in process

molsysmt/basic/remove.py

@@ -1,7 +1,7 @@
 from molsysmt._private.digestion import digest
 from molsysmt._private.structure_indices import complementary_structure_indices
 from molsysmt._private.atom_indices import complementary_atom_indices
-
+from molsysmt._private.variables import is_all
 
 @digest()
 def remove(molecular_system, selection=None, structure_indices=None, to_form=None, syntax='MolSysMT'):
@@ -61,7 +61,7 @@ def remove(molecular_system, selection=None, structure_indices=None, to_form=Non
 
     """
 
-    from . import select, extract
+    from . import select, extract, get
 
     atom_indices_to_be_kept = 'all'
     structure_indices_to_be_kept = 'all'
@@ -71,6 +71,9 @@ def remove(molecular_system, selection=None, structure_indices=None, to_form=Non
         atom_indices_to_be_kept = complementary_atom_indices(molecular_system, atom_indices_to_be_removed)
 
     if structure_indices is not None:
+        if is_all(structure_indices):
+            n_structures = get(molecular_system, element='system', n_structures=True)
+            structure_indices= list(range(n_structures))
         structure_indices_to_be_kept = complementary_structure_indices(molecular_system, structure_indices)
 
     tmp_item = extract(molecular_system, selection=atom_indices_to_be_kept,

molsysmt/element/atom/get_atom_type_from_atom_name.py

@@ -7,5 +7,8 @@ def get_atom_type_from_atom_name(atom_name):
     To be written soon...
     """
 
-    return atom_type[atom[atom_name]]
+    try:
+        return atom_type[atom[atom_name]]
+    except:
+        raise ValueError('Atom name '+atom_name+' has not known atom type.')
 

molsysmt/element/atom/names.py

@@ -1,6 +1,7 @@
 atom={
 'H'    : 'atH'    ,
 'HN'   : 'atH'    ,    # charmm.pdb
+'HN1'  : 'atH'    ,    #
 'H1'   : 'atH1'   ,
 'H2'   : 'atH2'   ,
 '2HH'  : 'atH2'   ,    # pymol.pdb
@@ -78,22 +79,28 @@
 'H8S'  : 'atH8S'  ,    # lipid POPC
 'H8X'  : 'atH8X'  ,    # lipid POPC 
 'H8Y'  : 'atH8Y'  ,    # lipid POPC 
+'H9R'  : 'atH9R'  ,    # lipid POPC 
+'H9S'  : 'atH9S'  ,    # lipid POPC 
 'H9X'  : 'atH9X'  ,    # lipid POPC 
 'H9Y'  : 'atH9Y'  ,    # lipid POPC 
+'H10R' : 'atH10R' ,    # lipid POPC 
+'H10S' : 'atH10S' ,    # lipid POPC 
 'H10X' : 'atH10X' ,    # lipid POPC 
 'H10Y' : 'atH10Y' ,    # lipid POPC 
 'H11A' : 'atH11A' ,    # lipid POPC
 'H11B' : 'atH11B' ,    # lipid POPC
 'H11R' : 'atH11R' ,    # lipid POPC 
+'H11S' : 'atH11S' ,    # lipid POPC 
 'H11X' : 'atH11X' ,    # lipid POPC 
 'H11Y' : 'atH11Y' ,    # lipid POPC 
-'H11S' : 'atH11S' ,    # lipid POPC 
 'H12A' : 'atH12A' ,    # lipid POPC
 'H12B' : 'atH12B' ,    # lipid POPC
 'H12R' : 'atH12R' ,    # lipid POPC 
 'H12S' : 'atH12S' ,    # lipid POPC 
+'H12T' : 'atH12T' ,    # lipid POPC 
 'H12X' : 'atH12X' ,    # lipid POPC 
 'H12Y' : 'atH12Y' ,    # lipid POPC 
+'H12Z' : 'atH12Z' ,    # lipid POPC 
 'H13A' : 'atH13A' ,    # lipid POPC
 'H13B' : 'atH13B' ,    # lipid POPC
 'H13C' : 'atH13C' ,    # lipid POPC
@@ -228,6 +235,7 @@
 'HH32' : 'atHH32' ,    # opls.gro
 '3HH3' : 'atHH33' ,
 'HH33' : 'atHH33' ,    # opls.gro
+'HR'   : 'atHR'   ,   # lipid
 'HS'   : 'atHS'   ,   # lipid POPC
 'HNT'  : 'atHT'   ,   # ACEMD (NME Terminal)
 'HX'   : 'atHX'   ,   # lipid POPC
@@ -500,35 +508,41 @@
 'atH8S' : 'H'   ,  
 'atH8X' : 'H'   ,  
 'atH8Y' : 'H'   ,  
+'atH9R' : 'H'   ,  
+'atH9S' : 'H'   ,  
 'atH9X' : 'H'   ,  
 'atH9Y' : 'H'   ,  
+'atH10R' : 'H'   ,  
+'atH10S' : 'H'   ,  
 'atH10X' : 'H'   ,  
 'atH10Y' : 'H'   ,  
+'atH11R' : 'H'   ,  
+'atH11S' : 'H'   ,  
 'atH11X' : 'H'   ,  
 'atH11Y' : 'H'   ,  
+'atH12S' : 'H'   ,  
+'atH12R' : 'H'   ,  
+'atH12T' : 'H'   ,  
 'atH12X' : 'H'   ,  
 'atH12Y' : 'H'   ,  
+'atH12Z' : 'H'   ,  
+'atH13R' : 'H'   ,  
+'atH13S' : 'H'   ,  
 'atH13X' : 'H'   ,  
 'atH13Y' : 'H'   ,  
+'atH14R' : 'H'   ,  
+'atH14S' : 'H'   ,  
 'atH14X' : 'H'   ,  
 'atH14Y' : 'H'   ,  
+'atH15R' : 'H'   ,  
+'atH15S' : 'H'   ,  
 'atH15X' : 'H'   ,  
 'atH15Y' : 'H'   ,  
+'atH16R' : 'H'   ,  
+'atH16S' : 'H'   ,  
 'atH16X' : 'H'   ,  
 'atH16Y' : 'H'   ,  
 'atH16Z' : 'H'   ,
-'atH11R' : 'H'   ,  
-'atH11S' : 'H'   ,  
-'atH12R' : 'H'   ,  
-'atH12S' : 'H'   ,  
-'atH13R' : 'H'   ,  
-'atH13S' : 'H'   ,  
-'atH14R' : 'H'   ,  
-'atH14S' : 'H'   ,  
-'atH15R' : 'H'   ,  
-'atH15S' : 'H'   ,  
-'atH16R' : 'H'   ,  
-'atH16S' : 'H'   ,  
 'atH17R' : 'H'   ,  
 'atH17S' : 'H'   ,  
 'atH18R' : 'H'   ,  
@@ -574,6 +588,7 @@
 'atHH31': 'H'   , 
 'atHH32': 'H'   , 
 'atHH33': 'H'   ,
+'atHR'  : 'H'   , 
 'atHS'  : 'H'   , 
 'atHT'  : 'H'   , 
 'atHT1' : 'H'   , 

molsysmt/form/parmed_Structure/__init__.py

@@ -19,6 +19,7 @@
 from .to_file_mol2 import to_file_mol2
 from .to_file_pdb import to_file_pdb
 from .to_file_psf import to_file_psf
+from .to_file_cif import to_file_cif
 from .to_mdtraj_Topology import to_mdtraj_Topology
 from .to_mdtraj_Trajectory import to_mdtraj_Trajectory
 from .to_nglview_NGLWidget import to_nglview_NGLWidget

molsysmt/form/parmed_Structure/attributes.py

@@ -2,6 +2,7 @@
 
 attributes = {ii:False for ii in _all_attributes}
 
+attributes['atom_index'] = True
 attributes['atom_index'] = True
 attributes['atom_id'] = True
 attributes['atom_name'] = True
@@ -23,8 +24,46 @@
 attributes['chain_id'] = True
 attributes['chain_name'] = True
 attributes['chain_type'] = True
-attributes['coordinates'] = True
+
+attributes['n_atoms'] = True
+attributes['n_groups'] = True
+attributes['n_components'] = True
+attributes['n_molecules'] = True
+attributes['n_chains'] = True
+attributes['n_entities'] = True
+attributes['n_aminoacids'] = True
+attributes['n_nucleotides'] = True
+attributes['n_ions'] = True
+attributes['n_waters'] = True
+attributes['n_small_molecules'] = True
+attributes['n_peptides'] = True
+attributes['n_proteins'] = True
+attributes['n_dnas'] = True
+attributes['n_rnas'] = True
+attributes['n_lipids'] = True
+attributes['n_oligosaccharides'] = True
+attributes['n_saccharides'] = True
+
+attributes['bond_index'] = True
+attributes['bond_id'] = False
+attributes['bond_type'] = True
+attributes['bond_order'] = True
+attributes['bonded_atoms'] = True
+attributes['inner_bond_index'] = True
+attributes['inner_bonded_atoms'] = True
+attributes['n_bonds'] = True
+attributes['n_inner_bonds'] = True
+
+
+attributes['structure_index'] = True
 attributes['box'] = True
+attributes['box_shape'] = True
+attributes['box_angles'] = True
+attributes['box_lengths'] = True
+attributes['box_volume'] = True
+attributes['coordinates'] = True
+attributes['n_structures'] = True
+attributes['b_factor'] = True
 
 
 del(_all_attributes)

molsysmt/form/parmed_Structure/get.py

@@ -5,6 +5,7 @@
 from molsysmt._private.execfile import execfile
 from molsysmt._private.exceptions import NotImplementedMethodError, NotWithThisFormError
 from molsysmt._private.digestion import digest
+from molsysmt._private.variables import is_all
 
 form='parmed.Structure'
 
@@ -63,7 +64,22 @@ def get_n_inner_bonds_from_atom(item, indices='all'):
 @digest(form=form)
 def get_coordinates_from_atom(item, indices='all', structure_indices='all'):
 
-    raise NotImplementedMethodError()
+    output = item.coordinates
+
+    if output is None:
+        return output
+
+    if not is_all(indices):
+        output = output[:,indices,:]
+    if not is_all(structure_indices):
+        output = output[structure_indices,:,:]
+
+    if not puw.is_quantity(output):
+        output = puw.quantity(output,'angstroms')
+
+    output = puw.standardize(output)
+
+    return output
 
 ## From group
 
@@ -191,22 +207,41 @@ def get_n_bonds_from_system(item):
 @digest(form=form)
 def get_n_structures_from_system(item, structure_indices='all'):
 
-    raise NotImplementedMethodError()
+    if is_all(structure_indices):
+        if item.coordinates is None:
+            return 0
+        else:
+            return item.coordinates.shape[0]
+    else:
+        return len(structure_indices)
 
 @digest(form=form)
 def get_box_from_system(item, structure_indices='all'):
 
-    raise NotImplementedMethodError()
+    output = item.box
+
+    if output is None:
+        return output
+
+    if not is_all(structure_indices):
+        output = output[structure_indices,:,:]
+
+    if not puw.is_quantity(output):
+        output = puw.quantity(output,'angstroms')
+
+    output = puw.standardize(output)
+
+    return output
 
 @digest(form=form)
 def get_time_from_system(item, structure_indices='all'):
 
-    raise NotImplementedMethodError()
+    return None
 
 @digest(form=form)
 def get_structure_id_from_system(item, structure_indices='all'):
 
-    raise NotImplementedMethodError()
+    return None
 
 ## From bond
 

molsysmt/form/parmed_Structure/to_file_cif.py

@@ -0,0 +1,14 @@
+from molsysmt._private.digestion import digest
+
+@digest(form='parmed.Structure')
+def to_file_cif(item, atom_indices='all', structure_indices='all', output_filename=None):
+
+    from . import extract
+
+    tmp_item = extract(item, atom_indices=atom_indices, structure_indices=structure_indices,
+            copy_if_all=False)
+    tmp_item.save(output_filename)
+    tmp_item = output_filename
+
+    return tmp_item
+

molsysmt/form/parmed_Structure/to_molsysmt_Topology.py

@@ -6,6 +6,7 @@ def to_molsysmt_Topology(item, atom_indices='all'):
     from molsysmt.native import Topology
     from numpy import empty, array, arange, reshape, where, unique, nan, sort, zeros
     from molsysmt.element.group import get_group_type_from_group_name
+    from molsysmt.element.atom import get_atom_type_from_atom_name
     from ..molsysmt_Topology import extract
 
     tmp_item = Topology()
@@ -33,25 +34,37 @@ def to_molsysmt_Topology(item, atom_indices='all'):
 
     atom_index = 0
 
+    aux_dict_chains={}
+
     for atom in item.atoms:
 
-        atom_index_array[atom_index] = atom._idx
+        atom_index_array[atom_index] = atom.idx
         atom_name_array[atom_index] = atom.name
         atom_id_array[atom_index] = atom.idx
-        atom_type_array[atom_index] = None
+        atom_type_array[atom_index] = get_atom_type_from_atom_name(atom.name)
         atom_partial_charge_array[atom_index] = atom.charge
         atom_formal_charge_array[atom_index] = atom.formal_charge
 
-        group_index_array[atom_index] = atom.residue._idx
+        group_index_array[atom_index] = atom.residue.idx
         group_name_array[atom_index] = atom.residue.name
         group_id_array[atom_index] = atom.residue.idx
         group_type_array[atom_index] = get_group_type_from_group_name(atom.residue.name)
 
+        chain_id = atom.residue.chain
+        if chain_id not in aux_dict_chains:
+            aux_dict_chains[chain_id]=len(aux_dict_chains)
+        chain_index = aux_dict_chains[chain_id]
+        chain_index_array[atom_index] = chain_index
+        chain_id_array[atom_index] = chain_id
+
         chain_index_array[atom_index] = 0
         chain_id_array[atom_index] = None
 
         atom_index+=1
 
+    if len(aux_dict_chains)==1:
+        if '' in aux_dict_chains:
+            chain_id_array[:]='A'
 
     tmp_item.atoms_dataframe["atom_index"] = atom_index_array
     tmp_item.atoms_dataframe["atom_name"] = atom_name_array