diff --git a/prody/atomic/atomic.py b/prody/atomic/atomic.py
index b4a6700f4..1541c1993 100644
--- a/prody/atomic/atomic.py
+++ b/prody/atomic/atomic.py
@@ -24,6 +24,15 @@
except:
continue
+CORE_AAMAP = AAMAP = {
+ 'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLN': 'Q',
+ 'GLU': 'E', 'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K',
+ 'MET': 'M', 'PHE': 'F', 'PRO': 'P', 'SER': 'S', 'THR': 'T', 'TRP': 'W',
+ 'TYR': 'Y', 'VAL': 'V'
+}
+
+invAAMAP = dict((v, k) for k, v in CORE_AAMAP.items())
+
AAMAP = {
'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLN': 'Q',
'GLU': 'E', 'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K',
@@ -242,17 +251,25 @@ def getTitle(self):
return ag._title
def getSequence(self, **kwargs):
- """Returns one-letter sequence string for amino acids.
+ """Returns one-letter sequence string for amino acids, unless *longSeq* is **True**.
When *allres* keyword argument is **True**, sequence will include all
residues (e.g. water molecules) in the chain and **X** will be used for
non-standard residue names."""
+ longSeq = kwargs.get('longSeq', False)
+
get = AAMAP.get
if hasattr(self, 'getResnames'):
- seq = ''.join([get(res, 'X') for res in self.getResnames()])
+ if longSeq:
+ seq = ' '.join(self.getResnames())
+ else:
+ seq = ''.join([get(res, 'X') for res in self.getResnames()])
else:
res = self.getResname()
- seq = get(res, 'X')
+ if longSeq:
+ seq = res
+ else:
+ seq = get(res, 'X')
return seq
diff --git a/prody/atomic/chain.py b/prody/atomic/chain.py
index d5534f783..db74231c9 100644
--- a/prody/atomic/chain.py
+++ b/prody/atomic/chain.py
@@ -8,9 +8,14 @@
__all__ = ['Chain']
-def getSequence(resnames):
- """Returns polypeptide sequence as from list of *resnames* (residue
- name abbreviations)."""
+def getSequence(resnames, **kwargs):
+ """Returns polypeptide sequence from a list of *resnames* using one-letter residue
+ name abbreviations by default, or long (usually three letter) abbrevations
+ if *longSeq* is **True**."""
+
+ longSeq = kwargs.get('longSeq', False)
+ if longSeq:
+ return ' '.join(resnames)
get = AAMAP.get
return ''.join([get(rn, 'X') for rn in resnames])
@@ -134,13 +139,16 @@ def getSequence(self, **kwargs):
if kwargs.get('allres', False):
get = AAMAP.get
- seq = ''.join([get(res.getResname(), 'X') for res in self])
+ if kwargs.get('longSeq', False):
+ seq = ' '.join([res.getResname() for res in self])
+ else:
+ seq = ''.join([get(res.getResname(), 'X') for res in self])
elif self._seq:
seq = self._seq
else:
calpha = self.calpha
if calpha:
- seq = getSequence(calpha.getResnames())
+ seq = getSequence(calpha.getResnames(), **kwargs)
else:
seq = ''
self._seq = seq
diff --git a/prody/atomic/flags.py b/prody/atomic/flags.py
index cee3c466a..56d9c4701 100644
--- a/prody/atomic/flags.py
+++ b/prody/atomic/flags.py
@@ -67,6 +67,8 @@
NONSTANDARD = {
'ASX': set(['acyclic', 'surface', 'polar', 'medium']),
'GLX': set(['acyclic', 'surface', 'large', 'polar']),
+ 'ASH': set(['acyclic', 'acidic', 'surface', 'polar', 'medium']),
+ 'GLH': set(['acyclic', 'acidic', 'surface', 'large', 'polar']),
'CSO': set(['acyclic', 'neutral', 'surface', 'medium', 'polar']),
'CYX': set(['acyclic', 'neutral', 'buried', 'medium', 'polar']),
'HIP': set(['cyclic', 'basic', 'surface', 'large', 'polar']),
@@ -75,6 +77,12 @@
'HSD': set(['cyclic', 'basic', 'surface', 'large', 'polar']),
'HSE': set(['cyclic', 'basic', 'surface', 'large', 'polar']),
'HSP': set(['cyclic', 'acidic', 'surface', 'large', 'polar']),
+ 'HISD': set(['cyclic', 'basic', 'surface', 'large', 'polar']),
+ 'HISE': set(['cyclic', 'basic', 'surface', 'large', 'polar']),
+ 'HISP': set(['cyclic', 'acidic', 'surface', 'large', 'polar']),
+ 'LYN': set(['acyclic', 'neutral', 'surface', 'large', 'polar']),
+ 'TYM': set(['cyclic', 'aromatic', 'surface', 'basic', 'large', 'polar']),
+ 'ARN': set(['acyclic', 'neutral', 'surface', 'large', 'polar']),
'MSE': set(['acyclic', 'neutral', 'buried', 'large']),
'CME': set(['acyclic', 'neutral', 'buried', 'large']),
'SEC': set(['acyclic', 'neutral', 'buried', 'polar', 'medium']),
diff --git a/prody/proteins/cifheader.py b/prody/proteins/cifheader.py
index dd4475a0b..d35f70e18 100644
--- a/prody/proteins/cifheader.py
+++ b/prody/proteins/cifheader.py
@@ -7,7 +7,8 @@
from prody import LOGGER
from prody.atomic import flags, AAMAP
-from prody.utilities import openFile, alignBioPairwise, GAP_PENALTY, GAP_EXT_PENALTY
+from prody.atomic.atomic import invAAMAP
+from prody.utilities import openFile, alignBioPairwise, GAP_EXT_PENALTY
from .localpdb import fetchPDB
from .header import (Chemical, Polymer, DBRef, _PDB_DBREF,
@@ -57,7 +58,7 @@ def _natomsFromFormulaPart(part):
return 1
return int("".join(digits))
-def parseCIFHeader(pdb, *keys):
+def parseCIFHeader(pdb, *keys, **kwargs):
"""Returns header data dictionary for *pdb*. This function is equivalent to
``parsePDB(pdb, header=True, model=0, meta=False)``, likewise *pdb* may be
an identifier or a filename.
@@ -119,14 +120,18 @@ def parseCIFHeader(pdb, *keys):
raise IOError('{0} is not a valid filename or a valid PDB '
'identifier.'.format(pdb))
pdb = openFile(pdb, 'rt')
- header = getCIFHeaderDict(pdb, *keys)
+ header = getCIFHeaderDict(pdb, *keys, **kwargs)
pdb.close()
return header
-def getCIFHeaderDict(stream, *keys):
+def getCIFHeaderDict(stream, *keys, **kwargs):
"""Returns header data in a dictionary. *stream* may be a list of PDB lines
- or a stream."""
+ or a stream.
+
+ Polymers have sequences that usually use one-letter residue name abbreviations by default.
+ To obtain long (usually three letter) abbrevations, set *longSeq* to **True**.
+ """
try:
lines = stream.readlines()
@@ -139,11 +144,17 @@ def getCIFHeaderDict(stream, *keys):
keys = list(keys)
for k, key in enumerate(keys):
if key in _PDB_HEADER_MAP:
- value = _PDB_HEADER_MAP[key](lines)
+ if key == 'polymers':
+ value = _PDB_HEADER_MAP[key](lines, **kwargs)
+ else:
+ value = _PDB_HEADER_MAP[key](lines)
keys[k] = value
else:
try:
- value = _PDB_HEADER_MAP['others'](lines, key)
+ if key == 'polymers':
+ value = _PDB_HEADER_MAP[key](lines, **kwargs)
+ else:
+ value = _PDB_HEADER_MAP[key](lines)
keys[k] = value
except:
raise KeyError('{0} is not a valid header data identifier'
@@ -761,8 +772,11 @@ def _getReference(lines):
return ref
-def _getPolymers(lines):
- """Returns list of polymers (macromolecules)."""
+def _getPolymers(lines, **kwargs):
+ """Returns list of polymers (macromolecules).
+
+ Sequence is usually one-letter abbreviations, but can be long
+ abbreviations (usually three letters) if *longSeq* is **True**"""
pdbid = _PDB_HEADER_MAP['identifier'](lines)
polymers = dict()
@@ -780,8 +794,28 @@ def _getPolymers(lines):
entities[entity].append(ch)
poly = polymers.get(ch, Polymer(ch))
polymers[ch] = poly
- poly.sequence += ''.join(item[
- '_entity_poly.pdbx_seq_one_letter_code_can'].replace(';', '').split())
+
+ longSeq = kwargs.get('longSeq', False)
+ if longSeq:
+ poly.sequence += ''.join(item[
+ '_entity_poly.pdbx_seq_one_letter_code'].replace(';', '').split())
+ else:
+ poly.sequence += ''.join(item[
+ '_entity_poly.pdbx_seq_one_letter_code_can'].replace(';', '').split())
+
+ if longSeq:
+ for poly in polymers.values():
+ seq = poly.sequence
+ resnames = []
+ for item in seq.split('('):
+ if item.find(')') != -1:
+ resnames.append(item[:item.find(')')])
+ letters = list(item[item.find(')')+1:])
+ else:
+ letters = list(item)
+ resnames.extend([invAAMAP[letter] for letter in letters])
+
+ poly.sequence = ' '.join(resnames)
# DBREF block 1
items2 = parseSTARSection(lines, '_struct_ref', report=False)
@@ -1240,13 +1274,17 @@ def _getOther(lines, key=None):
return data
-def _getUnobservedSeq(lines):
+def _getUnobservedSeq(lines, **kwargs):
+ """Get sequence of unobserved residues.
+
+ This sequence is usually using one-letter residue name abbreviations by default.
+ To obtain long (usually three letter) abbrevations, set *longSeq* to **True**."""
key_unobs = '_pdbx_unobs_or_zero_occ_residues'
try:
unobs = parseSTARSection(lines, key_unobs, report=False)
- polymers = _getPolymers(lines)
+ polymers = _getPolymers(lines, **kwargs)
except:
pass
diff --git a/prody/proteins/header.py b/prody/proteins/header.py
index ec83b77fc..4a48d45bf 100644
--- a/prody/proteins/header.py
+++ b/prody/proteins/header.py
@@ -235,7 +235,7 @@ def cleanString(string, nows=False):
return ' '.join(string.strip().split())
-def parsePDBHeader(pdb, *keys):
+def parsePDBHeader(pdb, *keys, **kwargs):
"""Returns header data dictionary for *pdb*. This function is equivalent to
``parsePDB(pdb, header=True, model=0, meta=False)``, likewise *pdb* may be
an identifier or a filename.
@@ -297,14 +297,17 @@ def parsePDBHeader(pdb, *keys):
raise IOError('{0} is not a valid filename or a valid PDB '
'identifier.'.format(pdb))
pdb = openFile(pdb, 'rt')
- header, _ = getHeaderDict(pdb, *keys)
+ header, _ = getHeaderDict(pdb, *keys, **kwargs)
pdb.close()
return header
-def getHeaderDict(stream, *keys):
+def getHeaderDict(stream, *keys, **kwargs):
"""Returns header data in a dictionary. *stream* may be a list of PDB lines
- or a stream."""
+ or a stream.
+
+ Polymers have sequences that usually use one-letter residue name abbreviations by default.
+ To obtain long (usually three letter) abbrevations, set *longSeq* to **True**."""
lines = defaultdict(list)
loc = 0
@@ -325,7 +328,10 @@ def getHeaderDict(stream, *keys):
keys = list(keys)
for k, key in enumerate(keys):
if key in _PDB_HEADER_MAP:
- value = _PDB_HEADER_MAP[key](lines)
+ if key == 'polymers':
+ value = _PDB_HEADER_MAP[key](lines, **kwargs)
+ else:
+ value = _PDB_HEADER_MAP[key](lines)
keys[k] = value
else:
raise KeyError('{0} is not a valid header data identifier'
@@ -587,8 +593,11 @@ def _getReference(lines):
return ref
-def _getPolymers(lines):
- """Returns list of polymers (macromolecules)."""
+def _getPolymers(lines, **kwargs):
+ """Returns list of polymers (macromolecules).
+
+ Polymers have sequences that usually use one-letter residue name abbreviations by default.
+ To obtain long (usually three letter) abbrevations, set *longSeq* to **True**."""
pdbid = lines['pdbid']
polymers = dict()
@@ -596,7 +605,14 @@ def _getPolymers(lines):
ch = line[11]
poly = polymers.get(ch, Polymer(ch))
polymers[ch] = poly
- poly.sequence += ''.join(getSequence(line[19:].split()))
+
+ longSeq = kwargs.get('longSeq', False)
+ if longSeq:
+ if poly.sequence != '':
+ poly.sequence += ' '
+ poly.sequence += getSequence(line[19:].split(), **kwargs)
+ else:
+ poly.sequence += ''.join(getSequence(line[19:].split(), **kwargs))
for i, line in lines['DBREF ']:
i += 1
diff --git a/prody/utilities/catchall.py b/prody/utilities/catchall.py
index 9e9c766c2..bf781770d 100644
--- a/prody/utilities/catchall.py
+++ b/prody/utilities/catchall.py
@@ -314,7 +314,7 @@ def calcTree(names, distance_matrix, method='upgma', linkage=False):
method = method.lower().strip()
- if method in ['ward', 'single', 'average', 'weighted', 'centroid', 'median']:
+ if method in ['ward', 'single', 'average', 'weighted', 'centroid', 'median', 'complete']:
from scipy.cluster.hierarchy import linkage as hlinkage
from scipy.spatial.distance import squareform