Merge pull request #27 from libefp2/jack

Jack

Author: Jacklaw441

doc/applied_efp.rst

@@ -34,7 +34,7 @@ The general procedure is to define the QM and EFP regions, fragment the residues
 EFP region, generate the starting fragment parameters, trim overlapping virtual/real atoms, 
 then create the final calculation input.
 
-.. image:: ../images/flowchart-1.png
+.. image:: ../images/flowchart.png
    :width: 500
    :align: center
 

examples/flex-EFP/Scripts/cut_qm.py

@@ -31,7 +31,7 @@ def get_specials(lines):
     and the atom indexes for which only the polarizable points should be removed.
     
     The function looks for keywords 'erased:' and 'remove:' in the lines.
-        -make_AAs_V2.py added these comments.
+        -make_AAs.py added these comments.
     
     Reads:
         lines: input file (.inp) lines.

examples/flex-EFP/Scripts/fragment_RMSD.py

@@ -18,7 +18,7 @@
 ang_cutoff = 0.20                        # Minimum RMSD allowed for a "good" match (in Angstroms)
 bohr_cutoff = ang_cutoff * 1.8897259886  # Convert Angstrom cutoff to Bohr
 
-#Add to these if there are more 
+#Add to these if there are more residue names than are listed
 amino_acid_dict = {
     'a': 'ala', 'r': 'arg', 'n': 'asn', 'd': 'asp', 'c': 'cys',
     'q': 'gln', 'e': 'glu', 'g': 'gly', 'h': 'hip', 'i': 'ile',

examples/flex-EFP/Scripts/make_AAs.py

@@ -26,7 +26,7 @@
 # Input Files and Command Line Arguments
 # ---------------------------
 # Get input filenames from command line
-# Sample execution: python make_AAs_V2.py efp_pair53004.g96 confout_pair53004.g96 user_defined.txt topol.top
+# Sample execution: python make_AAs.py efp_pair53004.g96 confout_pair53004.g96 user_defined.txt topol.top
 
 efp_g96 = sys.argv[1]     # EFP file ("efp_pair53004.g96")
 full_g96 = sys.argv[2]    # Full configuration file ("confout_pair53004.g96")

examples/flex-EFP/Scripts/make_bcls.py

@@ -21,7 +21,7 @@
 # Input files and cutting definitions
 # ---------------------------
 # Command-line arguments:
-# Sample execution: python make_bcls_V2.py efp_opt_83855.g96 optimized_83855.g96
+# Sample execution: python make_bcls.py efp_opt_83855.g96 optimized_83855.g96
 g96_file = sys.argv[1]        # EFP region file (e.g., "efp_opt_83855.g96")
 full_g96_file = sys.argv[2]   # Full configuration file (e.g., "optimized_83855.g96")