mmcif_reading works but outputs fatal error

headers/read_mmcif.h

@@ -20,6 +20,9 @@
 #include "libmolfile_plugin.h"
 #include "molfile_plugin.h"
 
-void open_mmcif(const char *filepath, const char *filetype, int natoms);
+s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_number, s_fparams *par);
 
+void print_molfile_atom_t(molfile_atom_t *at_in, molfile_timestep_t ts_in, int inatoms);
+void write_files(molfile_atom_t *at_in, molfile_timestep_t ts_in, int inatoms, int optflags, char *filetype);
+void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_number, s_fparams *params);
 #endif

plugins/LINUXAMD64/molfile/libmolfile_plugin.h

@@ -9,6 +9,9 @@ extern "C" {
 extern int molfile_abinitplugin_init(void);
 extern int molfile_abinitplugin_register(void *, vmdplugin_register_cb);
 extern int molfile_abinitplugin_fini(void);
+extern int molfile_amiraplugin_init(void);
+extern int molfile_amiraplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_amiraplugin_fini(void);
 extern int molfile_avsplugin_init(void);
 extern int molfile_avsplugin_register(void *, vmdplugin_register_cb);
 extern int molfile_avsplugin_fini(void);
@@ -201,9 +204,13 @@ extern int molfile_dtrplugin_fini(void);
 extern int molfile_maeffplugin_init(void);
 extern int molfile_maeffplugin_register(void *, vmdplugin_register_cb);
 extern int molfile_maeffplugin_fini(void);
+extern int molfile_orcaplugin_init(void);
+extern int molfile_orcaplugin_register(void *, vmdplugin_register_cb);
+extern int molfile_orcaplugin_fini(void);
 
 #define MOLFILE_INIT_ALL \
     molfile_abinitplugin_init(); \
+    molfile_amiraplugin_init(); \
     molfile_avsplugin_init(); \
     molfile_babelplugin_init(); \
     molfile_basissetplugin_init(); \
@@ -268,9 +275,11 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_init(); \
     molfile_dtrplugin_init(); \
     molfile_maeffplugin_init(); \
+    molfile_orcaplugin_init(); \
 
 #define MOLFILE_REGISTER_ALL(v, cb) \
     molfile_abinitplugin_register(v, cb); \
+    molfile_amiraplugin_register(v, cb); \
     molfile_avsplugin_register(v, cb); \
     molfile_babelplugin_register(v, cb); \
     molfile_basissetplugin_register(v, cb); \
@@ -335,9 +344,11 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_register(v, cb); \
     molfile_dtrplugin_register(v, cb); \
     molfile_maeffplugin_register(v, cb); \
+    molfile_orcaplugin_register(v, cb); \
 
 #define MOLFILE_FINI_ALL \
     molfile_abinitplugin_fini(); \
+    molfile_amiraplugin_fini(); \
     molfile_avsplugin_fini(); \
     molfile_babelplugin_fini(); \
     molfile_basissetplugin_fini(); \
@@ -402,6 +413,7 @@ extern int molfile_maeffplugin_fini(void);
     molfile_xyzplugin_fini(); \
     molfile_dtrplugin_fini(); \
     molfile_maeffplugin_fini(); \
+    molfile_orcaplugin_fini(); \
 
 #ifdef __cplusplus
 }

plugins/include/CVS/Entries

@@ -1,5 +1,5 @@
 /import_graphics_plugin.h/1.5/Fri Sep 21 19:43:10 2007//
 /vmdconio.h/1.4/Sun Oct 11 22:36:27 2015//
-/vmdplugin.h/1.33/Thu Oct 29 05:10:54 2015//
-/molfile_plugin.h/1.108/Fri Feb 26 03:17:01 2016//
+/vmdplugin.h/1.34/Wed May  2 03:12:56 2018//
+/molfile_plugin.h/1.112/Thu Oct 17 06:12:24 2019//
 D

plugins/include/molfile_plugin.h

@@ -11,7 +11,7 @@
  *
  *      $RCSfile: molfile_plugin.h,v $
  *      $Author: johns $       $Locker:  $             $State: Exp $
- *      $Revision: 1.108 $       $Date: 2016/02/26 03:17:01 $
+ *      $Revision: 1.112 $       $Date: 2019/10/17 06:12:24 $
  *
  ***************************************************************************/
 
@@ -57,8 +57,7 @@ typedef ssize_t molfile_ssize_t;      /**< for frame counts */
 #define MOLFILE_BUFSIZ           81   /**< maximum chars in string data  */
 #define MOLFILE_BIGBUFSIZ        4096 /**< maximum chars in long strings */
 
-#define MOLFILE_MAXWAVEPERTS     25   /**< maximum number of wavefunctions
-                                       *   per timestep */
+#define MOLFILE_MAXWAVEPERTS     25   /**< maximum number of wavefunctions per timestep */
 
 /**
  * Hard-coded direct-I/O page size constants for use by both VMD
@@ -106,12 +105,13 @@ typedef struct {
  */
 typedef struct {
   /* these fields absolutely must be set or initialized to empty */
+  char atom_type[8];
   char name[16];      /**< required atom name string             */
   char type[16];      /**< required atom type string             */
   char resname[8];    /**< required residue name string          */
   int resid;          /**< required integer residue ID           */
   char segid[8];      /**< required segment name string, or ""   */
-#if 0 && vmdplugin_ABIVERSION > 17
+#if 0 && vmdplugin_ABIVERSION > 10000
   /* The new PDB file formats allows for much larger structures, */
   /* which can therefore require longer chain ID strings.  The   */
   /* new PDBx/mmCIF file formats do not have length limits on    */
@@ -187,9 +187,54 @@ typedef struct molfile_timestep_metadata {
   int has_velocities;                  /**< if timesteps have velocities     */
 } molfile_timestep_metadata_t;
 
-/*
- * Per-timestep atom coordinates and periodic cell information
+
+/* 
+ *
+ * Per-timestep atom coordinates, velocities, forces, energies,
+ * and periodic cell information
+ *
  */ 
+
+#if 0
+/**
+ * Periodically stored energies of various kinds
+ */
+typedef struct {
+  int energyflags;         // XXX indicate use and semantics of data fields
+
+  double total_energy;     // XXX these copied from DESRES_READ_TIMESTEP2 case
+  double potential_energy;
+  double kinetic_energy;
+  double extended_energy;
+  double force_energy;
+  double total_pressure;
+
+  // Alchemical free energy methods need to store individual energy samples.
+  // We don't really want pre-averaged quantities, they lead to problems later.
+  double lambda;       // data gen sim parm: + aux scheduling + soft core parm
+  double temperature;  // temp set by thermostat
+  // either we use deltaU, or we store U and Uprime... 
+  double deltaU;       // Ulambda - Ulambdaprime
+  double Ulambda;      // U for lambda
+  double Ulambdaprime; // U for lambdaprime
+
+  // IDWS methods
+  // XXX both values of lambdaprime and required de-interleaving information
+
+  // Replica exchange methods
+  // XXX rectangle sample params?
+  
+  // REST2 method
+  // XXX 
+
+} molfile_energies_t;
+#endif
+
+
+/**
+ * Per-timestep atom coordinates, velocities, time, energies 
+ * and periodic cell info
+ */
 typedef struct {
   float *coords;        /**< coordinates of all atoms, arranged xyzxyzxyz   */
   float *velocities;    /**< space for velocities of all atoms; same layout */
@@ -839,6 +884,29 @@ typedef struct {
   int (* read_qm_rundata)(void *, molfile_qm_t *qmdata);
 
 
+  /**
+   * Query the molfile plugin to determine whether or not memory
+   * allocations used for atomic coordinates and PBC unit cell information
+   * need to be aligned to a particular virtual memory or filesystem 
+   * page size boundary to facilitate kernel-bypass unbuffered I/O,
+   * e.g., as used by jsplugin.  This API should be called prior to the
+   * first call to read a timestep.  The required page alignment size 
+   * (in bytes) is returned to the caller.  If this API has not been 
+   * called, then the molfile plugin should revert to standard 
+   * kernel-buffered I/O and suffer the associated performance loss.
+   * The caller can be assured that the plugin will not request any 
+   * page alignment size that is greater than the value of 
+   * MOLFILE_DIRECTIO_MAX_BLOCK_SIZE, both as a runtime sanity check,
+   * and to ensure that a caller that is unable to perform the max 
+   * aligned allocation doesn't call the API in the first place.
+   * If a page-aligned allocation is not required for the file being read,
+   * the plugin will return an alignment size of 1. 
+   */ 
+#if vmdplugin_ABIVERSION > 17
+  int (* read_timestep_pagealign_size)(void *, int *pagealignsize);
+#endif
+
+
   /**
    * Read the next timestep from the file.  Return MOLFILE_SUCCESS, or 
    * MOLFILE_EOF on EOF.  If the molfile_timestep_t or molfile_qm_metadata_t
@@ -862,6 +930,25 @@ typedef struct {
   int (* read_timestep_metadata)(void *, molfile_timestep_metadata_t *);
   int (* read_qm_timestep_metadata)(void *, molfile_qm_timestep_metadata_t *);
 
+
+#if defined(EXPERIMENTAL_DIRECTIO_APIS)
+  /**
+    * Calculate file offsets and I/O lengths for performing 
+    * kernel-bypass direct I/O or using GPU-Direct Storage APIs,
+    * thereby enabling peak I/O rates to be achieved for analysis 
+    * worksloads like clustering of trajectories.
+    */
+  int (* calc_fileoffsets_timestep)(void *, 
+                                    molfile_ssize_t frameindex, 
+                                    int firstatom, 
+                                    int lastatom,
+                                    int *firstatom, 
+                                    int *pageoffset,
+                                    molfile_ssize_t *startoffset,
+                                    molfile_ssize_t *readlen);
+#endif
+
+
 #if defined(DESRES_READ_TIMESTEP2)
   /**
     * Read a specified timestep!

plugins/include/render_plugin.h

@@ -0,0 +1,212 @@
+/***************************************************************************
+ *cr
+ *cr            (C) Copyright 1995-2006 The Board of Trustees of the
+ *cr                        University of Illinois
+ *cr                         All Rights Reserved
+ *cr
+ ***************************************************************************/
+
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ *      $RCSfile: molfile_plugin.h,v $
+ *      $Author: johns $       $Locker:  $             $State: Exp $
+ *      $Revision: 1.108 $       $Date: 2016/02/26 03:17:01 $
+ *
+ ***************************************************************************/
+
+/** @file 
+ * API for C extensions to define a way to control VMD rendering for inclusion
+ * in third-party rendering workflows.
+ */ 
+
+#ifndef RENDER_PLUGIN_H
+#define RENDER_PLUGIN_H
+
+#include "vmdplugin.h"
+
+/**
+ * Define a common plugin type to be used when registering the plugin.
+ */
+#define RENDER_PLUGIN_TYPE "render control"
+
+/* File plugin symbolic constants for better code readability */
+#define RENDER_SUCCESS           0   /**< succeeded in reading file      */
+#define RENDER_ERROR            -1   /**< error reading/opening a file   */
+
+/** 
+ * Camera definition in global coordinate system 
+ */
+typedef struct {
+  Vector pos;    /**< camera position */
+  Vector fwd;    /**< camera forward vector ("-Z" in OpenGL style) */
+  Vector up;     /**< camera up vector ("+Y" in OpenGL style) */
+  double fov_y;  /**< field-of-view in Y (vertical) axis (degrees) */
+
+  /** XXX work on these some more       
+  double scale;  /* global scale.  (in which sense?
+                  * Does cale=0.1 make the camera small, 
+                  * or make the world small?)
+                  */
+
+  int as_dome;    /**< 0=> planar projection, 1=> dome rendering */
+} vcam_camdef_t;
+
+
+/**
+ * global read-only values that would be nice to know
+ * Supposing there's a 4x4 matrix type called Matrix, and a 3-d Vector type
+ */
+typedef struct {
+  Matrix mrotate;
+  Matrix mcenter;
+  Matrix mscale;
+  Matrix mglobal;
+  Vector vback;    // "back" translation of camera 
+                   // (seems to be 0,0,-2 by default?)
+                   // other stuff?  framebuffer resolution?  
+                   // aspect ratio?   stereo separation in 
+                   // camera-coordinate units?  Global scale?
+} vcam_cam_globals_t;
+   
+
+// When we ask VMD to take a screen snapshot, what type?
+typedef enum {
+  SNAP_RGB8,        // grab a memory buffer and pass it to us, 
+                    // of 8-bit RGB/RGBA pixels
+                    // do we care about option of greater bit
+                    // depths, like 16-bit or float per-channel?  
+                    // Does VMD do rendering that would take 
+                    // advantage of it?
+
+
+  SNAP_PNG,         // Save as PNG image (or JPEG or TGA or PPM
+                    // or whatever you support) 
+                    // (with alpha if requested) JPEG? H264?
+
+  // XXX add these?
+  SNAP_PPM,         // 24-bit RGB PPM
+  SNAP_PPM48,       // 48-bit RGB PPM
+  SNAP_TGA,         // 24-bit RGB Targa
+ vcam_snaptype_t;
+
+
+// description of a snapshot after it's taken.
+typedef struct {
+   int xsize;         // image width
+   int ysize;
+   int channels;      // number of channels (3 or 4 for RGB vs RGBA)
+   int bpchan;        // bytes per channel value (1 for 8-bit, 2 for 16-bit, 4 for float?)
+   int bprow;         // bytes per row (may be bpchan*channels*xsize or a bit bigger if padded)
+
+   void *data;        // pointer to image array.  
+                      // Data owned by VMD - plugin shouldn't rely on 
+                      // it existing after return?  and shouldn't write
+                      // to it.  
+                      // data may be NULL if we asked for 
+                      // snapshot to be saved to an image file.
+} vcam_snap_t;
+
+
+// XXX I don't think we need this anymore
+#define VCAM_VERSION 0x0100
+
+// struct-full-of-callback-pointers, set at plugin initialization
+typedef struct { 
+  // magic number.  Allows checking for future-incompatible 
+  // versions of this interface
+  int version;
+
+  // Ask VMD to render next frame using this camera viewpoint/setup.
+  // I'm assuming we can't ask for a change in resolution, but 
+  // can ask for a different FOV or dome/planar setup... OK?
+  void (*set_cam)( vcam_camdef_t * );
+
+  // Ask VMD to take a screen snapshot of next rendered frame.
+  // VMD will call *us* back (vcam_snapped() below) when 
+  // it's done, and tell us image resolution etc.
+  // Assuming this is a one-shot - if we want more snapshots, 
+  // we have to call this again for each frame
+  // If VMD's framebuffer records alpha (even 0-vs-1 coverage),
+  // it might be nice to allow passing that along.
+  // If there's no alpha recorded there, then nevermind offering
+  // that option.
+  // filename would be NULL if we're asking for a raw RGB/RGBA buffer
+  void (*take_snap)( vcam_snaptype_t style, int withalpha, char *filename );
+
+  // ask for values of camera-related global variables, something like that?
+  void (*get_cam_globals)( vcam_cam_globals_t * );
+} vcam_init_t;
+
+
+Functions in the plugin that VMD may call:
+   void vcam_init( struct vcam_init_t * );
+     // called once at startup.
+     // If the plugin receives an interface version that it can't handle,
+     // then it should ignore calls to any of the other entry points.
+     void vcam_preframe();
+    
+     // may call the callbacks specified in the vcam_init_t structure
+     void vcam_snapped( vcam_snap_t * );
+     
+     // called by VMD after a requested snapshot is complete
+     void vcam_shutdown();
+  }
+
+
+
+
+
+/**
+ * Main file reader API.  Any function in this struct may be NULL
+ * if not implemented by the plugin; the application checks this to determine
+ * what functionality is present in the plugin. 
+ */ 
+typedef struct {
+  /**
+   * Required header 
+   */
+  vmdplugin_HEAD
+
+  /**
+   * Filename extension for this file type.  May be NULL if no filename 
+   * extension exists and/or is known.  For file types that match several
+   * common extensions, list them in a comma separated list such as:
+   *  "pdb,ent,foo,bar,baz,ban"
+   * The comma separated list will be expanded when filename extension matching
+   * is performed.  If multiple plugins solicit the same filename extensions,
+   * the one that lists the extension earliest in its list is selected. In the 
+   * case of a "tie", the first one tried/checked "wins".
+   */
+  const char *filename_extension;
+
+#if 0
+  // XXX insert stuff here
+
+
+
+#endif
+
+  /**
+   *  Console output, READ-ONLY function pointer.
+   *  Function pointer that plugins can use for printing to the host
+   *  application's text console.  This provides a clean way for plugins
+   *  to send message strings back to the calling application, giving the
+   *  caller the ability to prioritize, buffer, and redirect console messages
+   *  to an appropriate output channel, window, etc.  This enables the use of
+   *  graphical consoles like TkCon without losing console output from plugins.
+   *  If the function pointer is NULL, no console output service is provided
+   *  by the calling application, and the output should default to stdout
+   *  stream.  If the function pointer is non-NULL, all output will be
+   *  subsequently dealt with by the calling application.
+   *
+   *  XXX this should really be put into a separate block of
+   *      application-provided read-only function pointers for any
+   *      application-provided services
+   */
+  int (* cons_fputs)(const int, const char*);
+
+} molfile_plugin_t;
+
+#endif
+

plugins/include/vmdplugin.h

@@ -11,7 +11,7 @@
  *
  *      $RCSfile: vmdplugin.h,v $
  *      $Author: johns $       $Locker:  $             $State: Exp $
- *      $Revision: 1.33 $       $Date: 2015/10/29 05:10:54 $
+ *      $Revision: 1.34 $       $Date: 2018/05/02 03:12:56 $
  *
  ***************************************************************************/
 
@@ -144,7 +144,7 @@ typedef struct {
 /**
  * Use this macro to initialize the abiversion member of each plugin
  */
-#define vmdplugin_ABIVERSION  17
+#define vmdplugin_ABIVERSION  18
 
 /*@{*/
 /** Use this macro to indicate a plugin's thread-safety at registration time */

src/fparams.c

@@ -145,7 +145,7 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
             case 0:
                 break;
 
-            case M_PAR_CHAIN_AS_LIGAND :
+            case M_PAR_CHAIN_AS_LIGAND : /*option with -a "name of the chain" to be specified as a ligand*/
                 /*select the chains as ligand*/
                 status++;
                 strcpy(par->chain_as_ligand, optarg); /*par->chain_as_ligand contains the arg given in cmd line*/
@@ -163,7 +163,7 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
                 
                 break;
 
-            case M_PAR_DROP_CHAINS :
+            case M_PAR_DROP_CHAINS : /*option with -c "name of the chains"*/
             /*drop the selected chains from the pdb file*/
                 strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
                 //printf("%s and %s",par->custom_ligand,optarg);
@@ -180,7 +180,7 @@ s_fparams* get_fpocket_args(int nargs, char **args) {
                 status++;
                 break;
                 
-            case M_PAR_KEEP_CHAINS :
+            case M_PAR_KEEP_CHAINS : /*option with -k "name of the chains"*/
             /*drop the selected chains from the pdb file*/
                 
                 strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/

src/fpmain.c

@@ -56,12 +56,10 @@ static int register_cb(void *v, vmdplugin_t *p)
 int main(int argc, char *argv[])
 {
 
-        const char *cif_path = "/home/maels/fpocket/data/sample/2P0R.cif";
-        const char *cif_format = "pdbx";
-
-        int cif_nb;
-        open_mmcif(cif_path, cif_format, cif_nb);
+        
+        
         s_fparams *params = get_fpocket_args(argc, argv);
+        
         params->fpocket_running = 1;
         /* If parameters parsing is ok */
         if (params)
@@ -69,13 +67,14 @@ int main(int argc, char *argv[])
                 if (!params->db_run)
                         fprintf(stdout, "***** POCKET HUNTING BEGINS ***** \n");
                 //                print_fparams(params,stdout);
+                
                 if (params->pdb_lst != NULL)
                 {
                         /* Handle a list of pdb */
                         int i;
                         for (i = 0; i < params->npdb; i++)
                         {
-
+                                
                                 printf("> Protein %d / %d : %s", i, params->npdb,
                                        params->pdb_lst[i]);
                                 if (i == params->npdb - 1)
@@ -94,7 +93,8 @@ int main(int argc, char *argv[])
                                 print_pocket_usage(stdout);
                         }
                         else
-                        {
+                        {       
+                                
                                 process_pdb(params->pdb_path, params);
                         }
                 }
@@ -150,9 +150,14 @@ void process_pdb(char *pdbname, s_fparams *params)
         /* Try to open it */
         if (DEBUG)
                 print_number_of_objects_in_memory();
-        s_pdb *pdb = rpdb_open(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+      //  s_pdb *pdb2 = open_mmcif(pdbname, NULL, M_DONT_KEEP_LIG,params->model_number, params);
+      s_pdb *pdb = open_mmcif(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+        s_pdb *pdb_w_lig = open_mmcif(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
+        
+        
+       // s_pdb *pdb = rpdb_open(pdbname, NULL, M_DONT_KEEP_LIG, params->model_number, params);
 
-        s_pdb *pdb_w_lig = rpdb_open(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
+       // s_pdb *pdb_w_lig = rpdb_open(pdbname, NULL, M_KEEP_LIG, params->model_number, params);
         if (DEBUG)
                 print_number_of_objects_in_memory();
 
@@ -164,9 +169,14 @@ void process_pdb(char *pdbname, s_fparams *params)
         if (pdb)
         {
                 /* Actual reading of pdb data and then calculation */
-                rpdb_read(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
 
-                rpdb_read(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
+                read_mmcif(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+
+                read_mmcif(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
+
+                //rpdb_read(pdb, NULL, M_DONT_KEEP_LIG, params->model_number, params);
+
+                //rpdb_read(pdb_w_lig, NULL, M_KEEP_LIG, params->model_number, params);
 
                 //                        fprintf(stdout,"Init coordinate grid\n");
                 create_coord_grid(pdb);

src/rpdb.c

@@ -834,7 +834,7 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
         if (!strncmp(buf, "MODEL", 5) && model_number > 0)
         {
             cur_model_count++;
-            //printf("model : %d\n",cur_model_count);
+            printf("model : %d\n", cur_model_count);
             if (cur_model_count == model_number)
                 model_read = 1;
         }
@@ -892,12 +892,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                             pdb->n_xlig_atoms++;
                             fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
                         }
-                    }
 
-                    if (buf[21] == par->chain_as_ligand[0])
-                    {
-                        pdb->n_xlig_atoms++;
-                        //fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
+                        if (buf[21] == par->chain_as_ligand[0])
+                        {
+                            pdb->n_xlig_atoms++;
+                            //fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
+                        }
                     }
                 }
             }
@@ -926,7 +926,7 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         else if (ligan && strlen(ligan) == 1 && ligan[0] == buf[21])
                         {
                             if (keep_lig)
-                                natm_lig++;
+                            natm_lig++;
                             natoms++;
                         }
                         else
@@ -1208,7 +1208,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                             atom->radius = pte_get_vdw_ray(atom->symbol);
                             atom->electroneg = pte_get_enegativity(atom->symbol);
                             atom->sort_x = -1;
-
+                            //printf("type : %s, id : %d, name : %s, aloc : %c, res_name : %s, chain  : %s, res_id : %d, pdb_insert : %c, occupancy : %f, b_factor : %f, symbol : %s, charge : %d\n",
+                             //atom->type, atom->id,atom->name ,atom->pdb_aloc,atom->res_name,atom->chain,atom->res_id,atom->pdb_insert,atom->occupancy,atom->bfactor, atom->symbol,atom->charge);
+                            //printf("electroneg : %s\n",atom->symbol);
                             atoms_p[iatoms] = atom;
                             iatoms++;
                         }
@@ -1336,6 +1338,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                     {
 
                                         atom = atoms + iatoms;
+
                                         rpdb_extract_pdb_atom(pdb_line, atom->type, &(atom->id),
                                                               atom->name, &(atom->pdb_aloc), atom->res_name,
                                                               atom->chain, &(atom->res_id), &(atom->pdb_insert),
@@ -1348,7 +1351,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                         atom->radius = pte_get_vdw_ray(atom->symbol);
                                         atom->electroneg = pte_get_enegativity(atom->symbol);
                                         atom->sort_x = -1;
-
+                                        
                                         atoms_p[iatoms] = atom;
                                         pdb->lhetatm[ihetatm] = atom;
                                         ihetatm++;
@@ -1500,7 +1503,7 @@ void free_pdb_atoms(s_pdb *pdb)
  */
 int chains_to_delete(char *chains_selected, char *current_line_chain, int is_chain_kept)
 { /*deletes the chains selected by command -c, returns true if the chain correspond false if not*/
-    
+
     if (is_chain_kept == 0)
     {
         int is_deleted = 1;
@@ -1517,18 +1520,18 @@ int chains_to_delete(char *chains_selected, char *current_line_chain, int is_cha
         return is_deleted;
     }
     else
-    {      
-            int is_deleted = 0;
-            int i = 0;
-            for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+    {
+        int is_deleted = 0;
+        int i = 0;
+        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        {
+            if (chains_selected[i] == current_line_chain)
             {
-                if (chains_selected[i] == current_line_chain)
-                {
-                    //printf("%c_%c ", chains_selected[i],current_line_chain);
-                    is_deleted = 1;
-                }
+                //printf("%c_%c ", chains_selected[i],current_line_chain);
+                is_deleted = 1;
             }
-            //printf("\n");
-            return is_deleted;
+        }
+        //printf("\n");
+        return is_deleted;
     }
 }