packmol-memgen-minimal 1.1.16__py3-none-any.whl

packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py

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+#!/usr/bin/python
+
+###############################################################################
+# charmmlipid2amber.py
+# Version 2.0.3
+# 2014-06-05
+# Benjamin D. Madej
+#
+# Usage: 
+# charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o output.pdb
+#
+# Description:
+# Processes PDB files for use with Lipid14. This program processes only ATOM,
+# HETATM, and TER lines of a PDB file. Other lines will be removed from PDB.
+###############################################################################
+#Mod. by Stephan Schott V. // Added the possibility to recognize between
+#different chain IDs.
+
+
+# Includes
+import sys
+import csv
+import re
+import getopt
+import os
+
+# Main
+def charmmlipid2amber(inputpdb,outputpdb=None,csv_dict=os.path.abspath(os.path.dirname(sys.argv[0]))+"/charmmlipid2amber.csv"):
+    #print os.path.abspath(os.path.dirname(sys.argv[0]))+"/charmmlipid2amber.csv"
+    # Process options
+    input_file_name=inputpdb
+    if outputpdb is not None:
+        output_file_name=outputpdb
+    else:
+        output_file_name=inputpdb.replace(".pdb","_amber.pdb")
+    convert_file_name=csv_dict
+    if convert_file_name == '':
+        print("Error: charmmlipid2amber.py substitution file not set. Provide -c or pass a valid csv_dict path.")
+        print("Usage: charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o output.pdb")
+        sys.exit(2)
+    if os.path.isfile(convert_file_name) != True:
+        print("Error: No substitution file found. Check that the file set with -c is correct.")
+        sys.exit(1)
+    try:
+        input_file  = open(input_file_name, 'r') # File to be processed
+    except IOError as err:
+        print("Error: ", str(err))
+        sys.exit(1)
+    input_file_list = [] # File to be processed as a list
+    for line in input_file:
+        input_file_list.append(line)
+    input_file.close()
+
+    # Process residues
+    residue_list = [] # List of residue numbers
+    residue_start = [] # List of lines where residues start. Line numbers start at 1.
+    residue_end = [] # List of lines where residues end, including TER card if present. Line numbers start at 1.
+    it0 = 1
+    previous_residue = "" # Residue number of the previous line (including TER card). Set to "" if it is not an ATOM record or TER card.
+    current_residue = "" # Residue number of the current line (including TER card). Set to "" if it is not an ATOM record or TER card.
+    previous_chain = ""
+    current_chain = ""
+    # Split file into residues by checking columns 23-27 (<99999 residues):
+    # First line:
+    if (input_file_list[0][0:6] == "ATOM  " or
+        input_file_list[0][0:6] == "HETATM"):
+        residue_list.append(input_file_list[0][22:28])
+        residue_start.append(it0)
+        previous_residue = input_file_list[0][22:28] 
+        previous_chain = input_file_list[0][21:22]
+    elif line[0:3] == "TER":
+        previous_residue = ""
+        previous_chain = ""
+    else:
+        previous_residue = ""
+        previous_chain = ""
+    it0+=1
+#TER_trigger to separate residues according to TER flags. Only relevant when packing causes a single residue molecule 
+#to be packed at the beginning, and is not properly identified by residue number only
+    TER_trigger = False 
+    # Rest of lines:
+    for line in input_file_list[1:]:
+        if line[0:6] == "ATOM  " or line[0:6] == "HETATM":
+            current_residue = line[22:28]
+            current_chain = line[21:22]
+        elif line[0:3] == "TER":
+            current_residue = previous_residue
+            current_chain = previous_chain
+        else:
+            current_residue = ""
+            current_chain = ""
+        if previous_residue != current_residue  or previous_chain != current_chain or TER_trigger:
+            # Previous line was not an ATOM or TER:
+            if previous_residue == "" or previous_chain == "":
+                residue_list.append(current_residue)
+                residue_start.append(it0)
+                previous_residue = current_residue
+                previous_chain = current_chain
+            # Current line is not an ATOM or TER:
+            elif current_residue == "" or current_chain == "":
+                residue_end.append(it0-1)
+                previous_residue = current_residue
+                previous_chain = current_chain
+            # Previous and current line are ATOM or TER:
+            else:
+                residue_list.append(current_residue)
+                residue_start.append(it0)
+                residue_end.append(it0-1)
+                previous_residue = current_residue
+                previous_chain = current_chain
+            TER_trigger = False
+        it0+=1
+        if line[0:3] == "TER":
+            TER_trigger = True
+    # If the last residue is not closed, define the end:
+    if current_residue != "":
+        residue_end.append(it0-1)
+
+    # Process substition dictionaries
+    try:
+        csv_file = open(convert_file_name, 'r') # csv file with all substitutions
+    except IOError as err:
+        print("Error: ", str(err))
+        sys.exit(1)
+    # Skip header line of csv file. Line 2 contains dictionary keys:
+    csv_file.readline()
+    csv_file_reader = csv.DictReader(csv_file) # Dictionary csv reader
+    replace_dict = {} # Dictionary of atom name and residue name search and replace
+    order_dict = {} # Dictionary of atom name and residue name order
+    ter_dict = {} # Dictionary of whether residue should have a TER card based on atom name and residue name. All atom name and residue name in a residue with a TER card will return True.
+    num_atom_dict = {} # Dictionary of number of atoms in current residue for the search string
+    for line in csv_file_reader:
+        replace_dict[line["search"]] = line["replace"]
+        order_dict[line["search"]] = int(line["order"])
+        ter_dict[line["search"]] = (line["TER"] == "True")
+        num_atom_dict[line["search"]] = int(line["num_atom"])
+    csv_file.close()
+
+    # Do substitions
+    # The search and replace is columns 13-21 in the PDB file:
+    # 13-16: atom name
+    # 17:      alternate location indicator
+    # 18-20: residue name
+    # 21:      sometimes used for the residue name
+    output_file_list = [] # File to be written in list form (after processing)
+    residue_substituted = False # For error checking. True if a substitution occurs.
+    for it1 in range(0, len(residue_list)):
+        # residue_start and residue_end indices start at 1. 
+        # input_file_list indices start at 0.
+        input_residue = input_file_list[residue_start[it1]-1:
+            residue_end[it1]]
+        output_residue = []
+        # Process residue only if first atom is in the replacement dictionary:
+        if input_residue[0][12:21] in replace_dict:
+            residue_substituted = True
+            # Check if length of input_residue is correct:
+            # Count TER cards in residue for residue length arithmetic
+            n_TER_cards = 0
+            for line in input_residue:
+                if line[0:3] == "TER":
+                    n_TER_cards += 1
+            if len(input_residue)-n_TER_cards != num_atom_dict[input_residue[0][12:21]]:
+                print("Error: Number of atoms in residue does not match number of atoms in residue in replacement data file")
+                print(input_residue, num_atom_dict[input_residue[0][12:21]])
+                sys.exit(1)
+            output_residue = len(input_residue)*[0]
+            for it2 in range(0, len(input_residue)):
+                line = input_residue[it2]
+                if line[0:3] != "TER":
+                     search = line[12:21]
+                     output_residue[order_dict[search]] = re.sub(search, 
+                        replace_dict[search], line)
+                else:
+                     output_residue[it2] = "TER   \n"
+            if ter_dict[input_residue[0][12:21]] == True:
+                if input_residue[-1][0:3] != "TER":
+                    output_residue.append("TER   \n")
+        else:
+            output_residue = input_residue
+        output_file_list.extend(output_residue)
+    # Check if any residues were substituted:
+    if residue_substituted == False:
+        print("No residues substituted by charmmlipid2amber")
+        return input_file_name
+
+    # Write output
+    try:
+        output_file = open(output_file_name, 'w') # File to be written
+    except IOError as err:
+        print("Error: ", str(err))
+        sys.exit(1)
+    output_file.write("REMARK   Packmol generated pdb file, Packmol Memgen estimated parameters\n")
+    output_file.write("REMARK   charmmlipid2amber.py transformed file\n")
+    for line in output_file_list:
+        output_file.write(line)
+    output_file.write("END   \n")
+    output_file.close()
+    return output_file_name
+
+if __name__ == '__main__':
+    # Process options
+    input_file_name=''
+    output_file_name=''
+    convert_file_name=''
+    try:
+        myopts, args = getopt.getopt(sys.argv[1:],"i:o:c:")
+    except getopt.GetoptError as err:
+        print("Error: ", str(err))
+        print("Usage: charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o output.pdb")
+        sys.exit(2)
+    for o, a in myopts:
+        if o == "-i":
+            input_file_name = a
+        elif o == "-o":
+            output_file_name = a
+        elif o == "-c":
+            convert_file_name = a
+        else:
+            print("Usage: charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o output.pdb")
+            sys.exit(0)
+    if input_file_name == '' or output_file_name == '':
+        print("Usage: charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o output.pdb")
+        sys.exit(2)
+    charmmlipid2amber(input_file_name,outputpdb=output_file_name,csv_dict=os.path.abspath(os.path.dirname(sys.argv[0]))+"/charmmlipid2amber.csv")
+ 

packmol_memgen/lib/pdbremix/LICENSE

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+MIT License
+
+Copyright (c) 2018 Bosco Ho
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

packmol_memgen/lib/pdbremix/_version.py

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+0.9