Improve notebook and remove unused steps

notebooks/load_chemistrix_library.ipynb

 %% Cell type:markdown id: tags:
 
 # How to load new libraries to Chemical Checker infrastructure
 
 %% Cell type:markdown id: tags:
 
 
 ## Load library files to datasource table
 
 %% Cell type:code id: tags:
 
 ``` python
 import os
 import sys
 sys.path.append("/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker")
 
 os.environ["CC_CONFIG"] = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
 
 
 from chemicalchecker.util import Config
 
 from chemicalchecker.database import Datasource
 
 
 
 biur_real = {'name':"biur_real",'url':"file:///aloy/scratch/sbnb-adm/checker/local_downloads/BIUR_20100326.sdf",
              'permanent':True,'enabled':False,'user':"",'password':"",'description':"ChemistryX Biur real library",
              'molrepo_name':"biur_real",'molrepo_file':"BIUR_20100326.sdf",'is_db':False}
 biur_virtual = {'name':"biur_virtual",'url':"file:///aloy/scratch/sbnb-adm/checker/local_downloads/VIRTUAL_BIUR_POR_MW.tar.gz",
                 'permanent':True,'enabled':False,'user':"",'password':"",'description':"ChemistryX Biur virtual library",
                 'molrepo_name':"biur_virtual",'molrepo_file':"VIRTUAL_BIUR_POR_MW",'is_db':False}
 
 
 Datasource.add(biur_real)
 Datasource.add(biur_virtual)
 ```
 
 %% Cell type:markdown id: tags:
 
+## Add Library parser
+
+Check the *package/chemicalchecker/util/parser/parser.py* file and add a method for each one of the new libraries to parse those libraries.
+The new method to parse the library should have the same name as the **molrepo_name** used in the datasource table. The output of the method should be the same as the other methods used in the **parser.py** file.
+
+%% Cell type:markdown id: tags:
+
 ## Download  & parse datasource associated to library "biur_real"
 
 1. Download the datasource files
 2. Parse downloaded files and load it to the molrepo table
 
 %% Cell type:code id: tags:
 
 ``` python
 import os
 import sys
 sys.path.append("/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker")
 
 os.environ["CC_CONFIG"] = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
 
 
 from chemicalchecker.util import Config
 
 from chemicalchecker.database import Datasource, Molrepo
 
 # This method downloads all datasources related to this library
 # and parse the files to load the new data to the molrepo table
 
 Molrepo.from_molrepo_name("biur_real")
 ```
 
 %% Cell type:markdown id: tags:
 
 ## Download datasource associated to library "biur_virtual"
 
 1. Download the datasource files
 2. Parse downloaded files and load it to the molrepo table
 
 %% Cell type:code id: tags:
 
 ``` python
 import os
 import sys
 sys.path.append("/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker")
 
 os.environ["CC_CONFIG"] = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
 
 
 from chemicalchecker.util import Config
 
 from chemicalchecker.database import Datasource, Molrepo
 
 # This method downloads all datasources related to this library
 # and parse the files to load the new data to the molrepo table
 
 Molrepo.from_molrepo_name("biur_virtual")
 ```
 
 %% Cell type:markdown id: tags:
 
-## Add libraries to the structure table
-
-Get the inchikey-inchi pairs of the new libraries and add this information to the table structure. But only the molecules that are not already present in that table
-
-%% Cell type:code id: tags:
-
-``` python
-import os
-import sys
-import shutil
-
-sys.path.append("/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker")
-
-os.environ["CC_CONFIG"] = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
-
-
-from chemicalchecker.database import Structure, Molrepo
-
-# This method queries the molrepo table to get the fields that we want for the specified molrepo
-molrepo_ik_inchi = Molrepo.get_fields_by_molrepo_name("biur_real",["inchikey","inchi"])
-
-# This method add the inchikey-inchi pairs only for the molecules not present in the table
-Structure.add_missing_only(molrepo_ik_inchi)
-
-# This method queries the molrepo table to get the fields that we want for the specified molrepo
-molrepo_ik_inchi = Molrepo.get_fields_by_molrepo_name("biur_virtual",["inchikey","inchi"])
-
-# This method add the inchikey-inchi pairs only for the molecules not present in the table
-Structure.add_missing_only(molrepo_ik_inchi)
-```
-
-%% Cell type:markdown id: tags:
-
 ## Calculate the molecular properties and store them for library "biur_real"
 
+It will also add the missing molecules to the structure table
 It will create jobs to do this task in the cluster.
 It waits for a molecular property calculation to finish before submitting another one.
 
 %% Cell type:code id: tags:
 
 ``` python
 import os
 import sys
 import shutil
 
 sys.path.append("/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker")
 
 os.environ["CC_CONFIG"] = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
 
 
 from chemicalchecker.database import Molprop, Structure
 from chemicalchecker.database import Molrepo
 from chemicalchecker.util import HPC
 from chemicalchecker.util import Config
 
 
 molprops = ['fp2d','fp3d','subskeys','scaffolds','physchem']
 
 molrepo_ik_inchi = Molrepo.get_fields_by_molrepo_name("biur_real",["inchikey","inchi"])
 
 for mol in molprops:
 
     job_path = "/aloy/scratch/oguitart/jobs_molprop_" + mol
     if os.path.isdir(job_path):
         shutil.rmtree(job_path)
     os.mkdir(job_path)
 
     molprop = Molprop(mol)
 
     # This method sends the job and waits for the job to finish
     cluster = molprop.molprop_hpc(job_path,molrepo_ik_inchi)
 
 ```
 
 %% Cell type:markdown id: tags:
 
 ## Calculate the molecular properties and store them for library "biur_virtual"
 
 It will create jobs to do this task in the cluster.
 It waits for a molecular property calculation to finish before submitting another one.
 
 %% Cell type:code id: tags:
 
 ``` python
 import os
 import sys
 import shutil
 
 sys.path.append("/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker")
 
 os.environ["CC_CONFIG"] = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
 
 cc_config = '/aloy/home/oguitart/projects/source/chemical_checker/chemicalchecker/tests/data/config.json'
 
 from chemicalchecker.database import Molprop, Structure
 from chemicalchecker.database import Molrepo
 from chemicalchecker.util import HPC
 from chemicalchecker.util import Config
 
 
 molprops = ['fp2d','fp3d','subskeys','scaffolds','physchem']
 
 molrepo_ik_inchi = Molrepo.get_fields_by_molrepo_name("biur_virtual",["inchikey","inchi"])
 
 for mol in molprops:
 
     job_path = "/aloy/scratch/oguitart/jobs_molprop_" + mol
     if os.path.isdir(job_path):
         shutil.rmtree(job_path)
     os.mkdir(job_path)
 
     molprop = Molprop(mol)
 
     # This method sends the job and waits for the job to finish
     cluster = molprop.molprop_hpc(job_path,molrepo_ik_inchi)
 
 ```