diff --git a/.gitignore b/.gitignore
index 398bcbe..72d7fb3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,5 @@
 *.py[cod]
 # PIP stuff
 *.egg-info
+# Visual studio code
+.vscode
\ No newline at end of file
diff --git a/propka.cfg b/propka.cfg
deleted file mode 100644
index a12e38a..0000000
--- a/propka.cfg
+++ /dev/null
@@ -1,398 +0,0 @@
-# PropKa configuration file
-
-version version_A
-
-# Model pKa values
-model_pkas C-   3.20
-model_pkas ASP  3.80
-model_pkas GLU  4.50
-model_pkas HIS  6.50
-model_pkas CYS  9.00
-model_pkas TYR 10.00
-model_pkas LYS 10.50
-model_pkas ARG 12.50
-#model_pkas SER 14.20 Jack Kyte: Structure in Protein Chemistry, 1995, Garland Publishing, Inc New York and London
-model_pkas N+   8.00
-model_pkas CG  11.50
-model_pkas C2N 11.50
-model_pkas N30 10.00
-model_pkas N31 10.00
-model_pkas N32 10.00
-model_pkas N33 10.00
-model_pkas NAR  5.00
-model_pkas OCO  4.50
-model_pkas SH  10.00
-model_pkas OP   6.00
-
-# Custom ligand pKa values
-#  P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, and, J. Chattopadhyaya:
-#  Measurement of Nucleobase pKa Values in Model Mononucleotides 
-#  Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
-#  Journal of the American Chemical Society 2004 126 (9), 2862-2869
-# 
-custom_model_pkas DA-N1   3.82
-custom_model_pkas DA-N3   3.82
-custom_model_pkas DA-N7   3.82
-custom_model_pkas DA-OP1  1.00
-custom_model_pkas DA-OP2  1.00
-
-custom_model_pkas DG-N1   9.59
-custom_model_pkas DG-N3   9.59
-custom_model_pkas DG-N7   9.59
-custom_model_pkas DG-OP1  1.00
-custom_model_pkas DG-OP2  1.00
-
-custom_model_pkas DC-N3   4.34
-custom_model_pkas DC-OP1  1.00
-custom_model_pkas DC-OP2  1.00
-
-custom_model_pkas DT-N3  10.12
-custom_model_pkas DT-OP1  1.00
-custom_model_pkas DT-OP2  1.00
-
-
-# protein group mapping
-protein_group_mapping ASP-CG  COO
-protein_group_mapping GLU-CD  COO
-protein_group_mapping HIS-CG  HIS
-protein_group_mapping CYS-SG  CYS
-protein_group_mapping TYR-OH  TYR
-protein_group_mapping LYS-NZ  LYS
-protein_group_mapping ARG-CZ  ARG
-#protein_group_mapping SER-OG  SER
-protein_group_mapping THR-OG1 ROH
-protein_group_mapping SER-OG  ROH#
-protein_group_mapping ASN-CG  AMD
-protein_group_mapping GLN-CD  AMD
-protein_group_mapping TRP-NE1 TRP
-
-
-# matrix for propka interactions
-#   'N'   non-iterative interaction
-#   'I'   iterative interaction
-#   '-'   no interaction
-                      #CYS
-interaction_matrix CYS I#N+ 
-interaction_matrix N+  N I#HIS 
-interaction_matrix HIS I N I#LYS 
-interaction_matrix LYS N N N I#AMD 
-interaction_matrix AMD N - N - -#COO 
-interaction_matrix COO I N I N N I#ARG 
-interaction_matrix ARG N N N N - N I#TRP 
-interaction_matrix TRP N - - - - N - -#ROH 
-interaction_matrix ROH N - - - - N - - -#TYR 
-interaction_matrix TYR N I I I N N N N N I#SER
-interaction_matrix SER N N N N N N I N N N I #CG
-interaction_matrix CG  N N N N - N I - - N I I#C2N
-interaction_matrix C2N N N N N - N I - - N I I I#N30
-interaction_matrix N30 N I N N - N N - - I N I I I#N31
-interaction_matrix N31 N I N N - N N - - I N I I I I#N32
-interaction_matrix N32 N I N N - N N - - I N I I I I I#N33
-interaction_matrix N33 N I N N - N N - - I N I I I I I I#NAR
-interaction_matrix NAR I N I I N I N - - I N N N N N N N I#OCO
-interaction_matrix OCO I N I N N I N N N N N N N N N N N I I#NP1
-interaction_matrix NP1 N - N - - N - - - N N - - - - - - N N -#OH
-interaction_matrix OH  N - - - - N - - - N N - - - - - - - N - -#O3
-interaction_matrix O3  N - N - - N - - - N N - - - - - - N N - - -#CL
-interaction_matrix CL  N - N - - N - - - N N - - - - - - N N - - - -#F
-interaction_matrix F   N - N - - N - - - N N - - - - - - N N - - - - -#NAM
-interaction_matrix NAM N - N - - N - - - N N - - - - - - N N - - - - - -#N1
-interaction_matrix N1  N - N - - N - - - N N - - - - - - N N - - - - - - -#O2
-interaction_matrix O2  N - N - - N - - - N N - - - - - - N N - - - - - - - -#OP
-interaction_matrix OP  I N I N N I N N N N N N N N N N N I I N N N N N N N N I#SH
-interaction_matrix SH  I N N N N N N N N N N I I I I I I N N N N N N N N N N N I
-
-# Cutoff values for side chain interactions
-# default value
-sidechain_cutoffs default 3.0  4.0  
-# COO
-sidechain_cutoffs COO COO 2.5  3.5
-Sidechain_cutoffs COO SER 2.65 3.65
-sidechain_cutoffs COO ARG 1.85 2.85
-sidechain_cutoffs COO LYS 2.85 3.85
-sidechain_cutoffs COO HIS 2.0  3.0
-sidechain_cutoffs COO AMD 2.0  3.0
-sidechain_cutoffs COO TRP 2.0  3.0
-sidechain_cutoffs COO ROH 2.65 3.65
-sidechain_cutoffs COO TYR 2.65 3.65
-sidechain_cutoffs COO  N+ 2.85 3.85
-sidechain_cutoffs COO  CG 1.85 2.85
-sidechain_cutoffs COO C2N 1.85 2.85
-sidechain_cutoffs COO N30 2.85 3.85
-sidechain_cutoffs COO N31 2.85 3.85
-sidechain_cutoffs COO N32 2.85 3.85
-sidechain_cutoffs COO N33 2.85 3.85
-sidechain_cutoffs COO NAR 2.0  3.0
-sidechain_cutoffs COO OCO 2.5  3.5
-sidechain_cutoffs COO  OH 2.65 3.65
-sidechain_cutoffs COO NAM 2.0  3.0
-# SER
-sidechain_cutoffs SER SER 3.5  4.5
-sidechain_cutoffs SER ARG 2.5  4.0
-sidechain_cutoffs SER HIS 2.0  3.0
-sidechain_cutoffs SER AMD 2.5  3.5
-sidechain_cutoffs SER CYS 3.5  4.5
-sidechain_cutoffs SER TRP 2.5  3.5
-sidechain_cutoffs SER ROH 3.5  4.5
-sidechain_cutoffs SER  CG 2.5  4.0
-sidechain_cutoffs SER C2N 2.5  4.0
-sidechain_cutoffs SER NAR 2.0  3.0
-sidechain_cutoffs SER  OH 3.5  4.5
-sidechain_cutoffs SER  SH 3.5  4.5
-sidechain_cutoffs SER TYR 3.5  4.5
-sidechain_cutoffs SER  N+ 3.0  4.5
-sidechain_cutoffs SER NAM 2.5  3.5
-# ARG
-sidechain_cutoffs ARG CYS 2.5  4.0
-sidechain_cutoffs ARG TYR 2.5  4.0
-sidechain_cutoffs ARG OCO 1.85 2.85
-sidechain_cutoffs ARG  SH 2.5  4.0
-# HIS
-sidechain_cutoffs HIS AMD 2.0  3.0
-sidechain_cutoffs HIS TYR 2.0  3.0
-sidechain_cutoffs HIS OCO 2.0  3.0
-# CYS
-sidechain_cutoffs CYS CYS 3.0  5.0
-sidechain_cutoffs CYS TRP 2.5  3.5
-sidechain_cutoffs CYS ROH 3.5  4.5
-sidechain_cutoffs CYS AMD 2.5  3.5
-sidechain_cutoffs CYS TYR 3.5  4.5
-sidechain_cutoffs CYS  N+ 3.0  4.5
-sidechain_cutoffs CYS  CG 2.5  4.0
-sidechain_cutoffs CYS C2N 2.5  4.0
-sidechain_cutoffs CYS N30 3.0  4.5
-sidechain_cutoffs CYS N31 3.0  4.5
-sidechain_cutoffs CYS N32 3.0  4.5
-sidechain_cutoffs CYS N33 3.0  4.5
-sidechain_cutoffs CYS  OH 3.5  4.5
-sidechain_cutoffs CYS NAM 2.5  3.5
-sidechain_cutoffs CYS  SH 3.0  5.0
-# TYR
-sidechain_cutoffs TYR TYR 3.5  4.5
-sidechain_cutoffs TYR  N+ 3.0  4.5
-sidechain_cutoffs TYR AMD 2.5  3.5
-sidechain_cutoffs TYR TRP 2.5  3.5
-sidechain_cutoffs TYR ROH 3.5  4.5
-sidechain_cutoffs TYR  CG 2.5  4.0
-sidechain_cutoffs TYR C2N 2.5  4.0
-sidechain_cutoffs TYR OCO 2.65 3.65
-sidechain_cutoffs TYR NAR 2.0  3.0
-sidechain_cutoffs TYR  OH 3.5  4.5
-sidechain_cutoffs TYR NAM 2.5  3.5
-sidechain_cutoffs TYR  SH 3.5  4.5
-# N+
-sidechain_cutoffs  N+ OCO 2.85 3.85
-sidechain_cutoffs  N+  SH 3.0  4.5
-# LYS
-sidechain_cutoffs LYS OCO 2.85 3.85
-# OCO
-sidechain_cutoffs OCO OCO 2.5  3.5
-sidechain_cutoffs OCO TRP 2.0  3.0
-sidechain_cutoffs OCO ROH 2.65 3.65
-sidechain_cutoffs OCO AMD 2.0  3.0
-sidechain_cutoffs OCO  CG 1.85 2.85
-sidechain_cutoffs OCO C2N 1.85 2.85
-sidechain_cutoffs OCO N30 2.85 3.85
-sidechain_cutoffs OCO N31 2.85 3.85
-sidechain_cutoffs OCO N32 2.85 3.85
-sidechain_cutoffs OCO N33 2.85 3.85
-sidechain_cutoffs OCO NAR 2.0  3.0 
-sidechain_cutoffs OCO  OH 2.65 3.65
-sidechain_cutoffs OCO NAM 2.0  3.0
-# NAR
-sidechain_cutoffs NAR AMD 2.0  3.0
-# SH
-sidechain_cutoffs  SH ROH 3.5  4.5
-sidechain_cutoffs  SH TRP 2.5  3.5
-sidechain_cutoffs  SH AMD 2.5  3.5
-sidechain_cutoffs  SH NAM 2.5  3.5
-sidechain_cutoffs  SH  CG 2.5  4.0
-sidechain_cutoffs  SH C2N 2.5  4.0
-sidechain_cutoffs  SH  OH 3.5  4.5
-sidechain_cutoffs  SH  SH 3.0  5.0
-
-
-
-# Maximal interaction energies for side chains
-sidechain_interaction 0.85  
-
-# Angular dependent sidechain interactions
-angular_dependent_sidechain_interactions HIS
-angular_dependent_sidechain_interactions ARG
-angular_dependent_sidechain_interactions AMD
-angular_dependent_sidechain_interactions TRP
-
-# exception interaction values
-COO_HIS_exception 1.60
-OCO_HIS_exception 1.60
-CYS_HIS_exception 1.60
-CYS_CYS_exception 3.60
-
-# Coulomb interaction parameters
-coulomb_cutoff1  4.0  
-coulomb_cutoff2 10.0
-coulomb_diel    80.0
-
-# Backbone hydrogen bond parameters 
-backbone_NH_hydrogen_bond COO -0.85 2.00 3.00
-#backbone_NH_hydrogen_bond C-  -0.85 2.00 3.00
-backbone_NH_hydrogen_bond CYS -0.85 3.00 4.00
-backbone_NH_hydrogen_bond TYR -0.85 2.20 3.20
-backbone_NH_hydrogen_bond OCO -0.85 2.00 3.50
-backbone_NH_hydrogen_bond NAR -0.85 2.00 3.50
-
-backbone_CO_hydrogen_bond HIS  0.85 2.00 3.00
-backbone_CO_hydrogen_bond OCO  0.85 3.00 4.00
-backbone_CO_hydrogen_bond CG   0.85 2.00 4.00
-backbone_CO_hydrogen_bond C2N  0.85 2.00 4.00
-backbone_CO_hydrogen_bond N30  0.85 2.00 4.00
-backbone_CO_hydrogen_bond N31  0.85 2.00 4.00
-backbone_CO_hydrogen_bond N32  0.85 2.00 4.00
-backbone_CO_hydrogen_bond N33  0.85 2.00 4.00
-backbone_CO_hydrogen_bond NAR  0.85 2.00 3.50
-
-# Group charges
-charge COO -1
-charge HIS +1
-charge CYS -1
-charge TYR -1
-charge LYS +1
-charge ARG +1
-charge N+  +1
-charge C-  -1
-charge OCO -1
-charge SER -1
-charge CG  +1
-charge C2N +1
-charge N30 +1
-charge N31 +1
-charge N32 +1
-charge N33 +1
-charge NAR +1
-charge SH  -1
-charge OP  -1
-
-# list of acids
-acid_list ASP
-acid_list GLU
-acid_list CYS
-acid_list TYR
-acid_list SER
-acid_list C-
-acid_list OCO
-acid_list OP
-acid_list SH
-
-# list of bases
-base_list ARG
-base_list LYS
-base_list HIS
-base_list N+
-base_list CG
-base_list C2N
-base_list N30
-base_list N31
-base_list N32
-base_list N33
-base_list NAR
-
-# list of groups used in backbone reorganisation calculations
-backbone_reorganisation_list ASP
-backbone_reorganisation_list GLU
-
-# Residues that should be ignored
-ignore_residues HOH
-ignore_residues H2O
-ignore_residues HOH
-ignore_residues SO4
-ignore_residues PO4
-ignore_residues PEG
-ignore_residues EPE
-#ignore_residues NAG
-ignore_residues TRS
-
-# Relative Van der Waals volume parameters for the radial volume model
-# Radii adopted from Bondi, A. (1964). "Van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441-51
-VanDerWaalsVolume C  1.40  # radius: 1.70, volume: 20.58 all 'C' and 'CA' atoms
-VanDerWaalsVolume C4 2.64  # 38.79 hydrodphobic carbon atoms + unidentified atoms
-VanDerWaalsVolume N  1.06  # radius: 1.55, volume: 15.60 all nitrogen atoms
-VanDerWaalsVolume O  1.00  # radius: 1.52, volume: 14.71 all oxygen atoms
-VanDerWaalsVolume S  1.66  # radius: 1.80, volume: 24.43 all sulphur atoms
-VanDerWaalsVolume F  0.90  # raidus: 1.47, volume: 13.30 for fluorine 
-VanDerWaalsVolume Cl 1.53  # radius: 1.75, volume: 22.44 for chlorine
-VanDerWaalsVolume P  1.66  # radius: 1.80, volume: 24.42 for phosphorus
-
-# Other desolvation parameters
-desolvationSurfaceScalingFactor	   0.25
-desolvationPrefactor		  -13.0
-desolvationAllowance		    0.0
-desolv_cutoff 			   20.0
-buried_cutoff 			   15.0
-Nmin	      			    280
-Nmax	      			    560
-
-# Ligand groups
-ligand_typing groups 
-min_bond_distance_for_hydrogen_bonds 4
-
-# covalent coupling
-coupling_max_number_of_bonds     3
-shared_determinants              0
-common_charge_centre             0
-remove_penalised_group	         1
-
-# non-covalent coupling
-max_intrinsic_pKa_diff         2.0
-min_interaction_energy         0.5
-max_free_energy_diff           1.0
-min_swap_pka_shift             1.0
-min_pka                        0.0
-max_pka                       10.0
-pH                        variable
-reference                  neutral
-
-# ions
-ions 1P   1 # generic charged atoms
-ions 2P   2
-ions 1N  -1
-ions 2N  -2
-
-ions MG   2 #Magnesium Ion
-ions CA   2 #Calcium Ion
-ions ZN   2 #Zinc Ion
-ions NA   1 #Sodium Ion
-ions CL  -1 #Chloride Ion
-ions MN   2 #Manganese (ii) Ion
-ions K    1 #Potassium Ion
-ions CD   2 #Cadmium Ion
-ions FE   3 #Fe (iii) Ion
-ions SR   2 #Strontium Ion
-ions CU   2 #Copper (ii) Ion
-ions IOD -1 #Iodide Ion
-ions HG   2 #Mercury (ii) Ion
-ions BR  -1 #Bromide Ion
-ions CO   2 #Cobalt (ii) Ion
-ions NI   2 #Nickel (ii) Ion
-ions FE2  2 #Fe (ii) Ion
-
-# write out order of residues
-write_out_order ASP 
-write_out_order GLU
-write_out_order C-
-write_out_order HIS
-write_out_order CYS
-write_out_order TYR
-write_out_order LYS
-write_out_order ARG
-write_out_order SER
-write_out_order N+
-write_out_order CG
-write_out_order C2N
-write_out_order N30
-write_out_order N31
-write_out_order N32
-write_out_order N33
-write_out_order NAR
-write_out_order OCO
-write_out_order SH
-write_out_order OP
diff --git a/propka/__main__.py b/propka/__main__.py
new file mode 100644
index 0000000..3aa53ea
--- /dev/null
+++ b/propka/__main__.py
@@ -0,0 +1,8 @@
+"""Allow the PROPKA package to be run as a program.
+
+For example, `python -m propka`
+"""
+from .run import main
+
+if __name__ == "__main__":
+    main()
diff --git a/propka/lib.py b/propka/lib.py
index cd25446..1988fd8 100644
--- a/propka/lib.py
+++ b/propka/lib.py
@@ -222,7 +222,7 @@ def build_parser(parser=None):
     return parser
 
 
-def loadOptions(args):
+def loadOptions(args=None):
     """
     Load the arguments parser with options. Note that verbosity is set as soon
     as this function is invoked.
@@ -232,18 +232,11 @@ def loadOptions(args):
     Returns:
         argparse namespace
     """
-    # defining a 'usage' message
-    usage = "usage: %prog [options] filename"
-
     # loading the parser
     parser = build_parser()
 
     # parsing and returning options and arguments
-    if len(args) == 0:
-        # command line
-        options = parser.parse_args()
-    else:
-        options = parser.parse_args(args)
+    options = parser.parse_args(args)
 
     # adding specified filenames to arguments
     options.filenames.append(options.input_pdb)