more cleaning

added examples PDB
improved PDB reading function to read multiple structures is one file (each one with its own connectivity)

cosymlib/file_io/__init__.py

@@ -400,11 +400,13 @@ def get_geometry_from_file_pdb(file_name, read_multiple=False):
         for line in mol_section.split('\n'):
             if line.find('TITLE') > -1:
                 name = ' '.join(line.split()[1:])
-            if line.find('HETATM') > -1:
+            if line.find('HETATM') > -1 or line.find('ATOM') > -1:
                 coordinates.append([float(num) for num in line.split()[4:7]])
                 symbols.append(line.split()[2])
             if line.find('CONECT') > -1:
                 connect.append([int(num) for num in line.split()[2:]])
+            if line.find('TER') > -1 or line.find('END') > -1:
+                break
 
         connectivity = []
         for i, atom in enumerate(connect):

examples/methane.pdb

@@ -1,13 +1,26 @@
-TITLE      Molecule Name
+TITLE      Methane
 REMARK   1 File created by GaussView 5.0.9
 HETATM    1  C           0      -0.498  -0.179   0.000                       C
 HETATM    2  H           0      -0.141  -1.188   0.000                       H
 HETATM    3  H           0      -0.141   0.325   0.874                       H
 HETATM    4  H           0      -0.141   0.325  -0.874                       H
 HETATM    5  H           0      -1.568  -0.179   0.000                       H
+CONECT    1    2    3    4    5
+CONECT    2    1
+CONECT    3    1
+CONECT    4    1
+CONECT    5    1
 END
+TITLE      Methane distorted
+REMARK   1 File created by GaussView 5.0.9
+HETATM    1  C           0      -0.498  -0.179   0.100                       C
+HETATM    2  H           0      -0.141  -1.188   0.000                       H
+HETATM    3  H           0      -0.141   0.325   0.874                       H
+HETATM    4  H           0      -0.141   0.325  -0.874                       H
+HETATM    5  H           0      -1.568  -0.179   0.000                       H
 CONECT    1    2    3    4    5
 CONECT    2    1
 CONECT    3    1
 CONECT    4    1
 CONECT    5    1
+END

examples/python_api.py

@@ -24,16 +24,16 @@ def print_csm(data):
 
 
 # Get structures from files
-molecules_set = file_io.get_geometry_from_file_xyz('coord.xyz', read_multiple=True)
-fragments_set = file_io.get_geometry_from_file_cor('coord.cor', read_multiple=True)
+geometries_list = file_io.get_geometry_from_file_xyz('coord.xyz', read_multiple=True)
+fragments_list = file_io.get_geometry_from_file_cor('coord.cor', read_multiple=True)
 
 # Call shape as method of Geometry class
-print_shape_data(molecules_set)
-print_shape_data(fragments_set)
+print_shape_data(geometries_list)
+print_shape_data(fragments_list)
 
 
 # Check multiple calls of shape one calculatioin
-methane = molecules_set[0]
+methane = geometries_list[0]
 for i in range(100):
     measure = methane.get_shape_measure('SP-4', central_atom=1)
 
@@ -46,8 +46,8 @@ def print_csm(data):
 # test symgroup
 print('\nSYMMETRY\n--------')
 
-molecule = file_io.get_geometry_from_file_pdb('methane.pdb', read_multiple=False)
-print('measure C3: {} '.format(molecule.get_symmetry_measure('c3')))
+geometries_list = file_io.get_geometry_from_file_pdb('methane.pdb', read_multiple=True)
+print('measure C3: {} '.format(geometries_list[0].get_symmetry_measure('c3')))
 
 # Check multiple calls of symgroup one calculatioin
 for i in range(100):
@@ -65,30 +65,28 @@ def print_csm(data):
 print('\nWFNSYM\n--------')
 
 
-molecule = file_io.get_molecule_from_file_fchk('pirrol.fchk')
+molecule = file_io.get_molecule_from_file_fchk('pirrol.fchk', read_multiple=False)
 
-data = molecule.get_wf_symmetry('C2v',
-                                axis=[0.000000, 0.000000, 1.000000],  # valor defecte
-                                # vector_axis2=[-2.027247,  0.000133, -0.898469],
-                                center=[0.002440, -0.000122,  0.017307]
-                                )  # valor per defecte (CM)
-
-print_csm(data)
+measure_dict = molecule.get_wf_symmetry('C2v',
+                                        axis=[0.000000, 0.000000, 1.000000],  # valor defecte
+                                        # vector_axis2=[-2.027247,  0.000133, -0.898469],
+                                        center=[0.002440, -0.000122,  0.017307])
+print_csm(measure_dict)
 
 print('\nCOSYMLIB\n--------')
-molecules_set = file_io.get_geometry_from_file_xyz('coord_2.xyz', read_multiple=True)
-molecules_group = Cosymlib(molecules_set)
+geometries_list = file_io.get_geometry_from_file_xyz('coord_2.xyz', read_multiple=True)
+molecules_set = Cosymlib(geometries_list)
 print('\n\n***********{}************'.format('print_electronic_symmetry_measure()'))
-molecules_group.print_electronic_symmetry_measure('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+molecules_set.print_electronic_symmetry_measure('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
 
 
-molecules_set = file_io.read_generic_structure_file('pirrol.fchk', read_multiple=True)
-molecules_group = Cosymlib(molecules_set)
+molecules_list = file_io.read_generic_structure_file('pirrol.fchk', read_multiple=True)
+molecules_set = Cosymlib(molecules_list)
 print('\n\n***********{}************'.format('print_info()'))
-molecules_group.print_info()
+molecules_set.print_info()
 print('\n\n***********{}************'.format('print_wnfsym_irreducible_repr()'))
-molecules_group.print_wnfsym_irreducible_repr('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+molecules_set.print_wnfsym_irreducible_repr('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
 print('\n\n***********{}************'.format('print_wnfsym_sym_ovelap()'))
-molecules_group.print_wnfsym_sym_ovelap('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+molecules_set.print_wnfsym_sym_ovelap('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
 print('\n\n***********{}************'.format('print_wnfsym_sym_matrices()'))
-molecules_group.print_wnfsym_sym_matrices('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+molecules_set.print_wnfsym_sym_matrices('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])