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added (de)protonated AA #30

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added (de)protonated AA #30

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33 changes: 32 additions & 1 deletion aminoAcids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,15 @@ def __init__(self):
self.codes321 = {
'ALA': 'A',
'ARG': 'R',
'ARN': 'R',
'ASN': 'N',
'ASP': 'D',
'ASH': 'D',
'CYS': 'C',
'CYX': 'C',
'GLN': 'Q',
'GLU': 'E',
'GLH': 'E',
'GLY': 'G',
'HIS': 'H',
'HIE': 'H',
Expand All @@ -21,6 +25,7 @@ def __init__(self):
'ILE': 'I',
'LEU': 'L',
'LYS': 'K',
'LYN': 'K',
'MET': 'M',
'PHE': 'F',
'PRO': 'P',
Expand Down Expand Up @@ -69,6 +74,11 @@ def __init__(self):
O = 1,
C = 6,
),
'ARN': Counter(
N = 4,
O = 1,
C = 6,
),
'ASN': Counter(
N = 2,
O = 2,
Expand All @@ -79,12 +89,23 @@ def __init__(self):
O = 3,
C = 4
),
'ASH': Counter(
N = 1,
O = 3,
C = 4
),
'CYS': Counter(
N = 1,
O = 1,
C = 3,
S = 1
),
'CYX': Counter(
N = 1,
O = 1,
C = 3,
S = 1
),
'GLN': Counter(
N = 2,
O = 2,
Expand All @@ -95,6 +116,11 @@ def __init__(self):
O = 3,
C = 5
),
'GLH': Counter(
N = 1,
O = 3,
C = 5
),
'GLY': Counter(
N = 1,
O = 1,
Expand Down Expand Up @@ -135,6 +161,11 @@ def __init__(self):
O = 1,
C = 6
),
'LYN': Counter(
N = 2,
O = 1,
C = 6
),
'MET': Counter(
N = 1,
O = 1,
Expand Down Expand Up @@ -176,4 +207,4 @@ def __init__(self):
O = 1,
C = 5
)
}
}
14 changes: 11 additions & 3 deletions protein.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@

class System(object):
def __init__(self, **kwargs):
protein_res_names = ["ALA", "ARG", "ASN", "ASP", "CYS", "CYX", "GLN", "GLU", "GLY", "HIS",
"HIE", "HID", "HIP", "HISE", "HISD", "HISH", "ILE", "LEU", "LYS",
protein_res_names = ["ALA", "ARG","ARN", "ASN", "ASP", "ASH", "CYS", "CYX", "GLN", "GLH", "GLU", "GLY", "HIS",
"HIE", "HID", "HIP", "HISE", "HISD", "HISH", "ILE", "LEU", "LYS", "LYN",
"MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", ]

self.pdb = kwargs["pdb"]
Expand Down Expand Up @@ -249,7 +249,7 @@ def __init__(self, *args, **kwargs):

def _setRes(self):
"""
Change Histidines and Cysteins in pdb to the format preferred by gromacs.
Change Histidines and Cysteins and Protonated ASP and GLU and Deprotonated LYS pdb to the format preferred by gromacs.
"""
tgt = open(self.pdb.replace(".pdb", "-his.pdb"), "w")
self.pdb_his = tgt.name
Expand All @@ -264,6 +264,14 @@ def _setRes(self):
tgt.write(line.replace('HIP ','HISH'))
elif line.split()[3] == "CYX":
tgt.write(line.replace('CYX ','CYS '))
elif line.split()[3] == "ASH":
tgt.write(line.replace('ASH ','ASPH'))
elif line.split()[3] == "ASH":
tgt.write(line.replace('GLH ','GLUH'))
elif line.split()[3] == "LYN":
tgt.write(line.replace('LYN ','LYSN'))
elif line.split()[3] == "ARN":
tgt.write(line.replace('ARN ','ARGN'))
else:
tgt.write(line)
else:
Expand Down