diff --git a/Atom.cpp b/Atom.cpp index c187169..d46c1d0 100644 --- a/Atom.cpp +++ b/Atom.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Atom.h b/Atom.h index d161604..985ad78 100644 --- a/Atom.h +++ b/Atom.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _ATOM_GUARD diff --git a/AtomT.cpp b/AtomT.cpp index f0f9c21..9bbcab3 100644 --- a/AtomT.cpp +++ b/AtomT.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/AtomT.h b/AtomT.h index 2291e2f..a259460 100644 --- a/AtomT.h +++ b/AtomT.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _ATOM_TYPE_GUARD diff --git a/Bond.cpp b/Bond.cpp index d73ef5f..0343cb1 100644 --- a/Bond.cpp +++ b/Bond.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Bond.h b/Bond.h index bacf7d0..df283cd 100644 --- a/Bond.h +++ b/Bond.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _BOND_GUARD diff --git a/ConnectableAtom.cpp b/ConnectableAtom.cpp index c365252..92540f0 100644 --- a/ConnectableAtom.cpp +++ b/ConnectableAtom.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include "ConnectableAtom.h" diff --git a/ConnectableAtom.h b/ConnectableAtom.h index 936c60c..18e1922 100644 --- a/ConnectableAtom.h +++ b/ConnectableAtom.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _CONNECTABLE_ATOM_GUARD diff --git a/Constants.cpp b/Constants.cpp index 3d15def..9098b45 100644 --- a/Constants.cpp +++ b/Constants.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include "Constants.h" diff --git a/Constants.h b/Constants.h index ecfa273..d8bea71 100644 --- a/Constants.h +++ b/Constants.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _CONSTANTS_GUARD diff --git a/EdgeAggregator.h b/EdgeAggregator.h index bd1219e..335aed5 100644 --- a/EdgeAggregator.h +++ b/EdgeAggregator.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _EDGE_AGGREGATOR_GUARD diff --git a/EdgeAnnotation.h b/EdgeAnnotation.h index da72597..52cea43 100644 --- a/EdgeAnnotation.h +++ b/EdgeAnnotation.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _EDGE_ANNOTATION_GUARD diff --git a/EdgeDatabase.h b/EdgeDatabase.h index 31d4f9e..96d53c1 100644 --- a/EdgeDatabase.h +++ b/EdgeDatabase.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _EDGE_DATABASE_GUARD diff --git a/FixedSortedList.h b/FixedSortedList.h index 913aee8..73b48f0 100644 --- a/FixedSortedList.h +++ b/FixedSortedList.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _FIXED_SORTED_LIST_GUARD diff --git a/FragmentEdgeMap.cpp b/FragmentEdgeMap.cpp index 1260e57..f6fc552 100644 --- a/FragmentEdgeMap.cpp +++ b/FragmentEdgeMap.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include "FragmentEdgeMap.h" diff --git a/FragmentEdgeMap.h b/FragmentEdgeMap.h index 3b43dc6..827442c 100644 --- a/FragmentEdgeMap.h +++ b/FragmentEdgeMap.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _FRAGMENT_EDGE_MAP_GUARD diff --git a/IdFactory.cpp b/IdFactory.cpp index 2fbe90b..dae9e19 100644 --- a/IdFactory.cpp +++ b/IdFactory.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ diff --git a/IdFactory.h b/IdFactory.h index d9ad2f1..3f66a65 100644 --- a/IdFactory.h +++ b/IdFactory.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _ID_FACTORY_GUARD diff --git a/Instantiator.cpp b/Instantiator.cpp index f561d90..2e1f55d 100644 --- a/Instantiator.cpp +++ b/Instantiator.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Instantiator.h b/Instantiator.h index d7b48af..74b0ffc 100644 --- a/Instantiator.h +++ b/Instantiator.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _INSTANTIATOR_GUARD diff --git a/LevelHashMap.h b/LevelHashMap.h index ac62ae4..bf8d708 100644 --- a/LevelHashMap.h +++ b/LevelHashMap.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _LEVEL_HASH_MAP_GUARD diff --git a/LikeMoleculesContainer.h b/LikeMoleculesContainer.h index 0fcda8b..f760289 100644 --- a/LikeMoleculesContainer.h +++ b/LikeMoleculesContainer.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _LIKE_MOLECULES_CONTAINER_GUARD diff --git a/Linker.cpp b/Linker.cpp index 7c4bc92..4650c18 100644 --- a/Linker.cpp +++ b/Linker.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Linker.h b/Linker.h index 9d69c4f..8376efa 100644 --- a/Linker.h +++ b/Linker.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _LINKER_GUARD diff --git a/LinkerConnectableAtom.cpp b/LinkerConnectableAtom.cpp index 8c44d91..f25bf84 100644 --- a/LinkerConnectableAtom.cpp +++ b/LinkerConnectableAtom.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/LinkerConnectableAtom.h b/LinkerConnectableAtom.h index 531f32c..051fe5b 100644 --- a/LinkerConnectableAtom.h +++ b/LinkerConnectableAtom.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _LINKER_CONNECTABLE_ATOM_GUARD diff --git a/Main.cpp b/Main.cpp index 5e8377c..5b0467d 100644 --- a/Main.cpp +++ b/Main.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Makefile b/Makefile index 53c01f0..e5ed9c2 100644 --- a/Makefile +++ b/Makefile @@ -15,19 +15,27 @@ # along with synth. If not, see . # +CC=g++ +OPT= -O2 + +#Path to openbabel directory which contains the header (.h) files +OB_INC= ${HOME}/apps/openbabel-2.3.2-install/include/openbabel-2.0/ + +#Path to openbabel directory which contains the (.so) files +OB_LIB= ${HOME}/apps/openbabel-2.3.2-install/lib/ + + +GSL_LIB=/usr/lib64/ +GSL_INC=/usr/include/ +EXE = esynth + + +CFLAGS= $(OPT) -I$(GSL_INC) -L$(GSL_LIB) -I$(OB_INC) -L$(OB_LIB) -lz -lgsl -lgslcblas -lopenbabel -lpthread + + + +ODIR=./obj -OB_INC=../openbabel-2.3.2/include/ -OB_LIB_DIR=. -OB_LIB=openbabel -#GSL_DIR=/root/gsl-1.16/ -GSL_LIB=gsl -CBLAS_LIB=gslcblas -ZLIB=z - -IDIR =./ -CC=g++ -OPT= -O2 -g # -p -CFLAGS= $(OPT) -I$(IDIR) -I$(OB_INC) -L$(OB_LIB_DIR) -l$(ZLIB) -l$(GSL_LIB) -l$(CBLAS_LIB) -l$(OB_LIB) -lpthread ODIR=./obj DEPS = EdgeAggregator.h \ @@ -100,7 +108,7 @@ OBJ = $(patsubst %,$(ODIR)/%,$(_OBJ)) $(ODIR)/%.o: %.cpp $(DEPS) $(CC) -c -o $@ $< $(CFLAGS) -synth: $(OBJ) +$(EXE): $(OBJ) $(CC) $^ $(CFLAGS) -o $@ @@ -145,4 +153,4 @@ convertToSMI: $(TOSMI_OBJ) .PHONY: clean clean: - rm -f $(ODIR)/*.o *~ core synth.exe synth.exe.stackdump $(INCDIR)/*~ + rm -f $(ODIR)/*.o *~ core $(EXE) synth.stackdump $(INCDIR)/*~ diff --git a/MinimalMolecule.h b/MinimalMolecule.h index f4bf1ea..4dbc896 100644 --- a/MinimalMolecule.h +++ b/MinimalMolecule.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _MINIMAL_MOLECULE_GUARD diff --git a/Molecule.cpp b/Molecule.cpp index 78e8575..52ab547 100644 --- a/Molecule.cpp +++ b/Molecule.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include @@ -536,10 +536,14 @@ std::vector* Molecule::Compose(const Molecule& that) const std::vector* newMolecules = new std::vector(); // - // Pre-emptively check the molecular weight to see if there is a benefit - // to composing these molecules. + // Pre-emptively check the Lipinski characteristics to see if there is a benefit + // to composing these molecules; only perform this check if the user specified + // Lipinski compliance. // - if (Molecule::willExceedAdditiveThresholds(*this, that)) return newMolecules; + if (Options::USE_LIPINSKI) + { + if (Molecule::willExceedAdditiveThresholds(*this, that)) return newMolecules; + } // // Antecedent ids diff --git a/Molecule.h b/Molecule.h index f7d4b17..48768b5 100644 --- a/Molecule.h +++ b/Molecule.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _MOLECULE_GUARD @@ -39,7 +39,7 @@ #include "SmiMinimalMolecule.h" #include "EdgeDatabase.h" #include "Utilities.h" - +using namespace OpenBabel; class EdgeAggregator; class Rigid; diff --git a/MoleculeHashHypergraph.h b/MoleculeHashHypergraph.h index f845357..4bc68b7 100644 --- a/MoleculeHashHypergraph.h +++ b/MoleculeHashHypergraph.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _MOLECULE_HASH_HYPERGRAPH_GUARD diff --git a/OBWriter.cpp b/OBWriter.cpp index f1b3ffd..4a6fd5f 100644 --- a/OBWriter.cpp +++ b/OBWriter.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/OBWriter.h b/OBWriter.h index bbeab17..bea5193 100644 --- a/OBWriter.h +++ b/OBWriter.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _OB_WRITER_GUARD diff --git a/Options.cpp b/Options.cpp index 4144928..a4cb145 100644 --- a/Options.cpp +++ b/Options.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include @@ -34,6 +34,7 @@ bool Options::THREADED = false; bool Options::SERIAL = true; bool Options::OPENBABEL = true; bool Options::SMI_ONLY = false; +bool Options::USE_LIPINSKI = false; unsigned Options::OBGEN_THREAD_POOL_SIZE = 15; //unsigned Options::SMI_LEVEL_BOUND = 3; unsigned Options::PROBABILITY_PRUNE_LEVEL_START = 5; @@ -243,6 +244,12 @@ bool Options::handleOption(int& index) return true; } + if (strncmp(argv[index], "-lip", 4) == 0) + { + if (strcmp(argv[index], "-lip") == 0) + USE_LIPINSKI = true; + return true; + } /* diff --git a/Options.h b/Options.h index e6a7b4d..67d1a9e 100644 --- a/Options.h +++ b/Options.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _OPTIONS_GUARD @@ -43,6 +43,7 @@ class Options static bool THREADED; static bool SERIAL; static bool OPENBABEL; + static bool USE_LIPINSKI; //static unsigned SMI_LEVEL_BOUND; static unsigned PROBABILITY_PRUNE_LEVEL_START; static unsigned int OBGEN_THREAD_POOL_SIZE; diff --git a/README b/README index 29d9f3e..ded7348 100644 --- a/README +++ b/README @@ -1,21 +1,25 @@ Compiling: -The following libraries are required: - * openbabel (we used 2.3.2); modify the Makefile to update path accordingly. - * gsl (1.16) +The following libraries are required: modify the Makefile to update path accordingly. + * openbabel (we used 2.3.2) http://sourceforge.net/projects/openbabel/?source=typ_redirect + * gsl (1.16) http://www.linuxfromscratch.org/blfs/view/svn/general/gsl.html * gslcblas * z +NOTE: Openbabel.2.3.2 should be compiled from source code. (You might need to remove the generic instalation of OpenBabel to prevent path conflict) Object Files: All object files are compiled and places in the ./obj directory. 'make clean' will empty this folder. - +NOTE:before executing the esynth file, export LD_LIBRARY_PATH +example: + export LD_LIBRARY_PATH=${HOME}/apps/openbabel-2.3.2-install/lib/ + export LD_LIBRARY_PATH[to /gsl/lib] Executable: -'make' will create the synth application. +'make' will create the esynth application. All output of SMI molecules are dumped into the output directory (synth_output_dir). Each file will contain 250000 SMI molecules and wil l be compressed using the zlib compression algorithm. @@ -23,20 +27,33 @@ l be compressed using the zlib compression algorithm. Running (input): -./synth is the executable. +./esynth is the executable. Comamand-line arguments are specified with a prefix '-' and may include the following: * -serial : specified serial execution * -threaded : specifies a threaded execution; do not use. - * -odir specifies the name of the directory where output will be placed (./); default is ./synth_output_dir + * -odir specifies the name of the directory where output will be placed (./); default is ./esynth_output_dir * -tc defines the tanimoto coefficient as a value between 0 and 1; default is 0.95. * -smi-only ; species all molecules are to be handled as SMI objects. * -nopen ; specifies OpenBabel will not be used except for the first input from the SDF files and the resulting output in SMI format. * -prob-level ; specifies what level to begin pruning molecules for probability purposes. + * -lip ; Allows the user to turn on Lipinski compliance of molecules (Lipinski compliance defaults to off). -A typical run: ./synth -nopen -serial -smi-only - -Sample: ./synth -nopen -serial -smi-only -prob-level 2 l-test-linker1.sdf l-test-linker2.sdf r-test-rigid1.sdf r-test-rigid2.sdf +A typical run: ./esynth -nopen -serial -smi-only +Sample: ./esynth -nopen -serial -smi-only -prob-level 2 l-test-linker1.sdf l-test-linker2.sdf r-test-rigid1.sdf r-test-rigid2.sdf All data files (*.sdf) must exist in the same directory as the executable. + +Example run: +go to test directory located in example-fragments in esynth [esynth/example-fragments/test] + +PATH_TO_esynth/esynth `cat list` -nopen + +This is the simplest run, options can be added as explained above. The output smi molecules are in synth_output_dir + + + + + + diff --git a/README~ b/README~ new file mode 100644 index 0000000..c290e3f --- /dev/null +++ b/README~ @@ -0,0 +1,58 @@ +Compiling: + +The following libraries are required: modify the Makefile to update path accordingly. + * openbabel (we used 2.3.2) http://sourceforge.net/projects/openbabel/?source=typ_redirect + * gsl (1.16) http://www.linuxfromscratch.org/blfs/view/svn/general/gsl.html + * gslcblas + * z + +NOTE: Openbabel.2.3.2 should be compiled from source code. (You might need to remove the generic instalation of OpenBabel to prevent path conflict) + +Object Files: + +All object files are compiled and places in the ./obj directory. 'make clean' will empty this folder. + +NOTE:before executing the esynth file, export LD_LIBRARY_PATH +example: + export LD_LIBRARY_PATH=${HOME}/apps/openbabel-2.3.2-install/lib/ + export LD_LIBRARY_PATH[to /gsl/lib] + +Executable: + +'make' will create the esynth application. + +All output of SMI molecules are dumped into the output directory (synth_output_dir). Each file will contain 250000 SMI molecules and wil +l be compressed using the zlib compression algorithm. + + +Running (input): + +./esynth is the executable. + +Comamand-line arguments are specified with a prefix '-' and may include the following: + * -serial : specified serial execution + * -threaded : specifies a threaded execution; do not use. + * -odir specifies the name of the directory where output will be placed (./); default is ./esynth_output_dir + * -tc defines the tanimoto coefficient as a value between 0 and 1; default is 0.95. + * -smi-only ; species all molecules are to be handled as SMI objects. + * -nopen ; specifies OpenBabel will not be used except for the first input from the SDF files and the resulting output in SMI format. + * -prob-level ; specifies what level to begin pruning molecules for probability purposes. + +A typical run: ./esynth -nopen -serial -smi-only + +Sample: ./esynth -nopen -serial -smi-only -prob-level 2 l-test-linker1.sdf l-test-linker2.sdf r-test-rigid1.sdf r-test-rigid2.sdf + +All data files (*.sdf) must exist in the same directory as the executable. + +Example run: +go to test directory located in example-fragments in esynth [esynth/example-fragments/test] + +PATH_TO_esynth/esynth `cat list` -nopen + +This is the simplest run, options can be added as explained above. The output smi molecules are in synth_output_dir + + + + + + diff --git a/Rigid.cpp b/Rigid.cpp index 972db89..96ccc88 100644 --- a/Rigid.cpp +++ b/Rigid.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Rigid.h b/Rigid.h index b6c0e73..c09851e 100644 --- a/Rigid.h +++ b/Rigid.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _RIGID_GUARD diff --git a/RigidConnectableAtom.cpp b/RigidConnectableAtom.cpp index 725dd7c..8a951c4 100644 --- a/RigidConnectableAtom.cpp +++ b/RigidConnectableAtom.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/RigidConnectableAtom.h b/RigidConnectableAtom.h index 77267e8..19b4e8b 100644 --- a/RigidConnectableAtom.h +++ b/RigidConnectableAtom.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _RIGID_CONNECTABLE_ATOM_GUARD diff --git a/SimpleFragmentGraph.h b/SimpleFragmentGraph.h index 8af003d..0ce4579 100644 --- a/SimpleFragmentGraph.h +++ b/SimpleFragmentGraph.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _SIMPLE_FRAGMENT_GRAPH_GUARD diff --git a/SmiMinimalMolecule.h b/SmiMinimalMolecule.h index 0ae198e..c51c816 100644 --- a/SmiMinimalMolecule.h +++ b/SmiMinimalMolecule.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _SMI_MINIMAL_MOLECULE_GUARD diff --git a/Thread_Pool.h b/Thread_Pool.h index 1f8419b..3917355 100644 --- a/Thread_Pool.h +++ b/Thread_Pool.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _THREAD_POOL_GUARD diff --git a/TimedHashMap.cpp b/TimedHashMap.cpp index 8bac8b1..e696a69 100644 --- a/TimedHashMap.cpp +++ b/TimedHashMap.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include "TimedHashMap.h" diff --git a/TimedHashMap.h b/TimedHashMap.h index 9025346..fa20858 100644 --- a/TimedHashMap.h +++ b/TimedHashMap.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _TIMED_HASH_MAP_GUARD diff --git a/TimedLikeValueContainer.cpp b/TimedLikeValueContainer.cpp index ed3be17..2b4b098 100644 --- a/TimedLikeValueContainer.cpp +++ b/TimedLikeValueContainer.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include "TimedLikeValueContainer.h" diff --git a/TimedLikeValueContainer.h b/TimedLikeValueContainer.h index b2dfec2..be30b1e 100644 --- a/TimedLikeValueContainer.h +++ b/TimedLikeValueContainer.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _TIMED_LIKE_VALUE_CONTAINER_GUARD diff --git a/Utilities.cpp b/Utilities.cpp index 87d8277..57033e3 100644 --- a/Utilities.cpp +++ b/Utilities.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Utilities.h b/Utilities.h index cbdc442..db5a487 100644 --- a/Utilities.h +++ b/Utilities.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _UTILITIES_GUARD diff --git a/Validator.cpp b/Validator.cpp index 75b87a1..f13ee92 100644 --- a/Validator.cpp +++ b/Validator.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/Validator.h b/Validator.h index a28f4c6..a0ddaa9 100644 --- a/Validator.h +++ b/Validator.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _VALIDATOR_GUARD diff --git a/compliantwriter.cpp b/compliantwriter.cpp index b8790f3..4e16f30 100644 --- a/compliantwriter.cpp +++ b/compliantwriter.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/convertToSMI.cpp b/convertToSMI.cpp index 54f8ae8..3ccb7bb 100644 --- a/convertToSMI.cpp +++ b/convertToSMI.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include diff --git a/example-fragments/linkers/l-20914.sdf b/example-fragments/linkers/l-20914.sdf new file mode 100644 index 0000000..dc48dcf --- /dev/null +++ b/example-fragments/linkers/l-20914.sdf @@ -0,0 +1,21 @@ +z_outfile.coutfile001000.pdb + OpenBabel08201417113D + + 4 3 0 0 0 0 0 0 0 0999 V2000 + 5.9910 -1.9820 0.6350 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3110 -1.6010 1.5690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1520 -0.9520 1.3380 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7110 -0.7070 -0.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 1 0 0 0 0 +M END + + +> +0 O.2 +1 C.2 +1 N.am +3 C.3 + +$$$$ diff --git a/example-fragments/linkers/l-24839.sdf b/example-fragments/linkers/l-24839.sdf new file mode 100644 index 0000000..b8a4436 --- /dev/null +++ b/example-fragments/linkers/l-24839.sdf @@ -0,0 +1,18 @@ +z_outfile.coutfile001000.pdb + OpenBabel08201417143D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 4.3750 -1.6590 -2.8820 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8630 -0.6000 -2.2230 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9390 0.5690 -3.0660 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 3 2 1 0 0 0 0 +M END + + +> +2 N.3 +2 C.3 +1 S.3 + +$$$$ diff --git a/example-fragments/linkers/l-2515.sdf b/example-fragments/linkers/l-2515.sdf new file mode 100644 index 0000000..d5bc51e --- /dev/null +++ b/example-fragments/linkers/l-2515.sdf @@ -0,0 +1,18 @@ +z_outfile.coutfile001000.pdb + OpenBabel08201417093D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 1.7860 -4.8900 0.6080 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.7700 -4.1630 0.5810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8790 -4.6260 0.8100 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 3 2 0 0 0 0 +M END + + +> +0 O.co2 +1 C.2 +1 O.co2 + +$$$$ diff --git a/example-fragments/linkers/l-26242.sdf b/example-fragments/linkers/l-26242.sdf new file mode 100644 index 0000000..92dbd44 --- /dev/null +++ b/example-fragments/linkers/l-26242.sdf @@ -0,0 +1,21 @@ +z_outfile.coutfile003000.pdb + OpenBabel08201417043D + + 4 3 0 0 0 0 0 0 0 0999 V2000 + 0.0240 0.0350 2.3400 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0220 -0.6590 1.1230 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0180 1.5030 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 3 4 1 0 0 0 0 + 3 2 2 0 0 0 0 +M END + + +> +2 N.pl3 +0 N.2 +1 C.2 +3 C.3 + +$$$$ diff --git a/example-fragments/linkers/l-28568.sdf b/example-fragments/linkers/l-28568.sdf new file mode 100644 index 0000000..32638cf --- /dev/null +++ b/example-fragments/linkers/l-28568.sdf @@ -0,0 +1,19 @@ +z_outfile.coutfile003000.pdb + OpenBabel08201417083D + + 3 3 0 0 0 0 0 0 0 0999 V2000 + 0.1800 -6.5120 8.6920 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0080 -6.8610 10.1700 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3690 -7.0040 9.5190 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 3 1 0 0 0 0 + 1 2 1 0 0 0 0 + 3 2 1 0 0 0 0 +M END + + +> +2 C.3 +2 C.3 +2 C.3 + +$$$$ diff --git a/example-fragments/linkers/l-29718.sdf b/example-fragments/linkers/l-29718.sdf new file mode 100644 index 0000000..999b8a8 --- /dev/null +++ b/example-fragments/linkers/l-29718.sdf @@ -0,0 +1,21 @@ +z_outfile.coutfile001000.pdb + OpenBabel08201417093D + + 4 3 0 0 0 0 0 0 0 0999 V2000 + -1.4330 -0.5340 0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0190 1.5260 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6900 -0.4780 -1.2070 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2 3 1 0 0 0 0 + 2 1 1 0 0 0 0 + 4 2 1 0 0 0 0 +M END + + +> +3 C.3 +1 C.3 +3 C.3 +2 N.3 + +$$$$ diff --git a/example-fragments/linkers/l-5834.sdf b/example-fragments/linkers/l-5834.sdf new file mode 100644 index 0000000..1658658 --- /dev/null +++ b/example-fragments/linkers/l-5834.sdf @@ -0,0 +1,12 @@ +z_outfile.coutfile003000.pdb + OpenBabel08201417143D + + 1 0 0 0 0 0 0 0 0 0999 V2000 + -7.4970 -1.6430 -1.7410 C 0 0 0 0 0 0 0 0 0 0 0 0 +M END + + +> +4 C.3 + +$$$$ diff --git a/example-fragments/linkers/l-7932.sdf b/example-fragments/linkers/l-7932.sdf new file mode 100644 index 0000000..d1ac0b7 --- /dev/null +++ b/example-fragments/linkers/l-7932.sdf @@ -0,0 +1,21 @@ +z_outfile.coutfile001000.pdb + OpenBabel08201417103D + + 4 3 0 0 0 0 0 0 0 0999 V2000 + -0.0180 1.4650 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6000 -0.5160 -1.2390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7060 -0.5270 1.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 2 1 0 0 0 0 +M END + + +> +3 C.3 +0 N.3 +3 C.3 +3 C.3 + +$$$$ diff --git a/example-fragments/linkers/l-8012.sdf b/example-fragments/linkers/l-8012.sdf new file mode 100644 index 0000000..4bd66a7 --- /dev/null +++ b/example-fragments/linkers/l-8012.sdf @@ -0,0 +1,15 @@ +z_outfile.coutfile002001.pdb + OpenBabel08201417133D + + 2 1 0 0 0 0 0 0 0 0999 V2000 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0160 1.3060 0.0090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 3 0 0 0 0 +M END + + +> +1 C.1 +1 C.1 + +$$$$ diff --git a/example-fragments/rigids/r-11574.sdf b/example-fragments/rigids/r-11574.sdf new file mode 100644 index 0000000..a7149d1 --- /dev/null +++ b/example-fragments/rigids/r-11574.sdf @@ -0,0 +1,44 @@ +uz4.pdb-outfile00 + OpenBabel08201417103D + + 10 11 0 0 0 0 0 0 0 0999 V2000 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2140 -0.6840 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3960 0.0060 -0.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3910 1.4030 -0.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7640 1.9270 -0.0240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7150 0.7540 -0.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0790 3.0980 -0.0200 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1650 2.0890 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.8210 -0.4930 -0.0370 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0170 1.3870 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 10 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 9 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 8 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 2 0 0 0 0 + 6 9 2 0 0 0 0 + 8 10 2 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.2 +C.2 +O.2 +C.ar +C.2 +C.ar + +> +1 O.3 + +$$$$ diff --git a/example-fragments/rigids/r-15347.sdf b/example-fragments/rigids/r-15347.sdf new file mode 100644 index 0000000..556133b --- /dev/null +++ b/example-fragments/rigids/r-15347.sdf @@ -0,0 +1,32 @@ +uz4.pdb-outfile01 + OpenBabel08201417063D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 12.8080 -5.7880 1.4640 S 0 0 0 0 0 0 0 0 0 0 0 0 + 11.3470 -4.9740 1.8340 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.8060 -4.6830 3.0430 N 0 0 0 0 0 0 0 0 0 0 0 0 + 9.6050 -4.0130 3.0840 N 0 0 0 0 0 0 0 0 0 0 0 0 + 9.0010 -3.6640 1.9740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 10.1210 -4.2870 0.7310 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 2 6 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 +M END + + +> +S.2 +C.ar +N.ar +N.ar +C.ar +S.2 + +> +3 C.3 +5 C.ar + +$$$$ diff --git a/example-fragments/rigids/r-16928.sdf b/example-fragments/rigids/r-16928.sdf new file mode 100644 index 0000000..5a3661c --- /dev/null +++ b/example-fragments/rigids/r-16928.sdf @@ -0,0 +1,30 @@ +uz4.pdb-outfile00 + OpenBabel08201417103D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 5.4700 3.2460 -0.0290 N 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1390 1.9360 -0.0500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9700 0.9310 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7370 1.8060 -0.0240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.0910 3.0480 -0.0150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 5 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 +M END + + +> +N.am +C.3 +C.3 +C.2 +N.2 + +> +1 C.2 +2 C.ar +4 C.ar + +$$$$ diff --git a/example-fragments/rigids/r-21719.sdf b/example-fragments/rigids/r-21719.sdf new file mode 100644 index 0000000..7586b37 --- /dev/null +++ b/example-fragments/rigids/r-21719.sdf @@ -0,0 +1,41 @@ +uz4.pdb-outfile00 + OpenBabel08201417103D + + 9 10 0 0 0 0 0 0 0 0999 V2000 + 5.0690 -2.5950 -0.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.7600 -2.9210 -1.1650 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.0970 -3.3320 -0.7290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.1010 -3.2140 0.6730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2540 -3.5400 1.3810 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3730 -3.9730 0.7040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3630 -4.0870 -0.6790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2420 -3.7720 -1.3940 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.8560 -2.7590 1.0460 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 9 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 8 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 9 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +N.ar + +> +1 C.3 + +$$$$ diff --git a/example-fragments/rigids/r-21887.sdf b/example-fragments/rigids/r-21887.sdf new file mode 100644 index 0000000..b284ea6 --- /dev/null +++ b/example-fragments/rigids/r-21887.sdf @@ -0,0 +1,50 @@ +uz4.pdb-outfile00 + OpenBabel08201417083D + + 12 13 0 0 0 0 0 0 0 0999 V2000 + 9.5710 0.3520 -0.0750 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4410 -0.4010 -0.0730 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2030 0.2200 -0.0570 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.0480 -0.5490 -0.0550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1540 -1.9500 -0.0690 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9130 -2.7480 -0.0670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6860 -2.0430 -0.0500 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6950 -0.6830 -0.0370 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9440 -3.9670 -0.0790 O 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4080 -2.5600 -0.0850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8300 0.0320 -0.0450 O 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5370 -1.7910 -0.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 12 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 11 1 0 0 0 0 + 5 10 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 9 2 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 11 1 0 0 0 0 + 10 12 1 0 0 0 0 +M END + + +> +O.3 +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.2 +C.ar +O.2 +C.ar + +> +8 C.ar + +$$$$ diff --git a/example-fragments/rigids/r-2583.sdf b/example-fragments/rigids/r-2583.sdf new file mode 100644 index 0000000..41f0bef --- /dev/null +++ b/example-fragments/rigids/r-2583.sdf @@ -0,0 +1,67 @@ +uz4.pdb-outfile00 + OpenBabel08201417133D + + 17 19 0 0 0 0 0 0 0 0999 V2000 + -1.0500 -10.3780 3.8740 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6630 -9.1180 4.2880 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3000 -8.1490 3.3450 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3370 -8.4700 1.9880 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1120 -7.2700 0.7790 S 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0900 -5.6990 1.5740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0910 -5.6150 2.9680 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0700 -4.3540 3.5830 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0500 -3.2170 2.8290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0520 -3.3000 1.4330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0660 -4.5520 0.8120 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9340 -7.2530 -0.1830 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4640 -7.5310 0.4290 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7240 -9.7330 1.5850 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1160 -6.8180 3.8110 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5020 -6.7060 4.9580 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0800 -10.6860 2.5200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 17 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 3 15 1 0 0 0 0 + 4 5 1 0 0 0 0 + 4 14 2 0 0 0 0 + 5 12 2 0 0 0 0 + 5 13 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 11 2 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 7 15 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 11 10 1 0 0 0 0 + 14 17 1 0 0 0 0 + 15 16 2 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +S.O2 +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.2 +O.2 +C.ar +C.2 +O.2 +C.ar + +> +1 O.3 +10 C.ar + +$$$$ diff --git a/example-fragments/rigids/r-28607.sdf b/example-fragments/rigids/r-28607.sdf new file mode 100644 index 0000000..b42d5be --- /dev/null +++ b/example-fragments/rigids/r-28607.sdf @@ -0,0 +1,56 @@ +uz4.pdb-outfile00 + OpenBabel08201417123D + + 14 15 0 0 0 0 0 0 0 0999 V2000 + -0.3170 -4.4970 1.2570 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.8480 -3.1340 1.1780 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5910 -2.6470 2.1820 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1230 -1.4240 2.2150 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9850 -0.5160 1.2330 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1800 -0.8800 0.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1270 -0.7910 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8830 -2.0640 -0.0120 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0180 1.4610 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4990 0.5780 1.3310 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9070 -1.0470 3.3940 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7940 -3.3740 3.1350 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5660 -2.3040 -0.0040 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 14 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 3 13 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 12 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 11 2 0 0 0 0 + 6 14 2 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 10 1 0 0 0 0 + 8 9 2 0 0 0 0 + 9 14 1 0 0 0 0 +M END + + +> +C.3 +N.ar +C.ar +N.ar +C.ar +C.ar +N.ar +C.ar +N.ar +C.3 +O.2 +C.3 +O.2 +C.ar + +> +8 C.2 + +$$$$ diff --git a/example-fragments/rigids/r-29684.sdf b/example-fragments/rigids/r-29684.sdf new file mode 100644 index 0000000..280de01 --- /dev/null +++ b/example-fragments/rigids/r-29684.sdf @@ -0,0 +1,57 @@ +uz4.pdb-outfile00 + OpenBabel08201417103D + + 14 16 0 0 0 0 0 0 0 0999 V2000 + 2.6310 -4.5510 -0.0480 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4490 -3.5000 -0.0510 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9330 -2.2820 -0.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5350 -2.1320 -0.0240 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2130 -0.6830 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4150 0.0470 -0.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3810 1.4370 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1640 2.0980 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0170 1.3820 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7730 -3.2200 -0.0220 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5360 -0.9220 -0.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.7200 -0.6570 -0.0490 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3130 -4.3900 -0.0340 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 2 0 0 0 0 + 2 3 2 0 0 0 0 + 2 1 1 0 0 0 0 + 3 12 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 11 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 2 0 0 0 0 + 5 10 1 0 0 0 0 + 6 12 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 11 14 1 0 0 0 0 + 12 13 2 0 0 0 0 +M END + + +> +C.ar +N.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +N.ar +C.2 +O.2 +N.ar + +> +1 C.ar + +$$$$ diff --git a/example-fragments/rigids/r-30052.sdf b/example-fragments/rigids/r-30052.sdf new file mode 100644 index 0000000..20bd4c8 --- /dev/null +++ b/example-fragments/rigids/r-30052.sdf @@ -0,0 +1,53 @@ +uz4.pdb-outfile00 + OpenBabel08201417073D + + 13 14 0 0 0 0 0 0 0 0999 V2000 + 0.0660 -2.2340 3.5960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0530 -2.8970 2.3790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0380 -2.1690 1.1990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0240 -0.7630 1.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0060 -0.6950 -1.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0260 -2.1050 -1.1490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0300 -2.7120 -2.2040 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0110 0.0430 -2.4810 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0180 1.5030 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0260 -0.1110 2.4920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0410 -2.7950 0.0030 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0460 -0.8420 3.6440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 13 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 12 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 11 1 0 0 0 0 + 5 6 2 0 0 0 0 + 5 10 1 0 0 0 0 + 6 9 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 7 12 1 0 0 0 0 + 11 13 2 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.2 +C.3 +C.3 +C.ar +O.2 +C.ar + +> +1 O.3 + +$$$$ diff --git a/example-fragments/rigids/r-31553.sdf b/example-fragments/rigids/r-31553.sdf new file mode 100644 index 0000000..b1182c2 --- /dev/null +++ b/example-fragments/rigids/r-31553.sdf @@ -0,0 +1,31 @@ +uz4.pdb-outfile04 + OpenBabel08201417123D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 1.8710 2.0570 5.5720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0780 1.1700 6.6120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4260 1.6430 7.8640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5590 3.0020 8.0780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3480 3.8890 7.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0030 3.4160 5.7860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar + +> +1 C.3 + +$$$$ diff --git a/example-fragments/rigids/r-32216.sdf b/example-fragments/rigids/r-32216.sdf new file mode 100644 index 0000000..6d71e22 --- /dev/null +++ b/example-fragments/rigids/r-32216.sdf @@ -0,0 +1,48 @@ +uz4.pdb-outfile00 + OpenBabel08201417123D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 5.7530 -1.8470 2.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9520 -1.3980 4.1030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0970 -2.0730 5.2690 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3510 -2.4750 5.5910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2910 -2.7360 4.5740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5670 -3.2150 4.9120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9010 -3.3920 6.2220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9810 -3.1080 7.2310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7090 -2.6550 6.9170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1860 -0.4570 4.0080 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9470 -2.5070 3.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 11 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 10 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 4 9 1 0 0 0 0 + 5 11 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 +M END + + +> +C.ar +C.ar +O.2 +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.2 +C.ar + +> +1 C.2 +8 O.3 + +$$$$ diff --git a/example-fragments/rigids/r-3437.sdf b/example-fragments/rigids/r-3437.sdf new file mode 100644 index 0000000..642ebf8 --- /dev/null +++ b/example-fragments/rigids/r-3437.sdf @@ -0,0 +1,60 @@ +uz4.pdb-outfile00 + OpenBabel08201417073D + + 15 17 0 0 0 0 0 0 0 0999 V2000 + -0.0180 1.5030 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0220 -0.6700 1.1390 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0350 -1.9510 1.1970 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0400 -2.7040 0.1060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0590 -4.1770 -0.0960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0550 -4.4420 -1.4770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0340 -3.1440 -2.1890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0250 -2.9800 -3.3920 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0710 -5.7570 -1.9330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0880 -6.8020 -1.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0920 -6.5440 0.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0770 -5.2310 0.8020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0250 -2.0830 -1.1550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0060 -0.6940 -1.2070 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 15 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 14 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 13 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 10 1 0 0 0 0 + 8 9 2 0 0 0 0 + 8 14 1 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END + + +> +C.3 +C.ar +N.ar +N.ar +C.ar +C.ar +C.ar +C.2 +O.2 +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar + +> +12 O.3 + +$$$$ diff --git a/example-fragments/rigids/r-4045.sdf b/example-fragments/rigids/r-4045.sdf new file mode 100644 index 0000000..55ae519 --- /dev/null +++ b/example-fragments/rigids/r-4045.sdf @@ -0,0 +1,63 @@ +uz4.pdb-outfile00 + OpenBabel08201417133D + + 16 18 0 0 0 0 0 0 0 0999 V2000 + -4.3680 -1.6230 1.5570 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.5590 -2.0600 0.9910 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6100 -2.4580 1.8090 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.4490 -2.3890 3.2030 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.5820 -2.7940 4.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -8.8830 -2.9580 3.3760 C 0 0 0 0 0 0 0 0 0 0 0 0 + -8.9000 -2.9950 1.9730 C 0 0 0 0 0 0 0 0 0 0 0 0 + -10.1190 -3.1310 1.3170 C 0 0 0 0 0 0 0 0 0 0 0 0 + -11.2880 -3.2320 2.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + -11.2690 -3.2020 3.4300 C 0 0 0 0 0 0 0 0 0 0 0 0 + -12.4310 -3.3070 4.1280 O 0 0 0 0 0 0 0 0 0 0 0 0 + -10.0680 -3.0660 4.1020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.4540 -2.9800 5.2570 O 0 0 0 0 0 0 0 0 0 0 0 0 + -5.2490 -1.9460 3.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 + -7.7580 -2.9010 1.2610 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2210 -1.5680 2.9460 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 16 2 0 0 0 0 + 2 3 2 0 0 0 0 + 2 1 1 0 0 0 0 + 3 15 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 14 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 13 2 0 0 0 0 + 6 7 2 0 0 0 0 + 6 12 1 0 0 0 0 + 7 15 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 + 9 10 1 0 0 0 0 + 10 12 2 0 0 0 0 + 10 11 1 0 0 0 0 + 14 16 1 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.3 +C.ar +O.2 +C.ar +O.2 +C.ar + +> +1 C.ar + +$$$$ diff --git a/example-fragments/rigids/r-7756.sdf b/example-fragments/rigids/r-7756.sdf new file mode 100644 index 0000000..5bf3905 --- /dev/null +++ b/example-fragments/rigids/r-7756.sdf @@ -0,0 +1,46 @@ +uz4.pdb-outfile00 + OpenBabel08201417103D + + 11 12 0 0 1 0 0 0 0 0999 V2000 + 4.6510 0.0200 0.8630 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7360 -0.6750 -0.0530 C 0 0 2 0 0 0 0 0 0 0 0 0 + 2.3930 0.0060 -0.0250 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2080 -0.6940 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0170 1.3750 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1740 2.0780 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1550 -2.1990 -0.0050 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4930 -2.7860 -0.4520 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3720 1.3950 -0.0160 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6070 -2.1350 0.3760 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 1 0 0 0 + 2 3 1 0 0 0 0 + 2 11 1 0 0 0 0 + 3 10 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 8 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 10 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 11 1 0 0 0 0 +M END + + +> +N.3 +C.3 +C.ar +C.ar +C.ar +C.ar +C.ar +C.3 +C.3 +C.ar +C.3 + +> + +$$$$ diff --git a/example-fragments/rigids/r-8883.sdf b/example-fragments/rigids/r-8883.sdf new file mode 100644 index 0000000..d3570b8 --- /dev/null +++ b/example-fragments/rigids/r-8883.sdf @@ -0,0 +1,28 @@ +uz4.pdb-outfile03 + OpenBabel08201417073D + + 5 5 0 0 0 0 0 0 0 0999 V2000 + 7.2410 -2.6790 2.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.4020 -4.0170 2.7490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.7840 -4.2800 2.6610 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.4140 -3.0930 2.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.4720 -2.1070 2.5620 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 5 1 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +N.ar + +> +1 C.3 + +$$$$ diff --git a/example-fragments/test/l-5834.sdf b/example-fragments/test/l-5834.sdf new file mode 100644 index 0000000..1658658 --- /dev/null +++ b/example-fragments/test/l-5834.sdf @@ -0,0 +1,12 @@ +z_outfile.coutfile003000.pdb + OpenBabel08201417143D + + 1 0 0 0 0 0 0 0 0 0999 V2000 + -7.4970 -1.6430 -1.7410 C 0 0 0 0 0 0 0 0 0 0 0 0 +M END + + +> +4 C.3 + +$$$$ diff --git a/example-fragments/test/l-7932.sdf b/example-fragments/test/l-7932.sdf new file mode 100644 index 0000000..d1ac0b7 --- /dev/null +++ b/example-fragments/test/l-7932.sdf @@ -0,0 +1,21 @@ +z_outfile.coutfile001000.pdb + OpenBabel08201417103D + + 4 3 0 0 0 0 0 0 0 0999 V2000 + -0.0180 1.4650 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6000 -0.5160 -1.2390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.7060 -0.5270 1.1800 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 2 1 0 0 0 0 +M END + + +> +3 C.3 +0 N.3 +3 C.3 +3 C.3 + +$$$$ diff --git a/example-fragments/test/l-8012.sdf b/example-fragments/test/l-8012.sdf new file mode 100644 index 0000000..4bd66a7 --- /dev/null +++ b/example-fragments/test/l-8012.sdf @@ -0,0 +1,15 @@ +z_outfile.coutfile002001.pdb + OpenBabel08201417133D + + 2 1 0 0 0 0 0 0 0 0999 V2000 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0160 1.3060 0.0090 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 3 0 0 0 0 +M END + + +> +1 C.1 +1 C.1 + +$$$$ diff --git a/example-fragments/test/list b/example-fragments/test/list new file mode 100644 index 0000000..13beff8 --- /dev/null +++ b/example-fragments/test/list @@ -0,0 +1,7 @@ +l-5834.sdf +l-7932.sdf +l-8012.sdf +r-30052.sdf +r-31553.sdf +r-32216.sdf +r-3437.sdf diff --git a/example-fragments/test/r-30052.sdf b/example-fragments/test/r-30052.sdf new file mode 100644 index 0000000..20bd4c8 --- /dev/null +++ b/example-fragments/test/r-30052.sdf @@ -0,0 +1,53 @@ +uz4.pdb-outfile00 + OpenBabel08201417073D + + 13 14 0 0 0 0 0 0 0 0999 V2000 + 0.0660 -2.2340 3.5960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0530 -2.8970 2.3790 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0380 -2.1690 1.1990 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0240 -0.7630 1.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0060 -0.6950 -1.1670 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0260 -2.1050 -1.1490 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0300 -2.7120 -2.2040 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0110 0.0430 -2.4810 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0180 1.5030 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0260 -0.1110 2.4920 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0410 -2.7950 0.0030 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0460 -0.8420 3.6440 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 1 13 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 12 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 4 11 1 0 0 0 0 + 5 6 2 0 0 0 0 + 5 10 1 0 0 0 0 + 6 9 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 7 12 1 0 0 0 0 + 11 13 2 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.2 +C.3 +C.3 +C.ar +O.2 +C.ar + +> +1 O.3 + +$$$$ diff --git a/example-fragments/test/r-31553.sdf b/example-fragments/test/r-31553.sdf new file mode 100644 index 0000000..b1182c2 --- /dev/null +++ b/example-fragments/test/r-31553.sdf @@ -0,0 +1,31 @@ +uz4.pdb-outfile04 + OpenBabel08201417123D + + 6 6 0 0 0 0 0 0 0 0999 V2000 + 1.8710 2.0570 5.5720 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0780 1.1700 6.6120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4260 1.6430 7.8640 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5590 3.0020 8.0780 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3480 3.8890 7.0390 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0030 3.4160 5.7860 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 6 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 2 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 5 6 1 0 0 0 0 +M END + + +> +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar + +> +1 C.3 + +$$$$ diff --git a/example-fragments/test/r-32216.sdf b/example-fragments/test/r-32216.sdf new file mode 100644 index 0000000..6d71e22 --- /dev/null +++ b/example-fragments/test/r-32216.sdf @@ -0,0 +1,48 @@ +uz4.pdb-outfile00 + OpenBabel08201417123D + + 11 12 0 0 0 0 0 0 0 0999 V2000 + 5.7530 -1.8470 2.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9520 -1.3980 4.1030 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.0970 -2.0730 5.2690 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.3510 -2.4750 5.5910 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.2910 -2.7360 4.5740 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.5670 -3.2150 4.9120 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.9010 -3.3920 6.2220 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9810 -3.1080 7.2310 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7090 -2.6550 6.9170 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1860 -0.4570 4.0080 O 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9470 -2.5070 3.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 11 2 0 0 0 0 + 1 2 1 0 0 0 0 + 2 10 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 4 9 1 0 0 0 0 + 5 11 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 2 0 0 0 0 +M END + + +> +C.ar +C.ar +O.2 +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar +O.2 +C.ar + +> +1 C.2 +8 O.3 + +$$$$ diff --git a/example-fragments/test/r-3437.sdf b/example-fragments/test/r-3437.sdf new file mode 100644 index 0000000..642ebf8 --- /dev/null +++ b/example-fragments/test/r-3437.sdf @@ -0,0 +1,60 @@ +uz4.pdb-outfile00 + OpenBabel08201417073D + + 15 17 0 0 0 0 0 0 0 0999 V2000 + -0.0180 1.5030 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0220 -0.6700 1.1390 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0350 -1.9510 1.1970 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0400 -2.7040 0.1060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0590 -4.1770 -0.0960 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0550 -4.4420 -1.4770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0340 -3.1440 -2.1890 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0250 -2.9800 -3.3920 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0710 -5.7570 -1.9330 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0880 -6.8020 -1.0290 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0920 -6.5440 0.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0770 -5.2310 0.8020 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0250 -2.0830 -1.1550 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0060 -0.6940 -1.2070 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 15 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 4 5 1 0 0 0 0 + 5 14 2 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 13 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 10 1 0 0 0 0 + 8 9 2 0 0 0 0 + 8 14 1 0 0 0 0 + 10 11 2 0 0 0 0 + 11 12 1 0 0 0 0 + 12 13 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END + + +> +C.3 +C.ar +N.ar +N.ar +C.ar +C.ar +C.ar +C.2 +O.2 +C.ar +C.ar +C.ar +C.ar +C.ar +C.ar + +> +12 O.3 + +$$$$ diff --git a/obgen.cpp b/obgen.cpp index 6648bdf..cb73a4e 100644 --- a/obgen.cpp +++ b/obgen.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ /********************************************************************** diff --git a/obgen.h b/obgen.h index c82bdc6..c7c03f7 100644 --- a/obgen.h +++ b/obgen.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _OBGEN_GUARD diff --git a/obj/Atom.o b/obj/Atom.o new file mode 100644 index 0000000..4d6b9eb Binary files /dev/null and b/obj/Atom.o differ diff --git a/script.cpp b/script.cpp index 8815c8c..9330a0b 100644 --- a/script.cpp +++ b/script.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #include @@ -26,7 +26,7 @@ int main(int argc, char** argv) string sysCommand, scenarioFileName, scenarioName, moleculeFileName; ifstream scenarioFile, moleculesFile; ofstream logFile; - string synthCommand = "./synth"; + string synthCommand = "./esynth"; if (argc <= 1) { diff --git a/synthobgen.cpp b/synthobgen.cpp index 3a3dbab..d91b369 100644 --- a/synthobgen.cpp +++ b/synthobgen.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ /********************************************************************** diff --git a/zpipe.cpp b/zpipe.cpp index fa5fa47..e230825 100644 --- a/zpipe.cpp +++ b/zpipe.cpp @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ // Modified for use in synth: 6-20-2014 diff --git a/zpipe.h b/zpipe.h index 771a85e..af02c08 100644 --- a/zpipe.h +++ b/zpipe.h @@ -1,18 +1,18 @@ /* - * This file is part of synth. + * This file is part of esynth. * - * synth is free software: you can redistribute it and/or modify + * esynth is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * - * synth is distributed in the hope that it will be useful, + * esynth is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with synth. If not, see . + * along with esynth. If not, see . */ #ifndef _ZLIB_INTERFACE_GUARD