Merge pull request #2054 from baoilleach/updatedocstrings

Fix file format docstrings that were causing problems with Sphinx or GUI

src/formats/chemdrawcdx.cpp

@@ -135,15 +135,17 @@ class ChemDrawBinaryXFormat : OBMoleculeFormat
       "ChemDraw binary format\n"
       "Read only\n"
       "The whole file is read in one call.\n"
-      "Reactions if present are read and output as OBReaction objects.\n"
-      "Any molecules not involved in a reaction are output as OBMol objects.\n"
-      "Most molecule formats will output the reactants and products when\n"
-      "given an OBReaction object.\n"
+      "Note that a file may contain a mixture of reactions and\n"
+      "molecules.\n"
+
       "With the -ad option, a human-readable representation of the CDX tree\n"
-      "structure is output as an OBText object. Use textformat to view it:\n"
-      "    obabel input.cdx -otext -ad\n"
+      "structure is output as an OBText object. Use textformat to view it::\n\n"
+
+      "    obabel input.cdx -otext -ad\n\n"
+
       "Many reactions in CDX files are not fully specified with reaction data\n"
-      "structures, and may not be completely interpreted by this parser.\n"
+      "structures, and may not be completely interpreted by this parser.\n\n"
+
       "Read Options, e.g. -am\n"
       " m read molecules only; no reactions\n"
       " d output CDX tree to OBText object\n"

src/formats/mol2format.cpp

@@ -53,10 +53,10 @@ namespace OpenBabel
       return
         "Sybyl Mol2 format\n"
         "Read Options e.g. -ac\n"
-        "  c               Read UCSF Dock scores saved in comments preceeding molecules\n\n"
+        "  c               Read UCSF Dock scores saved in comments preceding molecules\n\n"
         "Write Options e.g. -xl\n"
-        "  l               Output ignores residue information (only ligands)\n\n"
-        "  c               Write UCSF Dock scores saved in comments preceeding molecules\n\n"
+        "  l               Output ignores residue information (only ligands)\n"
+        "  c               Write UCSF Dock scores saved in comments preceding molecules\n"
         "  u               Do not write formal charge information in UNITY records\n\n";
     };
 

src/formats/rinchiformat.cpp

@@ -43,6 +43,7 @@ namespace OpenBabel
     {
       return
         "RInChI\n"
+        "The Reaction InChI\n"
         "The Reaction InChI (or RInChI) is intended to be a unique\n"
         "string that describes a reaction. This may be useful for\n"
         "indexing and searching reaction databases. As with the InChI\n"

src/formats/smilesformat.cpp

@@ -166,16 +166,17 @@ namespace OpenBabel {
         "     This gives canonical labels 1,2,3,4 to atoms 4,2,1,3 respectively,\n"
         "     so that atom 4 will be visited first and the remaining atoms\n"
         "     visited in a depth-first manner following the lowest canonical labels.\n"
-        "  O  Store the SMILES atom order as a space-separated string in an\n"
-        "     OBPairData with the name 'SMILES Atom Order'\n"
+        "  O  Store the SMILES atom order as a space-separated string\n"
+        "     The string is stored as an OBPairData wth the name\n"
+        "     'SMILES Atom Order'.\n"
         "  F  <atom numbers> Generate SMILES for a fragment\n"
         "     The atom numbers should be specified like \"1 2 4 7\".\n"
         "  R  Do not reuse bond closure symbols\n"
         "  f  <atomno> Specify the first atom\n"
         "     This atom will be used to begin the SMILES string.\n"
         "  l  <atomno> Specify the last atom\n"
         "     The output will be rearranged so that any additional\n"
-        "     SMILES added to the end will be attached to this atom.\n\n"
+        "     SMILES added to the end will be attached to this atom.\n"
         "  T  <max seconds> Specify the canonicalization timeout\n"
         "     Canonicalization can take a while for symmetric molecules and a\n"
         "     timeout is used. The default is 5 seconds.\n\n"

src/formats/svgformat.cpp

@@ -104,10 +104,11 @@ class SVGFormat : public OBFormat
       " rows# number of rows in table(not displayed in GUI)\n"
       " N# max number objects to be output\n"
       " l draw grid lines\n"
-      " h <condition><color> highlight mol if condition is met\n"
+      " h <condition> highlight mol if condition is met\n"
       "    The condition can use descriptors and properties,\n"
       "    See documentation on ``--filter`` option for details.\n"
-      "    Specifying the highlight color is optional.\n"
+      "    To highlight in a particular color, follow the condition\n"
+      "    by a color.\n"
       " i add index to each atom\n"
       "    These indices are those in sd or mol files and correspond to the\n"
       "    order of atoms in a SMILES string.\n"

src/formats/vaspformat.cpp

@@ -90,16 +90,20 @@ namespace OpenBabel {
 
         "Both VASP 4.x and 5.x POSCAR formats are supported.\n\n"
 
+	"By default, atoms are written out in the order they are present in the input\n"
+	"molecule. To sort by atomic number specify ``-xw``. To specify the sort\n"
+	"order, use the ``-xz`` option.\n\n"
+
         "Read Options e.g. -as\n"
         "  s Output single bonds only\n"
         "  b Disable bonding entirely\n\n"
 
-        "Write Options e.g. -xw\n"
-        "  Atoms soring:\n"
-        "    no option: default order (presumably this is the order of atoms in the input molecule)\n"
-        "    -xw : Sort atoms by atomic number\n"
-        "    -xz 'atom1 atom2 ..': atom1 first, atom2 second ..., then default order\n"
-        "    -xw -xz 'atom1 atom2': atom1 first, atom2 second ..., then sort atoms by atomic number\n"
+        "Write Options e.g. -x4\n"
+        " w  Sort atoms by atomic number\n"
+        " z <list of atoms>  Specify the order to write out atoms\n"
+	"       'atom1 atom2 ...': atom1 first, atom2 second, etc. The remaining\n"
+	"       atoms are written in the default order or (if ``-xw`` is specified)\n"
+	"       in order of atomic number.\n"
         "  4 Write a POSCAR using the VASP 4.x specification.\n"
         "    The default is to use the VASP 5.x specification.\n\n"
         ;