Skip to content

L
libcifpp
Commit e0dc9f1c by maarten
Options

pdb2cif fixes 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@181 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent c5d277fb
Showing with 159 additions and 90 deletions
src/PDB2Cif.cpp
......@@ -181,42 +181,49 @@ int PDBRecord::vI(int columnFirst, int columnLast)
enum { start, digit, tail } state = start;
bool negate = false;
for (const char* p = mValue + columnFirst - 7; p < e; ++p)
try
{
switch (state)
for (const char* p = mValue + columnFirst - 7; p < e; ++p)
{
case start:
if (*p == '+')
state = digit;
else if (*p == '-')
{
negate = true;
state = digit;
}
else if (isdigit(*p))
{
result = *p - '0';
state = digit;
}
else if (not isspace(*p))
throw runtime_error("Not a valid integer in PDB record");
break;
switch (state)
{
case start:
if (*p == '+')
state = digit;
else if (*p == '-')
{
negate = true;
state = digit;
}
else if (isdigit(*p))
{
result = *p - '0';
state = digit;
}
else if (not isspace(*p))
throw runtime_error("Not a valid integer in PDB record");
break;
case digit:
if (isspace(*p))
state = tail;
else if (not isdigit(*p))
throw runtime_error("Not a valid integer in PDB record");
else
result = result * 10 + *p - '0';
break;
case digit:
if (isspace(*p))
state = tail;
else if (not isdigit(*p))
throw runtime_error("Not a valid integer in PDB record");
else
result = result * 10 + *p - '0';
break;
case tail:
if (not isspace(*p))
throw runtime_error("Not a valid integer in PDB record");
break;
case tail:
if (not isspace(*p))
throw runtime_error("Not a valid integer in PDB record");
break;
}
}
}
catch (...)
{
throw_with_nested(runtime_error("Trying to parse '" + string(mValue + columnFirst - 7, mValue + columnLast - 7) + '\''));
}
if (negate)
result = -result;
......@@ -645,14 +652,6 @@ class PDBFileParser
void GetNextRecord();
void Match(const string& expected);
// void Error(const string& msg) const
// {
// string lineNr;
// if (mRec != nullptr)
// lineNr = " (at line " + to_string(mRec->mLineNr) + ')';
//
// throw runtime_error("Error parsing PDB file" + lineNr + ": " + msg);
// }
void ParseTitle();
void ParseCitation(const string& id);
......@@ -695,37 +694,46 @@ class PDBFileParser
rx1(R"((\d{2})-(JAN|FEB|MAR|APR|MAY|JUN|JUL|AUG|SEP|OCT|NOV|DEC)-(\d{2}))"),
rx2(R"((JAN|FEB|MAR|APR|MAY|JUN|JUL|AUG|SEP|OCT|NOV|DEC)-(\d{2}))");
if (regex_match(s, m, rx1))
try
{
using namespace boost::gregorian;
if (regex_match(s, m, rx1))
{
using namespace boost::gregorian;
int day = stoi(m[1].str());
auto mi = kMonths.find(m[2].str());
if (mi == kMonths.end())
throw runtime_error("Invalid month: '" + m[2].str() + '\'');
int month = mi->second;
int year = 1900 + stoi(m[3].str());
if (year < 1950)
year += 100;
int day = stoi(m[1].str());
auto mi = kMonths.find(m[2].str());
if (mi == kMonths.end())
throw runtime_error("Invalid month: '" + m[2].str() + '\'');
int month = mi->second;
int year = 1900 + stoi(m[3].str());
if (year < 1950)
year += 100;
date dateOriginal(year, month, day);
date dateOriginal(year, month, day);
s = to_iso_extended_string(dateOriginal);
}
else if (regex_match(s, m, rx2))
{
auto mi = kMonths.find(m[1].str());
if (mi == kMonths.end())
throw runtime_error("Invalid month: '" + m[1].str() + '\'');
int month = mi->second;
int year = 1900 + stoi(m[2].str());
if (year < 1950)
year += 100;
s = to_iso_extended_string(dateOriginal);
s = (boost::format("%04d-%02d") % year % month).str();
}
else
ec = error::make_error_code(error::pdbErrors::invalidDate);
}
else if (regex_match(s, m, rx2))
catch (const exception& ex)
{
auto mi = kMonths.find(m[1].str());
if (mi == kMonths.end())
throw runtime_error("Invalid month: '" + m[1].str() + '\'');
int month = mi->second;
int year = 1900 + stoi(m[2].str());
if (year < 1950)
year += 100;
s = (boost::format("%04d-%02d") % year % month).str();
}
else
if (VERBOSE)
cerr << ex.what() << endl;
ec = error::make_error_code(error::pdbErrors::invalidDate);
}
return s;
}
......@@ -768,7 +776,7 @@ class PDBFileParser
{
smatch m;
if (not regex_match(s, m, sgRx))
throw runtime_error("invalid symmetry value");
throw runtime_error("invalid symmetry value '" + s + '\'');
s = m[1].str() + "_" + m[2].str();
}
......@@ -942,8 +950,16 @@ void PDBFileParser::PreParseInput(istream& is)
{
string cs = lookahead.substr(offset, len);
ba::trim(cs);
int result;
int result = cs.empty() ? 0 : stoi(cs);
try
{
result = cs.empty() ? 0 : stoi(cs);
}
catch (...)
{
throw runtime_error("Continuation string '" + cs + "' is not valid");
}
return result;
};
......@@ -1054,16 +1070,39 @@ void PDBFileParser::PreParseInput(istream& is)
}
else if (type == "FORMUL")
{
int compNr = stoi(value.substr(1, 3));
int n = 2;
while (lookahead.substr(0, 6) == type and
stoi(lookahead.substr(7, 3)) == compNr and
contNr(16, 2) == n)
try
{
value += lookahead.substr(19);
getline(is, lookahead);
++lineNr;
++n;
int compNr;
try
{
compNr = stoi(value.substr(1, 3));
}
catch (...)
{
throw_with_nested(runtime_error("Invalid component number '" + value.substr(1, 3) + '\''));
}
int n = 2;
try
{
while (lookahead.substr(0, 6) == type and
stoi(lookahead.substr(7, 3)) == compNr and
contNr(16, 2) == n)
{
value += lookahead.substr(19);
getline(is, lookahead);
++lineNr;
++n;
}
}
catch (const invalid_argument& ex)
{
throw_with_nested(runtime_error("Invalid component number '" + lookahead.substr(7, 3) + '\''));
}
}
catch (...)
{
throw_with_nested(runtime_error("When parsing FORMUL at line " + to_string(lineNr)));
}
}
else if (type == "HETNAM" or
......@@ -1117,7 +1156,7 @@ void PDBFileParser::PreParseInput(istream& is)
ba::replace_all(k, " ", " ");
ba::trim(v);
if (iequals(v, "NONE"))
if (iequals(v, "NONE") or iequals(v, "N/A") or iequals(v, "NAN"))
mRemark200[k] = ".";
else if (not iequals(v, "NULL"))
mRemark200[k] = v;
......@@ -1161,7 +1200,7 @@ void PDBFileParser::GetNextRecord()
void PDBFileParser::Match(const string& expected)
{
if (mRec->mName != expected)
throw runtime_error("At line " + to_string(mRec->mLineNr) + ": expected record " + expected + " but found " + mRec->mName);
throw runtime_error("Expected record " + expected + " but found " + mRec->mName);
}
vector<string> PDBFileParser::SplitCSV(const string& value)
......@@ -1239,17 +1278,13 @@ void PDBFileParser::ParseTitle()
}
// SPLIT
if (mRec->is("SPLIT"))
if (mRec->is("SPLIT "))
{
// 1 - 6 Record name "SPLIT "
// 9 - 10 Continuation continuation Allows concatenation of multiple records.
// 12 - 15 IDcode idCode ID code of related datablock.
throw runtime_error("SPLIT PDB files are not supported");
// if (VERBOSE)
// Error("skipping unimplemented SPLIT record");
// GetNextRecord();
}
// CAVEAT
......@@ -1406,7 +1441,13 @@ void PDBFileParser::ParseTitle()
cat = getCategory("exptl");
for (auto si = ba::make_split_iterator(mExpMethod, ba::token_finder(ba::is_any_of(";"), ba::token_compress_on)); not si.eof(); ++si)
vector<string> crystals;
ba::split(crystals, mRemark200["NUMBER OF CRYSTALS USED"], ba::is_any_of("; "));
if (crystals.empty())
crystals.push_back("");
auto ci = crystals.begin();
for (auto si = ba::make_split_iterator(mExpMethod, ba::token_finder(ba::is_any_of(";"), ba::token_compress_on)); not si.eof(); ++si, ++ci)
{
string expMethod(si->begin(), si->end());
ba::trim(expMethod);
......@@ -1417,7 +1458,7 @@ void PDBFileParser::ParseTitle()
cat->emplace({
{ "entry_id", mStructureId },
{ "method", expMethod },
{ "crystals_number", mRemark200["NUMBER OF CRYSTALS USED"] }
{ "crystals_number", ci != crystals.end() ? *ci : "" }
});
}
......@@ -2601,6 +2642,9 @@ void PDBFileParser::ParseRemark200()
if (ambientTemp.empty())
break;
if (ba::ends_with(ambientTemp, "K"))
ambientTemp.erase(ambientTemp.length() - 1, 1);
getCategory("diffrn")->emplace({
{ "id", diffrnNr },
{ "ambient_temp", ambientTemp },
......@@ -2673,8 +2717,11 @@ void PDBFileParser::ParseRemark200()
}
int wavelengthNr = 1;
for (auto& wl: diffrnWaveLengths)
for (auto wl: diffrnWaveLengths)
{
if (ba::ends_with(wl, "A"))
wl.erase(wl.length() - 1, 1);
getCategory("diffrn_radiation_wavelength")->emplace({
{ "id", wavelengthNr++ },
{ "wavelength", wl.empty() ? "." : wl },
......@@ -3208,6 +3255,8 @@ void PDBFileParser::ConstructEntities()
if (r->is("MODEL "))
{
modelNr = r->vI(11, 14);
if (modelNr != 1)
break;
continue;
}
......@@ -3311,6 +3360,14 @@ void PDBFileParser::ConstructEntities()
for (auto r = mData; r != nullptr; r = r->mNext)
{
if (r->is("MODEL "))
{
modelNr = r->vI(11, 14);
if (modelNr != 1)
break;
continue;
}
if (r->is("ATOM ") or r->is("HETATM"))
{ // 1 - 6 Record name "ATOM "
int serial = r->vI(7, 11); // 7 - 11 Integer serial Atom serial number.
......@@ -5184,7 +5241,10 @@ void PDBFileParser::PDBChain::AlignResToSeqRes()
int x, y;
const float kGapOpen = 10, gapExtend = 0.1;
const float
kMatchReward = 5,
kMismatchCost = -10,
kGapOpen = 10, gapExtend = 0.1;
float high = 0;
size_t highX = 0, highY = 0;
......@@ -5202,9 +5262,9 @@ void PDBFileParser::PDBChain::AlignResToSeqRes()
// score for alignment
float M;
if (a.mMonId == b.mMonId)
M = 1;
M = kMatchReward;
else
M = -10000;
M = kMismatchCost;
// gap open cost is zero if the PDB ATOM records indicate that a gap
// should be here.
......
src/PDB2CifRemark3.cpp
......@@ -1185,7 +1185,11 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
string line = getNextLine();
if (line != "REFINEMENT.")
throw runtime_error("Unexpected data in REMARK 3");
{
if (VERBOSE)
cerr << "Unexpected data in REMARK 3" << endl;
return false;
}
line = getNextLine();
......@@ -1193,7 +1197,12 @@ bool Remark3Parser::parse(const string& expMethod, PDBRecord* r, cif::Datablock&
smatch m;
if (not regex_match(line, m, rxp))
throw runtime_error("Expected valid PROGRAM line in REMARK 3");
{
if (VERBOSE)
cerr << "Expected valid PROGRAM line in REMARK 3" << endl;
return false;
}
line = m[1].str();
struct programScore
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment