Merge branch 'master' of github.com:ACRMGroup/bioplib

ACRMGroup · Aug 14, 2018 · 4c4609a · 4c4609a
2 parents 5f3e2ee + da24888
commit 4c4609a
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diff --git a/src/FitNCaCPDB.c b/src/FitNCaCPDB.c
@@ -3,12 +3,12 @@
 
    \file       FitNCaCPDB.c
    
-   \version    V1.5
-   \date       19.08.14
+   \version    V1.6
+   \date       07.08.18
    \brief      Fit two PDB linked lists. Also a weighted fit and support
                routines
    
-   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1993-6
+   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1993-2018
    \author     Dr. Andrew C. R. Martin
    \par
                Institute of Structural & Molecular Biology,
@@ -58,6 +58,7 @@
 -  V1.4  07.07.14 Use bl prefix for functions By: CTP
 -  V1.5  19.08.14 Added AsCopy suffix to calls to blSelectAtomsPDB() 
                   By: CTP
+-  V1.6  07.08.18 Removed erroneous check on sel[3]
 
 *************************************************************************/
 /* Doxygen
@@ -111,6 +112,8 @@
 -  07.07.14 Use bl prefix for functions By: CTP
 -  19.08.14 Added AsCopy suffix to calls to blSelectAtomsPDB() By: CTP
 -  03.11.17 Initialize RetVal! By: ACRM
+-  07.08.18 Removed erroneous check on sel[3]
+
 */
 BOOL blFitNCaCPDB(PDB *ref_pdb, PDB *fit_pdb, REAL rm[3][3])
 {
@@ -132,7 +135,7 @@ BOOL blFitNCaCPDB(PDB *ref_pdb, PDB *fit_pdb, REAL rm[3][3])
    SELECT(sel[0], "N   ");
    SELECT(sel[1], "CA  ");
    SELECT(sel[2], "C   ");
-   if((sel[0]==NULL)||(sel[1]==NULL)||(sel[2]==NULL)||(sel[3]==NULL))
+   if((sel[0]==NULL)||(sel[1]==NULL)||(sel[2]==NULL))
       return(FALSE);
    if( (ref_bb_pdb = blSelectAtomsPDBAsCopy(ref_pdb, 3, sel, &natoms))
        == NULL )

diff --git a/src/GetCofGPDBSCRange.c b/src/GetCofGPDBSCRange.c
@@ -3,11 +3,11 @@
 
    \file       GetCofGPDBSCRange.c
    
-   \version    V1.2
-   \date       07.07.14
+   \version    V1.3
+   \date       07.08.18
    \brief      Find CofG of a PDB linked list
    
-   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1992-4
+   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1992-2018
    \author     Dr. Andrew C. R. Martin
    \par
                Institute of Structural & Molecular Biology,
@@ -50,6 +50,7 @@
 -  V1.1  03.10.94 Added GetCofGPDBRange(), FindCofGPDBSCRange() and 
                   fixed NULL coord search in GetCofGPDB()
 -  V1.2  07.07.14 Use bl prefix for functions By: CTP
+-  V1.3  07.08.18 Initialized variable to silence gcc 7.3.1 with -O2
 
 *************************************************************************/
 /* Doxygen
@@ -97,11 +98,13 @@
    For Glycine, returns the CA coordinates.
 
 -  03.10.94 Original    By: ACRM
+-  07.08.18 Initialized ca to silence gcc 7.3.1 with -O2
 */
 void blGetCofGPDBSCRange(PDB *start, PDB *stop, VEC3F *cg)
 {
    int natom;
-   PDB *p, *ca;
+   PDB *p,
+       *ca = NULL;
 
    cg->x = 0.0;   
    cg->y = 0.0;   

diff --git a/src/HAddPDB.c b/src/HAddPDB.c
@@ -3,11 +3,11 @@
 
    \file       HAddPDB.c
    
-   \version    V2.22
-   \date       23.06.15
+   \version    V2.23
+   \date       07.08.18
    \brief      Add hydrogens to a PDB linked list
    
-   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1990-2015
+   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1990-2018
    \author     Dr. Andrew C. R. Martin
    \par
                Institute of Structural & Molecular Biology,
@@ -134,6 +134,8 @@
 -  V2.21 23.02.15 Uses new blRenumAtomsPDB()
 -  V2.22 23.06.15 Various calls to CLEAR_PDB() to fix problems with
                   uninitialized CONECT data
+-  V2.23 07.08.18 initialized and foce-terminated variables to silence
+                  gcc 7.3.1 with -O2
 
 *************************************************************************/
 /* Doxygen
@@ -616,14 +618,19 @@ preceeding the last residue\n");
 -  26.08.14 Used n and nt variables consistently instead of literal
             strings. Moved all use of 'ok' variable into SCREEN_INFO
 -  13.02.15 Added setting of element type
+-  07.08.18 initialized variables to silence gcc 7.3.1 with -O2
 */
 static PDB *makeh(int HType, REAL BondLen, REAL alpha, REAL beta, 
                   BOOL firstres)
 { 
    static char    *nt = "NT  ",
                   *n  = "N   ";
-   REAL           x1,y1,z1,x2,y2,z2,x3,y3,z3,
-                  x4,y4,z4,x5,y5,z5,x6,y6,z6,
+   REAL           x1 = 0.0, y1 = 0.0, z1 = 0.0,
+                  x2 = 0.0, y2 = 0.0, z2 = 0.0,
+                  x3 = 0.0, y3 = 0.0, z3 = 0.0,
+                  x4 = 0.0, y4 = 0.0, z4 = 0.0,
+                  x5 = 0.0, y5 = 0.0, z5 = 0.0,
+                  x6 = 0.0, y6 = 0.0, z6 = 0.0,
                   x21,y21,z21,r21,
                   x21p,y21p,z21p,r21p,
                   x23,y23,z23,r23,
@@ -1417,12 +1424,14 @@ been set.\n",DATAENV);
 -  05.12.02 Original   By: ACRM
 -  17.02.15 Terminates the out string when it is 4 or more characters
 -  18.03.15 Changed to use MAXLABEL
+-  07.08.18 Force terminated instr to silence gcc 7.3.1 with -O2
 */
 static void SetRawAtnam(char *out, char *in)
 {
    char instr[MAXLABEL];
 
    strncpy(instr, in, MAXLABEL-1);
+   instr[MAXLABEL-1] = '\0';
    TERMAT(instr, ' ');
 
    if(strlen(instr) > 3)

diff --git a/src/ReadPDB.c b/src/ReadPDB.c
@@ -3,11 +3,11 @@
 
    \file       ReadPDB.c
    
-   \version    V3.11
-   \date       01.07.15
+   \version    V3.12
+   \date       07.08.18
    \brief      Read coordinates from a PDB file 
    
-   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1988-2015
+   \copyright  (c) UCL / Dr. Andrew C. R. Martin 1988-2018
    \author     Dr. Andrew C. R. Martin
    \par
                Institute of Structural & Molecular Biology,
@@ -232,11 +232,13 @@ BUGS:  25.01.05 Note the multiple occupancy code won't work properly for
                   checks for failed XML extractions.
 -  V3.10 25.06.15 Fixed bug for pdbml parsing where residue number is set
                   to 0.  By: CTP
--  £3.11 01.07.15 Added ParseHeaderRecordsPDBML(). 
+-  V3.11 01.07.15 Added ParseHeaderRecordsPDBML(). 
                   ParseHeaderPDBML() broken into smaller functions: 
                   ParseTitlePDBML(), ParseCompndPDBML(), 
                   ParseSourcePDBML(), ParseResolPDBML(), 
                   ParseSeqresPDBML() and ParseModresPDBML().  By: CTP
+-  V3.12 07.08.18 Increased text buffer sizes to silence gcc 7.3.1 
+                  with -O2
 
 *************************************************************************/
 /* Doxygen
@@ -3317,6 +3319,7 @@ static STRINGLIST *ParseSeqresPDBML(xmlDoc *document)
    Parses PDBML header data and returns MODRES record.
 
 -  01.07.15 Original.  By: CTP
+-  07.08.18 Increased text buffer sizes to silence gcc 7.3.1 with -O2
 */
 static STRINGLIST *ParseModresPDBML(xmlDoc *document)
 {
@@ -3332,20 +3335,30 @@ static STRINGLIST *ParseModresPDBML(xmlDoc *document)
               *node      = NULL,
               *subnode   = NULL,
               *n         = NULL;
-   xmlChar    *content, *attribute;
-   double     content_lf = 0.0;
+   xmlChar    *content,
+              *attribute;
+   double     content_lf    = 0.0;
    STRINGLIST *modres_lines = NULL;
-   char       pdb_field[5]     = "";
+   char       pdb_field[8];
 
    /* modres                                                            */
-   char       modres_line[82]    =  "",
-              modres_resnam[8]   =  "",
-              modres_chain[8]    =  "",
-              modres_insert[2]   = " ",
-              modres_stdnam[8]   =  "",
-              modres_comment[42] =  "";
+   char       modres_line[160],
+              modres_resnam[8],
+              modres_chain[8], 
+              modres_insert[8],
+              modres_stdnam[8],
+              modres_comment[80];
    int        modres_seqnum      =   0;
 
+   modres_line[0]    = '\0';
+   modres_resnam[0]  = '\0';
+   modres_chain[0]   = '\0';
+   modres_insert[0]  = ' ';
+   modres_insert[1]  = '\0';
+   modres_stdnam[0]  = '\0';
+   modres_comment[0] = '\0';
+
+
    /* Parse Document Tree                                               */
    root_node = xmlDocGetRootElement(document);
    for(node = root_node->children; node; NEXT(node))
@@ -4232,7 +4245,7 @@ static STRINGLIST *SourceStringlist(STRINGLIST *stringlist,
    Creates SEQRES records in PDB-format.
 
 -  23.06.15 Original. By: CTP
-
+-  07.08.18 Increase size of buffers to silence gcc 7.3.1 with -O2
 */
 static STRINGLIST *SeqresStringlist(int nchains, char **chains, 
                                       STRINGLIST **residues)
@@ -4245,12 +4258,14 @@ static STRINGLIST *SeqresStringlist(int nchains, char **chains,
 #else
 
    STRINGLIST *stringlist = NULL,
-              *residue = NULL;
-   int i = 0, j = 0, nres = 0;
-   int nline = 0;
-   char seqres_line[82]  = "";
-   char residue_field[5] = "";
-   char sequence_field[53] = "";
+              *residue    = NULL;
+   int        i           = 0,
+              j           = 0,
+              nres        = 0,
+              nline = 0;
+   char       seqres_line[160],
+              residue_field[8],
+              sequence_field[80];
 
 
    /* process chains                                                    */

diff --git a/src/StripWatersPDB.c b/src/StripWatersPDB.c
@@ -3,11 +3,11 @@
 
    \file       StripWatersPDB.c
    
-   \version    V1.3
-   \date       19.04.15
+   \version    V1.4
+   \date       07.08.18
    \brief      
    
-   \copyright  (c) Dr. Andrew C. R. Martin, UCL, 2008-2014
+   \copyright  (c) Dr. Andrew C. R. Martin, UCL, 2008-2018
    \author     Dr. Andrew C. R. Martin
    \par
                Institute of Structural & Molecular Biology,
@@ -51,6 +51,7 @@
 -  V1.2  19.08.14 Renamed function blStripWatersPDB() to 
                   blStripWatersPDBAsCopy() By: CTP
 -  V1.3  19.04.15 Added call to blCopyConect()   By: ACRM
+-  V1.4  07.08.18 Initialized variable to silence gcc 7.3.1 with -O2
 
 *************************************************************************/
 /* Doxygen
@@ -95,12 +96,13 @@
 -  30.04.08 Original based on StripHPDB()   By: ACRM
 -  19.08.14 Renamed function to blStripWatersPDBAsCopy() By: CTP
 -  12.04.15 Added rebuild of CONECT data
+-  07.08.18 Initialized q to silence gcc 7.3.1 with -O2
 */
 PDB *blStripWatersPDBAsCopy(PDB *pdbin, int *natom)
 {
    PDB   *pdbout  = NULL,
          *p,
-         *q;
+         *q = NULL;
 
    *natom = 0;
 

diff --git a/src/WritePDB.c b/src/WritePDB.c
@@ -3,8 +3,8 @@
 
    \file       WritePDB.c
    
-   \version    V1.30
-   \date       09.02.18
+   \version    V1.31
+   \date       07.08.18
    \brief      Write a PDB file from a linked list
    
    \copyright  (c) UCL / Dr. Andrew C. R. Martin 1993-2018
@@ -113,6 +113,8 @@
                   Added ReadSeqresChainLabelWholePDB() and 
                   ReadSeqresResidueListWholePDB().  By: CTP
 -  V1.30 09.02.18 Corrected calls to ABS() in formal charges By: ACRM
+-  V1.31 07.08.18 Increased text buffer sizes to silence gcc 7.3.1 
+                  with -O2
 
 *************************************************************************/
 /* Doxygen
@@ -576,6 +578,7 @@ BOOL blWritePDBAsPDBML(FILE *fp, PDB  *pdb)
             in PDB. Set compound type to polymer. By:  CTP
 -  10.07.15 Added return value for no XML_SUPPORT  By: ACRM
 -  29.07.15 Added output of SEQRES records from wpdb->header.  By: CTP
+-  07.08.18 Increased text buffer sizes to silence gcc 7.3.1 with -O2
 */
 static BOOL blDoWritePDBAsPDBML(FILE *fp, WHOLEPDB  *wpdb, BOOL doWhole)
 {
@@ -596,7 +599,7 @@ static BOOL blDoWritePDBAsPDBML(FILE *fp, WHOLEPDB  *wpdb, BOOL doWhole)
                node        = NULL;
    xmlNsPtr    pdbx        = NULL,
                xsi         = NULL;
-   char        buffer[16], 
+   char        buffer[80], 
                *buffer_ptr;
    int         conect_id   = 0,
                i, j;
@@ -607,14 +610,14 @@ static BOOL blDoWritePDBAsPDBML(FILE *fp, WHOLEPDB  *wpdb, BOOL doWhole)
         pdbml_date[11] =   "",
         *title         = NULL;
 
-   COMPND    compound;
-   PDBSOURCE species;
-   int molid = 0;
-   HASHTABLE *chain_to_entity = NULL;
+   COMPND     compound;
+   PDBSOURCE  species;
+   int        molid             = 0;
+   HASHTABLE  *chain_to_entity  = NULL;
    int        seqres_nchains    =    0;
    char       **seqres_chain    = NULL;
    STRINGLIST **seqres_residues = NULL,
-              *s = NULL;
+              *s                = NULL;
 
    /* Create document                                                   */
    if((doc = xmlNewDoc((xmlChar *)"1.0"))==NULL)
@@ -1642,6 +1645,7 @@ void blWriteWholePDBHeader(FILE *fp, WHOLEPDB *wpdb)
 -  23.02.15  Added numTer parameter
 -  02.03.15  Padded END and CONECT
 -  06.08.15  Updated XML check. By: CTP
+-  07.08.18 Increased text buffer sizes to silence gcc 7.3.1 with -O2
 */
 void blWriteWholePDBTrailer(FILE *fp, WHOLEPDB *wpdb, int numTer)
 {
@@ -1660,7 +1664,7 @@ void blWriteWholePDBTrailer(FILE *fp, WHOLEPDB *wpdb, int numTer)
             int  i, 
                  nPrinted,
                  width=0;
-            char format[8];
+            char format[16];
 
             for(i=0, nPrinted=0; i<p->nConect; i++)
             {