initial commit

.gitignore

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+.*~
+*~
+.*.swp
+__pycache__
+*.log
+*.out
+*.err

__init__.py

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+from collections import OrderedDict
+
+def parse_pdb_line(l):
+    l = l.rstrip()
+    return OrderedDict(
+        [
+            # TODO support more than 100000 atoms
+            ("Record"    ,       l[ 0: 6] ),
+            ("serial"    ,   int(l[ 6:11])),
+            ("name"      ,       l[12:16] ),
+            ("altLoc"    ,       l[16:17] ),
+            ("resName"   ,       l[17:21] ),
+            ("chainID"   ,       l[21:22] ),
+            # TODO support more than 10000 residues
+            ("resSeq"    ,   int(l[22:26])),
+            ("iCode"     ,       l[26:27] ),
+            ("x"         , float(l[30:38])),
+            ("y"         , float(l[38:46])),
+            ("z"         , float(l[46:54])),
+            ("occupancy" , float(l[54:60])),
+            ("tempFactor", float(l[60:66])),
+            ("segment"   ,       l[72:76] ),
+            ("element"   ,       l[76:78] ),
+            ("charge"    ,       l[78:80] ),
+        ]
+    )
+
+def parse_pdb_file(filename):
+    with open(filename) as f:
+        rtn = []
+        for l in f:
+            if l[:6] in ["ATOM  ", "HETATM"]:
+                rtn.append(parse_pdb_line(l))
+    return rtn
+
+def write_pdb_line(entry):
+    name = entry["name"]
+    if len(name) < 4:
+        name = ' ' + name
+    mod_entry = entry.copy()
+    mod_entry["name"] = name
+    return '{: <6s}{: >5d} {: <4s}{:1s}{: <4s}{:1s}{: >4d}{:1s}   {: >8.3f}{: >8.3f}{: >8.3f}{: >6.2f}{: >6.2f}      {: <4s}{: >2s}{: >2s}'.format(*mod_entry.values()).rstrip() + '\n'
+
+def write_pdb_file(pdbdata):
+    return ''.join([write_pdb_line(entry) for entry in pdbdata])
+
+if __name__ == "__main__":
+    #parse_pdb_line("ATOM   1914  SOD SOD S1127       0.016  -3.389  -0.040  1.00 58.57      S   NA")
+    source = "/home/zhiwang/my_proj/charmm-gui_e86p_A51_drude/step2_drude.pdb"
+    source = "/home/zhiwang/my_proj/charmm-gui_e86p_A51/step5_assembly.namd.pdb"
+    #source = "orig.pdb"
+    pdb = (parse_pdb_file(source))
+    #print(pdb[6].values())
+    with open("dd.pdb", "w") as f:
+        f.write(write_pdb_file(pdb))
+    with open(source) as f:
+        with open('ref.pdb', 'w') as fout:
+            for l in f:
+                fout.write(l.rstrip() + '\n')