Passes tests

Lilly_Medchem_Rules.rb

@@ -1,24 +1,5 @@
 #!/usr/bin/env ruby
 
-#**************************************************************************
-
-#   Copyright (C) 2012  Eli Lilly and Company
-
-#   This program 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.
-
-#   This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
-
-#*************************************************************************/
-
 # Run the rejection/demerit rules
 
 ianhome=File.dirname($0)      # location for supporting files

Molecule/ISIS_Atom_List.cc

@@ -1,21 +1,3 @@
-/**************************************************************************
-
-    Copyright (C) 2011  Eli Lilly and Company
-
-    This program 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.
-
-    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
-
-**************************************************************************/
 #include <stdlib.h>
 #include <iomanip>
 using namespace std;
@@ -125,7 +107,7 @@ ISIS_Atom_List::create_from_ALS_record (const IWString & buffer)
       return 0;
     }
 
-    const Element * e = get_element_from_symbol_no_case_conversion (token);
+    const Element * e = get_element_from_symbol_no_case_conversion(token);
 
     if (NULL == e)   // should not happen
     {
@@ -206,6 +188,27 @@ ISIS_Atom_List::initialise_from_mdl_A_symbol ()
   return 1;
 }
 
+/*
+  Marvin adds AH, which is any atom, including Hydrogen
+*/
+
+int
+ISIS_Atom_List::initialise_from_mdl_AH_symbol ()
+{
+  _normal_list = 1;
+
+  initialise_from_mdl_Q_symbol();
+
+  _element.add(get_element_from_atomic_number(6));    // C
+  _element.add(get_element_from_atomic_number(1));    // H
+
+  return 1;
+}
+
+/*
+  Really don't like this, I should do something better with the Q symbol. Fix sometime...
+*/
+
 int
 ISIS_Atom_List::initialise_from_mdl_Q_symbol ()
 {
@@ -225,6 +228,16 @@ ISIS_Atom_List::initialise_from_mdl_Q_symbol ()
   return 1;
 }
 
+int
+ISIS_Atom_List::initialise_from_mdl_QH_symbol ()
+{
+  initialise_from_mdl_Q_symbol();
+
+  _element.add(get_element_from_atomic_number(1));
+
+  return 1;
+}
+
 int
 ISIS_Atom_List::convert_not_atom_lists_to_organic_lists ()
 {
@@ -308,8 +321,7 @@ ISIS_Atom_List::initialise_atom_list_from_symbol (const const_IWSubstring & s)
   const_IWSubstring token;
   while (mys.nextword(token, i, ','))
   {
-    int notused;
-    const Element * e = get_element_from_symbol(token, notused);
+    const Element * e = get_element_from_symbol_no_case_conversion(token);
     if (NULL == e)
     {
       cerr << "ISIS_Atom_List::initialise_atom_list_from_symbol:unrecognised element '" << token << "'\n";

Molecule/Makefile

@@ -11,12 +11,12 @@ LD = g++
 CXXFLAGS = -O2 -I . -I ../include -ffast-math -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
 
 # Some versions of gcc need the -std= directive, remove if it causes problems
-CXXFLAGS = -O2 -I . -I ../include -ffast-math -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 
+CXXFLAGS = -O2 -I . -I ../include -ffast-math -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DIW_IMPLEMENTATIONS_EXPOSED
 
 # Auto check gcc version from Raj Guha
 GCCVERSIONGTEQ4 := $(shell expr `gcc -dumpversion | cut -f1,2 -d.` \>= 4.3)
 ifeq "$(GCCVERSIONGTEQ4)" "1"
-    CXXFLAGS += -std=gnu++0x
+    CXXFLAGS += -std=c++11
 endif
 
 
@@ -26,11 +26,11 @@ CP = cp
 COMMON_OBJECTS = molecule.o moleculeb.o moleculeh.o element.o atom.o bond.o bond_list.o output.o ostream_and_type.o rmele.o etrans.o aromatic.o rwmolecule.o \
 	smi.o mdl.o mdl_v30.o parse_smarts_tmp.o mdl_file_data.o mdl_molecule.o mdl_atom_record.o isis_link_atom.o ISIS_Atom_List.o atom_alias.o molecule_smarts.o\
 	smiles.o smiles_support.o \
-	moleculer.o pearlman.o moleculed.o path.o frag.o unique.o chiral_centre.o charge_assigner.o target.o careful_frag.o \
+	moleculer.o pearlman.o moleculed.o path.o frag.o unique.o chiral_centre.o charge_assigner.o donor_acceptor.o target.o careful_frag.o \
 	iwrnm.o iwrcb.o set_of_atoms.o symm_class_can_rank.o ring_bond_iterator.o cis_trans_bond.o ematch.o coordinates.o dihedral.o\
 	iwsubstructure.o csubstructure.o substructure_a.o substructure_env.o ss_atom_env.o ss_bonds.o ss_ring.o ss_ring_base.o ss_ring_sys.o iwqry_wstats.o substructure_results.o substructure_spec.o substructure_chiral.o\
 	rwsubstructure.o substructure_nmab.o molecule_to_query.o is_actually_chiral.o tokenise_atomic_smarts.o temp_detach_atoms.o path_scoring.o \
-	element_hits_needed.o misc2.o standardise.o toggle_kekule_form.o
+	element_hits_needed.o numass.o misc2.o standardise.o toggle_kekule_form.o
 
 MC_FIRST_PASS_OBJECTS = mc_first_pass.o $(COMMON_OBJECTS)