From 4dc3d63fcdcbdb64a6e48da2780025b99ba88481 Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Tue, 19 Aug 2008 03:05:58 +0000
Subject: [PATCH] Update requirements. Minor cleanups in some cpps Finish the
 changes so that fileparsers don't throw exceptions unless the file is not
 found.

---
 .../PartialCharges/GasteigerCharges.cpp       |  2 +-
 Code/GraphMol/ROMol.h                         |  1 +
 Code/GraphMol/Wrap/rdmolfiles.cpp             | 34 ++++++-------------
 Code/RDBoost/Wrap/RDBase.cpp                  |  4 ++-
 Docs/SoftwareRequirements.txt                 |  6 ++--
 5 files changed, 19 insertions(+), 28 deletions(-)

diff --git a/Code/GraphMol/PartialCharges/GasteigerCharges.cpp b/Code/GraphMol/PartialCharges/GasteigerCharges.cpp
index e38fd2aac..342c9c35b 100755
--- a/Code/GraphMol/PartialCharges/GasteigerCharges.cpp
+++ b/Code/GraphMol/PartialCharges/GasteigerCharges.cpp
@@ -76,7 +76,7 @@ namespace Gasteiger {
 namespace RDKit {
   /*! \brief compute the gaseiger partial charges and return a new molecule with the charges set
    *
-   * Ref : J.Gasteiger, M. Marseli, "Iterative Equalization of Oribital Electronegatiity
+   * Ref : J.Gasteiger, M. Marsili, "Iterative Equalization of Oribital Electronegatiity
    *  A Rapid Access to Atomic Charges", Tetrahedron Vol 36 p3219 1980
    */
   void computeGasteigerCharges(const ROMol *mol, int nIter, bool throwOnParamFailure) {
diff --git a/Code/GraphMol/ROMol.h b/Code/GraphMol/ROMol.h
index e2d4f21cd..3addb383d 100755
--- a/Code/GraphMol/ROMol.h
+++ b/Code/GraphMol/ROMol.h
@@ -295,6 +295,7 @@ namespace RDKit{
     //@{
 
     //! returns a pointer to our RingInfo structure
+    //! <b>Note:</b> the client should not delete this.
     RingInfo *getRingInfo() const { return dp_ringInfo; };
 
     //! provides access to all neighbors around an Atom
diff --git a/Code/GraphMol/Wrap/rdmolfiles.cpp b/Code/GraphMol/Wrap/rdmolfiles.cpp
index 8b9807dfb..12f9bef94 100644
--- a/Code/GraphMol/Wrap/rdmolfiles.cpp
+++ b/Code/GraphMol/Wrap/rdmolfiles.cpp
@@ -43,10 +43,8 @@ namespace RDKit{
     } catch (...) {
       newM=0;
     }
+    return static_cast<ROMol *>(newM);
     if(!newM) return 0;
-    ROMol *res =new ROMol(*newM);
-    delete newM; 
-    return res;
   }
 
   ROMol *MolFromSmarts(const char *smarts,bool mergeHs=false){
@@ -56,10 +54,7 @@ namespace RDKit{
     } catch (...) {
       newM=0;
     }
-    if(!newM) return 0;
-    ROMol *res =new ROMol(*newM);
-    delete newM; 
-    return res;
+    return static_cast<ROMol *>(newM);
   }
    
   ROMol *MolFromTPLFile(const char *filename, bool sanitize=true,
@@ -67,13 +62,13 @@ namespace RDKit{
     RWMol *newM;
     try {
       newM = TPLFileToMol(filename,sanitize,skipFirstConf);
+    } catch (RDKit::BadFileException &e) {
+      PyErr_SetString(PyExc_IOError,e.message());
+      throw python::error_already_set();
     } catch (...) {
       newM=0;
     }
-    if(!newM) return 0;
-    ROMol *res =new ROMol(*newM);
-    delete newM; 
-    return res;
+    return static_cast<ROMol *>(newM);
   }
 
   ROMol *MolFromTPLBlock(std::string tplBlock, bool sanitize=true,
@@ -86,10 +81,7 @@ namespace RDKit{
     } catch (...) {
       newM=0;
     }
-    if(!newM) return 0;
-    ROMol *res =new ROMol(*newM);
-    delete newM; 
-    return res;
+    return static_cast<ROMol *>(newM);
   }
 
   ROMol *MolFromMolFile(const char *molFilename, bool sanitize=true, bool removeHs=true) {
@@ -99,11 +91,10 @@ namespace RDKit{
     } catch (RDKit::BadFileException &e) {
       PyErr_SetString(PyExc_IOError,e.message());
       throw python::error_already_set();
+    } catch (...) {
+      newM=0;
     }
-    if(!newM) return 0;
-    ROMol *res =new ROMol(*newM);
-    delete newM; 
-    return res;
+    return static_cast<ROMol *>(newM);
   }
 
   ROMol *MolFromMolBlock(std::string molBlock, bool sanitize=true, bool removeHs=true) {
@@ -115,10 +106,7 @@ namespace RDKit{
     } catch (...) {
       newM=0;
     }
-    if(!newM) return 0;
-    ROMol *res =new ROMol(*newM);
-    delete newM; 
-    return res;
+    return static_cast<ROMol *>(newM);
   }
 
 }
diff --git a/Code/RDBoost/Wrap/RDBase.cpp b/Code/RDBoost/Wrap/RDBase.cpp
index f0bdc937d..2d1e4a864 100755
--- a/Code/RDBoost/Wrap/RDBase.cpp
+++ b/Code/RDBoost/Wrap/RDBase.cpp
@@ -1,11 +1,13 @@
 // $Id$
 //
-// Copyright (c) 2004-2006 greg Landrum and Rational Discovery LLC
+// Copyright (c) 2004-2008 greg Landrum and Rational Discovery LLC
 //
 //   @@ All Rights Reserved  @@
 //
 #include <boost/python.hpp>
 #define PY_ARRAY_UNIQUE_SYMBOL rdbase_array_API
+#include <iostream>
+#include <fstream>
 #include <RDBoost/Wrap.h>
 #include "numpy/oldnumeric.h"
 
diff --git a/Docs/SoftwareRequirements.txt b/Docs/SoftwareRequirements.txt
index 49cff4318..cdb014604 100755
--- a/Docs/SoftwareRequirements.txt
+++ b/Docs/SoftwareRequirements.txt
@@ -4,9 +4,9 @@ By: Greg Landrum
 
 A. Required Python and the like:
    1) Python 2.3 or later 
-   2) Numeric Python (numpy.sourceforge.net)
-      binary versions for windows can be downloaded here:
-      http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe
+   2) NumPy (http://numpy.scipy.org/)
+      binary versions can be downloaded here:
+      http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103
    3) [not required with Python2.5 and later] A database wrapper, one of:
       - pyPgSQL (http://pypgsql.sourceforge.net/) 
       - pysqlite2 (http://www.initd.org/tracker/pysqlite/wiki/pysqlite)