flex efp scripts and fragment database

Author: slipchenko

CMakeLists.txt

@@ -2,10 +2,10 @@ cmake_minimum_required(VERSION 3.0)
 # project_VERSION* variables populated from project(... VERSION x.x.x) string
 cmake_policy(SET CMP0048 NEW)
 
-project(libefp VERSION 1.5.0 LANGUAGES C)
-set(libefp_AUTHORS "Ilya A. Kaliman")
+project(libefp VERSION 1.7.2 LANGUAGES C)
+set(libefp_AUTHORS "Ilya A. Kaliman, Lori A. Burns, Dmitry Morozov, Carlos H. Borca, Yen (Terri) Bui, Yongbin Kim, Lyudmila V. Slipchenko")
 set(libefp_DESCRIPTION "Parallel implementation of the Effective Fragment Potential method")
-set(libefp_URL "https://libefp.github.io/")
+set(libefp_URL "https://github.com/libefp2/libefp")
 set(libefp_LICENSE "BSD 2-clause")
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)

CONTRIBUTORS

@@ -5,5 +5,6 @@ Lori A. Burns
 Dmitry Morozov
 Carlos H. Borca
 Yen (Terri) Bui
+Yongbin Kim
 Lyudmila V. Slipchenko
 

fraglib/flex_efp_protein/README.md

@@ -0,0 +1,6 @@
+## Amino acid parameters as published 
+
+aa_flex_params_631Gd.tar.gz : parameters in 6-31G(d) basis
+aa_flex_params_631Gd-631+G3df2p.tar.gz: parameters in a hybrid 6-31G(d) / 6-31-+G(3df,2p) basis (diffuse functions on H atoms only)
+aa_flex_params_631Gd-6311++G3df2p.tar.gz: parameters in a hybrid 6-31G(d) / 6-311++G(3df,2p) basis (standard hybrid basis)
+

fraglib/flex_efp_protein/aa_flex_params_631Gd-631+G3df2p.tar.gz

@@ -1,3 +1,5 @@
 ## Scripts and tools
 
 Flexible_V5.py: flexible EFP script by Yongbin Kim
+
+create_hybrid_basis.py: generates a hybrid-basis potential from two original potentials in different basis sets; first (small) basis: elec, elec screening; second (large) basis: pol, disp, exrep, by Yongbin Kim 

fraglib/flex_efp_protein/aa_flex_params_631Gd-6311++G3df2p.tar.gz

@@ -0,0 +1,62 @@
+import sys,os
+
+def main(inputfile1,inputfile2):
+	pwd       = os.getcwd()+'/'
+	ifile1    = open(inputfile1,'r') # for elec
+	ifile2    = open(inputfile2,'r') # for rest
+	reflines1 = ifile1.readlines()
+	reflines2 = ifile2.readlines()
+
+	lineN = 0
+	for obj in reflines1:
+		line  = obj.strip()
+		lineN += 1
+		if 'POLARIZABLE' in line and 'DYNAMIC' not in line:
+			elec1 = lineN
+		elif 'SCREEN2' in line:
+			elec2 = lineN
+		else:
+			continue
+	print(inputfile1,inputfile2)
+	lineN = 0
+	for obj in reflines2:
+		line  = obj.strip()
+		lineN += 1
+		if 'POLARIZABLE' in line and 'DYNAMIC' not in line:
+			rest1 = lineN
+		elif 'SCREEN2' in line:
+			rest2 = lineN
+		else:
+			continue
+
+	lineN = 0
+	parm1,parm3 = [],[]
+	for obj in reflines1:
+		lineN += 1
+		if lineN < elec1:
+			if lineN == 4:
+				parm1.append('6-31G* elec, 6-31+xG(3df,2p) - else\n')
+			else:
+				parm1.append(obj)
+		elif lineN >= elec2:
+			parm3.append(obj)
+		else:
+			continue
+
+	lineN = 0
+	parm2 = []
+	for obj in reflines2:
+		lineN += 1
+		if lineN >= rest1 and lineN < rest2:
+			parm2.append(obj)
+		else:
+			continue
+
+
+	efparm = parm1+parm2+parm3
+	output = inputfile1.split('/')[1]
+	ofile = open(output,'w')
+	for i in range(len(efparm)):
+		ofile.write(efparm[i])
+
+main(sys.argv[1],sys.argv[2])