//#include <malloc.h>
#include <sstream>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <vector>
#include <iterator>
#include <algorithm>
#include <string>
#include <iomanip>
#include <map>
#include "pstream.h" // For reading gzip and bz2 compressed files
using namespace std;
void PrintErrorAndQuit(const string sErrorString)
{
cout << sErrorString << endl;
exit(1);
}
template <typename T> inline T getmin(const T &a, const T &b)
{
return b<a?b:a;
}
template <class A> void NewArray(A *** array, int Narray1, int Narray2)
{
*array=new A* [Narray1];
for(int i=0; i<Narray1; i++) *(*array+i)=new A [Narray2];
}
template <class A> void DeleteArray(A *** array, int Narray)
{
for(int i=0; i<Narray; i++)
if(*(*array+i)) delete [] *(*array+i);
if(Narray) delete [] (*array);
(*array)=NULL;
}
string AAmap(char A)
{
if (A=='A') return "ALA";
if (A=='B') return "ASX";
if (A=='C') return "CYS";
if (A=='D') return "ASP";
if (A=='E') return "GLU";
if (A=='F') return "PHE";
if (A=='G') return "GLY";
if (A=='H') return "HIS";
if (A=='I') return "ILE";
if (A=='K') return "LYS";
if (A=='L') return "LEU";
if (A=='M') return "MET";
if (A=='N') return "ASN";
if (A=='O') return "PYL";
if (A=='P') return "PRO";
if (A=='Q') return "GLN";
if (A=='R') return "ARG";
if (A=='S') return "SER";
if (A=='T') return "THR";
if (A=='U') return "SEC";
if (A=='V') return "VAL";
if (A=='W') return "TRP";
if (A=='Y') return "TYR";
if (A=='Z') return "GLX";
if ('a'<=A && A<='z') return " "+string(1,char(toupper(A)));
return "UNK";
}
char AAmap(const string &AA)
{
if (AA.compare("ALA")==0 || AA.compare("DAL")==0) return 'A';
if (AA.compare("ASX")==0) return 'B';
if (AA.compare("CYS")==0 || AA.compare("DCY")==0) return 'C';
if (AA.compare("ASP")==0 || AA.compare("DAS")==0) return 'D';
if (AA.compare("GLU")==0 || AA.compare("DGL")==0) return 'E';
if (AA.compare("PHE")==0 || AA.compare("DPN")==0) return 'F';
if (AA.compare("GLY")==0) return 'G';
if (AA.compare("HIS")==0 || AA.compare("DHI")==0) return 'H';
if (AA.compare("ILE")==0 || AA.compare("DIL")==0) return 'I';
if (AA.compare("LYS")==0 || AA.compare("DLY")==0) return 'K';
if (AA.compare("LEU")==0 || AA.compare("DLE")==0) return 'L';
if (AA.compare("MET")==0 || AA.compare("MED")==0 ||
AA.compare("MSE")==0) return 'M';
if (AA.compare("ASN")==0 || AA.compare("DSG")==0) return 'N';
if (AA.compare("PYL")==0) return 'O';
if (AA.compare("PRO")==0 || AA.compare("DPR")==0) return 'P';
if (AA.compare("GLN")==0 || AA.compare("DGN")==0) return 'Q';
if (AA.compare("ARG")==0 || AA.compare("DAR")==0) return 'R';
if (AA.compare("SER")==0 || AA.compare("DSN")==0) return 'S';
if (AA.compare("THR")==0 || AA.compare("DTH")==0) return 'T';
if (AA.compare("SEC")==0) return 'U';
if (AA.compare("VAL")==0 || AA.compare("DVA")==0) return 'V';
if (AA.compare("TRP")==0 || AA.compare("DTR")==0) return 'W';
if (AA.compare("TYR")==0 || AA.compare("DTY")==0) return 'Y';
if (AA.compare("GLX")==0) return 'Z';
if (AA.compare(0,2," D")==0) return tolower(AA[2]);
if (AA.compare(0,2," ")==0) return tolower(AA[2]);
return 'X';
}
/* split a long string into vectors by whitespace
* line - input string
* line_vec - output vector
* delimiter - delimiter */
void split(const string &line, vector<string> &line_vec,
const char delimiter=' ')
{
bool within_word = false;
for (size_t pos=0;pos<line.size();pos++)
{
if (line[pos]==delimiter)
{
within_word = false;
continue;
}
if (!within_word)
{
within_word = true;
line_vec.push_back("");
}
line_vec.back()+=line[pos];
}
}
/* strip white space at the begining or end of string */
string Trim(const string &inputString)
{
string result = inputString;
int idxBegin = inputString.find_first_not_of(" \n\r\t");
int idxEnd = inputString.find_last_not_of(" \n\r\t");
if (idxBegin >= 0 && idxEnd >= 0)
result = inputString.substr(idxBegin, idxEnd + 1 - idxBegin);
return result;
}
size_t get_PDB_lines(const string filename,
vector<vector<string> >&PDB_lines, vector<string> &chainID_list,
vector<int> &mol_vec, const int ter_opt, const int infmt_opt,
const string atom_opt, const bool autojustify, const int split_opt,
const int het_opt, const vector<string>&chain2parse,
const vector<string>&model2parse)
{
size_t i=0; // resi i.e. atom index
string line;
char chainID=0;
string resi="";
bool select_atom=false;
size_t model_idx=0;
vector<string> tmp_str_vec;
int compress_type=0; // uncompressed file
ifstream fin;
#ifndef REDI_PSTREAM_H_SEEN
ifstream fin_gz;
#else
redi::ipstream fin_gz; // if file is compressed
if (filename.size()>=3 &&
filename.substr(filename.size()-3,3)==".gz")
{
fin_gz.open("gunzip -c '"+filename+"'");
compress_type=1;
}
else if (filename.size()>=4 &&
filename.substr(filename.size()-4,4)==".bz2")
{
fin_gz.open("bzcat '"+filename+"'");
compress_type=2;
}
else
#endif
{
if (filename=="-") compress_type=-1;
else fin.open(filename.c_str());
}
if (infmt_opt==0||infmt_opt==-1) // PDB format
{
map<string,char> aa3to1;
aa3to1[" A"]=aa3to1[" DA"]='a';
aa3to1[" C"]=aa3to1[" DC"]='c';
aa3to1[" G"]=aa3to1[" DG"]='g';
aa3to1[" U"]=aa3to1["PSU"]='u';
aa3to1[" I"]=aa3to1[" DI"]='i';
aa3to1[" T"]='t';
aa3to1["ALA"]='A';
aa3to1["CYS"]='C';
aa3to1["ASP"]='D';
aa3to1["GLU"]='E';
aa3to1["PHE"]='F';
aa3to1["GLY"]='G';
aa3to1["HIS"]='H';
aa3to1["ILE"]='I';
aa3to1["LYS"]='K';
aa3to1["LEU"]='L';
aa3to1["MET"]=aa3to1["MSE"]='M';
aa3to1["ASN"]='N';
aa3to1["PRO"]='P';
aa3to1["GLN"]='Q';
aa3to1["ARG"]='R';
aa3to1["SER"]='S';
aa3to1["THR"]='T';
aa3to1["VAL"]='V';
aa3to1["TRP"]='W';
aa3to1["TYR"]='Y';
aa3to1["ASX"]='B';
aa3to1["GLX"]='Z';
aa3to1["SEC"]='U';
aa3to1["PYL"]='O';
string atom;
string resn;
string model_index="1";
map<string, char> alt_id_dict; // resi -> alt_id
string resi_chain;
while ((compress_type==-1)?cin.good():(compress_type?fin_gz.good():fin.good()))
{
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (infmt_opt==-1 && (line.compare(0,5,"loop_")==0 ||
line.compare(0,1,"#")==0)) // PDBx/mmCIF
return get_PDB_lines(filename,PDB_lines,chainID_list, mol_vec,
ter_opt, 3, atom_opt, autojustify, split_opt,het_opt,
chain2parse, model2parse);
if (model2parse.size())
{
if (line.size()>=6 && line.compare(0,5,"MODEL")==0)
model_index=Trim(line.substr(5,9));
else if (find(model2parse.begin(),model2parse.end(),
model_index)==model2parse.end()) continue;
}
if (i > 0)
{
if (ter_opt>=1 && line.compare(0,3,"END")==0) break;
else if (ter_opt>=3 && line.compare(0,3,"TER")==0) break;
}
if (line.compare(0,3,"END")==0)
{
if (split_opt) chainID=0;
map<string, char> ().swap(alt_id_dict);
}
if (line.size()>=54 && //(line[16]==' ' || line[16]=='A') &&
((line.compare(0, 6, "ATOM ")==0) ||
(line.compare(0, 6, "HETATM")==0 && het_opt==1) ||
(line.compare(0, 6, "HETATM")==0 && het_opt==2 &&
line.compare(17,3, "MSE")==0)))
{
atom=line.substr(12,4);
if (autojustify)
{
resn=line.substr(17,3);
if (aa3to1.count(resn))
{
atom=Trim(atom);
if (atom.size())
{
if (atom.size()>=2 && atom[atom.size()-1]=='*')
atom=atom.substr(0,atom.size()-1)+"'";
if (atom.size()==1) atom=" "+atom+" ";
else if (atom.size()==2) atom=" "+atom+" ";
else if (atom.size()==3) atom=" "+atom;
}
}
}
if (atom_opt=="auto")
{
if (line[17]==' ' && (line[18]=='D'||line[18]==' '))
select_atom=(atom==" C3'");
else select_atom=(atom==" CA ");
}
else if (atom_opt=="PC4'")
{
if (line[17]==' ' && (line[18]=='D'||line[18]==' '))
select_atom=(atom==" P ")||(atom==" C4'");
else select_atom=(atom==" CA ");
}
else select_atom=(atom==atom_opt);
if (select_atom)
{
resi_chain=line.substr(21,6);
if (alt_id_dict.count(resi_chain)==0)
alt_id_dict[resi_chain]=line[16];
else if (alt_id_dict[resi_chain]!=line[16]) continue;
if (chain2parse.size() && ( (line[21]==' ' &&
find(chain2parse.begin(),chain2parse.end(), "_"
)==chain2parse.end())|| (line[21]!=' ' &&
find(chain2parse.begin(), chain2parse.end(),
string(1,line[21]))==chain2parse.end()))) continue;
if (!chainID)
{
chainID=line[21];
model_idx++;
stringstream i8_stream;
i=0;
if (split_opt==2) // split by chain
{
if (chainID==' ')
{
if (ter_opt>=1) i8_stream << ":_";
else i8_stream<<':'<<model_idx<<",_";
}
else
{
if (ter_opt>=1) i8_stream << ':' << chainID;
else i8_stream<<':'<<model_idx<<','<<chainID;
}
chainID_list.push_back(i8_stream.str());
}
else if (split_opt==1) // split by model
{
i8_stream << ':' << model_idx;
chainID_list.push_back(i8_stream.str());
}
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
}
else if (ter_opt>=2 && chainID!=line[21]) break;
if (split_opt==2 && chainID!=line[21])
{
chainID=line[21];
i=0;
stringstream i8_stream;
if (chainID==' ')
{
if (ter_opt>=1) i8_stream << ":_";
else i8_stream<<':'<<model_idx<<",_";
}
else
{
if (ter_opt>=1) i8_stream << ':' << chainID;
else i8_stream<<':'<<model_idx<<','<<chainID;
}
chainID_list.push_back(i8_stream.str());
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
}
if (resi==line.substr(22,5) && atom_opt!="PC4'")
cerr<<"Warning! Duplicated residue "<<resi<<endl;
resi=line.substr(22,5); // including insertion code
PDB_lines.back().push_back(line);
if (line[17]==' ' && (line[18]=='D'||line[18]==' ')) mol_vec.back()++;
else mol_vec.back()--;
i++;
}
}
}
map<string,char>().swap(aa3to1);
map<string, char>().swap(alt_id_dict); // resi -> alt_id
string ().swap(resi_chain);
}
else if (infmt_opt==1) // SPICKER format
{
size_t L=0;
float x,y,z;
stringstream i8_stream;
while ((compress_type==-1)?cin.good():(compress_type?fin_gz.good():fin.good()))
{
if (compress_type==-1)
{
cin>>L>>x>>y>>z;
getline(cin, line);
if (!cin.good()) break;
}
else if (compress_type)
{
fin_gz>>L>>x>>y>>z;
getline(fin_gz, line);
if (!fin_gz.good()) break;
}
else
{
fin >>L>>x>>y>>z;
getline(fin, line);
if (!fin.good()) break;
}
model_idx++;
stringstream i8_stream;
i8_stream << ':' << model_idx;
chainID_list.push_back(i8_stream.str());
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
for (i=0;i<L;i++)
{
if (compress_type==-1) cin>>x>>y>>z;
else if (compress_type) fin_gz>>x>>y>>z;
else fin >>x>>y>>z;
i8_stream<<"ATOM "<<setw(4)<<i+1<<" CA UNK "<<setw(4)
<<i+1<<" "<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x<<setw(8)<<y<<setw(8)<<z;
line=i8_stream.str();
i8_stream.str(string());
PDB_lines.back().push_back(line);
}
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
}
}
else if (infmt_opt==2) // xyz format
{
size_t L=0;
stringstream i8_stream;
while ((compress_type==-1)?cin.good():(compress_type?fin_gz.good():fin.good()))
{
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
L=atoi(line.c_str());
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
for (i=0;i<line.size();i++)
if (line[i]==' '||line[i]=='\t') break;
if (!((compress_type==-1)?cin.good():(compress_type?fin_gz.good():fin.good()))) break;
chainID_list.push_back(':'+line.substr(0,i));
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
for (i=0;i<L;i++)
{
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
i8_stream<<"ATOM "<<setw(4)<<i+1<<" CA "
<<AAmap(line[0])<<" "<<setw(4)<<i+1<<" "
<<line.substr(2,8)<<line.substr(11,8)<<line.substr(20,8);
line=i8_stream.str();
i8_stream.str(string());
PDB_lines.back().push_back(line);
if (line[0]>='a' && line[0]<='z') mol_vec.back()++; // RNA
else mol_vec.back()--;
}
}
}
else if (infmt_opt==3) // PDBx/mmCIF format
{
bool loop_ = false; // not reading following content
map<string,int> _atom_site;
int atom_site_pos;
vector<string> line_vec;
string alt_id="."; // alternative location indicator
string asym_id="."; // this is similar to chainID, except that
// chainID is char while asym_id is a string
// with possibly multiple char
string prev_asym_id="";
string AA=""; // residue name
string atom="";
string prev_resi="";
string model_index=""; // the same as model_idx but type is string
stringstream i8_stream;
map<string, string> alt_id_dict; // resi -> alt_id
string resi_chain;
while ((compress_type==-1)?cin.good():(compress_type?fin_gz.good():fin.good()))
{
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (line.size()==0) continue;
if (loop_) loop_ = (line.size()>=2)?(line.compare(0,2,"# ")):(line.compare(0,1,"#"));
if (!loop_)
{
if (line.compare(0,5,"loop_")) continue;
while(1)
{
if (compress_type==-1)
{
if (cin.good()) getline(cin, line);
else PrintErrorAndQuit("ERROR! Unexpected end of -");
}
else if (compress_type)
{
if (fin_gz.good()) getline(fin_gz, line);
else PrintErrorAndQuit("ERROR! Unexpected end of "+filename);
}
else
{
if (fin.good()) getline(fin, line);
else PrintErrorAndQuit("ERROR! Unexpected end of "+filename);
}
if (line.size()) break;
}
if (line.compare(0,11,"_atom_site.")) continue;
loop_=true;
_atom_site.clear();
atom_site_pos=0;
_atom_site[Trim(line.substr(11))]=atom_site_pos;
while(1)
{
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (line.size()==0) continue;
if (line.compare(0,11,"_atom_site.")) break;
_atom_site[Trim(line.substr(11))]=++atom_site_pos;
}
if (_atom_site.count("group_PDB")*
_atom_site.count("label_atom_id")*
_atom_site.count("label_comp_id")*
(_atom_site.count("auth_asym_id")+
_atom_site.count("label_asym_id"))*
(_atom_site.count("auth_seq_id")+
_atom_site.count("label_seq_id"))*
_atom_site.count("Cartn_x")*
_atom_site.count("Cartn_y")*
_atom_site.count("Cartn_z")==0)
{
loop_ = false;
cerr<<"Warning! Missing one of the following _atom_site data items: group_PDB, label_atom_id, label_comp_id, auth_asym_id/label_asym_id, auth_seq_id/label_seq_id, Cartn_x, Cartn_y, Cartn_z"<<endl;
continue;
}
}
line_vec.clear();
split(line,line_vec);
if ((line_vec[_atom_site["group_PDB"]]!="ATOM" &&
line_vec[_atom_site["group_PDB"]]!="HETATM") ||
(line_vec[_atom_site["group_PDB"]]=="HETATM" &&
(het_opt==0 ||
(het_opt==2 && line_vec[_atom_site["label_comp_id"]]!="MSE")))
) continue;
atom=line_vec[_atom_site["label_atom_id"]];
if (atom[0]=='"') atom=atom.substr(1);
if (atom.size() && atom[atom.size()-1]=='"')
atom=atom.substr(0,atom.size()-1);
if (atom.size()==0) continue;
if (atom.size()==1) atom=" "+atom+" ";
else if (atom.size()==2) atom=" "+atom+" "; // wrong for sidechain H
else if (atom.size()==3) atom=" "+atom;
else if (atom.size()>=5) continue;
AA=line_vec[_atom_site["label_comp_id"]]; // residue name
if (AA.size()==1) AA=" "+AA;
else if (AA.size()==2) AA=" " +AA;
else if (AA.size()>=4) continue;
if (atom_opt=="auto")
{
if (AA[0]==' ' && (AA[1]=='D'||AA[1]==' ')) // DNA || RNA
select_atom=(atom==" C3'");
else select_atom=(atom==" CA ");
}
else if (atom_opt=="PC4'")
{
if (line[17]==' ' && (line[18]=='D'||line[18]==' '))
select_atom=(line.compare(12,4," P ")==0
)||(line.compare(12,4," C4'")==0);
else select_atom=(line.compare(12,4," CA ")==0);
}
else select_atom=(atom==atom_opt);
if (!select_atom) continue;
if (_atom_site.count("auth_asym_id"))
asym_id=line_vec[_atom_site["auth_asym_id"]];
else asym_id=line_vec[_atom_site["label_asym_id"]];
if (asym_id==".") asym_id=" ";
if (chain2parse.size() && ( (asym_id==" " &&
find(chain2parse.begin(),chain2parse.end(), "_"
)==chain2parse.end())|| (asym_id!=" " &&
find(chain2parse.begin(), chain2parse.end(),asym_id
)==chain2parse.end()))) continue;
if (model2parse.size() && _atom_site.count("pdbx_PDB_model_num") &&
find(model2parse.begin(), model2parse.end(),
line_vec[_atom_site["pdbx_PDB_model_num"]]
)==model2parse.end()) continue;
if (_atom_site.count("pdbx_PDB_model_num") &&
model_index!=line_vec[_atom_site["pdbx_PDB_model_num"]])
{
model_index=line_vec[_atom_site["pdbx_PDB_model_num"]];
if (PDB_lines.size() && ter_opt>=1) break;
if (PDB_lines.size()==0 || split_opt>=1)
{
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
prev_asym_id=asym_id;
if (split_opt==1 && ter_opt==0) chainID_list.push_back(
':'+model_index);
else if (split_opt==2 && ter_opt==0)
chainID_list.push_back(':'+model_index+','+asym_id);
else //if (split_opt==2 && ter_opt==1)
chainID_list.push_back(':'+asym_id);
//else
//chainID_list.push_back("");
}
map<string, string>().swap(alt_id_dict);
}
if (_atom_site.count("auth_seq_id"))
resi=line_vec[_atom_site["auth_seq_id"]];
else resi=line_vec[_atom_site["label_seq_id"]];
if (_atom_site.count("pdbx_PDB_ins_code") &&
line_vec[_atom_site["pdbx_PDB_ins_code"]]!="?")
resi+=line_vec[_atom_site["pdbx_PDB_ins_code"]][0];
else resi+=" ";
if (_atom_site.count("label_alt_id")) // in 39.4 % of entries
{
alt_id=line_vec[_atom_site["label_alt_id"]];
resi_chain=asym_id+resi;
if (alt_id_dict.count(resi_chain)==0)
alt_id_dict[resi_chain]=alt_id;
else if (alt_id_dict.count(resi_chain) && alt_id!=alt_id_dict[resi_chain])
continue;
//if (alt_id!="." && alt_id!="A") continue;
}
if (prev_asym_id!=asym_id)
{
if (prev_asym_id!="" && ter_opt>=2) break;
if (split_opt>=2)
{
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
if (split_opt==1 && ter_opt==0) chainID_list.push_back(
':'+model_index);
else if (split_opt==2 && ter_opt==0)
chainID_list.push_back(':'+model_index+','+asym_id);
else //if (split_opt==2 && ter_opt==1)
chainID_list.push_back(':'+asym_id);
//else
//chainID_list.push_back("");
}
}
if (prev_asym_id!=asym_id) prev_asym_id=asym_id;
if (AA[0]==' ' && (AA[1]=='D'||AA[1]==' ')) mol_vec.back()++;
else mol_vec.back()--;
if (prev_resi==resi && atom_opt!="PC4'")
cerr<<"Warning! Duplicated residue "<<resi<<endl;
prev_resi=resi;
i++;
i8_stream<<"ATOM "
<<setw(5)<<i<<" "<<atom<<" "<<AA<<" "<<asym_id[0]
<<setw(5)<<resi.substr(0,5)<<" "
<<setw(8)<<line_vec[_atom_site["Cartn_x"]].substr(0,8)
<<setw(8)<<line_vec[_atom_site["Cartn_y"]].substr(0,8)
<<setw(8)<<line_vec[_atom_site["Cartn_z"]].substr(0,8);
PDB_lines.back().push_back(i8_stream.str());
i8_stream.str(string());
}
_atom_site.clear();
line_vec.clear();
alt_id.clear();
asym_id.clear();
AA.clear();
map<string, string>().swap(alt_id_dict);
resi_chain.clear();
}
if (compress_type>=1) fin_gz.close();
else if (compress_type==0) fin.close();
line.clear();
if (!split_opt) chainID_list.push_back("");
return PDB_lines.size();
}
/* read fasta file from filename. sequence is stored into FASTA_lines
* while sequence name is stored into chainID_list.
* if ter_opt >=1, only read the first sequence.
* if ter_opt ==0, read all sequences.
* if split_opt >=1 and ter_opt ==0, each sequence is a separate entry.
* if split_opt ==0 and ter_opt ==0, all sequences are combined into one */
size_t get_FASTA_lines(const string filename,
vector<vector<string> >&FASTA_lines, vector<string> &chainID_list,
vector<int> &mol_vec, const int ter_opt=3, const int split_opt=0)
{
string line;
vector<string> tmp_str_vec;
size_t l;
int compress_type=0; // uncompressed file
ifstream fin;
#ifndef REDI_PSTREAM_H_SEEN
ifstream fin_gz;
#else
redi::ipstream fin_gz; // if file is compressed
if (filename.size()>=3 &&
filename.substr(filename.size()-3,3)==".gz")
{
fin_gz.open("gunzip -c '"+filename+"'");
compress_type=1;
}
else if (filename.size()>=4 &&
filename.substr(filename.size()-4,4)==".bz2")
{
fin_gz.open("bzcat '"+filename+"'");
compress_type=2;
}
else
#endif
{
if (filename=="-") compress_type=-1;
else fin.open(filename.c_str());
}
while ((compress_type==-1)?cin.good():(compress_type?fin_gz.good():fin.good()))
{
if (compress_type==-1) getline(cin, line);
else if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (line.size()==0 || line[0]=='#') continue;
if (line[0]=='>')
{
if (FASTA_lines.size())
{
if (ter_opt) break;
if (split_opt==0) continue;
}
FASTA_lines.push_back(tmp_str_vec);
FASTA_lines.back().push_back("");
mol_vec.push_back(0);
if (ter_opt==0 && split_opt)
{
line[0]=':';
chainID_list.push_back(line);
}
else chainID_list.push_back("");
}
else
{
FASTA_lines.back()[0]+=line;
for (l=0;l<line.size();l++) mol_vec.back()+=
('a'<=line[l] && line[l]<='z')-('A'<=line[l] && line[l]<='Z');
}
}
line.clear();
if (compress_type>=1) fin_gz.close();
else if (compress_type==0) fin.close();
return FASTA_lines.size();
}
int read_PDB(const vector<string> &PDB_lines, double **a, char *seq,
vector<string> &resi_vec, const int read_resi)
{
size_t i;
for (i=0;i<PDB_lines.size();i++)
{
a[i][0] = atof(PDB_lines[i].substr(30, 8).c_str());
a[i][1] = atof(PDB_lines[i].substr(38, 8).c_str());
a[i][2] = atof(PDB_lines[i].substr(46, 8).c_str());
seq[i] = AAmap(PDB_lines[i].substr(17, 3));
if (read_resi>=2) resi_vec.push_back(PDB_lines[i].substr(22,5)+
PDB_lines[i][21]);
if (read_resi==1) resi_vec.push_back(PDB_lines[i].substr(22,5));
}
seq[i]='\0';
return i;
}
double dist(double x[3], double y[3])
{
double d1=x[0]-y[0];
double d2=x[1]-y[1];
double d3=x[2]-y[2];
return (d1*d1 + d2*d2 + d3*d3);
}
double dot(double *a, double *b)
{
return (a[0] * b[0] + a[1] * b[1] + a[2] * b[2]);
}
void transform(double t[3], double u[3][3], double *x, double *x1)
{
x1[0]=t[0]+dot(&u[0][0], x);
x1[1]=t[1]+dot(&u[1][0], x);
x1[2]=t[2]+dot(&u[2][0], x);
}
void do_rotation(double **x, double **x1, int len, double t[3], double u[3][3])
{
for(int i=0; i<len; i++)
{
transform(t, u, &x[i][0], &x1[i][0]);
}
}
/* read user specified pairwise alignment from 'fname_lign' to 'sequence'.
* This function should only be called by main function, as it will
* terminate a program if wrong alignment is given */
void read_user_alignment(vector<string>&sequence, const string &fname_lign,
const int i_opt)
{
if (fname_lign == "")
PrintErrorAndQuit("Please provide a file name for option -i!");
// open alignment file
int n_p = 0;// number of structures in alignment file
string line;
ifstream fileIn(fname_lign.c_str());
if (fileIn.is_open())
{
while (fileIn.good())
{
getline(fileIn, line);
if (line.compare(0, 1, ">") == 0)// Flag for a new structure
{
if (n_p >= 2) break;
sequence.push_back("");
n_p++;
}
else if (n_p > 0 && line!="") sequence.back()+=line;
}
fileIn.close();
}
else PrintErrorAndQuit("ERROR! Alignment file does not exist.");
if (n_p < 2)
PrintErrorAndQuit("ERROR: Fasta format is wrong, two proteins should be included.");
if (sequence[0].size() != sequence[1].size())
PrintErrorAndQuit("ERROR! FASTA file is wrong. The length in alignment should be equal for the two aligned proteins.");
if (i_opt==3)
{
int aligned_resNum=0;
for (size_t i=0;i<sequence[0].size();i++)
aligned_resNum+=(sequence[0][i]!='-' && sequence[1][i]!='-');
if (aligned_resNum<3)
PrintErrorAndQuit("ERROR! Superposition is undefined for <3 aligned residues.");
}
line.clear();
return;
}
inline bool isfile(const string& filename)
{
if (FILE *fp = fopen(filename.c_str(), "r"))
{
fclose(fp);
return true;
}
else return false;
}
/* read list of entries from 'name' to 'chain_list'.
* dir_opt is the folder name (prefix).
* suffix_opt is the file name extension (suffix_opt).
* This function should only be called by main function, as it will
* terminate a program if wrong alignment is given */
void file2chainlist(vector<string>&chain_list, const string &name,
const string &dir_opt, const string &suffix_opt)
{
ifstream fp(name.c_str());
if (! fp.is_open())
PrintErrorAndQuit(("Can not open file: "+name+'\n').c_str());
string line;
string filename;
int a,b;
string sep;
while (fp.good())
{
getline(fp, line);
if (! line.size()) continue;
line=Trim(line);
for (a=0;a<=2;a++)
{
if (a==0) sep="";
else if (a==1) sep="/";
else if (a==2) sep="\\";
filename=dir_opt+sep+line+suffix_opt;
if (isfile(filename)) break;
if (suffix_opt.size())
{
filename=dir_opt+sep+line;
if (isfile(filename)) break;
}
else
{
filename=dir_opt+sep+line+".pdb";
if (isfile(filename)) break;
filename=dir_opt+sep+line+".cif";
if (isfile(filename)) break;
}
filename.clear();
}
if (filename.size()==0)
{
filename=dir_opt+line+suffix_opt;
cerr<<"WARNING! "<<filename<<" does not exist"<<endl;
}
else chain_list.push_back(filename);
line.clear();
filename.clear();
}
fp.close();
}
void file2chainpairlist(vector<string>&chain1_list, vector<string>&chain2_list,
const string &name, const string &dirpair_opt, const string &suffix_opt)
{
ifstream fp(name.c_str());
if (! fp.is_open())
PrintErrorAndQuit(("Can not open file: "+name+'\n').c_str());
string line;
string filename;
int a,b;
size_t i;
string sep,filename1,filename2;
vector<string> line_vec;
while (fp.good())
{
getline(fp, line);
if (! line.size()) continue;
line=Trim(line);
split(line, line_vec, '\t');
if (line_vec.size()==2)
{
filename1=line_vec[0];
filename2=line_vec[1];
for (i=0;i<2;i++) line_vec[i].clear(); line_vec.clear();
}
else
{
for (i=0;i<line_vec.size();i++) line_vec[i].clear(); line_vec.clear();
split(line, line_vec, ' ');
if (line_vec.size()==2)
{
filename1=line_vec[0];
filename2=line_vec[1];
for (i=0;i<2;i++) line_vec[i].clear(); line_vec.clear();
}
else
{
cerr<<"WARNING! not a chain pair: "<<line<<endl;
for (i=0;i<line_vec.size();i++) line_vec[i].clear(); line_vec.clear();
continue;
}
}
filename.clear();
for (a=0;a<=2;a++)
{
if (a==0) sep="";
else if (a==1) sep="/";
else if (a==2) sep="\\";
filename=dirpair_opt+sep+filename1+suffix_opt;
if (isfile(filename)) break;
if (suffix_opt.size())
{
filename=dirpair_opt+sep+line;
if (isfile(filename)) break;
}
else
{
filename=dirpair_opt+sep+line+".pdb";
if (isfile(filename)) break;
filename=dirpair_opt+sep+line+".cif";
if (isfile(filename)) break;
}
filename.clear();
}
if (filename.size()==0)
{
filename=dirpair_opt+filename1+suffix_opt;
cerr<<"WARNING! "<<filename<<" does not exist"<<endl;
continue;
}
else