issue-151 fix of chain reading atoms in read_mmcif & descriptor output writing

README.md

@@ -107,11 +107,6 @@ make ARCH=MACOSXX86_64
 sudo make install
 ```
 
-For M1 and M2, use the MACOSXARM64 architecture:
-```
-ARCH=MACOSXARM64 make
-```
-
 #### Using conda
 
 There's also a conda package of fpocket available thanks to Simon Bray. You can install fpocket using conda with:

headers/descriptors.h

@@ -81,8 +81,8 @@ typedef struct s_desc
                 characterChain2,                         /**< 0 if protein, 1 if nucl acid pocket, 2 if HETATM pocket*/
                 numResChain1,                            /**<number of resdiues on chain 1*/
                 numResChain2;                           /**<number of res on chain 2*/
-        char nameChain1[2],        /**<name of the first chain in contact with the pocket*/
-                nameChain2[2];     /**<name of the second chain in contact with the pocket, if there is*/
+        char nameChain1[255],        /**<name of the first chain in contact with the pocket*/
+                nameChain2[255];     /**<name of the second chain in contact with the pocket, if there is*/
         char ligTag[8];           /**<het atom tag of ligands situated in the pocket*/
         
 } s_desc ;

plugins/MACOSXARM64/molfile/libmolfile_plugin.h

@@ -1,415 +0,0 @@
-#ifndef LIBMOLFILE_PLUGIN_H
-#define LIBMOLFILE_PLUGIN_H
-#include "vmdplugin.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-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);
-extern int molfile_babelplugin_init(void);
-extern int molfile_babelplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_babelplugin_fini(void);
-extern int molfile_basissetplugin_init(void);
-extern int molfile_basissetplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_basissetplugin_fini(void);
-extern int molfile_bgfplugin_init(void);
-extern int molfile_bgfplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_bgfplugin_fini(void);
-extern int molfile_binposplugin_init(void);
-extern int molfile_binposplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_binposplugin_fini(void);
-extern int molfile_biomoccaplugin_init(void);
-extern int molfile_biomoccaplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_biomoccaplugin_fini(void);
-extern int molfile_brixplugin_init(void);
-extern int molfile_brixplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_brixplugin_fini(void);
-extern int molfile_carplugin_init(void);
-extern int molfile_carplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_carplugin_fini(void);
-extern int molfile_ccp4plugin_init(void);
-extern int molfile_ccp4plugin_register(void *, vmdplugin_register_cb);
-extern int molfile_ccp4plugin_fini(void);
-extern int molfile_corplugin_init(void);
-extern int molfile_corplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_corplugin_fini(void);
-extern int molfile_cpmdplugin_init(void);
-extern int molfile_cpmdplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_cpmdplugin_fini(void);
-extern int molfile_crdplugin_init(void);
-extern int molfile_crdplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_crdplugin_fini(void);
-extern int molfile_cubeplugin_init(void);
-extern int molfile_cubeplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_cubeplugin_fini(void);
-extern int molfile_dcdplugin_init(void);
-extern int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_dcdplugin_fini(void);
-extern int molfile_dlpolyplugin_init(void);
-extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_dlpolyplugin_fini(void);
-extern int molfile_dsn6plugin_init(void);
-extern int molfile_dsn6plugin_register(void *, vmdplugin_register_cb);
-extern int molfile_dsn6plugin_fini(void);
-extern int molfile_dxplugin_init(void);
-extern int molfile_dxplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_dxplugin_fini(void);
-extern int molfile_edmplugin_init(void);
-extern int molfile_edmplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_edmplugin_fini(void);
-extern int molfile_fs4plugin_init(void);
-extern int molfile_fs4plugin_register(void *, vmdplugin_register_cb);
-extern int molfile_fs4plugin_fini(void);
-extern int molfile_gamessplugin_init(void);
-extern int molfile_gamessplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_gamessplugin_fini(void);
-extern int molfile_graspplugin_init(void);
-extern int molfile_graspplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_graspplugin_fini(void);
-extern int molfile_grdplugin_init(void);
-extern int molfile_grdplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_grdplugin_fini(void);
-extern int molfile_gridplugin_init(void);
-extern int molfile_gridplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_gridplugin_fini(void);
-extern int molfile_gromacsplugin_init(void);
-extern int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_gromacsplugin_fini(void);
-extern int molfile_jsplugin_init(void);
-extern int molfile_jsplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_jsplugin_fini(void);
-extern int molfile_lammpsplugin_init(void);
-extern int molfile_lammpsplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_lammpsplugin_fini(void);
-extern int molfile_mapplugin_init(void);
-extern int molfile_mapplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_mapplugin_fini(void);
-extern int molfile_mdfplugin_init(void);
-extern int molfile_mdfplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_mdfplugin_fini(void);
-extern int molfile_mol2plugin_init(void);
-extern int molfile_mol2plugin_register(void *, vmdplugin_register_cb);
-extern int molfile_mol2plugin_fini(void);
-extern int molfile_moldenplugin_init(void);
-extern int molfile_moldenplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_moldenplugin_fini(void);
-extern int molfile_molemeshplugin_init(void);
-extern int molfile_molemeshplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_molemeshplugin_fini(void);
-extern int molfile_msmsplugin_init(void);
-extern int molfile_msmsplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_msmsplugin_fini(void);
-extern int molfile_namdbinplugin_init(void);
-extern int molfile_namdbinplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_namdbinplugin_fini(void);
-extern int molfile_offplugin_init(void);
-extern int molfile_offplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_offplugin_fini(void);
-extern int molfile_parm7plugin_init(void);
-extern int molfile_parm7plugin_register(void *, vmdplugin_register_cb);
-extern int molfile_parm7plugin_fini(void);
-extern int molfile_parmplugin_init(void);
-extern int molfile_parmplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_parmplugin_fini(void);
-extern int molfile_pbeqplugin_init(void);
-extern int molfile_pbeqplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_pbeqplugin_fini(void);
-extern int molfile_pdbplugin_init(void);
-extern int molfile_pdbplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_pdbplugin_fini(void);
-extern int molfile_pdbxplugin_init(void);
-extern int molfile_pdbxplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_pdbxplugin_fini(void);
-extern int molfile_phiplugin_init(void);
-extern int molfile_phiplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_phiplugin_fini(void);
-extern int molfile_pltplugin_init(void);
-extern int molfile_pltplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_pltplugin_fini(void);
-extern int molfile_plyplugin_init(void);
-extern int molfile_plyplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_plyplugin_fini(void);
-extern int molfile_pqrplugin_init(void);
-extern int molfile_pqrplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_pqrplugin_fini(void);
-extern int molfile_psfplugin_init(void);
-extern int molfile_psfplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_psfplugin_fini(void);
-extern int molfile_raster3dplugin_init(void);
-extern int molfile_raster3dplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_raster3dplugin_fini(void);
-extern int molfile_rst7plugin_init(void);
-extern int molfile_rst7plugin_register(void *, vmdplugin_register_cb);
-extern int molfile_rst7plugin_fini(void);
-extern int molfile_situsplugin_init(void);
-extern int molfile_situsplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_situsplugin_fini(void);
-extern int molfile_spiderplugin_init(void);
-extern int molfile_spiderplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_spiderplugin_fini(void);
-extern int molfile_stlplugin_init(void);
-extern int molfile_stlplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_stlplugin_fini(void);
-extern int molfile_tinkerplugin_init(void);
-extern int molfile_tinkerplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_tinkerplugin_fini(void);
-extern int molfile_uhbdplugin_init(void);
-extern int molfile_uhbdplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_uhbdplugin_fini(void);
-extern int molfile_vaspchgcarplugin_init(void);
-extern int molfile_vaspchgcarplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vaspchgcarplugin_fini(void);
-extern int molfile_vaspoutcarplugin_init(void);
-extern int molfile_vaspoutcarplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vaspoutcarplugin_fini(void);
-extern int molfile_vaspparchgplugin_init(void);
-extern int molfile_vaspparchgplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vaspparchgplugin_fini(void);
-extern int molfile_vaspposcarplugin_init(void);
-extern int molfile_vaspposcarplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vaspposcarplugin_fini(void);
-extern int molfile_vasp5xdatcarplugin_init(void);
-extern int molfile_vasp5xdatcarplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vasp5xdatcarplugin_fini(void);
-extern int molfile_vaspxdatcarplugin_init(void);
-extern int molfile_vaspxdatcarplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vaspxdatcarplugin_fini(void);
-extern int molfile_vaspxmlplugin_init(void);
-extern int molfile_vaspxmlplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vaspxmlplugin_fini(void);
-extern int molfile_vtkplugin_init(void);
-extern int molfile_vtkplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_vtkplugin_fini(void);
-extern int molfile_xbgfplugin_init(void);
-extern int molfile_xbgfplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_xbgfplugin_fini(void);
-extern int molfile_xsfplugin_init(void);
-extern int molfile_xsfplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_xsfplugin_fini(void);
-extern int molfile_xyzplugin_init(void);
-extern int molfile_xyzplugin_register(void *, vmdplugin_register_cb);
-extern int molfile_xyzplugin_fini(void);
-extern int molfile_dtrplugin_init(void);
-extern int molfile_dtrplugin_register(void *, vmdplugin_register_cb);
-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);
-
-#define MOLFILE_INIT_ALL \
-    molfile_abinitplugin_init(); \
-    molfile_amiraplugin_init(); \
-    molfile_avsplugin_init(); \
-    molfile_babelplugin_init(); \
-    molfile_basissetplugin_init(); \
-    molfile_bgfplugin_init(); \
-    molfile_binposplugin_init(); \
-    molfile_biomoccaplugin_init(); \
-    molfile_brixplugin_init(); \
-    molfile_carplugin_init(); \
-    molfile_ccp4plugin_init(); \
-    molfile_corplugin_init(); \
-    molfile_cpmdplugin_init(); \
-    molfile_crdplugin_init(); \
-    molfile_cubeplugin_init(); \
-    molfile_dcdplugin_init(); \
-    molfile_dlpolyplugin_init(); \
-    molfile_dsn6plugin_init(); \
-    molfile_dxplugin_init(); \
-    molfile_edmplugin_init(); \
-    molfile_fs4plugin_init(); \
-    molfile_gamessplugin_init(); \
-    molfile_graspplugin_init(); \
-    molfile_grdplugin_init(); \
-    molfile_gridplugin_init(); \
-    molfile_gromacsplugin_init(); \
-    molfile_jsplugin_init(); \
-    molfile_lammpsplugin_init(); \
-    molfile_mapplugin_init(); \
-    molfile_mdfplugin_init(); \
-    molfile_mol2plugin_init(); \
-    molfile_moldenplugin_init(); \
-    molfile_molemeshplugin_init(); \
-    molfile_msmsplugin_init(); \
-    molfile_namdbinplugin_init(); \
-    molfile_offplugin_init(); \
-    molfile_parm7plugin_init(); \
-    molfile_parmplugin_init(); \
-    molfile_pbeqplugin_init(); \
-    molfile_pdbplugin_init(); \
-    molfile_pdbxplugin_init(); \
-    molfile_phiplugin_init(); \
-    molfile_pltplugin_init(); \
-    molfile_plyplugin_init(); \
-    molfile_pqrplugin_init(); \
-    molfile_psfplugin_init(); \
-    molfile_raster3dplugin_init(); \
-    molfile_rst7plugin_init(); \
-    molfile_situsplugin_init(); \
-    molfile_spiderplugin_init(); \
-    molfile_stlplugin_init(); \
-    molfile_tinkerplugin_init(); \
-    molfile_uhbdplugin_init(); \
-    molfile_vaspchgcarplugin_init(); \
-    molfile_vaspoutcarplugin_init(); \
-    molfile_vaspparchgplugin_init(); \
-    molfile_vaspposcarplugin_init(); \
-    molfile_vasp5xdatcarplugin_init(); \
-    molfile_vaspxdatcarplugin_init(); \
-    molfile_vaspxmlplugin_init(); \
-    molfile_vtkplugin_init(); \
-    molfile_xbgfplugin_init(); \
-    molfile_xsfplugin_init(); \
-    molfile_xyzplugin_init(); \
-    molfile_dtrplugin_init(); \
-    molfile_maeffplugin_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); \
-    molfile_bgfplugin_register(v, cb); \
-    molfile_binposplugin_register(v, cb); \
-    molfile_biomoccaplugin_register(v, cb); \
-    molfile_brixplugin_register(v, cb); \
-    molfile_carplugin_register(v, cb); \
-    molfile_ccp4plugin_register(v, cb); \
-    molfile_corplugin_register(v, cb); \
-    molfile_cpmdplugin_register(v, cb); \
-    molfile_crdplugin_register(v, cb); \
-    molfile_cubeplugin_register(v, cb); \
-    molfile_dcdplugin_register(v, cb); \
-    molfile_dlpolyplugin_register(v, cb); \
-    molfile_dsn6plugin_register(v, cb); \
-    molfile_dxplugin_register(v, cb); \
-    molfile_edmplugin_register(v, cb); \
-    molfile_fs4plugin_register(v, cb); \
-    molfile_gamessplugin_register(v, cb); \
-    molfile_graspplugin_register(v, cb); \
-    molfile_grdplugin_register(v, cb); \
-    molfile_gridplugin_register(v, cb); \
-    molfile_gromacsplugin_register(v, cb); \
-    molfile_jsplugin_register(v, cb); \
-    molfile_lammpsplugin_register(v, cb); \
-    molfile_mapplugin_register(v, cb); \
-    molfile_mdfplugin_register(v, cb); \
-    molfile_mol2plugin_register(v, cb); \
-    molfile_moldenplugin_register(v, cb); \
-    molfile_molemeshplugin_register(v, cb); \
-    molfile_msmsplugin_register(v, cb); \
-    molfile_namdbinplugin_register(v, cb); \
-    molfile_offplugin_register(v, cb); \
-    molfile_parm7plugin_register(v, cb); \
-    molfile_parmplugin_register(v, cb); \
-    molfile_pbeqplugin_register(v, cb); \
-    molfile_pdbplugin_register(v, cb); \
-    molfile_pdbxplugin_register(v, cb); \
-    molfile_phiplugin_register(v, cb); \
-    molfile_pltplugin_register(v, cb); \
-    molfile_plyplugin_register(v, cb); \
-    molfile_pqrplugin_register(v, cb); \
-    molfile_psfplugin_register(v, cb); \
-    molfile_raster3dplugin_register(v, cb); \
-    molfile_rst7plugin_register(v, cb); \
-    molfile_situsplugin_register(v, cb); \
-    molfile_spiderplugin_register(v, cb); \
-    molfile_stlplugin_register(v, cb); \
-    molfile_tinkerplugin_register(v, cb); \
-    molfile_uhbdplugin_register(v, cb); \
-    molfile_vaspchgcarplugin_register(v, cb); \
-    molfile_vaspoutcarplugin_register(v, cb); \
-    molfile_vaspparchgplugin_register(v, cb); \
-    molfile_vaspposcarplugin_register(v, cb); \
-    molfile_vasp5xdatcarplugin_register(v, cb); \
-    molfile_vaspxdatcarplugin_register(v, cb); \
-    molfile_vaspxmlplugin_register(v, cb); \
-    molfile_vtkplugin_register(v, cb); \
-    molfile_xbgfplugin_register(v, cb); \
-    molfile_xsfplugin_register(v, cb); \
-    molfile_xyzplugin_register(v, cb); \
-    molfile_dtrplugin_register(v, cb); \
-    molfile_maeffplugin_register(v, cb); \
-
-#define MOLFILE_FINI_ALL \
-    molfile_abinitplugin_fini(); \
-    molfile_amiraplugin_fini(); \
-    molfile_avsplugin_fini(); \
-    molfile_babelplugin_fini(); \
-    molfile_basissetplugin_fini(); \
-    molfile_bgfplugin_fini(); \
-    molfile_binposplugin_fini(); \
-    molfile_biomoccaplugin_fini(); \
-    molfile_brixplugin_fini(); \
-    molfile_carplugin_fini(); \
-    molfile_ccp4plugin_fini(); \
-    molfile_corplugin_fini(); \
-    molfile_cpmdplugin_fini(); \
-    molfile_crdplugin_fini(); \
-    molfile_cubeplugin_fini(); \
-    molfile_dcdplugin_fini(); \
-    molfile_dlpolyplugin_fini(); \
-    molfile_dsn6plugin_fini(); \
-    molfile_dxplugin_fini(); \
-    molfile_edmplugin_fini(); \
-    molfile_fs4plugin_fini(); \
-    molfile_gamessplugin_fini(); \
-    molfile_graspplugin_fini(); \
-    molfile_grdplugin_fini(); \
-    molfile_gridplugin_fini(); \
-    molfile_gromacsplugin_fini(); \
-    molfile_jsplugin_fini(); \
-    molfile_lammpsplugin_fini(); \
-    molfile_mapplugin_fini(); \
-    molfile_mdfplugin_fini(); \
-    molfile_mol2plugin_fini(); \
-    molfile_moldenplugin_fini(); \
-    molfile_molemeshplugin_fini(); \
-    molfile_msmsplugin_fini(); \
-    molfile_namdbinplugin_fini(); \
-    molfile_offplugin_fini(); \
-    molfile_parm7plugin_fini(); \
-    molfile_parmplugin_fini(); \
-    molfile_pbeqplugin_fini(); \
-    molfile_pdbplugin_fini(); \
-    molfile_pdbxplugin_fini(); \
-    molfile_phiplugin_fini(); \
-    molfile_pltplugin_fini(); \
-    molfile_plyplugin_fini(); \
-    molfile_pqrplugin_fini(); \
-    molfile_psfplugin_fini(); \
-    molfile_raster3dplugin_fini(); \
-    molfile_rst7plugin_fini(); \
-    molfile_situsplugin_fini(); \
-    molfile_spiderplugin_fini(); \
-    molfile_stlplugin_fini(); \
-    molfile_tinkerplugin_fini(); \
-    molfile_uhbdplugin_fini(); \
-    molfile_vaspchgcarplugin_fini(); \
-    molfile_vaspoutcarplugin_fini(); \
-    molfile_vaspparchgplugin_fini(); \
-    molfile_vaspposcarplugin_fini(); \
-    molfile_vasp5xdatcarplugin_fini(); \
-    molfile_vaspxdatcarplugin_fini(); \
-    molfile_vaspxmlplugin_fini(); \
-    molfile_vtkplugin_fini(); \
-    molfile_xbgfplugin_fini(); \
-    molfile_xsfplugin_fini(); \
-    molfile_xyzplugin_fini(); \
-    molfile_dtrplugin_fini(); \
-    molfile_maeffplugin_fini(); \
-
-#ifdef __cplusplus
-}
-#endif
-#endif

src/descriptors.c

@@ -65,7 +65,6 @@ s_desc* allocate_s_desc(void)
 	s_desc *desc = (s_desc*)my_malloc(sizeof(s_desc)) ;
 	
 	reset_desc(desc) ;
-
 	return desc ;
 }
 
@@ -364,7 +363,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
 		nb_res_ids = 0 ;	/* Current number of residus */
 
 	int nb_polar_atm = 0 ;
-        char curChainName[2];
+        char *curChainName = (char*)my_malloc(255*sizeof(char));
         
         if(atoms && natoms>1){
             firstatom=atoms[0];
@@ -373,8 +372,8 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
             if(element_in_std_res(firstatom->res_name))             desc->characterChain1=0;
             else if(element_in_nucl_acid(firstatom->res_name))      desc->characterChain1=1;
             else if(element_in_kept_res(firstatom->res_name))       desc->characterChain1=2;
-            strncpy(desc->nameChain1,firstatom->chain,2);
-            strncpy(curChainName,firstatom->chain,2);
+            strcpy(desc->nameChain1,firstatom->chain);
+            strcpy(curChainName,firstatom->chain);
             desc->numResChain1 = countResidues(all_atoms,all_natoms,firstatom->chain);
 
             for(i = 0 ; i < natoms ; i++) {
@@ -384,7 +383,7 @@ void set_atom_based_descriptors(s_atm **atoms, int natoms, s_desc *desc,s_atm *a
                             desc->interChain = 1;
                             if(!desc->numResChain2){
                                 desc->numResChain2 = countResidues(all_atoms,all_natoms,curatom->chain);
-                                strncpy(curChainName,curatom->chain,1);
+                                strcpy(curChainName,curatom->chain);
                             }
                         }
 

src/read_mmcif.c

@@ -124,9 +124,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             if (par->xlig_resnumber > -1)
             {
 
-                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && 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]) || (par->xlig_chain_code!=NULL && 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])))
+                // if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && 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]) || (par->xlig_chain_code!=NULL && 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])))
+                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth,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]) || (par->xlig_chain_code!=NULL && 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++;
+
                 }
             }
         }
@@ -630,9 +634,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
 
                 unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
 
-                if (is_chain_ligand || (params->xlig_chain_code !=NULL && 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]) || (params->xlig_chain_code!=NULL && 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]))
-                {
-                                        
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && strcmp(at_in[i].chain_auth, 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]) || (params->xlig_chain_code!=NULL && strcmp(at_in[i].chain_auth, 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]))
+                {                      
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
                     *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];