<commit_before><cg_molecule> <!-- this file is used to convert an atomistic to coarse-grained trajectory -->
	<name>A</name> <!-- name of the CG molecule -->
	<ident>Protein</ident> <!-- name of the atomistic molecule -->
	<topology>
 		<cg_beads>
			<cg_bead>
				<name>NIT1</name> <!-- name of the first CG bead -->
				<type>DCV2T</type> <!-- type of the bead -->
				<mapping>NIT</mapping> <!-- mapping to determine the bead center -->
				<beads> <!-- list of atoms resnum:resname:atomname -->
				1:NIT:N1 1:NIT:CN1 1:NIT:N2 1:NIT:CN2 1:NIT:CC1 1:NIT:C1 1:NIT:HN1
				</beads>
				<symmetry>3</symmetry> <!-- gyration is used for orientation -->
			<qm>
				<name>DCV2T</name> <!-- type of the conjugated seg -->
				<position>1</position> <!-- position in the conjugated segment -->
			</qm>
			</cg_bead>
			<cg_bead>
                                <name>THI2</name> <!-- name of the second CG bead -->
				<type>DCV2T</type>
                                <mapping>THI</mapping>
                                <beads>
				2:THI:S1 2:THI:CA1 2:THI:CA2 2:THI:CB1 2:THI:CB2 2:THI:HC1 2:THI:HC2
                                </beads>
                                <symmetry>3</symmetry>
			<qm>
				<name>DCV2T</name>
                                <position>2</position>
                        </qm>
                        </cg_bead>
			<cg_bead>
				<name>THI3</name>
				<type>DCV2T</type>
				<mapping>THI</mapping>
                                <beads>
				3:THI:S1 3:THI:CA1 3:THI:CA2 3:THI:CB1 3:THI:CB2 3:THI:HC1 3:THI:HC2
                                </beads>
                                <symmetry>3</symmetry>
			<qm>
				<name>DCV2T</name>
                                <position>3</position>
                        </qm>
                        </cg_bead>
			<cg_bead>
				<name>NIT4</name>
				<type>DCV2T</type>
				<mapping>NIT</mapping>
                                <beads>
				4:NIT:N1 4:NIT:CN1 4:NIT:N2 4:NIT:CN2 4:NIT:CC1 4:NIT:C1 4:NIT:HN1
				</beads>
                                <symmetry>3</symmetry>
			<qm>
				<name>DCV2T</name>
                                <position>4</position>
                        </qm>
                        </cg_bead>
		</cg_beads>
	</topology>
	<maps><commit_msg>manual for the new code<commit_after><cg_molecule> <!-- this file is used to convert an atomistic to coarse-grained trajectory -->
	<name>A</name> <!-- name of the CG molecule -->
	<ident>Protein</ident> <!-- name of the atomistic molecule -->
	<topology>
 		<cg_beads>
			<cg_bead>
				<name>NIT1</name> <!-- name of the rigid fragment (used by CSG only) -->
				<type>NIT</type> <!-- type of the rigid fragment (used by CSG only) -->
				<mapping>NIT</mapping> <!-- mapping to determine the fragment center -->
				<beads> <!-- list of atoms resnum:resname:atomname -->
				  1:NIT:N1 1:NIT:CN1 1:NIT:N2 1:NIT:CN2 1:NIT:CC1 1:NIT:C1 1:NIT:HN1
				</beads>
				<symmetry>3</symmetry> <!-- gyration is used for orientation -->
				<segment>
                                  <type>DCV2T</type> <!-- type of the segment the fragment belongs to -->
				  <name>DCVT</name> <!-- name of this segment in a molecule -->
				  <position>1</position> <!-- position of the fragment in the segment -->
				</segment>
			</cg_bead>
			<cg_bead>
                                <name>THI1</name> <!-- name of the second rigid fragment -->
				<type>THI</type>
                                <mapping>THI</mapping>
                                <beads>
				2:THI:S1 2:THI:CA1 2:THI:CA2 2:THI:CB1 2:THI:CB2 2:THI:HC1 2:THI:HC2
                                </beads>
                                <symmetry>3</symmetry>
				<segment>
				  <type>DCV2T</type>
				  <name>DCVT</name>
                                  <position>2</position>
                        	</segment>
                        </cg_bead>
			<cg_bead>
				<name>THI2</name>
				<type>THI</type>
				<mapping>THI</mapping>
                                <beads>
				  3:THI:S1 3:THI:CA1 3:THI:CA2 3:THI:CB1 3:THI:CB2 3:THI:HC1 3:THI:HC2
                                </beads>
                                <symmetry>3</symmetry>
				<segment>
				  <type>DCV2T</type>
				  <name>DCVT</name>
                                  <position>3</position>
                        	</segment>
                        </cg_bead>
			<cg_bead>
				<name>NIT2</name>
				<type>THI</type>
				<mapping>NIT</mapping>
                                <beads>
				4:NIT:N1 4:NIT:CN1 4:NIT:N2 4:NIT:CN2 4:NIT:CC1 4:NIT:C1 4:NIT:HN1
				</beads>
                                <symmetry>3</symmetry>
				<segment>
				  <type>DCV2T</type>
				  <name>DCVT</name>
                                  <position>4</position>
                        	</segment>
                        </cg_bead>
		</cg_beads>
	</topology>
	<maps>
{'fraction_non_alphanumeric': 0.14838576158940397, 'fraction_numerical': 0.030629139072847682, 'mean_word_length': 1.4080717488789238, 'pattern_counts': {'":': 0, '<': 198, '<?xml version=': 0, '>': 198, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4642398', 'n_tokens_mistral': 1983, 'n_tokens_neox': 1661, 'n_words': 319}