# recgen-rust
Rust Wrapper of ReCGen

## Logs
- v0.1.1: Apple M1 dynamically linking
- v0.1.0: intialized, ecfp-build done

## Environmental Variables
- RECGEN_INCL:  header files for compiling
- RECGEN_LIB:   lib files for compiling
- RECGEN_DB:    sqlite database file
- RECGEN_INPUT: directory where input files exist

## Using conda to install openbabel and sqlite3
openbabel requires boost.
```
conda install -y -c anaconda sqlite 
conda install -y -c conda-forge boost-cpp openbabel
ln -s /Users/qw/miniconda3/envs/openbabel/lib/libboost_iostreams.dylib /usr/local/lib
export RECGEN_INCL=~/miniconda3/envs/openbabel/include
export RECGEN_LIB=~/miniconda3/envs/openbabel/lib
```

## Findings about ReCGen
- table "_s" includes id, smarts and content of SDF.
- table "_f" includes id, smarts, fingerprints and number of overlap.

## Make building works
### from OB2.0 to OB3.0
- [OBElementTable has been removed](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#handling-of-elements-and-related-information), use OBElements:: instead
- OBAtom::GetHvyDegree() (OB 2.x GetHvyValence())
- The “Unset” methods for molecule, atom and bond flags have been removed, OBMol::UnsetAromaticPerceived() in OB 2.x is now OBMol::SetAromaticPerceived(false).

### Code improvement: 
WrapSQLit_Base deconstructor try to close the db connection. add a marker is_opened, try to close when it has been opened


## About the Databse

### what is column nof in the table frag_f?
WrapSQLite.cpp line 162, size of a vector of Overlap from BBMol.GetOverlap

how is Overlap created?
```
void Insert(deque<ECMol> &frags, int &nn)
bmol.SetOverlapFragments_Ref();
const int ECMol::he2[12]={85,100,101,102,104,105,106,107,108,109,110,111};
// At, Fm, Md, No, Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg
while (tmp.find("[No]") != string::npos) tmp.replace(tmp.find("[No]"), 3, "[A;!R]");
while (tmp.find("[Fm]") != string::npos) tmp.replace(tmp.find("[Fm]"), 4, "a");
while (tmp.find("[Md]") != string::npos) tmp.replace(tmp.find("[Md]"), 4, "[A;R]");
while (tmp.find("[At]") != string::npos) tmp.replace(tmp.find("[At]"), 4, "*");
void ECMol::MkSMARTS(bool AddH) // specific SMART rule
void BBMol::SetOverlapFragments_Ref()
void SetOverlapFragments_Ref(int ele);
void SetOverlapFragments_Ref(string attr, int val);
void SetOverlapFragments_Fra();
```