diff --git a/common/python/nomadcore/md_data_access/MDDataAccess.py b/common/python/nomadcore/md_data_access/MDDataAccess.py
index 715854a262b927492bb9e847a376b46736a71f47..d762bc805aff5c48fde1eca2b7d1f5282c8c902e 100644
--- a/common/python/nomadcore/md_data_access/MDDataAccess.py
+++ b/common/python/nomadcore/md_data_access/MDDataAccess.py
@@ -2269,194 +2269,3 @@ if __name__ == "__main__":
atom = MDdata.iread()
print(i)
- if "mdanalysis" in MDdata.topocode:
-
- def getseg(seg):
- regex = re.compile(r"^seg_[0-9]+_b")
- if regex.findall(seg.segid):
- segname = bytes(re.sub(r"^seg_[0-9]+_b","",seg.segid).replace("'",""), "utf-8").decode("utf-8")
- else:
- segname = seg.segid
- return [seg.ix,segname]
-
- def get_atomseg(atom):
- return [atom.segment.ix,atom.segment.segname.decode('utf-8')]
-
- def getres(atom):
- return [atom.resname.decode('utf-8'),atom.resid]
-
- def getatom(atom):
- atmid = atom.ix
- atmname = atom.name.decode('utf-8')
- atmtyp = atom.type.decode('utf-8')
- atmres = atom.resname.decode('utf-8')
- atmresid = atom.resid
- atmsegid = atom.segid
- return [atmid,atmname,atmtyp,atmres,atmresid,atmsegid]
-
- def residuepairs(atom1,atom2):
- return [getres(atom1),getres(atom2)]
-
- def atompairs(atom1,atom2):
- return [getatom(atom1),getatom(atom2)]
-
- print(MDdata.topohandler.atoms)
- attrlist = dir(MDdata.topohandler.atoms)
- if "names" in attrlist:
- print("Atom Names:",MDdata.topohandler.atoms.names)
- if "types" in attrlist:
- print("Atom Types:",MDdata.topohandler.atoms.types)
- if "masses" in attrlist:
- print("Atom Masses:",MDdata.topohandler.atoms.masses)
- if "charges" in attrlist:
- print("Atom Charges:",MDdata.topohandler.atoms.charges)
- if "radiuses" in attrlist:
- print("Atom Radiuses:",MDdata.topohandler.atoms.radiuses)
- if "bfactors" in attrlist:
- print("Atom bFactors:",MDdata.topohandler.atoms.bfactors)
- print("Atom List:",[mda.topology.guessers.guess_atom_element(getatom(a)[1]) for a in MDdata.topohandler.atoms])
- print("Atom Residues:",MDdata.topohandler.atoms.residues)
- print("Atom Residue ids:",MDdata.topohandler.atoms.residues.ix)
- print("Atom Residue Names:",[a.resname for a in MDdata.topohandler.atoms.residues])
- print("Atom Segments:",MDdata.topohandler.atoms.segments)
- print("Atom Bonds:",MDdata.topohandler.atoms.bonds)
- print("Atom Angles:",MDdata.topohandler.atoms.angles)
- print("Atom Dihedrals:",MDdata.topohandler.atoms.dihedrals)
- print("Atom Impropers:",MDdata.topohandler.atoms.impropers)
- print(MDdata.topohandler.bonds)
- topd = MDdata.topohandler.bonds.topDict
- topdk = topd.keys()
- for key in topdk:
- topt = topd[key]
- for b in topt:
- reslist=residuepairs(b.atoms[0],b.atoms[1])
- atmlist=atompairs(b.atoms[0],b.atoms[1])
- if str(reslist[0][0]) != str(reslist[1][0]):
- print("RES:",reslist,
- "ATM:",atmlist)
-
-
- #print("Bonds:",[ [a[0].ix,a[1].ix] for a in MDdata.topohandler.bonds])
- print(MDdata.topohandler.angles)
- #print("Angles:",[ [a[0].ix,a[1].ix,a[2].ix] for a in MDdata.topohandler.angles])
- print(MDdata.topohandler.residues)
- #print("Residue bonds:",[a.bonds for a in MDdata.topohandler.residues])
- #for r in MDdata.topohandler.residues:
- # print(r.resname,r.resid)
- print([getseg(seg)[1] for seg in MDdata.topohandler.segments])
- #print("Segment Names:",[a.segment for a in MDdata.topohandler.segments])
- #print("Residue Names:",MDdata.topohandler.residues.names)
- #print("Residue Types:",MDdata.topohandler.residues.names)
- #print("Residue Bonds:",MDdata.topohandler.residues.bonds)
- #print("Residue Angles:",MDdata.topohandler.residues.angles)
-
-
- print(mda.topology.guessers.guess_atom_element("BERK"))
-
- #angles = mdtraj.compute_angles(mytopology)
- #dihedrals = mdtraj.compute_dihedrals(mytopology)
- #print(dihedrals)
- #print(' Chains: %s' % [res for res in mytopology.chains])
- #print(' Residues: %s' % [res for res in mytopology.residues])
- #print(' Atoms: %s' % [res for res in mytopology.atoms])
- #print(' Bonds: %s' % [res for res in mytopology.bonds])
- #print(mytopology.chain(0))
- table, bonds = mytopology.to_dataframe()
- print(bonds)
- print(len(bonds))
- array = table.get("resSeq")
- #print([res for res in array])
- mydict = table.to_dict(orient='list')
- mylist = mydict["resSeq"]
- print('mylist')
- print(mylist)
- print('mylist')
- atomindex = np.arange(len(mylist))
- passarray = np.zeros((len(mylist), 2), dtype=int)
- passarray[:,0] = atomindex
- passarray[:,1] = mylist
- print(table)
- print(passarray)
- #print(bonds)
- #for bond in bonds:
- # print(bond)
- mol_to_mol_bond = []
- mol_to_mol_bond_num = []
- atom_in_mol_bond = []
- atom_in_mol_bond_num = []
- index=0
- print(len([res for res in mytopology.bonds]))
- for res in mytopology.bonds:
- molname1, molatom1 = str(res[0]).split('-')
- molname2, molatom2 = str(res[1]).split('-')
- if molname1 in molname2:
- atom_in_mol_bond.append(res)
- atom_in_mol_bond_num.append(bonds[index])
- else:
- mol_to_mol_bond.append(res)
- mol_to_mol_bond_num.append(bonds[index])
- index += 1
- print(mol_to_mol_bond)
- print(np.array(mol_to_mol_bond_num))
-
- atom_list = list(set(mydict["name"]))
- atom_type_dict = {}
- print(atom_list)
- print(len(atom_list))
- masses = {}
- for ielm in range(len(atom_list)):
- elm = atom_list[ielm]
- atom_type_dict.update({elm : ielm})
- for atom in mytopology.atoms:
- if elm == atom.name:
- masses.update({atom.name : atom.element})
- print([atom_list, masses])
- interDict = {}
- interTypeDict = {}
- for elm in atom_list:
- bondList = []
- typeList = []
- bondid = 0
- for bond in mytopology.bonds:
- molname1, molatom1 = str(bond[0]).split('-')
- molname2, molatom2 = str(bond[1]).split('-')
- if (elm == str(molatom1) or elm == str(molatom2)):
- bondList.append(list(bonds[bondid]))
- #typeList.append(list([molatom1,molatom2]))
- typeList.append(list([
- atom_type_dict[str(molatom1)],
- atom_type_dict[str(molatom2)]
- ]))
- interDict.update({elm : bondList})
- interTypeDict.update({elm : typeList})
- bondid += 1
-
- # print(interDict)
- print(interDict["CH3"])
- print(interTypeDict["CH3"])
- print(len(interDict["CH3"][0]))
-
- # print([[atom.element.radius, atom.index, atom.name, atom.residue.name, atom.element] for atom in mytopology.atoms])
-
- # Atom labels:
- print(table)
- # for atom in mytopology.atoms:
- # print(atom)
- labellist = mydict["element"]
- #print(labellist)
- # atomlabels = np.arange(len(labellist))
- # labelarray = np.zeros((len(labellist), 2), dtype=int)
- # labelarray[:,0] = atomlabels
- # labelarray[:,1] = labellist
- # print(labelarray)
- # print(readdata.unitcell_lengths)
- latticevectors = readdata.iread().unitcell_vectors
- box = readdata.iread().unitcell_lengths
- step = 0
- for latvec in latticevectors:
- print(step, latvec)
- step += 1
- for pbc in box:
- print(step, box)
- step += 1
-