pdbxpluging update

headers/pertable.h

@@ -28,6 +28,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 float pte_get_vdw_ray(const char *symbol) ;
 float pte_get_mass(const char *symbol) ;
 float pte_get_enegativity(const char *symbol) ;
+float pte_get_enegativity_from_number(int atomicnumber) ;
+char *pte_get_element_from_number(int atomicnumber);
 int is_valid_element(const char *str, int ignore_case) ;
 int element_in_std_res(char *res_name);
 int element_in_nucl_acid(char *res_name);

plugins/include/molfile_plugin.h

@@ -120,10 +120,12 @@ typedef struct {
   /* chains for existing PDBx/mmCIF files.                       */
   char chain[4];      /**< required chain name, or ""            */
 #else
-  char chain[2];      /**< required chain name, or ""            */
+  char chain[16];      /**< required chain name, or ""            */
 #endif
   /* rest are optional; use optflags to specify what's present   */
   char altloc[2];     /**< optional PDB alternate location code  */
+  char chain_auth[16];      /**< optional author chain name ""            */
+  int resid_auth;          /**< optional author integer residue ID           */
   char insertion[2];  /**< optional PDB insertion code           */
   float occupancy;    /**< optional occupancy value              */
   float bfactor;      /**< optional B-factor value               */
@@ -131,6 +133,7 @@ typedef struct {
   float charge;       /**< optional charge value                 */
   float radius;       /**< optional radius value                 */
   int atomicnumber;   /**< optional element atomic number        */
+  int modelnumber;    /**< optional model number                 */
 
 #if 0
   char complex[16];
@@ -165,6 +168,8 @@ typedef struct {
 #define MOLFILE_ALTLOC        0x0040 /**< Multiple conformations present   */
 #define MOLFILE_ATOMICNUMBER  0x0080 /**< Atomic element number provided   */
 #define MOLFILE_BONDSSPECIAL  0x0100 /**< Only non-standard bonds provided */
+#define MOLFILE_CHAIN_AUTH    0x0120 /**< if Author chain id provided      */
+#define MOLFILE_RESID_AUTH    0x0120 /**< if Author resid id provided      */
 #if defined(DESRES_CTNUMBER)
 #define MOLFILE_CTNUMBER      0x0200 /**< ctnumber provided */
 #endif

plugins/include/vmdplugin.h

@@ -0,0 +1,191 @@
+/***************************************************************************
+ *cr
+ *cr            (C) Copyright 1995-2006 The Board of Trustees of the
+ *cr                        University of Illinois
+ *cr                         All Rights Reserved
+ *cr
+ ***************************************************************************/
+
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ *      $RCSfile: vmdplugin.h,v $
+ *      $Author: johns $       $Locker:  $             $State: Exp $
+ *      $Revision: 1.34 $       $Date: 2018/05/02 03:12:56 $
+ *
+ ***************************************************************************/
+
+/** @file
+ * This header must be included by every VMD plugin library.  It defines the
+ * API for every plugin so that VMD can organize the plugins it finds.  
+ */
+
+#ifndef VMD_PLUGIN_H
+#define VMD_PLUGIN_H
+
+
+/* 
+ * Preprocessor tricks to make it easier for us to redefine the names of
+ * functions when building static plugins.
+ */
+#if !defined(VMDPLUGIN)
+/** 
+  * macro defining VMDPLUGIN if it hasn't already been set to the name of 
+  * a static plugin that is being compiled.  This is the catch-all case.
+  */
+#define VMDPLUGIN vmdplugin
+#endif
+/** concatenation macro, joins args x and y together as a single string */
+#define xcat(x, y) cat(x, y)
+/** concatenation macro, joins args x and y together as a single string */
+#define cat(x, y) x ## y 
+
+/*
+ *  macros to correctly define plugin function names depending on whether 
+ *  the plugin is being compiled for static linkage or dynamic loading. 
+ *  When compiled for static linkage, each plugin needs to have unique
+ *  function names for all of its entry points.  When compiled for dynamic
+ *  loading, the plugins must name their entry points consistently so that
+ *  the plugin loading mechanism can find the register, register_tcl, init,
+ *  and fini routines via dlopen() or similar operating system interfaces.
+ */
+/*@{*/
+/** Macro names entry points correctly for static linkage or dynamic loading */
+#define VMDPLUGIN_register     xcat(VMDPLUGIN, _register)
+#define VMDPLUGIN_register_tcl xcat(VMDPLUGIN, _register_tcl)
+#define VMDPLUGIN_init         xcat(VMDPLUGIN, _init)
+#define VMDPLUGIN_fini         xcat(VMDPLUGIN, _fini)
+/*@}*/
+
+
+/** "WIN32" is defined on both WIN32 and WIN64 platforms... */
+#if (defined(WIN32)) 
+#define WIN32_LEAN_AND_MEAN
+#include <windows.h>
+
+#if !defined(STATIC_PLUGIN)
+#if defined(VMDPLUGIN_EXPORTS)
+/** 
+ *  Only define DllMain for plugins, not in VMD or in statically linked plugins
+ *  VMDPLUGIN_EXPORTS is only defined when compiling dynamically loaded plugins
+ */
+BOOL APIENTRY DllMain( HANDLE hModule,
+                       DWORD ul_reason_for_call,
+                       LPVOID lpReserved
+                     )
+{
+  return TRUE;
+}
+
+#define VMDPLUGIN_API __declspec(dllexport)
+#else
+#define VMDPLUGIN_API __declspec(dllimport)
+#endif /* VMDPLUGIN_EXPORTS */
+#else  /* ! STATIC_PLUGIN */
+#define VMDPLUGIN_API
+#endif /* ! STATIC_PLUGIN */
+#else
+/** If we're not compiling on Windows, then this macro is defined empty */
+#define VMDPLUGIN_API 
+#endif
+
+/** define plugin linkage correctly for both C and C++ based plugins */
+#ifdef __cplusplus
+#define VMDPLUGIN_EXTERN extern "C" VMDPLUGIN_API
+#else
+#define VMDPLUGIN_EXTERN extern VMDPLUGIN_API
+#endif  /* __cplusplus */
+
+/* 
+ * Plugin API functions start here 
+ */
+
+
+/** 
+ * Init routine: called the first time the library is loaded by the 
+ * application and before any other API functions are referenced.
+ * Return 0 on success.
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_init(void);
+
+/**
+ * Macro for creating a struct header used in all plugin structures.
+ * 
+ * This header should be placed at the top of every plugin API definition 
+ * so that it can be treated as a subtype of the base plugin type.
+ *
+ * abiversion: Defines the ABI for the base plugin type (not for other plugins)
+ * type: A string descriptor of the plugin type.
+ * name: A name for the plugin.
+ * author: A string identifier, possibly including newlines.
+ * Major and minor version.  
+ * is_reentrant: Whether this library can be run concurrently with itself.
+ */
+#define vmdplugin_HEAD \
+  int abiversion; \
+  const char *type; \
+  const char *name; \
+  const char *prettyname; \
+  const char *author; \
+  int majorv; \
+  int minorv; \
+  int is_reentrant; 
+
+/** 
+  * Typedef for generic plugin header, individual plugins can
+  * make their own structures as long as the header info remains 
+  * the same as the generic plugin header, most easily done by 
+  * using the vmdplugin_HEAD macro.
+  */
+typedef struct {
+  vmdplugin_HEAD
+} vmdplugin_t;
+
+/**
+ * Use this macro to initialize the abiversion member of each plugin
+ */
+#define vmdplugin_ABIVERSION  18
+
+/*@{*/
+/** Use this macro to indicate a plugin's thread-safety at registration time */
+#define VMDPLUGIN_THREADUNSAFE 0
+#define VMDPLUGIN_THREADSAFE   1
+/*@}*/
+
+/*@{*/
+/** Error return code for use in the plugin registration and init functions */
+#define VMDPLUGIN_SUCCESS      0
+#define VMDPLUGIN_ERROR       -1
+/*@}*/
+
+/** 
+ * Function pointer typedef for register callback functions
+ */
+typedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
+
+/**
+ * Allow the library to register plugins with the application.
+ * The callback should be called using the passed-in void pointer, which
+ * should not be interpreted in any way by the library.  Each vmdplugin_t
+ * pointer passed to the application should point to statically-allocated
+ * or heap-allocated memory and should never be later modified by the plugin.
+ * Applications must be permitted to retain only a copy of the the plugin
+ * pointer, without making any deep copy of the items in the struct.
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_register(void *, vmdplugin_register_cb);
+
+/**
+ * Allow the library to register Tcl extensions.  
+ * This API is optional; if found by dlopen, it will be called after first
+ * calling init and register.  
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl(void *, void *tcl_interp, 
+    vmdplugin_register_cb);
+
+/**
+ * The Fini method is called when the application will no longer use 
+ * any plugins in the library.  
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_fini(void);
+
+#endif   /* VMD_PLUGIN_H */

src/pertable.c

@@ -242,6 +242,60 @@ float pte_get_enegativity(const char *symbol)
 	return -1 ;
 }
 
+
+
+/**
+   ## FUNCTION:
+	pte_get_element_from_number
+  
+   ## SPECIFICATION:
+	Returns the symbol for a given element through the atomic number
+  
+   ## PARAMETERS:	
+	@ const char *symbol: The symbol of the element in the periodic table
+  
+   ## RETURN:
+	char*: atom element symbol
+  
+*/
+char *pte_get_element_from_number(int atomicnumber)
+{
+	char tmp[3] ;
+	if(atomicnumber>0 && atomicnumber<112){
+	
+		tmp[0] = ST_pte_symbol[atomicnumber][0] ;
+		tmp[1] = ST_pte_symbol[atomicnumber][1] ;
+		tmp[2] = '\0';
+		return tmp;
+	} 
+	return -1 ;
+}
+
+/**
+   ## FUNCTION:
+	pte_get_enegativity_from_number
+  
+   ## SPECIFICATION:
+	Returns the electronegativity (Pauling) value for a given element
+  
+   ## PARAMETERS:	
+	@ const char *symbol: The symbol of the element in the periodic table
+  
+   ## RETURN:
+	float: electrobegativity of Pauling corresponding to symbol
+  
+*/
+float pte_get_enegativity_from_number(int atomicnumber)
+{
+	if(atomicnumber>0 && atomicnumber<112)
+		return ST_pte_electronegativity[atomicnumber] ;
+		
+	
+
+	return -1 ;
+}
+
+
 /**
    ## FUNCTION:
 	is_valid_element

src/read_mmcif.c

@@ -74,132 +74,118 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
     rc2 = api->read_structure(h_in, &optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
-    //printf("%s | %s |%d\n", fpath, filetype, inatoms);
-    //print_molfile_atom_t(at_in, ts_in, inatoms);
-
-    /*-----------------------------------------------------------*/
-    //printf("Model Number : %d\n",model_number);
-    if (model_number > 0)
-        model_flag = 1; /*here we indicate that a particular model should be read only*/
-
+    if(!model_number) model_number=1;
+    model_flag=1;
     for (i = 0; i < inatoms; i++) /*loop to go through all atoms*/
     {
-        //printf("%d/%d\n", i, inatoms);
-        if (model_flag == 0 || model_read == 1)
+        if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
+            at_in[i].altloc[0] = ' ';
+        if (at_in[i].modelnumber==model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
         {
-            if (at_in[i].altloc[0] == '.')
-                at_in[i].altloc[0] = ' ';
-            if (!strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
+
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
             {
-                if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
+                if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
                 {
-
-                    //printf("TYPE : %s ` %d \n",at_in[i].name,i );
-
-                    if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
+                    /* Atom entry: check if there is a ligand in there (just in case)... */
+                    if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
                     {
-                        /* Atom entry: check if there is a ligand in there (just in case)... */
-                        if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
-                        {
-                            if (keep_lig)
-                            {
-                                natm_lig++;
-                                natoms++;
-                            }
-                            /*check this function*/
-                        }
-                        else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
-                        { /*here we have a protein chain defined as ligand...a bit more complex then*/
-                            if (keep_lig)
-                            {
-                                natm_lig++;
-                                natoms++;
-                            }
-                        }
-                        else
-                        {
-                            natoms++;
-                        }
-                    }
-                    if (par->xlig_resnumber > -1)
-                    {
-
-                        //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
-                        //fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
-
-                        if (at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])
-                        {
-                            pdb->n_xlig_atoms++;
-                            //fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
-                        }
-
-                        if (is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
-                        {
-                            pdb->n_xlig_atoms++;
-                            //fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
-                        }
-                    }
-                }
-            }
-            else if (!strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(par->chain_as_ligand,at_in[i].chain[0])))
-            {
-
-                if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
-                {
-
-                    if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
-                    {
-                        if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
+                        if (keep_lig)
                         {
                             natm_lig++;
                             natoms++;
                         }
-                        else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                        /*check this function*/
+                    }
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    { /*here we have a protein chain defined as ligand...a bit more complex then*/
+                        if (keep_lig)
                         {
-                            if (keep_lig)
-                                natm_lig++;
+                            natm_lig++;
                             natoms++;
                         }
-                        else
-                        {
-                            /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                            if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand,at_in[i].chain[0])))
-                            {
-                                //printf("N hetatm : %d\n", nhetatm);
-                                //printf("%s|%c ",resb,buf[21]);
-                                natoms++;
-                                nhetatm++;
-                            }
-                            else if (!is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
-                            {
-                                for (j = 0; j < ST_nb_keep_hetatm; j++)
-                                {
-                                    if (ST_keep_hetatm[j][0] == at_in[i].resname[0] && ST_keep_hetatm[j][1] == at_in[i].resname[1] && ST_keep_hetatm[j][2] == at_in[i].resname[2])
-                                    {
-                                        nhetatm++;
-                                        natoms++;
-                                        break;
-                                    }
-                                }
-                            }
-                        }
                     }
-                    if (par->xlig_resnumber > -1)
+                    else
                     {
+                        natoms++;
+                    }
+                }
+                if (par->xlig_resnumber > -1)
+                {
+
+                    //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
+                    //fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
 
                         if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
-                        {
-                            pdb->n_xlig_atoms++;
-                        }
+                    {
+                        pdb->n_xlig_atoms++;
+                        //fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
                     }
+
                     if (is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
                     {
                         pdb->n_xlig_atoms++;
-                        //fprintf(stdout, "H%d\t", pdb->n_xlig_atoms);
+                        //fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
                     }
                 }
             }
         }
+        else if (at_in[i].modelnumber==model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(par->chain_as_ligand,at_in[i].chain[0])))
+        {
+
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' )
+            {
+
+                if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
+                {
+                    if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
+                    {
+                        natm_lig++;
+                        natoms++;
+                    }
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    {
+                        if (keep_lig)
+                            natm_lig++;
+                        natoms++;
+                    }
+                    else
+                    {
+                        /* Keep specific HETATM given in the static list ST_keep_hetatm */
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand,at_in[i].chain[0])))
+                        {
+
+                            natoms++;
+                            nhetatm++;
+                        }
+                        else if (!is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
+                        {
+                            for (j = 0; j < ST_nb_keep_hetatm; j++)
+                            {
+                                if (ST_keep_hetatm[j][0] == at_in[i].resname[0] && ST_keep_hetatm[j][1] == at_in[i].resname[1] && ST_keep_hetatm[j][2] == at_in[i].resname[2])
+                                {
+                                    nhetatm++;
+                                    natoms++;
+                                    break;
+                                }
+                            }
+                        }
+                    }
+                }
+                if (par->xlig_resnumber > -1)
+                {
+                    if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+                    {
+                        pdb->n_xlig_atoms++;
+                    }
+                }
+                if (is_ligand(par->chain_as_ligand,at_in[i].chain[0]))
+                {
+                    pdb->n_xlig_atoms++;
+                }
+            }
+        }
+        
     }
 
     if (pdb->n_xlig_atoms)
@@ -290,23 +276,19 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
     //printf("READ : %s | %s |%d\n", pdb->fname, filetype, inatoms);
     /* Loop over the pdb file */
-    if (model_number > 0)
-        model_flag = 1; /*here we indicate that a particular model should be read only*/
+    model_flag=1;
+    if (!model_number ) model_number = 1;
+    ; /*here we indicate that a particular model should be read only*/
     for (i = 0; i < inatoms; i++)
     {
-        if (at_in[i].altloc[0] == '.')
+        if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
             at_in[i].altloc[0] = ' ';
-        //printf("%d/%d \n", i, inatoms);
-        if (model_flag == 0 || model_read == 1)
-        {
-            //printf("%c \n",at_in[i].altloc[0]);
-            if (!strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand,at_in[i].chain[0]))
+
+            if (at_in[i].modelnumber==model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand,at_in[i].chain[0]))
             {
-                //printf("TYPE : %s ` %d \n",at_in[i].name,i );
-                //printf("%c \n",at_in[i].altloc[0]); /* column 16 check for configuration of the residue e.g A,B */
-                if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
+
+                if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
                 { /*if within first occurence*/
-                    //printf("%c \n",at_in[i].altloc[0]);
                     /* Enter this if when arg in command line is -r */
                     if (pdb->n_xlig_atoms)
                     {
@@ -350,7 +332,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                 atom->z = ts_in.coords[(3 * i) + 2];
                                 atom->occupancy = at_in[i].occupancy;
                                 atom->bfactor = at_in[i].bfactor;
-                                strcpy(atom->symbol, at_in[i].name);
+                                strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+
 
                                 atom->charge = at_in[i].charge;
                                 atom->mass = at_in[i].mass;
@@ -387,7 +370,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                 atom->z = ts_in.coords[(3 * i) + 2];
                                 atom->occupancy = at_in[i].occupancy;
                                 atom->bfactor = at_in[i].bfactor;
-                                strcpy(atom->symbol, at_in[i].name);
+                                strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+
 
                                 atom->charge = at_in[i].charge;
                                 atom->mass = at_in[i].mass;
@@ -430,17 +414,19 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             //printf("ins:%s",at_in[i].insertion);
+                            
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
                             atom->z = ts_in.coords[(3 * i) + 2];
                             atom->occupancy = at_in[i].occupancy;
                             atom->bfactor = at_in[i].bfactor;
-                            strcpy(atom->symbol, at_in[i].name);
-
+                            strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+                            
                             atom->charge = at_in[i].charge;
                             atom->mass = at_in[i].mass;
                             atom->radius = at_in[i].radius;
-                            atom->electroneg = pte_get_enegativity(atom->symbol);
+                            
+                            atom->electroneg = pte_get_enegativity_from_number(at_in[i].atomicnumber);
                             guess_flag +=1;
 
                             /* Store additional information not given in the pdb */
@@ -452,16 +438,16 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
 
                             atoms_p[iatoms] = atom;
                             iatoms++;
+
                         }
                     }
                 }
             }
-            else if (!strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(params->chain_as_ligand,at_in[i].chain[0])))
+            else if (at_in[i].modelnumber==model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(params->chain_as_ligand,at_in[i].chain[0])))
             {
 
-                if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
+                if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A'  || at_in[i].altloc[0] == '1')
                 { /*first occurence*/
-                    //printf("ATOM TYPE: %s",at_in[i].atom_type);
                     if (pdb->n_xlig_atoms)
                     {
                         if ((at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
@@ -506,7 +492,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             atom->z = ts_in.coords[(3 * i) + 2];
                             atom->occupancy = at_in[i].occupancy;
                             atom->bfactor = at_in[i].bfactor;
-                            strcpy(atom->symbol, at_in[i].name);
+                            strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+
 
                             atom->charge = at_in[i].charge;
                             atom->mass = at_in[i].mass;
@@ -543,7 +530,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                 atom->z = ts_in.coords[(3 * i) + 2];
                                 atom->occupancy = at_in[i].occupancy;
                                 atom->bfactor = at_in[i].bfactor;
-                                strcpy(atom->symbol, at_in[i].name);
+                                strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+
 
                                 atom->charge = at_in[i].charge;
                                 atom->mass = at_in[i].mass;
@@ -581,7 +569,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                 atom->z = ts_in.coords[(3 * i) + 2];
                                 atom->occupancy = at_in[i].occupancy;
                                 atom->bfactor = at_in[i].bfactor;
-                                strcpy(atom->symbol, at_in[i].name);
+                                strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+
 
                                 atom->charge = at_in[i].charge;
                                 atom->mass = at_in[i].mass;
@@ -619,7 +608,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                         atom->z = ts_in.coords[(3 * i) + 2];
                                         atom->occupancy = at_in[i].occupancy;
                                         atom->bfactor = at_in[i].bfactor;
-                                        strcpy(atom->symbol, at_in[i].name);
+                                        strncpy(atom->symbol, pte_get_element_from_number(at_in[i].atomicnumber),3);
+
 
                                         atom->charge = at_in[i].charge;
                                         atom->mass = at_in[i].mass;
@@ -646,11 +636,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                 rpdb_extract_cryst1(pdb_line, &(pdb->alpha), &(pdb->beta), &(pdb->gamma),
                                     &(pdb->A), &(pdb->B), &(pdb->C));
             }
-            else if (model_read == 1 && !strncmp(at_in[i].atom_type, "ENDMDL", 6))
-                model_read = 0;
-            else if (model_number == 0 && !strncmp(at_in[i].atom_type, "END ", 3))
+            else if (!strncmp(at_in[i].atom_type, "END ", 3))
                 break;
-        }
     }
 
     pdb->avg_bfactor = 0.0;