From f5acb7f9710b308f071bdbce0d50f877481e9013 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 5 Jan 2024 15:49:11 +0100
Subject: [PATCH] feat: optionally ignore reserved compounds
---
modules/conop/src/chemdict_tool.cc | 24 +++++++++++++--------
modules/io/src/mol/chemdict_parser.cc | 30 +++++++++++++++++++++++++--
modules/io/src/mol/chemdict_parser.hh | 8 +++++--
3 files changed, 49 insertions(+), 13 deletions(-)
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 404f50b8a..eff12c73e 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -35,30 +35,36 @@ using namespace ost;
void PrintUsage()
{
- std::cout << "usage: chemdict_tool action <compound-dict> <db> (pdb|charmm|amber|opls)" << std::endl;
+ std::cout << "usage: chemdict_tool ACTION <compound-dict> <db> [DIALECT] [OPTIONS]" << std::endl;
std::cout << "supported actions are:" << std::endl;
std::cout << " create - creates a new db " << std::endl;
std::cout << " update - update existing db" << std::endl;
+ std::cout << "supported dialects are: pdb, charmm, amber, opls" << std::endl;
+ std::cout << "supported options are:" << std::endl;
+ std::cout << " -i - ignore compounds reserved by the PDB (01-99, DRG, INH, LIG)" << std::endl;
}
int main(int argc, char const *argv[])
{
- if (argc!=4 && argc!=5) {
+ if (argc!=4 && argc!=5 && argc!=6) {
PrintUsage();
return 0;
}
conop::Compound::Dialect dialect=conop::Compound::PDB;
- if (argc==5) {
- String format=argv[4];
+ bool ignore_reserved=false;
+ for (int i = 4; i < argc; i++) {
+ String param=argv[i];
- if (format=="charmm") {
+ if (param=="charmm") {
dialect=conop::Compound::CHARMM;
- } else if (format=="pdb") {
+ } else if (param=="pdb") {
dialect=conop::Compound::PDB;
- } else if (format=="opls") {
+ } else if (param=="opls") {
dialect=conop::Compound::OPLS;
- } else if (format=="amber") {
+ } else if (param=="amber") {
dialect=conop::Compound::AMBER;
+ } else if (param=="-i") {
+ ignore_reserved=true;
} else {
PrintUsage();
return 0;
@@ -75,7 +81,7 @@ int main(int argc, char const *argv[])
filtered_istream.push(boost::iostreams::gzip_decompressor());
}
filtered_istream.push(istream);
- io::ChemdictParser cdp(filtered_istream, dialect);
+ io::ChemdictParser cdp(filtered_istream, dialect, ignore_reserved);
conop::CompoundLibPtr compound_lib;
bool in_mem=false;
if (!strncmp(argv[1], "create", 6)) {
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index a6e6b71db..d838d232a 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -17,8 +17,13 @@ bool ChemdictParser::OnBeginData(const StringRef& data_name)
std::cout << last_ << std::flush;
}
atom_map_.clear();
- insert_=true;
- return true;
+ if (ignore_reserved_ && IsNameReserved(data_name)) {
+ insert_=false;
+ }
+ else {
+ insert_=true;
+ }
+ return true;
}
bool ChemdictParser::OnBeginLoop(const StarLoopDesc& header)
@@ -252,4 +257,25 @@ void ChemdictParser::InitPDBXTypeMap()
xtm_["?"]=mol::ChemType(mol::ChemType::UNKNOWN);
}
+bool ChemdictParser::IsNameReserved(const StringRef& data_name)
+{
+ // This checks if the compound name is one of the reserved name that will
+ // never be used in the PDB. See
+ // https://www.rcsb.org/news/feature/630fee4cebdf34532a949c34
+ if ( // Check if in range 01-99
+ (data_name.length() == 2 &&
+ data_name[0] >= '0' && data_name[0] <= '9' &&
+ data_name[1] >= '0' && data_name[1] <= '9' &&
+ data_name != StringRef("00", 2)) ||
+ data_name == StringRef("DRG", 3) ||
+ data_name == StringRef("INH", 3) ||
+ data_name == StringRef("LIG", 3)
+ )
+ {
+ std::cout << "Ignoring reserved compound " << data_name << std::endl;
+ return true;
+ }
+ return false;
+}
+
}}
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
index f33ee72fb..00a395b98 100644
--- a/modules/io/src/mol/chemdict_parser.hh
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -40,9 +40,11 @@ typedef enum {
class DLLEXPORT_OST_IO ChemdictParser : public StarParser {
public:
- ChemdictParser(std::istream& stream, conop::Compound::Dialect dialect):
+ ChemdictParser(std::istream& stream, conop::Compound::Dialect dialect,
+ bool ignore_reserved=false):
StarParser(stream), compound_(new conop::Compound("UNK")),
- last_(0), loop_type_(DONT_KNOW), dialect_(dialect)
+ last_(0), loop_type_(DONT_KNOW), dialect_(dialect),
+ ignore_reserved_(ignore_reserved)
{
this->InitTypeMap();
this->InitPDBXTypeMap();
@@ -66,6 +68,7 @@ public:
private:
void InitTypeMap();
void InitPDBXTypeMap();
+ bool IsNameReserved(const StringRef& data_name);
conop::CompoundLibPtr lib_;
conop::CompoundPtr compound_;
typedef enum {
@@ -92,6 +95,7 @@ private:
LoopType loop_type_;
conop::AtomSpec atom_;
conop::Compound::Dialect dialect_;
+ bool ignore_reserved_;
};
--
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